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Sample records for heptaphylla novos constituintes

  1. New constituents from the trunk bark of Tabebuia heptaphylla; Novos constituintes quimicos das cascas do caule de Tabebuia heptaphylla

    Energy Technology Data Exchange (ETDEWEB)

    Garcez, Fernanda Rodrigues; Garcez, Walmir Silva; Mahmoud, Talal Suleiman; Figueiredo, Patricia de Oliveira [Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Dept. de Quimica]. E-mail: frgarcez@nin.ufms.br; Resende, Ubirazilda Maria [Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Dept. de Biologia

    2007-07-01

    A new triterpene, 3beta,6beta,21beta-trihydroxyolean-12-ene and a new iridoid, 8alpha-methyl-8beta-hydroxy-6beta-(3',4'-dimethoxy)benzoyloxy-1alpha, 3alpha-dimethoxy-octahydro-cyclopenta[c]pyran were isolated from the trunk bark of a specimen of Tabebuia heptaphylla (Bignoniaceae) collected in the 'Pantanal' of Mato Grosso do Sul, Brazil. Twelve known compounds were also obtained in this work, comprising four iridoids, 6-O-p-hydroxybenzoylajugol, 6-O-p-methoxybenzoylajugol, 6-O-3{sup ,}4{sup -}dimethoxybenzoylajugol, 8alpha-methyl-8beta-hydroxy-6beta-(4'-hydroxy)benzoyloxy-1alpha, 3alpha-dimethoxy-octahydro-cyclopenta[c]pyran, a cyclopentene dialdehyde, 2-formyl-5-(3',4'-dimethoxybenzoyloxy) -3-methyl-2-cyclopentene-1-acetaldehyde, a phenylethanoid glycoside, verbascoside and three benzoic acid derivatives, p-hydroxybenzoic, pmethoxybenzoic and 3,4-dimethoxybenzoic acids, in addition to squalene, sitostenone and sitosterol. The antioxidant properties of the isolated compounds were also evaluated in this work. (author)

  2. Triterpenoid saponins from the stem barks of Schefflera heptaphylla.

    Science.gov (United States)

    Wu, Chun; Duan, Ying-Hui; Li, Man-Mei; Tang, Wei; Wu, Xia; Wang, Guo-Cai; Ye, Wen-Cai; Zhou, Guang-Xiong; Li, Yao-Lan

    2013-09-01

    Nine new triterpenoid saponins, including four ursane-type triterpenoid saponins named heptursosides A-D (1-4), four oleanane-type triterpenoid saponins named heptoleosides A-D (5-8), and one dammarane-type triterpenoid saponin, heptdamoside A (9), along with two known saponins, asiaticoside D (10) and scheffoleoside B (11), were isolated from the stem barks of Schefflera heptaphylla. Their structures were determined on the basis of spectroscopic analysis and chemical methods. It is noteworthy in this study that the aglycone of 1-6 is reported for the first time, and to the best of our knowledge, this is the first report for the presence of the tetracyclic triterpenoid saponin from Schefflera. All the saponins were evaluated for their inhibitory effects on lipopolysaccharide-induced nitric oxide production in RAW264.7 cells, and 2, 6, 7, and 10 showed anti-inflammatory activities under their noncytotoxic concentrations. Georg Thieme Verlag KG Stuttgart · New York.

  3. Antibacterial, antifungal and antioxidant activities of the ethanol extract of the stem bark of Clausena heptaphylla

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    Fakruddin Md

    2012-11-01

    Full Text Available Abstract Background There is wide spread interest in drugs derived from plants as green medicine is believed to be safe and dependable, compared with costly synthetic drugs that have adverse effects. Methods We have attempted to evaluate the antioxidant, In vitro thrombolytic, antibacterial, antifungal and cytotoxic effects of Clausena heptaphylla (Rutaceae stem bark extract ethanol extract. Results Ethanolic stem bark extract of Clausena heptaphylla (CHET contains flavonoids, alkaloids, saponins and steroids but it lacks tannins, anthraquinones and resins. Phenol content of the extract was 13.42 mg/g and flavonoid content was 68.9 mg/g. CHET exhibited significant DPPH free radical scavenging activity with IC50 value of 3.11 μg/ml. Reducing power of CHET was also moderately stronger. In the cytotoxicity assay, LC50 and Chi-square value of the ethanolic extract against brine shrimp nauplii were 144.1461 μg/ml and 0.8533 demonstrating potent cytotoxic effect of the extract. In vitro thrombolytic activity of CHET is significant with 45.38% clot lysis capability compared to that of Streptokinase (65.78%. In antibacterial screening, moderate zone of inhibition (6.5-9.0 mm in diameter was observed against gram-positive Bacillus subtilis ATCC 11774, Bacillus cereus ATCC 10876, Staphylococcus aureus ATCC 25923, Bacillus polymyxa ATCC 842 and Bacillus megaterium ATCC 13578 and less promising zone of inhibition (3.0-4.5 mm in diameter against gram-negative Salmonella typhi ATCC 65154, Shigella flexneri ATCC 12022, Proteus vulgaris ATCC 13315 and Escherichia coli ATCC 25922. Shigella sonnei ATCC 8992 did not show any sensitivity. The MIC values against these bacteria were ranged from 2,000 to 3,500 μg/ml. The extract showed significant zone of inhibition against Rhizopus oryzae DSM 2200, Aspergillus niger DSM 737 and Aspergillus ochraceus DSM 824 in antifungal assay. Conclusions Further advanced research is necessary to isolate and characterize the

  4. Seco-limonoid derived from Raputia heptaphylla promotes the control of cutaneous leishmaniasis in hamsters (Mesocricetus auratus).

    Science.gov (United States)

    Granados-Falla, Diana; Gomez-Galindo, Angela; Daza, Alejandro; Robledo, Sara; Coy-Barrera, Carlos; Cuca, Luis; Delgado, Gabriela

    2016-03-01

    The rational search of novel bioactive molecules against pathogens with immunomodulatory activity is presently one of the most significant approaches to discover and design new therapeutic agents for effective control of infectious diseases, such as the infection caused by Leishmania parasites. In the present study, we evaluated the therapeutic efficacy of the recently characterized immunomodulatory compound 11α,19β-dihydroxy-7-acetoxy-7-deoxoichangin, a seco-limonoid derived from the bark of Raputia heptaphylla (Pittier) using: (1) peritoneal macrophages and (2) Mesocricetus auratus hamsters infected with Leishmania (V.) panamensis and Leishmania (L.) amazonensis. We observed the ability of this seco-limonoid to induce the effective control of the parasite either in vitro [determining an effective concentration 50 (EC50) of 59 µ m at the infection model] and in vivo (inducing clinical improvement or even cure in infected animals treated compared with the groups of animals treated with vehicle solution or meglumine antimoniate).

  5. A construção do Estado republicano e a "crise de trabalho" na Assembleia Nacional Constituinte (1911

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    Teresa NUNES

    2014-12-01

    Full Text Available A denominada "crise de trabalho", resultante do conjunto complexo de transformações económicas e comerciais em curso nos finais do séc. XIX, constituiu um aspecto estruturante da realidade portuguesa desde os anos 80. Esta circunstância, uma determinante na conjuntura nacional, influenciou largamente a propaganda do Partido Republicano Português. Uma vez implantado o regime republicano, a construção do novo estado, discutido no contexto da Assembleia Nacional Constituinte, confrontava-se com as características de uma realidade social complexa, tanto no espaço urbano como rural, dominada pela "crise de trabalho", pelas reivindicações laborais acompanhadas pelo surto grevista, cujas consequências políticas e económicas conflituavam com a imagem de tranquilidade interna desejada no contexto, difícil, do reconhecimento externo do novo regime.

  6. Conservação de sementes de ipê-roxo Preservation of Tabebuia heptaphylla (Vell. Toledo seeds

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    Leila Martins

    2012-01-01

    Full Text Available O objetivo desta pesquisa foi estudar o comportamento fisiológico de sementes de ipê-roxo (Tabebuia heptaphylla (Vell. Toledo durante o amazenamento. Frutos colhidos manualmente de 15 plantas-matrizes foram colocados em ambiente sombreado para secagem complementar e posterior extração manual das sementes; primeiro, determinou-se o grau de umidade inicial das sementes (15,6% e, em seguida, as sementes remanescentes foram submetidas a secagem para obtenção dos demais graus de umidade desejados (11,5, 8,0 e 4,3%. As amostras correspondentes aos diferentes graus de umidade foram armazenadas em câmaras, na temperaturas de 10, 20 e -196 °C. No início e após 120, 240 e 360 dias de armazenamento, as sementes foram submetidas a diversas avaliações fisiológicas. O delineamento experimental foi o inteiramente casualizado, em esquema fatorial, com 4 tratamentos (grau de umidade no início do armazenamento e 12 tratamentos (4 grau de umidade x 3 condições térmicas, em cada época de avaliação, durante o armazenamento. A comparação das médias foi realizada pelo Teste de Tukey a 5%. A conservação das sementes de ipê-roxo com teores de água de 15,6, 11,5, 8,1 e 4,3% é favorecida no armazenamento a 10 e -196 °C.The objective of this research was to study the physiological performance of Tabebuia heptaphylla (Vell. Toledo seeds during storage. Fruits from 15 mother plants were hand picked and placed under shade to finish drying and to ease further manual extraction of seeds. Firstly, the initial moisture content of the seeds was determined, which was 15.6%. Following that, the remaining seeds were submitted to drying at ambient temperature inside a glass desicator in order to obtain the other desired moisture contents (11.5, 8.1 and 4.3%. The samples, corresponding to the different moisture contents were stored inside chambers at temperatures of 10, 20 and -196 °C. At the beginning and after 120, 240 and 360 days of storage, the seeds

  7. Licanol, um novo flavanol, e outros constituintes de Licania macrophylla Benth

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    Fernando Antônio de Medeiros

    2012-01-01

    Full Text Available The phytochemical investigation of L. macrophylla Benth led to the isolation of a new flavanol named licanol: (--4'-O-methyl-epigallocatechin-3'-O-α-L-rhamnoside, along with nine known compounds, identified as: (--4'-O-methyl-epigallocatechin, pheophytin A, 13²-hydroxy-(13²-S-pheophytin A, pheophytin B, sitosterol, stigmasterol, sitosterol-β-O-glucoside, betulinic alcohol and oleanolic acid. The structures were established based on IR, HR-ESI-MS, and NMR spectrometric data analysis with the aid of 2D techniques. The methanolic extracts of leaves and stem bark as well as the compounds licanol, 13²-hidroxi-(13²-S-feofitina A, and betulinic alcohol demonstrated antimicrobial activity against several bacterial strains.

  8. A FILOSOFIA ROUSSEAUNIANA E SUA INFLUÊNCIA PARA A TEORIZAÇÃO DO PODER CONSTITUINTE

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    Ilana Alcântara Monteiro da Fonseca

    2010-08-01

    Full Text Available É assente na doutrina que o Poder Constituinte sempre existiu. Todavia, a elaboração de uma teoria que legitimasse a existência do Poder Constituinte só teve início no século XVIII, a partir do livro Que é o Terceiro Estado? escrito por Sieyès. Entretanto, a partir dos estudos empreendidos por Rousseau que resultaram na obra Do Contrato Social notam-se inúmeros aspectos da teorização do Poder Constituinte realizada por Sieyès. Neste trabalho, iremos expor características da filosofia rousseauniana, a evolução do Poder Constituinte e, ainda, faremos uma breve análise Do Contrato Social e a influência que este exerceu na teorização do Poder Constituinte.

  9. Os comunistas e a Constituinte de 1946: por ocasião do 60º aniversário da Constituição de 1946

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    Prestes, Anita Leocádia

    2006-01-01

    Full Text Available Neste artigo faz-se uma apreciação do contexto sócio-político presente no Brasil durante o ano de 1945. Destaca-se a atividade dos comunistas, voltada para a luta pela convocação de uma Assembléia Constituinte livremente eleita. Com a convocação de eleições para a Assembléia Constituinte, os comunistas elegem uma bancada, cuja atuação na Constituinte de 1946 é analisada no artigo

  10. Avaliação da atividade antioxidante e quantificação dos principais constituintes bioativos de algumas variedades de frutas cítricas

    OpenAIRE

    Duzzioni, Alexandra Gelsleichter [UNESP

    2009-01-01

    As frutas cítricas são muito consumidas e apreciadas por todo o mundo, não só devido ao seu paladar agradável como também ao seu valor nutricional. São fontes de constituintes bioativos que podem atuar como antioxidantes em defesa ao nosso organismo. Existem relatos principalmente sobre os fitoquímicos e o potencial antioxidante das laranjas, no entanto as tangerinas, que também apresentam estes constituintes e atividade antioxidante, ainda são pouco estudadas. O Brasil se destaca na produção...

  11. De Novo Histoid Leprosy

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    Pooja Pandey

    2015-01-01

    Full Text Available Histoid leprosy is an uncommon entity with specific clinical, histopathological and bacteriological features. Histoid lepromas are sudden eruption of dome shaped lesions usually associated with dapsone resistance, as a variant of lepromatous leprosy or rarely arising de novo. We report a case who presented for the first time with histoid features with no history of taking dapsone/antileprosy treatment earlier in an elderly male with small to large lesions over normal skin in the post-leprosy elimination era.

  12. Coccidioidomicose: novo caso brasileiro

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    Moraes Mário A.P.

    1998-01-01

    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.

  13. Crescimento de cordeiros abatidos com diferentes pesos: 2. Constituintes corporais Growth of lambs slaughtered at different weights: 2. Body constituents

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    Cleber Cassol Pires

    2000-10-01

    Full Text Available O experimento foi realizado no Setor de Ovinocultura do Departamento de Zootecnia da Universidade Federal de Santa Maria, com o objetivo de determinar o crescimento de órgãos e outros constituintes do corpo de cordeiros, e suas proporções em relação ao peso vivo (PV e peso de corpo vazio (PCV. Utilizaram-se 22 cordeiros machos inteiros, filhos de carneiros Texel e ovelhas cruzas (Texel x Ideal. Desses, quatro foram abatidos ao nascimento, e os restantes ao desmame e aos 28 e 33kg. A determinação do crescimento dos constituintes corporais foi realizada através de equações alométricas, utilizando-se o logaritmo do peso de cada componente corporal, em função do logaritmo do PCV. As proporções do trato gastrintestinal (TGI, do conjunto de órgãos internos (COI, da gordura interna (GOI e da carcaça aumentaram com a elevação do PV e PCV (PThis experiment was developed at the Animal Science Department, at Federal University of Santa Maria, Brazil with the aim of determining the growth of the organs and other body constituents of lambs, and their proportion in the live weight (LW and empty body weight (EBW. Twenty-two intact male lambs, from crossbreed Texel x Ideal dams sired by Texel males were used. Four lambs were slaughtered at the beginning of the experiment (24 hours after birth and groups of six lambs were slaughtered at weaning and when reaching 28 or 33kg of body weight. To study the relative growth of the different body constituents, the halometric equations between the log of the weight of each component, and of the log of the EBW were fitted. The proportions of alimentary tract (AT, other internal organs (GOI, internal fat (IF and carcass increased with increasing LW and EBW (P<0.05, whereas heart, liver, spleen, kidney, lung with trachea, blood, feet and head decreased (P<0.05. One group of constituents was early maturity (heart, kidney, lung with trachea, feet, blood and head, and another was of late maturity (rumen

  14. 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...

  15. Ordenação de constituintes em construções categorial, tética e apresentativa Constituent ordering in categorical, thetic and presentative constructions

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    Erotilde Goreti Pezatti

    2012-01-01

    Full Text Available A ordenação de constituintes oracionais nas variedades portuguesas é aqui tratada considerando-se três moldes de conteúdo, Tético, Apresentativo e Categorial. A linearização das estruturas oracionais refletem decisões assumidas na formulação do Nível Interpessoal e configuram predominantemente Molde de Conteúdo Categorial Tópico-orientado, com o constituinte Tópico ocupando a posição P I, a palavra verbal, a posição P M, e os outros constituintes, as posições à direita e à esquerda de P M. Em Construções Téticas, a oração toda, por ser focal, ocupa o domínio de P F, já em Construções Apresentativas a cópula vazia assume a posição absoluta P M, e o sintagma nominal Tópico/Foco posiciona-se em P F.The ordering of clausal constituents in Portuguese varieties is treated here considering three content frames recognized in FDG model, thetic, presentative and categorical. The clausal linearization reflects decisions taken in the formulation of the Interpersonal Level and predominantly represents Topic-oriented content frame in which the constituent in the Topic function occupies the position P I, the verb, the P M position, and other remaining constituents occupy the left and right positions of P M. Thetic constructions, whose whole clause performs focal and topical function, occupies the P F area, while presentative constructions have the grammatical word 'copula' taking the absolute position P M and the Topic/Focus Noun phrase taking the P F position.

  16. De novo peroxisome biogenesis revisited

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    Marten Veenhuis

    2014-04-01

    Full Text Available We describe an alternative peroxisome formation pathway in yeast pex3 and pex19 cells, which relies on the existence of small peroxisomal remnants that are present in these cells. This groundbreaking result challenges current models prescribing that peroxisomes derive de novo from the ER. Our data also has major implications for the sorting pathway of specific peroxisomal membrane proteins (PMPs. We propose a novel sorting pathway for the PMPs Pex13 and Pex14 that is independent of the known Pex3/Pex19 machinery.

  17. De novo trisomy 16p

    Energy Technology Data Exchange (ETDEWEB)

    Juan, J.L.C.; Cigudosa, J.C.; Gomez, A.O. [Univ. of La Laguna, Tenerife, Canary Islands (Spain)] [and others

    1997-01-20

    We report on a patient with psychomotor retardation and a pattern of malformations comprising single umbilical artery, craniofacial anomalies, severe truncal hypotonia, and lower-limb hyporreflexia. G-banding cytogenetics demonstrated a 16p+ chromosome. Parental chromosomes were normal. The use of fluorescent in situ hybridization (FISH) showed that this extra material derived from chromosome 16. High-resolution G-banding demonstrated a duplicated segment on the 16p arm, confirming our suspicion of a de novo tandem duplication; hence, the cytogenetic diagnosis was given as 46,XY,dir dup(16)(p11.2{r_arrow}p12). 9 refs., 3 figs.

  18. De novo peptide sequencing by deep learning.

    Science.gov (United States)

    Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

    2017-07-18

    De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7-22.9% higher accuracy at the amino acid level and 38.1-64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5-100% coverage and 97.2-99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming.

  19. Os motivos da censura em Feliz Ano Novo, de Rubem Fonseca

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    Deivis Jhones Garlet

    2015-06-01

    Full Text Available Ao considerar como premissa a relação existente entre literatura e história, necessariamente enfatizamos o diálogo entre ambas, no qual elementos extraestéticos constituintes do meio ideológico que circunda o escritor em dado momento são transmutados no ato estético para o interior do plano narrativo, por meio das operações de reflexo e de refração, passando por uma avaliação axiológica e desempenhando uma determinada função estética e, em retorno, uma dialogicidade com o contexto material. É com esse entendimento que propomos uma análise do conto Feliz Ano Novo, de Rubem Fonseca, que foi censurado pela Ditadura Civil-Militar em 1975. O objetivo consiste em construir, com o recurso de conceitos do Círculo de Bakhtin e das leis sobre censura da época, uma explicação dos motivos que podem ter levado ao corte da narrativa, salientando-se o matiz explicativo, mas não justificativo. Entendemos que esse estudo contribui para a compreensão da ideologia da Ditadura Civil-Militar e do contraponto simbólico efetuado no fazer artístico de Rubem Fonseca. Além disso, ao estudarmos a especificidade do literário em consonância com outros ramos do saber, como a história, a ciência política e a jurídica, inscrevemos nosso trabalho no âmbito maior dos estudos comparados em literatura, sempre tendo no horizonte como paradigma o diálogo nas relações do fazer humano.

  20. Psicolingüística e educação: um novo paradigma para a pesquisa aplicada

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    Prucha, Jan

    1995-01-01

    Full Text Available Não há dúvida que a psicolingüística é uma fonte importante para a explicação de problemas educacionais. Isso se deve ao fato de que linguagem e comunicação são elementos constituintes de processos educacionais. Como conseqüência, uma área interdisciplinar chamada psicolingüística aplicada a educação se desenvolveu. Áreas de aplicação da psicolingüística no estudo de processos educacionais foram descritas alhures (Prucha, 1988. A metodologia da pesquisa em educação e outras ciências sociais têm passado por mudanças importantes durante as duas últimas décadas. Uma das mudanças mais relevantes é uma orientação nova de pesquisa empírica que é geralmente rotulada como paradigma pós-positivista. O novo paradigma foi elaborado em novas abordagens de pesquisa, geralmente chamadas qualitativas, etnográficas, naturalistas, entre outras. Quanto à pesquisa educacional, o novo paradigma já foi manifestado em alguns estudos empíricos (ver, entre outros, o "International Journal of Qualitative Studies in Education". O foco principal deste trabalho é explicar a relevância do paradigma pós-positivista (qualitativo na pesquisa educacional. O argumento do autor é que estudos empíricos na área de psicolingüística aplicada à educação deveriam utilizar a metodologia qualitativa como um importante instrumento de investigação da comunicação humana

  1. 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.

  2. De novo Transcriptome Analysis in Perennial Ryegrass

    DEFF Research Database (Denmark)

    Farrell, Jacqueline Danielle; Byrne, Stephen; Asp, Torben

    Perennial ryegrass (Lolium perenne L.) is an important grass species for both forage and amenity purposes for temperate regions worldwide. It is envisaged that breeding efforts may be enhanced with the assistance of new breeding technologies such as genomic selection. A major step towards genomic...... of functional markers for improved ryegrass breeding. Therefore, the goal of this study is to analyze a de novo assembly of the perennial ryegrass transcriptome from the same inbred genotype being used for de novo genome assembly. Furthermore, we also conducted de novo transcriptome assembly with other...

  3. Constituintes químicos fixos e voláteis dos talos e frutos de Piper tuberculatum Jacq. e das raízes de P. hispidum H. B. K.

    OpenAIRE

    Facundo,Valdir Alves; Pollli,Aline Roberta; Rodrigues,Rosely Valéria; Militão,Júlio S. L Teixeira; Stabelli,Rodrigo Guerino; Cardoso,Cosuelo Tamiris

    2008-01-01

    Os óleos essenciais dos frutos e talos finos de Piper tuberculatum e das raízes de P. hispidum, coletados no estado de Rondônia, foram obtidos por hidrodestilação e analisados por GC e GC-MS. Foram identificados como constituintes majoritários, nos óleos dos frutos e talos finos de P. tuberculatum, o óxido de cariofileno (32,1%) e (26,6%) e o (E)-cariofileno (17,7%) e (12,3%), respectivamente. No óleo essencial das raízes de P. hispidum, foram identificados, como constituintes majoritários, o...

  4. 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.

  5. Atividade fungitóxica in vitro dos óleos essenciais de Lippia sidoides Cham., Cymbopogon citratus(D.C. Stapf. e de seus constituintes majoritários no controle de Rhizoctonia solani e Sclerotium rolfsii

    Directory of Open Access Journals (Sweden)

    A.H. GONÇALVES

    2015-01-01

    Full Text Available RESUMO O objetivo deste estudo foi avaliar o potencial fungitóxicos dos óleos essenciais de Cymbopogon citratus, Lippia sidoides, e de seus constituintes majoritários, sobre o crescimento micelial dos fitopatógenos Rhizoctonia solani e Sclerotium rolfsii. A caracterização química do óleo de L. sidoides demonstrou a presença do carvacrol (33,27% e o 1,8-cineol (24,41% como seus componentes majoritários. Enquanto que o citral (77,6% foi o constituinte majoritário do óleo essencial de C. citratus. A avaliação do potencial fungitóxico dos óleos essenciais e de seus constituintes majoritários foi realizada por meio de ensaios in vitro, avaliando a inibição do crescimento micelial dos microrganismos. Ambos os óleos essenciais inibiram totalmente o crescimento micelial de R. solani na concentração de 400 µg mL-1. O crescimento micelial de S. rolfsii foi inibido pelo óleo essencial de C. citratus na concentração de 300 µg mL-1 e pelo óleo essencial de L. sidoides na concentração de 400 µg mL-1. Em relação aos constituintes majoritários, o 1,8-cineol não apresentou efeito fungitóxico nas concentrações avaliadas. No entanto, o carvacrol e o citral foram mais efetivos que os óleos essenciais havendo ausência de crescimento micelial de R. solani e de S. rolfsii nas concentrações de 200 µg mL-1 e 225 µg mL-1, respectivamente.

  6. De novo Families: Lesbian Motherhood.

    Science.gov (United States)

    Hayman, Brenda; Wilkes, Lesley

    2017-01-01

    The aim of this recent Australian study was to explore the experiences of lesbian women choosing motherhood. Participants included 30 self-identifying lesbian mothers. Data were collected via interviews, data collection sheets, and online journaling. The interview and journaling data were analyzed using constant comparative analysis and subsequently illuminated three main themes: becoming mothers, constructing motherhood, and legitimizing our family. These papers described the journey to motherhood and specifically explored the various methods of conception and other decisions that participants made when planning their family, the challenge of heteronormativity in health care, and legitimizing the role of the non-birth mother in de novo families. This article aims to present the participants' experiences of motherhood that was a constant topic found woven throughout all three of the identified themes. Participants identified that they had a unique opportunity to create their own mothering roles in the absence of significant "lesbian mother" role models and that they were able to adjust and to adapt their roles depending on fluctuating circumstances.

  7. Relação entre os constituintes do solo e seu comportamento espectral Relationship between the soil constituents and its spectral behavior

    Directory of Open Access Journals (Sweden)

    Ricardo Simão Diniz Dalmolin

    2005-04-01

    Full Text Available A reflectância espectral de solos é a expressão que registra o fluxo de radiação eletromagnética refletida pelo solo em relação ao fluxo radiante. Como os solos apresentam diferentes constituintes, os mesmos podem ser identificados e em certos casos quantificados pela análise de sua resposta espectral. Os principais constituintes dos solos que influenciam seu comportamento espectral são a matéria orgânica, óxidos de ferro, argilominerais, além da distribuição granulométrica e umidade. A utilização da reflectância espectral visando obter informações na identificação e quantificação de características do solo de maneira rápida e não invasiva, tanto em nível laboratorial como em nível orbital, tem ocorrido principalmente em países desenvolvidos. No Brasil, o interesse de pesquisadores pelo estudo do comportamento espectral de solos vem crescendo desde a década de 80 do século passado, sendo esta linha de pesquisa relativamente jovem e necessitada de suporte de pesquisa para melhor entendimento dos efeitos da interação da energia eletromagnética entre os diferentes componentes do solo.The spectral soil reflectance is an expression that characterizes the electromagnetic radiation reflected by soil surface. Most of the soil constituents can be identified and sometimes quantified by the spectral behavior. The main soil constituents that influence its spectral behavior are the organic matter, iron oxides, mineralogy and clay content and moisture. The use of soil reflectance allows to obtain information to quickly identify and quantify the soil characteristics, both in laboratory and orbital levels, but it has been tested and used mainly in developed countries. In Brazil, the research interest for the study of the soil spectral reflectance started in the 1980’s, being a recent research area which needs research support to achieve a better understanding of the spectral interaction among the different components of

  8. O voto de saias: a Constituinte de 1934 e a participação das mulheres na política

    Directory of Open Access Journals (Sweden)

    Rita de Cássia Barbosa de Araújo

    2003-12-01

    Full Text Available ESTE artigo trata da participação política da mulher, no quadro das transformações trazidas pela Revolução de 1930 e, sobretudo, pela perspectiva da eleição da Assembléia Nacional Constituinte, em 1934. Situado no campo da chamada microhistória, a análise está baseada nos resultados de uma enquete, realizada pelo Diario de Pernambuco, no início de 1933. Dezenove mulheres de classe média e da elite urbanas de Pernambuco, Paraíba e Alagoas, e duas associações femininas foram ouvidas pelo jornal, a propósito do momento político, das tarefas da futura Constituinte, do papel político e do lugar que julgavam dever ser o da mulher no processo de transformação vivenciado no Brasil, naquele período. Este importante e pouco conhecido material foi tratado com o objetivo da fazer falar as depoentes de então, embora trazendo o aporte histórico que as situa e as contextualiza.this article analyzes the political participation of women, in the set of deep changes brought by the Revolution of 1930 and, especially, by the perspective of the elections to the National Constitutional Assembly in 1934. This analysis, of the so-called micro-history style, is based on the results of a research conducted by the daily newspaper Diário de Pernambuco, in the beginning of 1933. Nineteen middle and upper class women of Pernambuco, Paraíba e Alagoas, as well as two women's associations, were interviewed on the political momentum, the task of the future Assembly, the political role and the space they believed women should occupy in the changing Brazilian scene of the 30's. This important, and widely unknown, material was studied with the purpose of enabling the original interviewees to speak up their minds, given the due consideration of their context.

  9. Constituintes químicos voláteis e não-voláteis de Moringa oleifera Lam., Moringaceae

    Directory of Open Access Journals (Sweden)

    Milena B. Barreto

    Full Text Available O estudo fitoquímico do extrato etanólico das folhas de Moringa oleifera Lam., Moringaceae, resultou no isolamento dos derivados benzilnitrilas niazirina, niazirinina e 4-hidroxifenil-acetonitrila, enquanto que das cascas dos frutos somente o octacosano foi obtido. Os óleos essenciais das folhas, flores e frutos foram analisados por cromatografia gasosa acoplada a espectrometria de massa. Os constituintes principais identificados foram: fitol (21,6% e timol (9,6% nas folhas, octadecano (27,4% e ácido hexadecanóico (18,4% nas flores e docosano (32,7% e tetracosano (24,0% nos frutos. As estruturas dos compostos isolados foram identificadas a partir de técnicas espectroscópicas (RMN, IV e EM. A 4-hidroxifenil-acetonitrila está sendo citada pela primeira vez para o gênero Moringa e os óleos essenciais das flores e frutos estão sendo citados pela primeira vez para a espécie M. oleifera.

  10. Elementos básicos constituintes do desenvolvimento endógeno/local/regional/territorial: redes, atores e território

    Directory of Open Access Journals (Sweden)

    Luisa Cristina Pieniz

    2013-07-01

    Full Text Available Este trabalho apresenta elementos constituintes no processo de Desenvolvimento, dando enfoque a possibilidade de promoção do desenvolvimento local, endógeno a partir dos atores envolvidos e suas formas de organização. Levando-se sempre em consideração as potencialidades e fragilidades deste Território, seja sobre os aspectos econômicos, seja sob o ponto de vista social. Neste sentido aparece o estado com papel importante de resolver através de suas funções públicas as desigualdades, sejam de infraestrutura, como de saúde, educação, entre outras. A cooperação através de Redes surge como estratégias para que os atores possam resolver suas limitações e promovam estratégias de competitividade no cenário que estão envolvidos, para que objetivo primordial de promoção do desenvolvimento a partir de dentro ocorra.

  11. Identificação de itens alimentares constituintes da dieta dos peixes-boi marinhos (Trichechus manatus na região Nordeste do Brasil

    Directory of Open Access Journals (Sweden)

    João Carlos Gomes Borges

    2008-01-01

    Full Text Available http://dx.doi.org/10.5007/2175-7925.2008v21n2p77 Os peixes-boi marinhos são considerados herbívoros oportunistas, consumindo uma grande variedade de itens alimentares. Objetivou-se com este trabalho identificar os itens alimentares constituintes da dieta dos peixe-boi marinhos em vida livre, na região Nordeste do Brasil. Para tanto  foram coletadas amostras de conteúdo estomacal, provenientes de seis carcaças de peixes-boi marinhos, além de amostras fecais de 11 animais nativos e cinco espécimes reintroduzidos. O material foi identificado ao nível de gênero e/ou espécie, através de aspectos morfo-anatômicos, sendo identificadas 21 espécies entre macroalgas, fanerógamas e cnidários. Através destas análi ses, foi possível observar que os peixes-boi marinhos alimentaram-se de uma grande diversidade de plantas aquáticas, com predominância das algas vermelhas.

  12. Exploiting sparseness in de novo genome assembly.

    Science.gov (United States)

    Ye, Chengxi; Ma, Zhanshan Sam; Cannon, Charles H; Pop, Mihai; Yu, Douglas W

    2012-04-19

    The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.

  13. Novos paradigmas literários

    OpenAIRE

    Guimarães,Denise Azevedo Duarte

    2005-01-01

    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 consti...

  14. Proteomics-grade de novo sequencing approach

    DEFF Research Database (Denmark)

    Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank

    2005-01-01

    -80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly...... were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies....

  15. Constituintes voláteis das folhas e dos galhos de Cinnamomum zeylanicum Blume (Lauraceae Volatile constituents from leaves and branches of Cinnamomum zeylanicum Blume (Lauraceae

    Directory of Open Access Journals (Sweden)

    Maria da Paz Lima

    2005-09-01

    Full Text Available Os óleos essenciais das folhas e dos galhos de Cinnamomum zeylanicum coletada no município de Manaus, estado do Amazonas, foram obtidos por hidrodestilação e analisados através de CG-EM. Vinte e três constituintes foram identificados nas folhas, dos quais o eugenol foi o que apresentou maior porcentagem (60%. Nos galhos foram identificados trinta e seis componentes, com predominância dos monoterpenos alfa- e beta-pineno (9,9%; 3,5%, alfa-felandreno (9,2%, p-cimeno (6,2%, limoneno (7,9%, linalol (10,6%; os sesquiterpenos alfa-copaeno (3,3%, (beta -cariofileno (6,7%, óxido de cariofileno (3,1% e os alilbenzenos (E-cinamaldeído (7,8% e acetato de (E-cinamila (9,7%.The essential oils of the leaves and branches "of Cinnamomum zeylanicum, collected at Manaus, state of Amazonas, were obtained by hydrodistillation and analyzed by GC-MS. Twenty-three components were identified, of which eugenol, was the major (60%. Thirty-six components were identified in the branch oil, among them the monoterpenes alpha-pinene (9.9 %, beta-pinene (3.5 %, alpha phellandrene (9.2 %, p-cymene (6.2%, limonene (7.9%, linalool (10.6% were the most abundant, followed by the sesquiterpenes alpha-copaene (3.3%, (beta-caryophyllene (6.7%, caryophyllene oxide (3.1% and the allybenzenes (E-cinnamaldehyde (7.8%, (E-cinnamyl acetate (9.7%.

  16. De novo mutations in human genetic disease

    NARCIS (Netherlands)

    Veltman, J.A.; Brunner, H.G.

    2012-01-01

    New mutations have long been known to cause genetic disease, but their true contribution to the disease burden can only now be determined using family-based whole-genome or whole-exome sequencing approaches. In this Review we discuss recent findings suggesting that de novo mutations play a prominent

  17. 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...

  18. [Surgical treatment of de-novo scoliosis].

    Science.gov (United States)

    Putzier, M; Pumberger, M; Halm, H; Zahn, R K; Franke, J

    2016-09-01

    De-novo scoliosis is most commonly associated with chronic back pain and in 70 % of cases with neurological symptoms of the lower extremities. In recent literature, the occurrence and severity of segmental lateral listhesis has been discussed as being an important prognostic factor of sagittal and frontal deformity progression. In general, operative interventions in patients with de-novo scoliosis are associated with a high rate of complications. Therefore, conservative treatment modalities are recommended at early stages of the disease. If conservative management fails and a sufficient reduction of the patient's symptoms cannot be achieved, depending on the symptoms, a selective decompression, short-segment fusion or long-instrumented reduction and fusion are indicated. Additionally to the patient's symptoms, specific imaging diagnostics are necessary to develop an adequate surgical treatment strategy. Selective decompression without fusion is indicated in patients with a fixed deformity and primarily neurologic pain or deficits. In conditions of a focal pathology as cause of significant low back pain and/or neurologic symptoms at early stages of deformity, a short segment fusion is the treatment of choice. However, short-segment fusion as a less-invasive procedure must not be performed in biplanar unbalanced patients and/or advanced de-novo scoliosis. In advanced degenerative de-novo scoliosis a long-segment reposition and fusion following an alignment correction are needed. Standardized pre-operative planning and perioperative management are highly critical to the post-operative success. All operative treatment strategies in patients with de-novo scoliosis can be successful but they require sophisticated and individual surgical indication.

  19. 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.

  20. Evaluation of the antimicrobial activity of crude extracts and isolated constituents from Chresta scapigera Avaliação da atividade antimicrobiana dos extratos brutos e dos constituintes de Chresta scapigera

    Directory of Open Access Journals (Sweden)

    Elisandra C. Schinor

    2007-03-01

    Full Text Available Crude extracts and eight isolated compounds from Chresta scapigera were evaluated for antibacterial and antifungal activities by the agar-well diffusion method. Twenty strains, including Gram-positive and Gram-negative bacteria and yeasts were used in the bioassay. Hexane extracts presented the best results while ethanol extracts did not indicate inhibition of the microbial growth. Amongst the evaluated compounds b-amyrin acetate, tiliroside and luteolin showed the strongest antimicrobial effect.Os extratos brutos e oito constituintes isolados de Chresta scapigera foram avaliados para as atividades antibacteriana e antifúngica, utilizando o método de difusão em ágar. Vinte cepas indicadoras, incluindo bactérias (Gram-positivas e Gram-negativas e leveduras, foram utilizadas no bioensaio. Os melhores resultados foram obtidos para os extratos hexânicos, enquanto os extratos etanólicos não inibiram o crescimento microbiano. Acetato de b-amirina, tilirosídeo e luteolina foram os mais eficazes dentre os constituintes avaliados.

  1. De novo lipogenesis in health and disease.

    Science.gov (United States)

    Ameer, Fatima; Scandiuzzi, Lisa; Hasnain, Shahida; Kalbacher, Hubert; Zaidi, Nousheen

    2014-07-01

    De novo lipogenesis (DNL) is a complex and highly regulated metabolic pathway. In normal conditions DNL converts excess carbohydrate into fatty acids that are then esterified to storage triacylglycerols (TGs). These TGs could later provide energy via β-oxidation. In human body this pathway is primarily active in liver and adipose tissue. However, it is considered to be a minor contributor to the serum lipid homeostasis. Deregulations in the lipogenic pathway are associated with diverse pathological conditions. The present review focuses on our current understanding of the lipogenic pathway with special reference to the causes and consequences of aberrant DNL. The deregulation of DNL in the major lipogenic tissues of the human body is often observed in various metabolic anomalies - including obesity, non-alcoholic fatty liver disease and metabolic syndrome. In addition to that de novo lipogenesis is reported to be exacerbated in cancer tissues, virus infected cells etc. These observations suggest that inhibitors of the DNL pathway might serve as therapeutically significant compounds. The effectiveness of these inhibitors in treatment of cancer and obesity has been suggested by previous works. De novo lipogenesis - which is an intricate and highly regulated pathway - can lead to adverse metabolic consequences when deregulated. Therapeutic targeting of this pathway may open a new window of opportunity for combating various lipogenesis-driven pathological conditions - including obesity, cancer and certain viral infections. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. De novo psychogenic seizures after epilepsy surgery: case report

    Directory of Open Access Journals (Sweden)

    MONTENEGRO MARIA AUGUSTA

    2000-01-01

    Full Text Available The occurrence of de novo psychogenic seizures after epilepsy surgery is rare, and is estimated in 1.8% to 3.6%. Seizures after epilepsy surgery should be carefully evaluated, and de novo psychogenic seizures should be considered especially when there is a change in the ictal semiology. We report a patient with de novo psychogenic seizures after anterior temporal lobe removal for refractory temporal lobe epilepsy. Once psychogenic seizures were diagnosed and psychiatric treatment was started, seizures stopped.

  3. 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.

  4. Novos valores ou nova hierarquia de valores?

    Directory of Open Access Journals (Sweden)

    Vera Rudge Werneck

    2010-04-01

    Full Text Available O artigo tem por objetivo mostrar que não existem novos valores mas sim novas hierarquias de valores. Cada geração em cada tempo e lugar vai hierarquizar os valores diferentemente. Tece uma análise das várias modalidades de valores considerando a sensibilidade como o processo cognitivo próprio para o seu conhecimento. Fundamentando-se teoricamente em Max Scheler, passando para Yvan Gobry, até concluir com um exemplo de hierarquização de valores.

  5. De novo membrane protein structure prediction.

    Science.gov (United States)

    Nugent, Timothy

    2015-01-01

    Recent advances in identifying residue-residue contacts from large multiple sequence alignments have enabled impressive gains to be made in the field of protein structure prediction. In this chapter, we discuss these advances and provide a step-by-step guide to applying the latest tools to the de novo modelling of alpha-helical transmembrane proteins. As a practical example, we demonstrate the process of building an accurate 3D model of a G protein-coupled receptor, correctly orientated in the membrane, using only its primary protein sequence.

  6. Efeito de um extrato de Ganoderma lucidum (Reishi) na marcação de constituintes sanguíneos com tecnécio-99M e na sobrevivência de Escherichia coli

    OpenAIRE

    Agostinho, Raquel Terra

    2009-01-01

    Avaliações clínicas têm sido possíveis com radiobiocomplexos marcados com tecnécio-99m (99mTc). Drogas naturais ou sintéticas são capazes de interferir na marcação de estruturas sanguíneas com 99mTc, e também tem sido descrita a toxicidade de vários produtos naturais. O objetivo deste estudo foi avaliar o efeito de um extrato de Ganoderma lucidum (Reishi) na marcação de constituintes sanguíneos sangüíneas com 99mTc e na sobrevivência de Escherichia coli. Amostras de sangue de ratos Wistar for...

  7. Constituintes voláteis de cafés "gourmet" e mole do cerrado do triângulo mineiro em função da torra

    Directory of Open Access Journals (Sweden)

    Nascimento Evandro Afonso do

    2003-01-01

    Full Text Available Neste trabalho foi estudada a variação da composição dos voláteis de dois cafés "gourmet" e de um café mole em função do grau de torrefação. Os cafés provenientes de Araguari, cerrado do Triângulo Mineiro, foram submetidos à torra americana (grãos marrons claros, média (grãos marrons e forte (grãos pretos e, em seguida, moídos e submetidos a uma destilação por arraste de vapor em contra-corrente com diclorometano. A análise de cromatografia gasosa acoplada à espectrometria de massas (CG-EM dos constituintes voláteis mostrou que piridina, pirazina e derivados, furfural e derivados são os principais constituintes voláteis dos cafés analisados. Mostrou ainda que não é possível diferenciar os três tipos de café pelos compostos dominantes (concentração acima de 1% no aroma. Foi observado também que a torra afeta sensivelmente os resultados, sendo que a torra americana, usada normalmente na prova da xícara para classificação sensorial de cafés, produz alguns voláteis de forte impacto no aroma que não aparecem na torra média nem na forte, além de apresentar concentrações dos componentes mais comuns muito diferentes daquelas observadas nas outras duas torras.

  8. De Novo Lipogenesis Products and Endogenous Lipokines.

    Science.gov (United States)

    Yilmaz, Mustafa; Claiborn, Kathryn C; Hotamisligil, Gökhan S

    2016-07-01

    Recent studies have shown that in addition to their traditionally recognized functions as building blocks, energy stores, or hazardous intermediates, lipids also have the ability to act as signaling molecules with potent effects on systemic metabolism and metabolic diseases. This Perspective highlights this somewhat less apparent biology of lipids, especially focusing on de novo lipogenesis as a process that gives rise to key messenger molecules mediating interorgan communication. Elucidating the mechanisms of lipid-dependent coordination of metabolism promises invaluable insights into the understanding of metabolic diseases and may contribute to the development of a new generation of preventative and therapeutic approaches. © 2016 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  9. [De novo lipogenesis: role in hepatocellular carcinoma].

    Science.gov (United States)

    Calvisi, D F

    2011-11-01

    Hepatocellular carcinoma (HCC) is one of the most frequent and lethal tumors worldwide. Thus, there is an urgent need to elucidate its molecular pathogenesis in order to develop novel diagnostic, preventive and therapeutic strategies for this deadly disease. Mounting evidence implies a pivotal role of proteins involved in lipid biosynthesis in the development and progression of human HCC. This review summarizes the data available on the pathogenetic relevance of lipogenic proteins in the growth of liver cancer cells, the mechanisms responsible for unrestrained lipid biosynthesis in HCC and the possible clinical implications arising from these discoveries. Altogether the data implicate the AKT-mTORC1-RPS6 signaling pathway as the main inducer of aberrant lipid synthesis in HCC and are indicative of therapeutic strategies aimed at inhibiting de novo lipogenesis for the treatment of human liver cancer.

  10. De Novo Gastric Cancer After Liver Transplantation.

    Science.gov (United States)

    Gong, Chung-Sik; Yoo, Moon-Won; Kim, Beom-Su; Hwang, Shin; Kim, Ki-Hun; Yook, Jeong-Hwan; Kim, Byung-Sik; Lee, Sung-Gyu

    2016-06-23

    BACKGROUND In South Korea, which has a high incidence of gastric cancer, the most common de novo malignancy associated with liver transplantation is gastric cancer. This study sought to identify clinicopathologic characteristics in gastric cancer patients after liver transplantation, and to help manage these cases. MATERIAL AND METHODS We investigated gastric cancer patients after liver transplantation at Asan Medical Center. We analyzed sex, age, cause of liver transplantation, initiating immunosuppressant, pre-transplantation gastric fibroscopy findings, time interval between transplantation and gastric cancer occurrence, follow-up period, existence of gastric cancer screening, Helicobacter pylori infection, family cancer history, gastric cancer treatment, cancer location, size of tumor, macroscopic gross type, WHO histologic type, Lauren's classification, TNM stage, and survival. RESULTS Of 2968 adult liver transplantation patients at our hospital, 19 were diagnosed with gastric cancer. The mean age at the time of gastric cancer diagnosis was 60.2±6.8 (46-71) years and mean time interval between liver transplantation and diagnosis of gastric cancer was 56.0±30.7 (3.20-113) months. Endoscopic submucosal dissection was done for 10 patients, 4 of whom underwent surgical resection. Surgical resection as an initial treatment was done in 8 patients. One patient received chemotherapy first. The standard incidence ratio of gastric cancer in these patients was 1036 per 100 000 persons (95% CI, 623.7-1,619) in men and 318.9 per 100 000 (95% CI, 4.170-1,774) in women. CONCLUSIONS For long-term survival of liver transplant patients, early detection of de novo cancer is necessary. Therefore, annual screening for gastric cancer after liver transplantation is needed, especially in areas where the incidence of gastric cancer is high, such as South Korea.

  11. [Clinical significance of micromegakaryocytes in de novo AML].

    Science.gov (United States)

    Kobayashi, S; Seki, K; Katayama, N; Akiba, C; Yamamoto, T; Sakai, K; Yamaguchi, M; Maruta, A; Noguchi, T; Ogawa, K

    1993-03-01

    Bone marrow specimens obtained from 54 patients with de novo AML and 7 patients with AML evolving from MDS were retrospectively examined for the presence of micromegakaryocytes defined as cells of less than 30 microns in diameter with one or two nuclei. At least 25 megakaryocytes were counted in each patient. Micromegakaryocytes were found in 17 cases (31%), M1:1/11, M2:5/18, M3:0/4, M4:5/12, M5:1/4, M6:4/4, M7:1/1. The median age of the patients was higher in de novo AML with micromegakaryocytes (57 years) than in de novo AML without micromegakaryocytes (41 years) (p = 0.014). Chromosomal analysis revealed that deletion of 5 or 5q-, 7 or 7q- was recognized only in the group of de novo AML with micromegakaryocytes and that t(15;17), t(8:21) and inv (16) were not recognized in this group. Micromegakaryocytes were identified in each bone marrow specimen obtained from 9 of 10 patients with de novo AML with trilineage myelodysplasia. The complete remission rate was significantly lower in de novo AML with micromegakaryocytes (33%) than in de novo AML without micromegakaryocytes (86%) (p = 0.001). The duration of survival of the patients with de novo AML with micromegakaryocytes was shown to be shorter than that of the patients with de novo AML without micromegakaryocytes (p = 0.017). Micromegakaryocytes were recognized in all of 7 patients with AML evolving from MDS. The presence of micromegakaryocytes in bone marrow of the patients with AML indicates a subset of AML with poor prognosis that may be closely associated with myelodysplastic syndrome.

  12. 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...... trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably...

  13. 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

  14. Marcelo Caetano : últimas razones del Estado Novo

    Directory of Open Access Journals (Sweden)

    Hipólito de la Torre Gómez

    2007-01-01

    Full Text Available El reformismo de Marcelo Caetano, ensayado durante sus años de gobierno, resultó insuficiente para responder a los desafíos de la sociedad portuguesa, que acabaron por desembocar en la ruptura del 25 de Abril. Las razones del fracaso de la reforma marcelista se han atribuido a menudo a las dificultades del Presidente del Consejo para maniobrar, prácticamente sin margen y sin tiempo, entre poderosas presiones políticas contrapuestas. Sin embargo, el análisis de su pensamiento político, expreso en las manifestaciones realizadas durante los años de su Gobierno, revelan que en lo sustancial su ideario nunca se salió de los parámetros ideológicos y políticos del Estado Novo. Su reformismo no iba más allá de un intento honesto de relegitimar el régimen mediante un proceso de efectiva institucionalización de la actividad política, de dinamización representativa, de modernización socioeconómica y de aperturismo liberalizador.The reformist policy of Marcelo Caetano was incapable of overcoming the challenges of Portuguese society that eventually led to the outbreak of 25th April. The reasons for this failure have been often linked to the President’s difficulties to implement changes in the midst of powerful and opposed political pressures. Nevertheless, the analysis of his political thought expressed in the speeches and statements produced during his government period, shows that essentially marcelist’s ideas never exceeded the «Estado Novo» ideological framework. So, his reforming policy never went beyond an honest attempt to renew the regime throughout a more institutionalised and representative political practice, a deeper tolerance of public liberties and an economic and social modernization. All that could at the ouset raise popular hopes, but it could never flow into democracy.

  15. De-novo Histoid Hansen cases

    Directory of Open Access Journals (Sweden)

    Rita Vipul Vora

    2014-01-01

    Full Text Available Histoid leprosy is a rare form of multibacillary leprosy with distinct clinical and histopathological features. It is a variant of lepromatous leprosy with a very high bacterial index. It appears in patients as a relapse after dapsone monotherapy, in the presence of dapsone resistance or rarely ′de-novo′. It is a matter of concern as we found three cases of de-novo Histoid that too in 3 months from February 2013 to April 2013; in post-global leprosy elimination era. We report three cases presenting with ′de-novo′ Histoid Hansen′s disease, with no history of leprosy or exposure to dapsone/multi-drug therapy, with heavy bacillary index. The above cases proved to be an eye opener to us in more than one senses. We are reporting these cases just to create awareness and avoid misdiagnosis which will help in prompt treatment and avoid its spread as well as avoid complications and deformities associated with it.

  16. Novos caminhos e alternativas para a Webometria

    Directory of Open Access Journals (Sweden)

    Fabio Castro Gouveia

    2012-12-01

    Full Text Available Com cerca de 15 anos de existência a webometria vivencia hoje um cenário de crise e novos desafios diante das restrições de acesso a informação impostos pelos mecanismos de busca comerciais, colocando em cheque as tradicionais análises de hiperlinks. Historicamente, o link foi a unidade central de informação da webometria por ser e a ligação direta entre os atores (páginas que compõem Web. Diante deste cenário, como obter daqui para frente dados webométricos? Neste momento crítico, novas oportunidades são geradas pelo desenvolvimento de metodologias para o campo. Neste artigo apontamos algumas reflexões e exploramos possibilidades que vem sendo discutidas entre os pesquisadores, como retorno ao uso de web crawlers e a citação da URL e de palavras em mecanismos de busca comerciais, além de trazer uma abordagem ainda pouco explorada, por meio do uso de um operador do Google, o allinanchor.

  17. ATIVIDADE BIOLÓGICA DE UM NOVO TRITERPENO ISOLADO DE Guarea cannata (MELIACEAE)

    OpenAIRE

    PEREIRA Júnior, Orlando L; WOLTER Filho, Wilson; WOLTER, Esther L. Aguiar; ZOGHBI, Maria das Graças B.; SIQUEIRA, Jane B. G.; PINHEIRO, Carlos C.S.

    1993-01-01

    Do cerne de Guarea carinata foi isolado como principal constituinte um triterpeno di-acetilado (I). do grupo dos protolimonóides, derivado do apo-tirucalol e que mostrou atividade no controle biológico das larvas de Urbanus acawoioa(WILLIAMS, R. C, 1926) (Lepidoptera Hesperiidac). From the bark of Guarea carinata was isolated as main constituent a diacetilated triterpen (I) of protolimonoids type, derived from apo-tirucalol, that showed antifeedant activity in biological control of Urbanus...

  18. 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

  19. RAMPART: a workflow management system for de novo genome assembly

    National Research Council Canada - National Science Library

    Mapleson, Daniel; Drou, Nizar; Swarbreck, David

    2015-01-01

    ... assembly for publication. Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good...

  20. 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?

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

    OpenAIRE

    Junjie Li; Ji-Xin Cheng

    2014-01-01

    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 ...

  2. Convergent De Novo Synthesis of Vineomycinone B2 Methyl Ester

    OpenAIRE

    Chen, Qian; Zhong, Yashan; O’Doherty, George A.

    2013-01-01

    An efficient de novo synthesis of vineomycinone B2 methyl ester has been achieved. The longest linear route required only 14 steps from achiral commercially available starting materials (4.0% overall yield). The key transformations included the de novo asymmetric synthesis of two key fragments, which were joined by a convergent late stage Suzuki’s glycosylation for the construction of the aryl β-C-glycoside. A subsequent BBr3 one-pot debenzylation, demethylation and air oxidation provided vin...

  3. Global Innovation – Lessons Learned from the Novo Nordisk Case

    Directory of Open Access Journals (Sweden)

    Nina BIRKMOSE

    2011-06-01

    Full Text Available This paper looks at the possibilities of Western multinationals to efficiently and effectively relocate research and development to emerging markets. In order to exemplify the findings, we will use the case of Danish pharmaceutical company Novo Nordisk and their approach to the Chinese market. Thus, the research question of this paper is: Which lessons are to be learned from the case of Novo Nordisk in China?

  4. De novo lipogenesis in Atlantic salmon adipocytes.

    Science.gov (United States)

    Bou, Marta; Todorčević, Marijana; Torgersen, Jacob; Škugor, Stanko; Navarro, Isabel; Ruyter, Bente

    2016-01-01

    Carnivorous teleost fish utilize glucose poorly, and the reason for this is not known. It is possible that the capacity of adipocytes to synthesize lipids from carbohydrate precursors through a process known as "de novo lipogenesis" (DNL) is one of the factors that contributes to glucose intolerance in Atlantic salmon. Primary adipocytes from Atlantic salmon differentiated in vitro were incubated with radiolabelled glucose in order to explore the capacity of salmon adipocytes to synthesize and deposit lipids from glucose through DNL. The lipid-storage capacity of adipocytes incubated with glucose was compared with that of cells incubated with the fatty acid palmitic acid. Quantitative PCR and immunohistochemistry were used to assess changes of genes and proteins involved in glucose and lipid transport and metabolism. Less than 0.1% of the radiolabelled glucose was metabolized to the fatty acids 16:0 and the stearoyl-CoA desaturase products 16:1 and 18:1 by DNL, whereas approximately 40% was converted to glycerol to form the triacylglycerol backbone of lipids. Transcriptional analysis indicated that adipocytes ensure the availability of necessary cofactors and other substrates for lipid synthesis and storage from glycolysis, the pentose phosphate pathway and glyceroneogenesis. We have shown for the first time that the DNL pathway is active in fish adipocytes. The capacity of the pathway to convert glucose into cellular lipids for storage is relatively low. The limited capacity of adipocytes to utilize glucose as a substrate for lipid deposition may contribute to glucose intolerance in salmonids. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. 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 

  6. 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

  7. 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

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

    Science.gov (United States)

    Willsey, A Jeremy; Fernandez, Thomas V; Yu, Dongmei; King, Robert A; Dietrich, Andrea; Xing, Jinchuan; Sanders, Stephan J; Mandell, Jeffrey D; Huang, Alden Y; Richer, Petra; Smith, Louw; Dong, Shan; Samocha, Kaitlin E; Neale, Benjamin M; Coppola, Giovanni; Mathews, Carol A; Tischfield, Jay A; Scharf, Jeremiah M; State, Matthew W; Heiman, Gary A

    2017-05-03

    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 trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably damaging missense) are overrepresented in probands (RR 1.37, p = 0.003). We identify four likely risk genes with multiple de novo damaging variants in unrelated probands: WWC1 (WW and C2 domain containing 1), CELSR3 (Cadherin EGF LAG seven-pass G-type receptor 3), NIPBL (Nipped-B-like), and FN1 (fibronectin 1). Overall, we estimate that de novo damaging variants in approximately 400 genes contribute risk in 12% of clinical cases. VIDEO ABSTRACT. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. RAMPART: a workflow management system for de novo genome assembly.

    Science.gov (United States)

    Mapleson, Daniel; Drou, Nizar; Swarbreck, David

    2015-06-01

    The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication. Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available. RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART. © The Author 2015. Published by Oxford University Press.

  10. Genetic variation and the de novo assembly of human genomes.

    Science.gov (United States)

    Chaisson, Mark J P; Wilson, Richard K; Eichler, Evan E

    2015-11-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation.

  11. Pathway design using de novo steps through uncharted biochemical spaces.

    Science.gov (United States)

    Kumar, Akhil; Wang, Lin; Ng, Chiam Yu; Maranas, Costas D

    2018-01-12

    Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously considering any combination of the aforementioned design criteria. First, we track and codify as rules all reaction centers using a prime factorization-based encoding technique (rePrime). Reaction rules and known biotransformations are then simultaneously used by the pathway design algorithm (novoStoic) to trace both metabolites and molecular moieties through balanced bio-conversion strategies. We demonstrate the use of novoStoic in bypassing steps in existing pathways through putative transformations, assembling complex pathways blending both known and putative steps toward pharmaceuticals, and postulating ways to biodegrade xenobiotics.

  12. Wood Anatomy of the Neotropical Sapotaceae. XXXVII. Genus Novo?

    Science.gov (United States)

    1982-10-01

    anatomy of the secondary xylem of the neotropical Sapotaceae. The earlier papers, all by the same author and under the same general heading, include: I...L AD-R122 937 WIOOD ANATOMY OF THE NEOTROPICAL SAPOTACERE XXXVII GENUS i/i y NOVO?(U) FOREST-PRODUCTS LAB MADISON W~I B F KUKRCHKA OCT 82 FSRP-FPL...ja WOOD ANATOMY * OF THE NEOTROPICAL SAPOTACEAE .;\\. , XXXVII. GENUS NOVO? RESEARCH PAPER FPL 425 FOREST PRODUCTS LABORATORY FOREST SERVICE U.S

  13. Lipoexpediency: de novo lipogenesis as a metabolic signal transmitter.

    Science.gov (United States)

    Lodhi, Irfan J; Wei, Xiaochao; Semenkovich, Clay F

    2011-01-01

    De novo lipogenesis, the production of fats from simple precursors, is often dismissed as irrelevant to the pathobiology of obesity caused by positive energy balance due to typical high fat diets. However, emerging data implicate de novo lipogenesis in the generation of metabolic signals that alter disease risk. Exploiting this signaling pathway represents lipoexpediency. Lipoexpediency is the concept of directing fats toward benefit even in the setting of lipid overload, and represents a strategy to complement efforts aimed at improving energy balance. Optimizing lipid signals initiated by key lipogenic enzymes such as fatty acid synthase might limit morbidity in people who are unlikely to abandon the lifestyle of the sedentary gourmand.

  14. Convergent de novo synthesis of vineomycinone B2 methyl ester.

    Science.gov (United States)

    Chen, Qian; Zhong, Yashan; O'Doherty, George A

    2013-08-04

    An efficient de novo synthesis of vineomycinone B2 methyl ester has been achieved. The longest linear route required only 14 steps from achiral commercially available starting materials (4.0% overall yield). The key transformations included the de novo asymmetric synthesis of two key fragments, which were joined by a convergent late stage Suzuki's glycosylation for the construction of the aryl β-C-glycoside. A subsequent BBr3 one-pot debenzylation, demethylation and air oxidation provided vineomycinone B2 methyl ester.

  15. Análise da madeira de Pinus oocarpa parte I: estudo dos constituintes macromoleculares e extrativos voláteis Chemical analysis of Pinus oocarpa wood part I: quantification of macromolecular components and volatile extractives

    Directory of Open Access Journals (Sweden)

    Sérgio Antônio Lemos de Morais

    2005-06-01

    Full Text Available Neste estudo foram analisados os principais componentes químicos da madeira de Pinus oocarpa, cultivado na região do cerrado. A composição química dessa madeira foi: 59,05% de a-celulose, 21,22% de hemiceluloses A e B, 25,18% de lignina, 2,78% de extrativos em diclorometano, 4,38% de extrativos em etanol:tolueno, 4,31% de extrativos em água quente e 1,26% de cinzas. O conteúdo de celulose foi relativamente elevado, indicando que essa madeira possui grande potencial para produção de pasta de celulose. Investigou-se, também, a composição dos extrativos. Os principais constituintes do extrato diclorometano dessa madeira foram os ácidos diterpênicos, além dos ácidos palmítico e oléico. No óleo essencial, extraído por aparelho de Clevenger, os principais componentes identificados foram aromadendreno, ledano, hexadecanal e ácido oléico.The chemical composition of Pinus oocarpa wood cultivated in the Brazilian cerrado was established. The obtained results were: a-cellulose (59.05%, hemicelluloses A and B (21.22%, lignin (25.18%, dichloromethane extractives (2.78%, ethanol:toluene extractives (4.38%, hot water extractives (4.31% and ash (1.26%. The cellulose content was high. This result opens perspectives for using Pinus oocarpa wood in pulp and paper industries. Most of the dichloromethane extractives were diterpenic, palmitic and oleic acids. The volatile composition, obtained by means of the Clevenger method followed by GC-MS analysis was constituted mainly by aromadendrene, ledane, hexadecanal and oleic acid.

  16. Illumina-based de novo transcriptome sequencing and analysis of ...

    Indian Academy of Sciences (India)

    2017-12-18

    Dec 18, 2017 ... 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 ...

  17. 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...

  18. 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...

  19. De Novo Mutations in YWHAG Cause Early-Onset Epilepsy

    NARCIS (Netherlands)

    Guella, Ilaria; McKenzie, Marna B.; Evans, Daniel M.; Buerki, Sarah E.; Toyota, Eric B.; Van Allen, Margot I.; Adam, Shelin; Boelman, Cyrus; Bolbocean, Corneliu; Candido, Tara; Eydoux, Patrice; Horvath, Gabriella; Huh, Linda; Nelson, Tanya N.; Sinclair, Graham; van Karnebeek, Clara D M; Vercauteren, Suzanne; Suri, Mohnish; Elmslie, Frances; Simon, Marleen E.H.|info:eu-repo/dai/nl/413981282; van Gassen, Koen L.I.|info:eu-repo/dai/nl/304819417; Héron, Delphine; Keren, Boris; Nava, Caroline; Connolly, Mary B.; Demos, Michelle; Farrer, Matthew J.

    2017-01-01

    Massively parallel sequencing has revealed many de novo mutations in the etiology of developmental and epileptic encephalopathies (EEs), highlighting their genetic heterogeneity. Additional candidate genes have been prioritized in silico by their co-expression in the brain. Here, we evaluate rare

  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. Wnt signaling, de novo lipogenesis, adipogenesis and ectopic fat

    National Research Council Canada - National Science Library

    Song, Kangxing; Wang, Shuxia; Mani, Mitra; Mani, Arya

    2014-01-01

    ...). Following we will describe our most pertinent findings related to Wnt/LRP6 regulation of de novo lipogenesis and adipogenesis and the role of impaired Wnt signaling in generation of ectopic fat, insulin resistance, elevated plasma lipids and non-alcoholic fatty liver disease (NAFLD).

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

    NARCIS (Netherlands)

    Willsey, A. Jeremy; Fernandez, Thomas V.; Yu, Dongmei; King, Robert A.; Dietrich, Andrea; Xing, Jinchuan; Sanders, Stephan J.; Mandell, Jeffrey D.; Huang, Alden Y.; Richer, Petra; Smith, Louw; Dong, Shan; Samocha, Kaitlin E.; Neale, Benjamin M.; Coppola, Giovanni; Mathews, Carol A.; Tischfield, Jay A.; Scharf, Jeremiah M.; State, Matthew W.; Heiman, Gary A.

    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

  3. Preliminary Data from a De Novo Trauma Registry

    African Journals Online (AJOL)

    Accidental injury at home or on the roads was the most common cause of admission with majority of patients not receiving any pre-hospital care. Sixteen percent of patients died while admitted. Conclusion: The data obtained from this de novo registry largely aligns to previous institutional reports while revealing data points ...

  4. 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 ...

  5. A de novo X;13 translocation with abnormal phenotype.

    OpenAIRE

    Hodgson, S V; Barber, J C; Dowie, A; Dubowitz, V

    1986-01-01

    We describe a female infant who presented with hypotonia and developmental delay. Her karyotype showed a de novo balanced translocation between the X chromosome and chromosome 13, with breakpoints at Xq13 and 13p11. The normal X was late replicating in all cells examined. The cause of this patient's abnormal phenotype is discussed.

  6. Whole exome sequencing reveals a MLL de novo mutation ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Whole exome sequencing reveals a de novo mutation associated with mild developmental delay ... Keywords. Wiedemann–Steiner syndrome; whole exome sequencing; hairy elbows; hypertrichosis cubiti; gene; KMT2A; developmental delay; children.

  7. 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...

  8. Genes from scratch – the evolutionary fate of de novo genes

    Science.gov (United States)

    Schlötterer, Christian

    2015-01-01

    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. PMID:25773713

  9. Novos conhecimentos sobre a flora bacteriana vaginal Vaginal bacterial flora: up to date

    Directory of Open Access Journals (Sweden)

    Iara Moreno Linhares

    2010-01-01

    Full Text Available O objetivo desta revisão foi apresentar os novos conhecimentos sobre o ecossistema vaginal, enfatizando os métodos não cultiváveis de identificação microbiana (amplificação de genes, as várias espécies de Lactobacillus que podem compor a flora vaginal e a interação desta com os mecanismos locais de imunidade inata e adquirida, dependentes dos constituintes genéticos. Foram pesquisados no Medline (Pubmed os artigos relacionados ao tema publicados entre 1997 e 2009, selecionando-se apenas os considerados relevantes. A utilização de técnicas não cultiváveis (técnicas de amplificação de genes tem possibilitado o melhor conhecimento sobre a composição do ecossistema vaginal. Na maioria das mulheres no menacme predominam na vagina uma ou mais espécies de Lactobacillus: L. crispatus, . L. inners e L gasseri. Entretanto, em outras mulheres aparentemente saudáveis pode haver deficiência ou mesmo ausência de Lactobacillus, que são substituídos por outras bactérias produtoras de ácido lático: espécies de Atopobium, Megasphaera e/ou Leptotrichia. A infecção e/ou a proliferação de bactérias patogênicas na vagina são suprimidas pela produção de ácido lático, por produtos gerados pelas bactérias e pela atividade local das imunidades inata e adquirida. As células epiteliais vaginais produzem diversos componentes com atividade antimicrobiana. Tais células ainda possuem receptores de membrana ("Toll-like receptors" que reconhecem padrões moleculares associados aos patógenos. O reconhecimento leva à produção de citocinas proinflamatórias e à estimulação da imunidade antigenoespecífica. A produção de anticorpos IgG e IgA também pode ser iniciada na endocérvice e na vagina em resposta à infecção. Conclui-se que a composição da flora vaginal e os mecanismos de imunidade representam importantes mecanismos de defesa. Os critérios de "flora normal" e "flora anormal" devem ser revistos; os polimorfismos

  10. De novo transcriptome assembly of heavy metal tolerant Silene dioica

    OpenAIRE

    Cegan, Radim; Hudzieczek, Vojtech; Hobza, Roman

    2017-01-01

    Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) databa...

  11. Whole exome sequencing reveals a MLL de novo mutation ...

    Indian Academy of Sciences (India)

    Bernardini L. et al. 2014 Wide spectrum of congenital anomalies including choanal atresia, malformed extremities, and brain and spinal malformations in a girl with a de novo 5.6-Mb deletion of. 13q12.11–13q12.13. Am. J. Med. Genet. A 164, 1734–1743. Polizzi A., Pavone P., Ciancio E., La Rosa C., Sorge G. and Ruggieri.

  12. Posterior amorphous corneal dystrophy caused by a de novo deletion.

    Science.gov (United States)

    Odent, S; Casteels, I; Cassiman, C; Dieltiëns, M; Hua, M-T; Devriendt, K

    2017-01-01

    We present a newborn diagnosed with posterior amorphous corneal dystrophy (PACD). PACD is a rare disorder with partial or complete posterior lamellar corneal opacification. Genetic screening showed a deletion of chromosome 12q21.33-q22 containing the identified four small leucine-rich proteoglycans (SLRP's) associated with this particular dystrophy. Neither parents were carrier of the deletion. To our knowledge, this is the first report of a de novo mutation causing PACD.

  13. 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.

  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. Tinindo Trincando: Contracultura e rock no samba dos Novos Baianos

    Directory of Open Access Journals (Sweden)

    VARGAS, Herom

    2011-12-01

    Full Text Available The aim of this article is to discuss aspects linked to counterculture and rock in musical production of the Brazilian band Novos Baianos in the 70’s. Having the context of Brazilian popular music from that decade as a background, two points will be discussed: 1 the particular understanding of counterculture made by the band, and 2 the experimental mix between rock and Brazilian popular musical genres. The counterculture aspects – according to Roszak (1972, Muggiatti (1981, Goffman e Joy (2007, Risério (2005, Dunn (2001; 2002 – will be observed from memories of one of the band’s leaders, the lyricist Luiz Galvão, in his book Anos 70: novos e baianos (1997, and from the scenes of the movie Novos Baianos F.C., directed by Solano Ribeiro (1973. On musical experimentation, some of their songs recorded in the 70’s point the ways of use of rock’s aesthetic elements, especially in guitar arrangements of the musician Pepeu Gomes

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    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. Outros constituintes isolados de Licania arianeae (Chrysobalanaceae

    Directory of Open Access Journals (Sweden)

    Mário G. de Carvalho

    Full Text Available O ácido flavona-6-sulfônico, 4'-O-metil-5,7-diidroxi-flavona-6-sulfonato, conhecido como niruriflavona, e a saponina, ácido 3-O-[6'-O-4-hidroxibenzoil]-²-D-galactopiranosil-ursa-12-en-28-óico, foram isolados, respectivamente, de madeira e folhas de Licania arianeae. As estruturas foram estabelecidas através da análise de espectros de massas e RMN incluindo experimentos bidimensionais.

  19. De novo assembly of highly diverse viral populations

    Directory of Open Access Journals (Sweden)

    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.

  20. De novo assembly of highly diverse viral populations.

    Science.gov (United States)

    Yang, Xiao; Charlebois, Patrick; Gnerre, Sante; Coole, Matthew G; Lennon, Niall J; Levin, Joshua Z; Qu, James; Ryan, Elizabeth M; Zody, Michael C; Henn, Matthew R

    2012-09-13

    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. 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. 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.

  1. De Novo Designed Imaging Agents Based on Lanthanide Peptides Complexes.

    Science.gov (United States)

    Peacock, A F A

    2016-01-01

    Herein are discussed a selection of lanthanide peptide/protein complexes in view of their potential applications as imaging agents, both in terms of luminescence detection and magnetic resonance imaging. Though this chapter covers a range of different peptides and protein, if focuses specifically on the opportunities afforded by the de novo design of coiled coils, miniature protein scaffolds, and the development on lanthanide-binding sites into these architectures. The requirements for lanthanide coordination and the challenges that need to be addressed when preparing lanthanide peptides with a view to their potential adoption as clinical imaging applications, will be highlighted. © 2016 Elsevier Inc. All rights reserved.

  2. De novo pathway-based biomarker identification

    DEFF Research Database (Denmark)

    Alcaraz, Nicolas; List, Markus; Batra, Richa

    2017-01-01

    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...... 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...

  3. Sonhos de Nabucodonosor: aspectos da propaganda do Estado Novo Pernambucano

    OpenAIRE

    Maria Gomes de Souza Neto, José

    2005-01-01

    Este trabalho tem por objetivo explorar as diversas formas e imagens criadas e utilizadas pela propaganda oficial do Estado Novo pernambucano durante seu período de vigência, entre 1937 e 1945, mais particularmente em seus primeiros cinco anos, a grosso modo, o período em que o Brasil ainda não se envolvera na II Guerra Mundial. Durante estes oito anos, Pernambuco foi governado pelo interventor federal Agamenon Magalhães. A partir da análise do que ainda resta do vasto mater...

  4. [De novo growth of a capillary hemangioma of the conjunctiva].

    Science.gov (United States)

    Fernández-Vega Cueto, L; Tresserra, F; de la Paz, M F

    2014-03-01

    A 22-year-old woman patient, diagnosed with an inclusion cyst of the conjunctiva in the nasal sector of the left eye, who after 2 shot/needle injections in the lesion came to our clinic with a dense subconjunctival hemorrhage in four quadrants and with severe pain. After excision biopsy, a capillary hemangioma of the conjunctiva was diagnosed. Conjunctival capillary hemangioma is mainly a benign lesion, asymptomatic and mostly congenital in origin, its progression or de novo growth is rare in adulthood. Copyright © 2012 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

  5. Perspectivas aos "novos designers de moda" no mercado de trabalho

    OpenAIRE

    Venturelli, Valéria Gomes Denelle

    2010-01-01

    Este trabalho tem como objetivo investigar os jovens que escolhem o curso de Negócios da Moda (com o foco em criação) na Universidade Anhembi Morumbi que conseguem trabalhar nessa área quando se formam e como é este processo. Sabemos que isto engloba entender de que forma a produção criativa desse novo designer de moda é assimilada pelo mercado de trabalho. Uma primeira entrevista foi realizada com o intuito de identificar o grupo de 33 alunos que optaram pelo curso de Negócios da Moda na Uni...

  6. Novos táxons de Apomecynini (Coleoptera, Cerambycidae, Lamiinae

    Directory of Open Access Journals (Sweden)

    Ubirajara R. Martins

    2008-01-01

    Full Text Available Novos táxons descritos: Tethystola cincta sp. nov. e Rosalba formosa sp. nov. da Bolívia (Santa Cruz; Adetus stellatus sp. nov. da Costa Rica (Cartago; Acrepidopterum capilosum sp. nov. de Honduras (Ilha Roatán; Irundiaba gen. nov. espécie-tipo, I. waorani sp. nov. do Equador (Napo. Novo nome Neopoticatuca é proposto para Potiatuca Martins & Galileo, 2007 (Cerambycinae, Ibidionini non Potiatuca Galileo & Martins, 2006 (Lamiinae, Apomecynini; Neopotiatuca brevis (Martins & Galileo, 2007 comb. nov.New taxa on Apomecynini (Coleoptera, Cerambycidae, Lamiinae. New taxa described: Tethystola cincta sp. nov. and Rosalba formosa sp. nov. from Bolívia (Santa Cruz; Adetus stellatus sp. nov. from Costa Rica (Cartago; Acrepidopterum capilosum sp. nov. from Honduras (Ilha Roatán; Irundiaba gen. nov. type species, I. waorani sp. nov. from Ecuador (Napo. A new name, Neopoticatuca is proposed to Potiatuca Martins & Galileo, 2007 (Cerambycinae, Ibidionini non Potiatuca Galileo & Martins, 2006 (Lamiinae, Apomecynini; Neopotiatuca brevis (Martins & Galileo, 2007 comb. nov.

  7. Montaigne, a descoberta do Novo Mundo e o ceticismo moderno

    Directory of Open Access Journals (Sweden)

    Danilo Marcondes

    2012-12-01

    Full Text Available O descobrimento do Novo Mundo é um dos fatores fundamentais de ruptura com a tradição, na inauguração do pensamento moderno. A descoberta de povos no novo continente com culturas radicalmente diferentes da europeia leva a um questionamento cético sobre a universalidade da natureza humana, o que denominamos "argumento antropológico". Montaigne é o mais importante pensador deste contexto a discutir esta questão nos Ensaios. Examinamos aqui alguns dos aspectos centrais de sua reflexão a este respeito.The Discovery of the New World is one of the central causes of the breakdown with tradition that opens the way to modern thought. The first contact of the Europeans with the native peoples of the New World shows radically different cultures giving rise to doubts about the universality of human nature, what might be called an "anthropological argument" in a skeptic sense. Michel de Montaigne is the major philosopher in this context to discuss these issues in his Essays and I shall examine some of the more relevant aspects of this discussion.

  8. Molecular characterization of de novo secondary trisomy 13

    Energy Technology Data Exchange (ETDEWEB)

    Shaffer, L.G.; McCaskill, C.; Han, Jin-Yeong [Baylor College of Medicine, Houston, TX (United States); Choo, K.H.A. [Murdoch Institute, Melbourne (Australia); Cutillo, D.M.; Donnenfeld, A.E. [Pennyslvania Hospital, PA (United States); Weiss, L.; Van Dyke, D.L. [Henry Ford Hospital, Detroit, MI (United States)

    1994-11-01

    Unbalanced Robertsonian translocations are a significant cause of mental retardation and fetal wastage. The majority of homologous rearrangements of chromosome 21 in Down syndrome have been shown to be isochromosomes. Aside from chromosome 21, very little is known about other acrocentric homologous rearrangements. In this study, four cases of de novo secondary trisomy 13 are presented. FISH using alpha-satellite sequences, rDNA, and a pTRI-6 satellite I sequence specific to the short arm of chromosome 13 showed all four rearrangements to be dicentric an apparently devoid of ribosomal genes. Three of four rearrangements retained the pTRI-6 satellite I sequence. Case 1 was the exception, showing a deletion of this sequence in the rearrangement, although both parental chromosomes 13 had strong positive hybridization signals. Eleven microsatellite markers from chromosome 13 were also used to characterize the rearrangements. Of the four possible outcomes, one maternal Robertsonian translocation, two paternal isochromosomes, and one maternal isochromosomes were observed. A double recombination was observed in the maternally derived rob(13q13q). No recombination events were detected in any isochromosome. The parental origins and molecular chromosomal structure of these cases are compared with previous studies of de novo acrocentric rearrangements. 20 refs., 3 figs., 2 tabs.

  9. Multi-nucleotide de novo Mutations in Humans.

    Directory of Open Access Journals (Sweden)

    Søren Besenbacher

    2016-11-01

    Full Text Available Mutation of the DNA molecule is one of the most fundamental processes in biology. In this study, we use 283 parent-offspring trios to estimate the rate of mutation for both single nucleotide variants (SNVs and short length variants (indels in humans and examine the mutation process. We found 17812 SNVs, corresponding to a mutation rate of 1.29 × 10-8 per position per generation (PPPG and 1282 indels corresponding to a rate of 9.29 × 10-10 PPPG. We estimate that around 3% of human de novo SNVs are part of a multi-nucleotide mutation (MNM, with 558 (3.1% of mutations positioned less than 20kb from another mutation in the same individual (median distance of 525bp. The rate of de novo mutations is greater in late replicating regions (p = 8.29 × 10-19 and nearer recombination events (p = 0.0038 than elsewhere in the genome.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Bovine-associated mucoprotein: de novo synthesis by nonmammary tissues.

    Science.gov (United States)

    Pringnitz, D J; Butler, J E

    1985-08-01

    Bovine tissues were cultured in vitro in the presence of carbon-14 amino acids and tritiated hexosamine to examine the de novo synthesis of the milk fat globule glycoprotein bovine-associated mucoprotein, by selected tissues. Among tissues examined, the relative synthesis of bovine-associated mucoprotein was highest in mammary tissue. The de novo synthesized bovine-associated mucoprotein in mammary and lacrimal gland cultures when examined for incorporation of carbon-14, had similar sedimentation profiles in sucrose density gradients and incorporated the same relative amount of carbohydrate. The bovine-associated mucoprotein synthesized by lung and spleen cultures sedimented in similar fashion to mammary gland bovine-associated mucoprotein when incorporation of carbon-14 was used as the marker, but it displayed greater heterogeneity when evaluated for tritium incorporation. Bovine-associated mucoprotein in the lung and spleen incorporated relatively less carbohydrate than that synthesized by mammary tissue. These findings support the concept of intertissue heterogeneity, which had been suggested by previous studies.

  12. A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

    Directory of Open Access Journals (Sweden)

    Shuaibin Lian

    2014-01-01

    Full Text Available Background. Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses. Up to now, the performances of assembling repeats of these current assemblers are very poor. Results. To improve this problem, we proposed a new genome assembly algorithm, named SWA, which has four properties: (1 assembling repeats and nonrepeats; (2 adopting a new overlapping extension strategy to extend each seed; (3 adopting sliding window to filter out the sequencing bias; and (4 proposing a compensational mechanism for low coverage datasets. SWA was evaluated and validated in both simulations and real sequencing datasets. The accuracy of assembling repeats and estimating the copy numbers is up to 99% and 100%, respectively. Finally, the extensive comparisons with other eight leading assemblers show that SWA outperformed others in terms of completeness and correctness of assembling repeats and nonrepeats. Conclusions. This paper proposed a new de novo genome assembly method for resolving complex repeats. SWA not only can detect where repeats or nonrepeats are but also can assemble them completely from NGS data, especially for assembling repeats. This is the advantage over other assemblers.

  13. Novo-desenvolvimento, capital social e desigualdade social

    Directory of Open Access Journals (Sweden)

    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

  14. Donor transmitted and de novo cancer after liver transplantation.

    Science.gov (United States)

    Desai, Rajeev; Neuberger, James

    2014-05-28

    Cancers in solid organ recipients may be classified as donor transmitted, donor derived, de novo or recurrent. The risk of donor-transmitted cancer is very low and can be reduced by careful screening of the donor but cannot be abolished and, in the United Kingdom series is less than 0.03%. For donors with a known history of cancer, the risks will depend on the nature of the cancer, the interventions given and the interval between diagnosis and organ donation. The risks of cancer transmission must be balanced against the risks of death awaiting a new graft and strict adherence to current guidelines may result increased patient death. Organs from selected patients, even with high-grade central nervous system (CNS) malignancy and after a shunt, can, in some circumstances, be considered. Of potential donors with non-CNS cancers, whether organs may be safely used again depends on the nature of the cancer, the treatment and interval. Data are scarce about the most appropriate treatment when donor transmitted cancer is diagnosed: sometimes substitution of agents and reduction of the immunosuppressive load may be adequate and the impact of graft removal should be considered but not always indicated. Liver allograft recipients are at increased risk of some de novo cancers, especially those grafted for alcohol-related liver disease and hepatitis C virus infection. The risk of lymphoproliferative disease and cancers of the skin, upper airway and bowel are increased but not breast. Recipients should be advised to avoid risk behavior and monitored appropriately.

  15. Materiais avançados: novos produtos e novos processos na indústria automobilística

    Directory of Open Access Journals (Sweden)

    Heloisa V. de Medina

    1998-06-01

    Full Text Available Esse artigo mostra o desenvolvimento recente dos materiais novos e avançados e seus impactos na organização insustrial exigindo flexibilidade em todas as fases: P&D, projeto e produção. Essas mudanças estão gerando produtos novos e melhorados e atendendo também aos requisitos ambientais. Discute-se o conceito de materiais avançados e apresenta-se os desenvolvimentos recentes nesse campo. O desenvolvimento de materiais especiais para o setor automobilístico é também enfatizado como exemplo significativo da revolução dos materiais e seus impactos inovadores na estrutura industrial deste setor vital.This article shows the recent development of new and advanced materials and its impatcs on the industrial organization, asking for flexiblility from the R&D through the design fase until the production level. These changes are enabling new and better products and also meeting environmental requirements. The concept of advanced material is discussed and the recent progresses on materials field are presented.. The development of special materials and its new applications in the automotive industry is also stressed as a significant exemple of the materials revolution and its innovative impacts on the industrial structure of this core sector.

  16. 76 FR 68767 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Science.gov (United States)

    2011-11-07

    ...] [FR Doc No: 2011-28766] 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... entitled ``Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

  17. 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...

  18. 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.

  19. De novo lipogenesis in human fat and liver is linked to ChREBP-beta and metabolic health

    National Research Council Canada - National Science Library

    Eissing, L; Scherer, T; Todter, K; Knippschild, U; Greve, J.W; Buurman, W.A; Pinnschmidt, H.O; Rensen, S.S; Wolf, A.M; Bartelt, A; Heeren, J; Buettner, C; Scheja, L

    2013-01-01

    Clinical interest in de novo lipogenesis has been sparked by recent studies in rodents demonstrating that de novo lipogenesis specifically in white adipose tissue produces the insulin-sensitizing fatty acid palmitoleate...

  20. Neoplastic disease after liver transplantation: Focus on de novo neoplasms.

    Science.gov (United States)

    Burra, Patrizia; Rodriguez-Castro, Kryssia I

    2015-08-07

    De novo neoplasms account for almost 30% of deaths 10 years after liver transplantation and are the most common cause of mortality in patients surviving at least 1 year after transplant. The risk of malignancy is two to four times higher in transplant recipients than in an age- and sex-matched population, and cancer is expected to surpass cardiovascular complications as the primary cause of death in transplanted patients within the next 2 decades. Since exposure to immunosuppression is associated with an increased frequency of developing neoplasm, long-term immunosuppression should be therefore minimized. Promising results in the prevention of hepatocellular carcinoma (HCC) recurrence have been reported with the use of mTOR inhibitors including everolimus and sirolimus and the ongoing open-label prospective randomized controlled SILVER. Study will provide more information on whether sirolimus-containing vs mTOR-inhibitor-free immunosuppression is more efficacious in reducing HCC recurrence.

  1. Neoplastic disease after liver transplantation: Focus on de novo neoplasms

    Science.gov (United States)

    Burra, Patrizia; Rodriguez-Castro, Kryssia I

    2015-01-01

    De novo neoplasms account for almost 30% of deaths 10 years after liver transplantation and are the most common cause of mortality in patients surviving at least 1 year after transplant. The risk of malignancy is two to four times higher in transplant recipients than in an age- and sex-matched population, and cancer is expected to surpass cardiovascular complications as the primary cause of death in transplanted patients within the next 2 decades. Since exposure to immunosuppression is associated with an increased frequency of developing neoplasm, long-term immunosuppression should be therefore minimized. Promising results in the prevention of hepatocellular carcinoma (HCC) recurrence have been reported with the use of mTOR inhibitors including everolimus and sirolimus and the ongoing open-label prospective randomized controlled SILVER. Study will provide more information on whether sirolimus-containing vs mTOR-inhibitor-free immunosuppression is more efficacious in reducing HCC recurrence. PMID:26269665

  2. 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.

  3. Accurate de novo design of hyperstable constrained peptides

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D.; Gilmore, Jason M.; Harvey, Peta J.; Cheneval, Olivier; Buchko, Garry W.; Pulavarti, Surya V. S. R. K.; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A.; Greisen, Per Jr; Rocklin, Gabriel J.; Song, Yifan; Linsky, Thomas W.; Watkins, Andrew; Rettie, Stephen A.; Xu, Xianzhong; Carter, Lauren P.; Bonneau, Richard; Olson, James M.; Coutsias, Evangelos; Correnti, Colin E.; Szyperski, Thomas; Craik, David J.; Baker, David

    2016-09-14

    Covalently-crosslinked peptides present attractive opportunities for developing new therapeutics. Lying between small molecule and protein therapeutics in size, natural crosslinked peptides play critical roles in signaling, virulence and immunity. Engineering novel peptides with precise control over their three-dimensional structures is a significant challenge. Here we describe the development of computational methods for de novo design of conformationally-restricted peptides, and the use of these methods to design hyperstable disulfide-stabilized miniproteins, heterochiral peptides, and N-C cyclic peptides. Experimentally-determined X-ray and NMR structures for 12 of the designs are nearly identical to the computational models. The computational design methods and stable scaffolds provide the basis for a new generation of peptide-based drugs.

  4. De novo synthesis of a sunscreen compound in vertebrates.

    Science.gov (United States)

    Osborn, Andrew R; Almabruk, Khaled H; Holzwarth, Garrett; Asamizu, Shumpei; LaDu, Jane; Kean, Kelsey M; Karplus, P Andrew; Tanguay, Robert L; Bakalinsky, Alan T; Mahmud, Taifo

    2015-05-12

    Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics.

  5. Wnt signaling, de novo lipogenesis, adipogenesis and ectopic fat.

    Science.gov (United States)

    Song, Kangxing; Wang, Shuxia; Mani, Mitra; Mani, Arya

    2014-11-30

    Wnt signaling is as a major regulator of adipogenesis. It differentially regulates the fate of mesenchymal stem cells (MSC) by promoting osteogenesis and myogenesis, and inhibiting adipogenesis[1]. Its loss of function has been associated with impaired osteogenesis[2] and diverse congenital and adult cardiovascular disorders[3,4]. Our group has identified loss of function mutations in Wnt coreceptor LRP6 that underlie autosomal dominant early onset coronary artery (CAD), osteoporosis and most features of the metabolic syndrome, including high plasma triglyceride and LDL-C, diabetes, hypertension, hyperuricemia and fatty liver disease (unpublished data). Following we will describe our most pertinent findings related to Wnt/LRP6 regulation of de novo lipogenesis and adipogenesis and the role of impaired Wnt signaling in generation of ectopic fat, insulin resistance, elevated plasma lipids and non-alcoholic fatty liver disease (NAFLD).

  6. 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.

  7. 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.

  8. Katome: de novo DNA assembler implemented in rust

    Science.gov (United States)

    Neumann, Łukasz; Nowak, Robert M.; Kuśmirek, Wiktor

    2017-08-01

    Katome is a new de novo sequence assembler written in the Rust programming language, designed with respect to future parallelization of the algorithms, run time and memory usage optimization. The application uses new algorithms for the correct assembly of repetitive sequences. Performance and quality tests were performed on various data, comparing the new application to `dnaasm', `ABySS' and `Velvet' genome assemblers. Quality tests indicate that the new assembler creates more contigs than well-established solutions, but the contigs have better quality with regard to mismatches per 100kbp and indels per 100kbp. Additionally, benchmarks indicate that the Rust-based implementation outperforms `dnaasm', `ABySS' and `Velvet' assemblers, written in C++, in terms of assembly time. Lower memory usage in comparison to `dnaasm' is observed.

  9. Reasons for treating secondary AML as de novo AML

    DEFF Research Database (Denmark)

    Ostgård, Lene Sofie Granfeldt; Kjeldsen, Eigil; Holm, Mette Skov

    2010-01-01

    In a Danish bi-regional registry-based study, we conducted an analysis of the incidence and clinical importance of secondary acute myeloid leukaemia (AML). In a total of 630 cases of AML, we found 157 (25%) cases of secondary AML. The secondary leukaemia arose from MDS (myelodysplastic syndrome......) in 77 cases (49%), CMPD (chronic myeloproliferative disorder) in 43 cases (27%) and was therapy-related AML (t-AML) in 37 cases (24%). Median age at diagnosis of AML was 69 yr in secondary cases when compared to 66 yr in de novo cases (P = 0.006). In univariate analyses, secondary AML was associated...... of age, cytogenetic abnormalities, performance status and leucocyte count (WBC), presence of secondary AML completely lost prognostic significance. We conclude that the presence of secondary AML does not per se convey an unfavourable prognosis and that patients with secondary AML should be offered...

  10. 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.

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

    DEFF Research Database (Denmark)

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang

    2015-01-01

    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...... 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...... 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...

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

    OpenAIRE

    Wilson de Oliveira Souza

    1999-01-01

    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 bloco...

  13. 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.

  14. Factors Associated With Ambulatory Activity in De Novo Parkinson Disease.

    Science.gov (United States)

    Christiansen, Cory; Moore, Charity; Schenkman, Margaret; Kluger, Benzi; Kohrt, Wendy; Delitto, Anthony; Berman, Brian; Hall, Deborah; Josbeno, Deborah; Poon, Cynthia; Robichaud, Julie; Wellington, Toby; Jain, Samay; Comella, Cynthia; Corcos, Daniel; Melanson, Ed

    2017-04-01

    Objective ambulatory activity during daily living has not been characterized for people with Parkinson disease prior to initiation of dopaminergic medication. Our goal was to characterize ambulatory activity based on average daily step count and examine determinants of step count in nonexercising people with de novo Parkinson disease. We analyzed baseline data from a randomized controlled trial, which excluded people performing regular endurance exercise. Of 128 eligible participants (mean ± SD = 64.3 ± 8.6 years), 113 had complete accelerometer data, which were used to determine daily step count. Multiple linear regression was used to identify factors associated with average daily step count over 10 days. Candidate explanatory variable categories were (1) demographics/anthropometrics, (2) Parkinson disease characteristics, (3) motor symptom severity, (4) nonmotor and behavioral characteristics, (5) comorbidities, and (6) cardiorespiratory fitness. Average daily step count was 5362 ± 2890 steps per day. Five factors explained 24% of daily step count variability, with higher step count associated with higher cardiorespiratory fitness (10%), no fear/worry of falling (5%), lower motor severity examination score (4%), more recent time since Parkinson disease diagnosis (3%), and the presence of a cardiovascular condition (2%). Daily step count in nonexercising people recruited for this intervention trial with de novo Parkinson disease approached sedentary lifestyle levels. Further study is warranted for elucidating factors explaining ambulatory activity, particularly cardiorespiratory fitness, and fear/worry of falling. Clinicians should consider the costs and benefits of exercise and activity behavior interventions immediately after diagnosis of Parkinson disease to attenuate the health consequences of low daily step count.Video Abstract available for more insights from the authors (see Video, Supplemental Digital Content 1, http://links.lww.com/JNPT/A170).

  15. De novo synthesis of milk triglycerides in humans.

    Science.gov (United States)

    Mohammad, Mahmoud A; Sunehag, Agneta L; Haymond, Morey W

    2014-04-01

    Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. To test the hypothesis that the incorporation of (13)C carbons from [U-(13)C]glucose into fatty acids (FA) and glycerol in triglycerides (TG) will be greater: 1) in milk than plasma TG, 2) during a high-carbohydrate (H-CHO) diet than high-fat (H-FAT) diet, and 3) during feeding than fasting. Seven healthy, lactating women were studied on two isocaloric, isonitrogenous diets. On one occasion, subjects received diets containing H-FAT or H-CHO diet for 1 wk. Incorporation of (13)C from infused [U-(13)C]glucose into FA and glycerol was measured using GC-MS and gene expression in RNA isolated from milk fat globule using microarrays. Incorporation of (13)C2 into milk FA increased with increased FA chain length from C2:0 to C12:0 but progressively declined in C14:0 and C16:0 and was not detected in FA>C16. During feeding, regardless of diets, enrichment of (13)C2 in milk FA and (13)C3 in milk glycerol were ∼ 3- and ∼ 7-fold higher compared with plasma FA and glycerol, respectively. Following an overnight fast during H-CHO and H-FAT diets, 25 and 6%, respectively, of medium-chain FA (MCFA, C6-C12) in milk were derived from glucose but increased to 75 and 25% with feeding. Expression of genes involved in FA or glycerol synthesis was unchanged regardless of diet or fast/fed conditions. The human MG is capable of de novo lipogenesis of primarily MCFA and glycerol, which is influenced by the macronutrient composition of the maternal diet.

  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.

    Science.gov (United States)

    Simcha, David; Price, Nathan D; Geman, Donald

    2012-01-01

    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 the LR and ALR

  18. 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

  19. 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

    Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large...... 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...

  20. 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

  1. Comportamento de progênies de cafeeiro cultivar mundo novo Mundo novo coffee (Coffea arabica L. cultivar progenies evaluation

    Directory of Open Access Journals (Sweden)

    Gladyston Rodrigues Carvalho

    2006-10-01

    Full Text Available Com o objetivo de avaliar o comportamento de algumas progênies da cultivar Mundo Novo, em relação à produção de café instalou-se em Machado-MG, em 1988, o presente trabalho. O experimento foi coordenado pela Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG em parceria com a Universidade Federal de Lavras, Universidade Federal de Viçosa e Instituto Agronômico de Campinas, sendo conduzido na Fazenda Experimental da EPAMIG. Foram utilizadas 24 progênies da Cultivar Mundo Novo, avaliadas durante 14 colheitas. O delineamento experimental utilizado foi em blocos casualizados, sendo os tratamentos compostos por 24 progênies, com três repetições. Cada parcela foi constituída de uma fileira de nove plantas, sendo todas consideradas úteis. O espaçamento utilizado foi de 3,0 x 1,0 m, com uma planta por cova. Avaliou-se a produção de grãos em sacas de 60 kg de café beneficiado/ha. Realizou-se a análise de variância com parcelas subdivididas, em que cada biênio foi considerado como uma subparcela. Posteriormente, as médias foram comparadas pelo teste de Scott Knott a 5% de probabilidade. Os resultados obtidos permitiram verificar ampla variação entre as progênies sendo a IAC 376-4-26 C807, IAC 388-6-16-2 C499 EP108, IAC 464-1 C12, IAC376-4-30, IAC 388-6-14, IAC 379-19-2SSP, IAC 464-2, IAC 502-9-P13 IV , IAC 388-6-13 C1138, IAC 502-11, IAC 376-4-36 e IAC 501-5-801 como as de maior potencial produtivo enquanto que, as progênies de Mundo Novo IAC 379-19 P-19I e IAC 474-5 apresentaram a menor produtividade. As progênies que detiveram a maiores produtividades médias ao longo das 14 colheitas também foram as de melhor desempenho nas primeiras colheitas.The objective of this work is to evaluate the behavior of some progenies from cultivar Mundo Novo, in relation to production. For this purpose an experiment was conduted in Machado-MG, in 1988. The research was coordenated by Empresa de Pesquisa Agropecuária de Minas Gerais

  2. Ultrafast de novo docking combining pharmacophores and combinatorics.

    Science.gov (United States)

    Gastreich, Marcus; Lilienthal, Markus; Briem, Hans; Claussen, Holger

    2006-12-01

    We report on a successful de novo design approach which relies on the combination of multi-million compound combinatorial docking under receptor-based pharmacophore constraints. Inspired by a rationale by A.R. Leach et al., we document on the unification of two steps into one for ligand assembly. In the original work, fragments known to bind in protein active sites were connected forming novel ligand compounds by means of generic skeleton linkers and following a combinatorial approach. In our approach, the knowledge of fragments binding to the protein has been expressed in terms of a receptor-based pharmacophore definition. The combinatorial linking step is performed in situ during docking, starting from combinatorial libraries. Three sample scenarios growing in size and complexity (combinatorial libraries of 1 million, 1.3 million, and 22.4 million compounds) have been created to illustrate the method. Docking could be accomplished between minutes and several hours depending on the outset; the results were throughout promising. Technically, a module compatibility between FlexX(C) and FlexX-Pharm has been established. The background is explained, and the crucial points from an information scientist's perspective are highlighted.

  3. 8-oxoguanine causes spontaneous de novo germline mutations in mice

    Science.gov (United States)

    Ohno, Mizuki; Sakumi, Kunihiko; Fukumura, Ryutaro; Furuichi, Masato; Iwasaki, Yuki; Hokama, Masaaki; Ikemura, Toshimichi; Tsuzuki, Teruhisa; Gondo, Yoichi; Nakabeppu, Yusaku

    2014-04-01

    Spontaneous germline mutations generate genetic diversity in populations of sexually reproductive organisms, and are thus regarded as a driving force of evolution. However, the cause and mechanism remain unclear. 8-oxoguanine (8-oxoG) is a candidate molecule that causes germline mutations, because it makes DNA more prone to mutation and is constantly generated by reactive oxygen species in vivo. We show here that endogenous 8-oxoG caused de novo spontaneous and heritable G to T mutations in mice, which occurred at different stages in the germ cell lineage and were distributed throughout the chromosomes. Using exome analyses covering 40.9 Mb of mouse transcribed regions, we found increased frequencies of G to T mutations at a rate of 2 × 10-7 mutations/base/generation in offspring of Mth1/Ogg1/Mutyh triple knockout (TOY-KO) mice, which accumulate 8-oxoG in the nuclear DNA of gonadal cells. The roles of MTH1, OGG1, and MUTYH are specific for the prevention of 8-oxoG-induced mutation, and 99% of the mutations observed in TOY-KO mice were G to T transversions caused by 8-oxoG; therefore, we concluded that 8-oxoG is a causative molecule for spontaneous and inheritable mutations of the germ lineage cells.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

    Science.gov (United States)

    Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

    2017-12-01

    Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

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

    Science.gov (United States)

    Matra, Deden Derajat; Kozaki, Toshinori; Ishii, Kazuo; Poerwanto, Roedhy; Inoue, Eiichi

    2016-12-01

    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.

  10. 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

    2017-10-01

    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.

  11. De Novo Methylation of Repeated Sequences in Coprinus Cinereus

    Science.gov (United States)

    Freedman, T.; Pukkila, P. J.

    1993-01-01

    We have examined the stability of duplicated DNA sequences in the sexual phase of the life cycle of the basidiomycete fungus, Coprinus cinereus. We observed premeiotic de novo methylation in haploid nuclei containing either a triplication, a tandem duplication, or an ectopic duplication. Methylation changes were not observed in unique sequences. Repeated sequences underwent methylation changes during the dikaryotic stage. In one cross, 27% of the segregants exhibited methylation-directed gene inactivation. However, all auxotrophs eventually reverted to prototrophy. C to T transition mutations were not observed in this study. Our studies also revealed one inversion that occurred in 50% of the segregants in a single triplication cross, and a single pop-out event that occurred during vegetative growth. These alterations were similar to changes reported in experiments with duplicated sequences in Neurospora crassa and Ascobolus immersus. However, significant differences were also noted. First, the extent of methylation was much less in C. cinereus than in the other two fungi. Second, CpG sequences appeared to be the preferred targets of methylation. PMID:8244000

  12. 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.

  13. Molecular genetic diagnosis of de novo and recurrent bladder cancer.

    Science.gov (United States)

    Steiner, G; Reinschmidt, G; Müller, S C

    1999-02-01

    Bladder cancer, the second most common urological tumor, is usually diagnosed by endoscopy and biopsy of the lower urinary tract. However, this procedure is expensive, can cause discomfort to the patient and is a source of infection. Commercially available diagnostic systems measure protein byproducts of bladder carcinoma in voided urine; their sensitivity is only between 60-80%. Polymerase chain reaction (PCR)-based microsatellite analysis of the urine sediment (MAUS) is a noninvasive, inexpensive and easily performed analytical method which was introduced in the de novo diagnosis and follow-up of bladder cancer. By utilizing the PCR with 20 polymorphic microsatellite markers on different chromosomes and separating PCR products by electrophoresis on 7% denaturing polyacrylamide-formamide-urea slab gels, a 91% diagnostic sensitivity could be achieved. In order to minimize costs and analysis time, the separation and detection of PCR products was carried out by capillary array electrophoresis and two-color fluorescent primer labeling/laser beam detection in another study. The accuracy of both methods was the same. In either detection system, MAUS is an accurate and promising tool in the noninvasive diagnosis of bladder cancer.

  14. Growth Hormone Inhibits Hepatic De Novo Lipogenesis in Adult Mice

    Science.gov (United States)

    Cordoba-Chacon, Jose; Majumdar, Neena; List, Edward O.; Diaz-Ruiz, Alberto; Frank, Stuart J.; Manzano, Anna; Bartrons, Ramon; Puchowicz, Michelle; Kopchick, John J.

    2015-01-01

    Patients with nonalcoholic fatty liver disease (NAFLD) are reported to have low growth hormone (GH) production and/or hepatic GH resistance. GH replacement can resolve the fatty liver condition in diet-induced obese rodents and in GH-deficient patients. However, it remains to be determined whether this inhibitory action of GH is due to direct regulation of hepatic lipid metabolism. Therefore, an adult-onset, hepatocyte-specific, GH receptor (GHR) knockdown (aLivGHRkd) mouse was developed to model hepatic GH resistance in humans that may occur after sexual maturation. Just 7 days after aLivGHRkd, hepatic de novo lipogenesis (DNL) was increased in male and female chow-fed mice, compared with GHR-intact littermate controls. However, hepatosteatosis developed only in male and ovariectomized female aLivGHRkd mice. The increase in DNL observed in aLivGHRkd mice was not associated with hyperactivation of the pathway by which insulin is classically considered to regulate DNL. However, glucokinase mRNA and protein levels as well as fructose-2,6-bisphosphate levels were increased in aLivGHRkd mice, suggesting that enhanced glycolysis drives DNL in the GH-resistant liver. These results demonstrate that hepatic GH actions normally serve to inhibit DNL, where loss of this inhibitory signal may explain, in part, the inappropriate increase in hepatic DNL observed in NAFLD patients. PMID:26015548

  15. 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.

  16. De Novo MS/MS Sequencing of Native Human Antibodies.

    Science.gov (United States)

    Guthals, Adrian; Gan, Yutian; Murray, Laura; Chen, Yongmei; Stinson, Jeremy; Nakamura, Gerald; Lill, Jennie R; Sandoval, Wendy; Bandeira, Nuno

    2017-01-06

    One direct route for the discovery of therapeutic human monoclonal antibodies (mAbs) involves the isolation of peripheral B cells from survivors/sero-positive individuals after exposure to an infectious reagent or disease etiology, followed by single-cell sequencing or hybridoma generation. Peripheral B cells, however, are not always easy to obtain and represent only a small percentage of the total B-cell population across all bodily tissues. Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/MS spectra against databases derived from genetic sequencing of B cells from the same patient. In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required without the need for sequencing of genetic material. Peripheral pAbs from a cytomegalovirus-exposed individual were purified by glycoprotein B antigen affinity and de novo sequenced from MS/MS data. Purely MS-derived mAbs were then manufactured in mammalian cells to validate potency via antigen-binding ELISA. Interestingly, we found that these mAbs accounted for 1 to 2% of total donor IgG but were not detected in parallel sequencing of memory B cells from the same patient.

  17. De novo assembly and analysis of crow lungs transcriptome.

    Science.gov (United States)

    Vijayakumar, Periyasamy; Raut, Ashwin Ashok; Kumar, Pushpendra; Sharma, Deepak; Mishra, Anamika

    2014-09-01

    The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.

  18. 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.

  19. 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.

  20. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler.

    Science.gov (United States)

    Bankar, Kiran Gopinath; Todur, Vivek Nagaraj; Shukla, Rohit Nandan; Vasudevan, Madavan

    2015-09-01

    Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.

  1. Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

    Science.gov (United States)

    Sen, K. Ilker; Tang, Wilfred H.; Nayak, Shruti; Kil, Yong J.; Bern, Marshall; Ozoglu, Berk; Ueberheide, Beatrix; Davis, Darryl; Becker, Christopher

    2017-05-01

    Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

  2. De novo lipogenesis in the differentiating human adipocyte can provide all fatty acids necessary for maturation

    NARCIS (Netherlands)

    Collins, Jennifer M.; Neville, Matt J.; Pinnick, Katherine E.; Hodson, Leanne; Ruyter, Bente; van Dijk, Theo H.; Reijngoud, Dirk-Jan; Fielding, Mark D.; Frayn, Keith N.

    The primary products of de novo lipogenesis (DNL) are saturated fatty acids, which confer adverse cellular effects. Human adipocytes differentiated with no exogenous fat accumulated triacylglycerol (TG) in lipid droplets and differentiated normally. TG composition showed the products of DNL

  3. De novo histoid leprosy: A case report from a post-elimination area

    Directory of Open Access Journals (Sweden)

    Yasmeen J Bhat

    2015-01-01

    Full Text Available Histoid leprosy is an uncommon variant of lepromatous leprosy that usually follows treatment failure. Occasionally it occurs de novo without any history of previous inadequate or irregular treatment. We, hereby, report a case of de novo histoid leprosy in a 25-year-old man from the post-elimination area of Kashmir, where the prevalence rate of the disease was reported to be 0.17/10000 in March, 2013 (NLEP.

  4. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia

    Science.gov (United States)

    Yu, Lan; Sawle, Ashley D.; Wynn, Julia; Aspelund, Gudrun; Stolar, Charles J.; Arkovitz, Marc S.; Potoka, Douglas; Azarow, Kenneth S.; Mychaliska, George B.; Shen, Yufeng; Chung, Wendy K.

    2015-01-01

    Congenital diaphragmatic hernia (CDH) is a serious birth defect that accounts for 8% of all major birth anomalies. Approximately 40% of cases occur in association with other anomalies. As sporadic complex CDH likely has a significant impact on reproductive fitness, we hypothesized that de novo variants would account for the etiology in a significant fraction of cases. We performed exome sequencing in 39 CDH trios and compared the frequency of de novo variants with 787 unaffected controls from the Simons Simplex Collection. We found no significant difference in overall frequency of de novo variants between cases and controls. However, among genes that are highly expressed during diaphragm development, there was a significant burden of likely gene disrupting (LGD) and predicted deleterious missense variants in cases (fold enrichment = 3.2, P-value = 0.003), and these genes are more likely to be haploinsufficient (P-value = 0.01) than the ones with benign missense or synonymous de novo variants in cases. After accounting for the frequency of de novo variants in the control population, we estimate that 15% of sporadic complex CDH patients are attributable to de novo LGD or deleterious missense variants. We identified several genes with predicted deleterious de novo variants that fall into common categories of genes related to transcription factors and cell migration that we believe are related to the pathogenesis of CDH. These data provide supportive evidence for novel genes in the pathogenesis of CDH associated with other anomalies and suggest that de novo variants play a significant role in complex CDH cases. PMID:26034137

  5. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia.

    Science.gov (United States)

    Yu, Lan; Sawle, Ashley D; Wynn, Julia; Aspelund, Gudrun; Stolar, Charles J; Arkovitz, Marc S; Potoka, Douglas; Azarow, Kenneth S; Mychaliska, George B; Shen, Yufeng; Chung, Wendy K

    2015-08-15

    Congenital diaphragmatic hernia (CDH) is a serious birth defect that accounts for 8% of all major birth anomalies. Approximately 40% of cases occur in association with other anomalies. As sporadic complex CDH likely has a significant impact on reproductive fitness, we hypothesized that de novo variants would account for the etiology in a significant fraction of cases. We performed exome sequencing in 39 CDH trios and compared the frequency of de novo variants with 787 unaffected controls from the Simons Simplex Collection. We found no significant difference in overall frequency of de novo variants between cases and controls. However, among genes that are highly expressed during diaphragm development, there was a significant burden of likely gene disrupting (LGD) and predicted deleterious missense variants in cases (fold enrichment = 3.2, P-value = 0.003), and these genes are more likely to be haploinsufficient (P-value = 0.01) than the ones with benign missense or synonymous de novo variants in cases. After accounting for the frequency of de novo variants in the control population, we estimate that 15% of sporadic complex CDH patients are attributable to de novo LGD or deleterious missense variants. We identified several genes with predicted deleterious de novo variants that fall into common categories of genes related to transcription factors and cell migration that we believe are related to the pathogenesis of CDH. These data provide supportive evidence for novel genes in the pathogenesis of CDH associated with other anomalies and suggest that de novo variants play a significant role in complex CDH cases. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Patterns and rates of exonic de novo mutations in autism spectrum disorders.

    Science.gov (United States)

    Neale, Benjamin M; Kou, Yan; Liu, Li; Ma'ayan, Avi; Samocha, Kaitlin E; Sabo, Aniko; Lin, Chiao-Feng; Stevens, Christine; Wang, Li-San; Makarov, Vladimir; Polak, Paz; Yoon, Seungtai; Maguire, Jared; Crawford, Emily L; Campbell, Nicholas G; Geller, Evan T; Valladares, Otto; Schafer, Chad; Liu, Han; Zhao, Tuo; Cai, Guiqing; Lihm, Jayon; Dannenfelser, Ruth; Jabado, Omar; Peralta, Zuleyma; Nagaswamy, Uma; Muzny, Donna; Reid, Jeffrey G; Newsham, Irene; Wu, Yuanqing; Lewis, Lora; Han, Yi; Voight, Benjamin F; Lim, Elaine; Rossin, Elizabeth; Kirby, Andrew; Flannick, Jason; Fromer, Menachem; Shakir, Khalid; Fennell, Tim; Garimella, Kiran; Banks, Eric; Poplin, Ryan; Gabriel, Stacey; DePristo, Mark; Wimbish, Jack R; Boone, Braden E; Levy, Shawn E; Betancur, Catalina; Sunyaev, Shamil; Boerwinkle, Eric; Buxbaum, Joseph D; Cook, Edwin H; Devlin, Bernie; Gibbs, Richard A; Roeder, Kathryn; Schellenberg, Gerard D; Sutcliffe, James S; Daly, Mark J

    2012-04-04

    Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. To identify further genetic risk factors, here we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n = 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant, and the overall rate of mutation is only modestly higher than the expected rate. In contrast, the proteins encoded by genes that harboured de novo missense or nonsense mutations showed a higher degree of connectivity among themselves and to previous ASD genes as indexed by protein-protein interaction screens. The small increase in the rate of de novo events, when taken together with the protein interaction results, are consistent with an important but limited role for de novo point mutations in ASD, similar to that documented for de novo copy number variants. Genetic models incorporating these data indicate that most of the observed de novo events are unconnected to ASD; those that do confer risk are distributed across many genes and are incompletely penetrant (that is, not necessarily sufficient for disease). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.

  7. Impact of modern chemotherapy on the survival of women presenting with de novo metastatic breast cancer

    OpenAIRE

    Pal Sumanta K; Dehaven Mary; Nelson Rebecca A; Onami Susan; Hsu JoAnn; Waliany Sarah; Kruper Laura; Mortimer Joanne

    2012-01-01

    Abstract Background Data that directly associate utilization of novel systemic therapies with survival trends in metastatic breast cancer (MBC) are limited. In the setting of de novo MBC, large registry analyses cite positive temporal trends in survival, but the extent to which advances in systemic therapy have contributed to these gains is not clear. Methods The City of Hope Cancer Registry was used to identify a consecutive series of patients with de novo MBC who received their first line o...

  8. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

    OpenAIRE

    Gent, Jonathan I.; Ellis, Nathanael A.; Guo, Lin; Harkess, Alex E.; Yao, Yingyin; Zhang, Xiaoyu; Dawe, R. Kelly

    2013-01-01

    Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylat...

  9. 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....

  10. Paternal origin of the de novo deleted chromosome 4 in Wolf-Hirschhorn syndrome.

    OpenAIRE

    Tupler, R.; Bortotto, L; Bühler, E M; Alkan, M; Malik, N J; Bösch-Al Jadooa, N; Memo, L; Maraschio, P

    1992-01-01

    The parental origin of the de novo deleted chromosome 4 was studied in five cases of Wolf-Hirschhorn syndrome using polymorphic probes mapping in the 4p16.3 region. In all the patients the deleted chromosome was found to be of paternal origin and these results, together with similar ones obtained by another group, make the preferential paternal origin of the de novo chromosome 4 deletion highly significant.

  11. Reference-guided de novo assembly approach improves genome reconstruction for related species.

    Science.gov (United States)

    Lischer, Heidi E L; Shimizu, Kentaro K

    2017-11-10

    The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.

  12. Constituintes químicos fixos e voláteis dos talos e frutos de Piper tuberculatum Jacq. e das raízes de P. hispidum H. B. K. Fixed and volatile chemical constituents from stems and fruits of Piper tuberculatum Jacq. and from roots of P. hispidum H. B. K.

    Directory of Open Access Journals (Sweden)

    Valdir Alves Facundo

    2008-12-01

    Full Text Available Os óleos essenciais dos frutos e talos finos de Piper tuberculatum e das raízes de P. hispidum, coletados no estado de Rondônia, foram obtidos por hidrodestilação e analisados por GC e GC-MS. Foram identificados como constituintes majoritários, nos óleos dos frutos e talos finos de P. tuberculatum, o óxido de cariofileno (32,1% e (26,6% e o (E-cariofileno (17,7% e (12,3%, respectivamente. No óleo essencial das raízes de P. hispidum, foram identificados, como constituintes majoritários, o dilapiol (57,5%, a elemicina (24,5% e o apiol (10,2%. Do extrato etanólico dos frutos de P. tuberculatum, foram isolados os esteróides β-sitosterol e estigmasterol, as amidas piplartina e dihidropiplartina e um derivado do ácido cinâmico, o ácido 3,4,5-trimetoxi-dihidrocinâmico.The essential oils of the fruits and fine stems of Piper tuberculatum and of the roots of P. hispidum, collected in the state of Rondônia, had been gotten by hydrodistillation and analyzed by GC and GC-MS. Caryophyllene oxide - 32,1% in fruits and 26,6% in fine stem, and (E-caryophyllene - 17,7% in fruits and 12,3% in fine stems, were identified as the major constituents in such parts of P. tuberculatum. In the essential oil of the roots of P. hispidum, dillapiol (57,5%, elemicine (24,5% and apiole (10,2% were identified as the most abundant constituents. From the ethanolic extract of the fruits of P. tuberculatum, the steroids β-sitosterol and stigmasterol, the amides piplartine and dihidropiplartine and the derivative of the cinâmico acid 3,4,5-trimethoxy-dihidrocinâmic acid were isolated.

  13. Second-generation de novo design: a view from a medicinal chemist perspective

    Science.gov (United States)

    Zaliani, Andrea; Boda, Krisztina; Seidel, Thomas; Herwig, Achim; Schwab, Christof H.; Gasteiger, Johann; Claußen, Holger; Lemmen, Christian; Degen, Jörg; Pärn, Juri; Rarey, Matthias

    2009-08-01

    For computational de novo design, a general retrospective validation work is a very challenging task. Here we propose a comprehensive workflow to de novo design driven by the needs of computational and medicinal chemists and, at the same time, we propose a general validation scheme for this technique. The study was conducted combining a suite of already published programs developed within the framework of the NovoBench project, which involved three different pharmaceutical companies and four groups of developers. Based on 188 PDB protein-ligand complexes with diverse functions, the study involved the ligand reconstruction by means of a fragment-based de-novo design approach. The structure-based de novo search engine FlexNovo showed in five out of eight total cases the ability to reconstruct native ligands and to rank them in four cases out of five within the first five candidates. The generated structures were ranked according to their synthetic accessibilities evaluated by the program SYLVIA. This investigation showed that the final candidate molecules have about the same synthetic complexity as the respective reference ligands. Furthermore, the plausibility of being true actives was assessed through literature searches.

  14. Second-generation de novo design: a view from a medicinal chemist perspective.

    Science.gov (United States)

    Zaliani, Andrea; Boda, Krisztina; Seidel, Thomas; Herwig, Achim; Schwab, Christof H; Gasteiger, Johann; Claussen, Holger; Lemmen, Christian; Degen, Jörg; Pärn, Juri; Rarey, Matthias

    2009-08-01

    For computational de novo design, a general retrospective validation work is a very challenging task. Here we propose a comprehensive workflow to de novo design driven by the needs of computational and medicinal chemists and, at the same time, we propose a general validation scheme for this technique. The study was conducted combining a suite of already published programs developed within the framework of the NovoBench project, which involved three different pharmaceutical companies and four groups of developers. Based on 188 PDB protein-ligand complexes with diverse functions, the study involved the ligand reconstruction by means of a fragment-based de-novo design approach. The structure-based de novo search engine FlexNovo showed in five out of eight total cases the ability to reconstruct native ligands and to rank them in four cases out of five within the first five candidates. The generated structures were ranked according to their synthetic accessibilities evaluated by the program SYLVIA. This investigation showed that the final candidate molecules have about the same synthetic complexity as the respective reference ligands. Furthermore, the plausibility of being true actives was assessed through literature searches.

  15. 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.

  16. 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".

  17. Growth Hormone Inhibits Hepatic De Novo Lipogenesis in Adult Mice.

    Science.gov (United States)

    Cordoba-Chacon, Jose; Majumdar, Neena; List, Edward O; Diaz-Ruiz, Alberto; Frank, Stuart J; Manzano, Anna; Bartrons, Ramon; Puchowicz, Michelle; Kopchick, John J; Kineman, Rhonda D

    2015-09-01

    Patients with nonalcoholic fatty liver disease (NAFLD) are reported to have low growth hormone (GH) production and/or hepatic GH resistance. GH replacement can resolve the fatty liver condition in diet-induced obese rodents and in GH-deficient patients. However, it remains to be determined whether this inhibitory action of GH is due to direct regulation of hepatic lipid metabolism. Therefore, an adult-onset, hepatocyte-specific, GH receptor (GHR) knockdown (aLivGHRkd) mouse was developed to model hepatic GH resistance in humans that may occur after sexual maturation. Just 7 days after aLivGHRkd, hepatic de novo lipogenesis (DNL) was increased in male and female chow-fed mice, compared with GHR-intact littermate controls. However, hepatosteatosis developed only in male and ovariectomized female aLivGHRkd mice. The increase in DNL observed in aLivGHRkd mice was not associated with hyperactivation of the pathway by which insulin is classically considered to regulate DNL. However, glucokinase mRNA and protein levels as well as fructose-2,6-bisphosphate levels were increased in aLivGHRkd mice, suggesting that enhanced glycolysis drives DNL in the GH-resistant liver. These results demonstrate that hepatic GH actions normally serve to inhibit DNL, where loss of this inhibitory signal may explain, in part, the inappropriate increase in hepatic DNL observed in NAFLD patients. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  18. Novos conceitos em cuidados paliativos na unidade de terapia intensiva

    Directory of Open Access Journals (Sweden)

    Cristina Bueno Terzi Coelho

    Full Text Available RESUMO Alguns dos pacientes admitidos em uma unidade de terapia intensiva podem enfrentar condições de doença terminal, que geralmente levam à morte. O conhecimento sobre cuidados paliativos é recomendado para os profissionais de saúde encarregados do cuidado destes pacientes. Em muitas situações, os pacientes devem ser avaliados diariamente, já que a introdução de novos tratamentos pode ou não ser benéfica para eles. As discussões entre os membros da equipe de saúde, relacionadas ao prognóstico e aos objetivos do tratamento, devem ser avaliadas cuidadosamente em cooperação com os pacientes e seus familiares. A adoção na unidade de terapia intensiva de protocolos relacionados a pacientes em final da vida é fundamental. É importante ter uma equipe multidisciplinar para determinar se é necessário deixar de iniciar ou mesmo retirar tratamentos avançados. Além disto, pacientes e familiares devem ser informados de que os cuidados paliativos envolvem o melhor tratamento possível para aquela situação específica, assim como respeitar suas vontades e considerar as bases sociais e espirituais dos mesmos. Assim, o objetivo desta revisão foi apresentar os cuidados paliativos como uma opção razoável para dar suporte à equipe da unidade de terapia intensiva na assistência a pacientes com doença terminal. São apresentadas atualizações com relação a dieta, ventilação mecânica e diálise nestes pacientes. Ainda, discutiremos o programa, comum nos Estados Unidos, conhecido como filosofia hospice, como alternativa ao ambiente da unidade de terapia intensiva/hospital.

  19. 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.

  20. THE PERITONEAL DIALYSIS TREATMENT IN DIALYSIS CENTRE NOVO MESTO

    Directory of Open Access Journals (Sweden)

    Mateja Globokar

    2004-12-01

    Full Text Available Background. In the article the development, basic principle and technical basis of peritoneal dialysis (PD, as one of the three methods of renal replacement therapy (RRT, are presented. In addition the PD treatment in dialysis centre Novo mesto from 1994 to 2003 is described.Methods. All available hospital records of 40 patients treated with PD over 9 years in dialysis centre were reviewed retrospectively. The authors were interested in age structure of patients, the causes of end-stage renal disease (ESRD, the course of treatment and complications that had arisen with PD.Results. PD was the first treatment option for 35 patients. There were 28.6% older than 55 years and 17.1% older than 65. The leading causes of ESRD are diabetic nephropathy and the group of glomerular diseases (especially IgA nephropathy – both in 25% of patients, as well as polycystic kidney disease (in 15%. The noninfectious complications and peritonitis are presented. The incidence of the latter is 1 episode/62,69 patient – months. The Gram-positive organisms were responsible in 45.5% and Gram-negative organisms in 13.6%. 3 patients had peritonitis caused by multiple microorganisms,with extremely severe course. In 6 patients renal transplantation was performed, 8 patients were transferred to hemodialysis (HD. Among the dead patients, there was a high percentage of patients with diabetes mellitus, the leading cause of death was cardiovascular complications.Conclusions. PD is highly recommended as first option in RRT in younger, compliant patients. Patients with diabetes and older patients with atherosclerosis are problematic, as various complications commonly arise.

  1. Further Insights into Brevetoxin Metabolism by de Novo Radiolabeling

    Directory of Open Access Journals (Sweden)

    Kevin Calabro

    2014-06-01

    Full Text Available The toxic dinoflagellate Karenia brevis, responsible for early harmful algal blooms in the Gulf of Mexico, produces many secondary metabolites, including potent neurotoxins called brevetoxins (PbTx. These compounds have been identified as toxic agents for humans, and they are also responsible for the deaths of several marine organisms. The overall biosynthesis of these highly complex metabolites has not been fully ascertained, even if there is little doubt on a polyketide origin. In addition to gaining some insights into the metabolic events involved in the biosynthesis of these compounds, feeding studies with labeled precursors helps to discriminate between the de novo biosynthesis of toxins and conversion of stored intermediates into final toxic products in the response to environmental stresses. In this context, the use of radiolabeled precursors is well suited as it allows working with the highest sensitive techniques and consequently with a minor amount of cultured dinoflagellates. We were then able to incorporate [U-14C]-acetate, the renowned precursor of the polyketide pathway, in several PbTx produced by K. brevis. The specific activities of PbTx-1, -2, -3, and -7, identified by High-Resolution Electrospray Ionization Mass Spectrometer (HRESIMS, were assessed by HPLC-UV and highly sensitive Radio-TLC counting. We demonstrated that working at close to natural concentrations of acetate is a requirement for biosynthetic studies, highlighting the importance of highly sensitive radiolabeling feeding experiments. Quantification of the specific activity of the four, targeted toxins led us to propose that PbTx-1 and PbTx-2 aldehydes originate from oxidation of the primary alcohols of PbTx-7 and PbTx-3, respectively. This approach will open the way for a better comprehension of the metabolic pathways leading to PbTx but also to a better understanding of their regulation by environmental factors.

  2. Prevalence and origin of De Novo duplications in Charcot-Marie-Tooth disease type 1A: First report of a De Novo duplication with a maternal origin

    Energy Technology Data Exchange (ETDEWEB)

    Blair, I.P.; Nash, J.; Gordon, M.J.; Nicholson, G.A. [Univ. of Sydney, New South Wales (United Kingdom)

    1996-03-01

    Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. Sporadic cases of CMT have been described since the earliest reports of the disease. The most frequent form of the disorder, CMT1A, is associated with a 1.5-Mb DNA duplication on chromosome 17p11.2, which segregates with the disease. In order to investigate the prevalence of de novo CMT1A duplications, this study examined 118 duplication-positive CMT1A families. In 10 of these families it was demonstrated that the disease had arisen as the result of a de novo mutation. By taking into account the ascertainment of families, it can be estimated that {>=}10% of autosomal dominant CMT1 families are due to de novo duplications. The CMT1A duplication is thought to be the product of unequal crossing over between parental chromosome 17 homologues during meiosis. Polymorphic markers from within the duplicated region were used to determine the parental origin of these de novo duplications in eight informative families. Seven were of paternal and one of maternal origin. This study represents the first report of a de novo duplication with a maternal origin and indicates that it is not a phenomenon associated solely with male meioses. Recombination fractions for the region duplicated in CMT1A are larger in females than in males. That suggests that oogenesis may be afforded greater protection from misalignment during synapsis, and/or that there may be lower activity of those factors or mechanisms that lead to unequal crossing over at the CMT1A locus. 41 refs., 2 figs.

  3. Retrospective study on de novo postoperative urinary incontinence after pelvic organ prolapse surgery.

    Science.gov (United States)

    Ugianskiene, Aiste; Kjærgaard, Niels; Inger Lindquist, Anna Sofie; Larsen, Thomas; Glavind, Karin

    2017-12-01

    Reported incidences of de novo urinary incontinence (UI) following pelvic organ prolapse (POP) surgery in preoperatively continent women vary between 2% and 43%. The aim of this study was to investigate the incidence and the types of de novo UI and differences between operations in different compartments. Retrospective study of 678 women with POP surgery using native tissue repair during a 3-year period. Patients completed three modified prolapse questions from the International Consultation on Incontinence-Vaginal Symptoms (ICIQ-VS) and the International Consultation on Incontinence Questionnaire- Urinary Incontinence Short Form (ICIQ-UI SF) before undergoing surgery and 3 months postoperatively. Patients who were totally dry and scored 0 on ICIQ-UI SF before surgery were included in the study (N=299). The patients developing new onset UI on ICIQ-UI SF postoperatively were interviewed by telephone after median 30 months. A total of 33 patients (11%) developed subjective de novo UI at 3 months follow-up. The majority of patients (N=16) reported stress UI. The risk of developing de novo UI increased with parity (p=0.03). We found no difference between operations in different compartments. At long-term follow-up 12 patients became continent without incontinence surgery or medical treatment leaving only 21 patients (7%) incontinent. The risk of developing de novo UI after prolapse surgery with native tissue repair is low and improves over time. Parity is significantly associated with the risk of developing de novo UI. There is no difference in the incidence of de novo incontinence between operations in different compartments. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. De novo lipogenesis in human fat and liver is linked to ChREBP-β and metabolic health

    OpenAIRE

    Eissing, Leah; Scherer, Thomas; Tödter, Klaus; Knippschild, Uwe; Greve, Jan Willem; Buurman, Wim A.; Pinnschmidt, Hans O.; Rensen, Sander S.; Wolf, Anna M.; Bartelt, Alexander; Heeren, Joerg; Buettner, Christoph; Scheja, Ludger

    2013-01-01

    Clinical interest in de novo lipogenesis has been sparked by recent studies in rodents demonstrating that de novo lipogenesis specifically in white adipose tissue produces the insulin-sensitizing fatty acid palmitoleate. By contrast, hepatic lipogenesis is thought to contribute to metabolic disease. How de novo lipogenesis in white adipose tissue versus liver is altered in human obesity and insulin resistance is poorly understood. Here we show that lipogenic enzymes and the glucose transporte...

  5. Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype

    Directory of Open Access Journals (Sweden)

    Kanavakis Emanuel

    2008-07-01

    Full Text Available Abstract Background Carriers of apparently balanced translocations are usually phenotypically normal; however in about 6% of de novo cases, an abnormal phenotype is present. In the current study we investigated 12 patients, six de novo and six familial, with apparently balanced translocations and mental retardation and/or congenital malformations by applying 1 Mb resolution array-CGH. In all de novo cases, only the patient was a carrier of the translocation and had abnormal phenotype. In five out of the six familial cases, the phenotype of the patient was abnormal, although the karyotype appeared identical to other phenotypically normal carriers of the family. In the sixth familial case, all carriers of the translocations had an abnormal phenotype. Results Chromosomal and FISH analyses suggested that the rearrangements were "truly balanced" in all patients. However, array-CGH, revealed cryptic imbalances in three cases (3/12, 25%, two de novo (2/12, 33.3% and one familial (1/12, 16.6%. The nature and type of abnormalities differed among the cases. In the first case, what was identified as a de novo t(9;15(q31;q26.1, a complex rearrangement was revealed involving a ~6.1 Mb duplication on the long arm of chromosome 9, an ~10 Mb deletion and an inversion both on the long arm of chromosome 15. These imbalances were located near the translocation breakpoints. In the second case of a de novo t(4;9(q25;q21.2, an ~6.6 Mb deletion was identified on the short arm of chromosome 7 which is unrelated to the translocation. In the third case, of a familial, t(4;7(q13.3;p15.3, two deletions of ~4.3 Mb and ~2.3 Mb were found, each at one of the two translocation breakpoints. In the remaining cases the translocations appeared balanced at 1 Mb resolution. Conclusion This study investigated both de novo and familial apparently balanced translocations unlike other relatively large studies which are mainly focused on de novo cases. This study provides additional

  6. 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.

  7. Subthalamic nucleus--sensorimotor cortex functional connectivity in de novo and moderate Parkinson's disease.

    Science.gov (United States)

    Kurani, Ajay S; Seidler, Rachael D; Burciu, Roxana G; Comella, Cynthia L; Corcos, Daniel M; Okun, Michael S; MacKinnon, Colum D; Vaillancourt, David E

    2015-01-01

    Previous research has indicated increased functional connectivity between subthalamic nucleus (STN) and sensorimotor cortex in off-medication Parkinson's disease (PD) compared with control subjects. It is not clear if the increase in functional connectivity between STN and sensorimotor cortex occurs in de novo PD, which is before patients begin dopamine therapy. Resting-state functional magnetic resonance imaging was carried out in 20 de novo (drug naïve) patients with PD (Hoehn and Yahr stage: I-II), 19 patients with moderate PD (Hoehn and Yahr stage: II-III), and 19 healthy controls. The functional connectivity analysis in de novo and moderate PD patients focused on the connectivity of the more affected STN and the sensorimotor cortex. Using resting-state functional connectivity analysis, we provide new evidence that people with de novo PD and off-medicated moderate PD have increased functional connectivity between the more affected STN and different regions within the sensorimotor cortex. The overlapping sensorimotor cortex found in both de novo and moderate PD had functional connectivity values that correlated positively with the Unified Parkinson's Disease Rating Scale part III. This key finding suggests that changes in functional connectivity between STN and sensorimotor cortex occur early in the disease following diagnosis and before dopamine therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Surgical Treatment and Outcome of Patients with De Novo Lung Cancer After Liver Transplantation.

    Science.gov (United States)

    Shoji, Fumihiro; Toyokawa, Gouji; Harada, Noboru; Itoh, Shinji; Harimoto, Norifumi; Ikegami, Toru; Okamoto, Tatsuro; Soejima, Yuji; Yoshizumi, Tomoharu; Maehara, Yoshihiko

    2017-05-01

    De novo malignancy, including primary lung cancer, is one of the limitations to long-term survival after liver transplantation. The purpose of this study was to describe patients who developed de novo lung cancer after living-donor liver transplantation (LDLT) and investigate their clinicopathological features as well as the feasibility of surgical resection. We investigated 554 patients who underwent LDLT. De novo lung cancer after LDLT was observed in five (0.9%) out of 554 studied patients: four men and one woman, aged 61-78 years (mean=67 years). All four men had a smoking history. Clinical stages of de novo lung cancer were stage IA in three patients, and stage IB and IV in one patient each. Three out of five patients underwent pulmonary lobectomy and pathological stage was IA in two patients and IIA in one. All patients who underwent surgery stopped immunosuppressive therapy 1 day preoperatively and restarted on postoperative day 1. There were no serious postoperative complications. All three patients are still alive without any recurrence, with survival ranging from 8 to 29 months, with an average of 16.3 months after diagnosis of lung cancer. Although the study population was small, these results suggest that pulmonary lobectomy of de novo lung cancer after LDLT, even under immunosuppressive conditions, is a feasible procedure and may yield a survival benefit. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  9. De-novo learning of genome-scale regulatory networks in S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Sisi Ma

    Full Text Available De-novo reverse-engineering of genome-scale regulatory networks is a fundamental problem of biological and translational research. One of the major obstacles in developing and evaluating approaches for de-novo gene network reconstruction is the absence of high-quality genome-scale gold-standard networks of direct regulatory interactions. To establish a foundation for assessing the accuracy of de-novo gene network reverse-engineering, we constructed high-quality genome-scale gold-standard networks of direct regulatory interactions in Saccharomyces cerevisiae that incorporate binding and gene knockout data. Then we used 7 performance metrics to assess accuracy of 18 statistical association-based approaches for de-novo network reverse-engineering in 13 different datasets spanning over 4 data types. We found that most reconstructed networks had statistically significant accuracies. We also determined which statistical approaches and datasets/data types lead to networks with better reconstruction accuracies. While we found that de-novo reverse-engineering of the entire network is a challenging problem, it is possible to reconstruct sub-networks around some transcription factors with good accuracy. The latter transcription factors can be identified by assessing their connectivity in the inferred networks. Overall, this study provides the gene network reverse-engineering community with a rigorous assessment of the accuracy of S. cerevisiae gene network reconstruction and variability in performance of various approaches for learning both the entire network and sub-networks around transcription factors.

  10. Citologia do desenvolvimento dos frutos sem sementes no café "mundo novo" Cytology of the development of empty fruits in the mundo novo coffee

    Directory of Open Access Journals (Sweden)

    A. J. T. Mendes

    1954-01-01

    Full Text Available Uma pequena porcentagem de frutos sem sementes é comum às plantas de tôdas as variedades de Coffea arabica, parecendo tratar-se de um fenômeno puramente fisiológico. No café Mundo Novo porém, além dêste tipo de plantas, há outras com elevada porcentagem de lojas vazias ("chochos". Constituindo isto um grave defeito para uma variedade comercial, procurou-se estudar a sua causa. As observações feitas no processo da microsporogênese mostraram irregularidades na distribuição dos cromossômios. Sendo encontradas tanto nas plantas de alta porcentagem como nas de baixa porcentagem de chochos, não deve residir nessas anomalias a causa procurada. Em estudos comparativos dos dois tipos de plantas do Mundo Novo e da variedade bourbon, pôde-se verificar : a que, em linhas gerais, o processo da formação do saco embrionário e o desenvolvimento do endosperma e do embrião são idênticos, havendo um ligeiro atrazo para as plantas Mundo Novo ; b que nestas últimas existem anormalidades diversas no saco embrionário, em proporção muito mais elevada do que no bourbon. Ocorrendo com igual freqüência nos dois tipos de plantas do café Mundo Novo, estas anormalidades também não devem se relacionar com a formação de chochos. Estudos realizados em frutos de diversas idades, permitiram relacionar a alta freqüência de lojas vazias com o aparecimento de uma estrutura anormal, em forma de disco, encontrada no interior dos restos de perisperma. Êste "disco" (com cêrca de 3 mm de diâmetro só apareceu na planta de alta freqüência de chochos, não tendo sido constatado na planta Mundo Novo de baixa freqüência de chochos, nem na planta bourbon. O exame citológico revelou que essa estrutura é constituida de endosperma, contendo um embrião anormal ; de côr clara a princípio, torna-se pardacenta à medida que degenera ; recebeu a denominação de "endosperma discóide". De oito plantas examinadas a seguir, encontrou-se endosperma disc

  11. 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...... of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y...

  12. Serine Hydroxymethyltransferase Anchors de Novo Thymidylate Synthesis Pathway to Nuclear Lamina for DNA Synthesis*

    Science.gov (United States)

    Anderson, Donald D.; Woeller, Collynn F.; Chiang, En-Pei; Shane, Barry; Stover, Patrick J.

    2012-01-01

    The de novo thymidylate biosynthetic pathway in mammalian cells translocates to the nucleus for DNA replication and repair and consists of the enzymes serine hydroxymethyltransferase 1 and 2α (SHMT1 and SHMT2α), thymidylate synthase, and dihydrofolate reductase. In this study, we demonstrate that this pathway forms a multienzyme complex that is associated with the nuclear lamina. SHMT1 or SHMT2α is required for co-localization of dihydrofolate reductase, SHMT, and thymidylate synthase to the nuclear lamina, indicating that SHMT serves as scaffold protein that is essential for complex formation. The metabolic complex is enriched at sites of DNA replication initiation and associated with proliferating cell nuclear antigen and other components of the DNA replication machinery. These data provide a mechanism for previous studies demonstrating that SHMT expression is rate-limiting for de novo thymidylate synthesis and indicate that de novo thymidylate biosynthesis occurs at replication forks. PMID:22235121

  13. 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.

  14. Reflexões sobre o Novo Desenvolvimentismo e o Desenvolvimentismo Clássico

    Directory of Open Access Journals (Sweden)

    LUIZ CARLOS BRESSER-PEREIRA

    2016-06-01

    Full Text Available RESUMO Este artigo, inicialmente, distingue, o Novo Desenvolvimentismo, um novo sistema teórico que está em criação, do desenvolvimentismo realmente existente, que foi responsável pelo desenvolvimento original de muitos países, mas muitas vezes é apenas uma forma de populismo fi ou keynesianismo vulgar. Segundo, distingue o Desenvolvimentismo Clássico, que o precedeu. Terceiro, brevemente analisa o chamado "social-desenvolvimentismo" e nada vê ali que se aproxime de uma teoria. Finalmente, o artigo fornece um resumo do Novo Desenvolvimentismo - seus principais argumentos no campo da economia política, da teoria econômica e da política econômica.

  15. 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...

  16. 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.

  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

    2011-06-02

    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.

  18. 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

    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...... for development of more sustainable production systems in healthcare”. Future R&D performed within the framework of our NOVO network should substantiate this hypothesis. In practical terms, this necessitates expanded research protocols....... 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...

  19. Recurrent and de novo glomerulonephritis following renal transplantation: higher rates of rejection and lower graft survival.

    Science.gov (United States)

    Mirioglu, Safak; Caliskan, Yasar; Goksoy, Yagmur; Gulcicek, Sibel; Ozluk, Yasemin; Sarihan, Irem; Seyahi, Nurhan; Kilicaslan, Isin; Turkmen, Aydin; Sever, Mehmet Sukru

    2017-12-01

    In this retrospective study with case-control design, we aimed to determine the clinical and pathological characteristics of post-transplant glomerulonephritis (GN), and their effects on transplant recipients. One hundred and twenty renal transplant recipients with biopsy-proven recurrent or de novo primary GN were compared with two matched control groups including 120 transplant recipients with nonrecurrent primary GN (nonrecurrent GN group) and 120 transplant recipients with non-GN etiology (non-GN group). Primary outcome was allograft loss, and secondary outcomes were biopsy-confirmed cellular or antibody-mediated rejection. In recurrent/de novo GN, nonrecurrent GN and non-GN groups, 54.2% (n = 65), 16.7% (n = 20) and 8.3% (n = 10) of patients reached primary outcome after a median follow-up of 96 (IQR: 56-149) months, respectively. Allograft loss was significantly higher in recurrent/de novo GN group compared to nonrecurrent GN and non-GN groups (p < 0.001). At 10 years, allograft loss rates in recurrent/de novo GN group were 54.2% for focal segmental glomerulosclerosis, 53.2% for membranoproliferative glomerulonephritis, and 33.4% for IgA nephropathy cases. Biopsy-confirmed rejection rate was significantly higher in the recurrent/de novo GN group (n = 25, 20.8%) compared to non-GN (n = 8, 6.7%) group (p = 0.001). Recurrent/de novo GN is associated with higher risk of rejection and worse allograft survival.

  20. 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.

  1. Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors.

    Science.gov (United States)

    Schneider, Gisbert; Geppert, Tim; Hartenfeller, Markus; Reisen, Felix; Klenner, Alexander; Reutlinger, Michael; Hähnke, Volker; Hiss, Jan A; Zettl, Heiko; Keppner, Sarah; Spänkuch, Birgit; Schneider, Petra

    2011-03-01

    De novo design of drug-like compounds with a desired pharmacological activity profile has become feasible through innovative computer algorithms. Fragment-based design and simulated chemical reactions allow for the rapid generation of candidate compounds as blueprints for organic synthesis. We used a combination of complementary virtual-screening tools for the analysis of de novo designed compounds that were generated with the aim to inhibit inactive polo-like kinase 1 (Plk1), a target for the development of cancer therapeutics. A homology model of the inactive state of Plk1 was constructed and the nucleotide binding pocket conformations in the DFG-in and DFG-out state were compared. The de novo-designed compounds were analyzed using pharmacophore matching, structure-activity landscape analysis, and automated ligand docking. One compound was synthesized and tested in vitro. The majority of the designed compounds possess a generic architecture present in known kinase inhibitors. Predictions favor kinases as targets of these compounds but also suggest potential off-target effects. Several bioisosteric replacements were suggested, and de novo designed compounds were assessed by automated docking for potential binding preference toward the inactive (type II inhibitors) over the active conformation (type I inhibitors) of the kinase ATP binding site. One selected compound was successfully synthesized as suggested by the software. The de novo-designed compound exhibited inhibitory activity against inactive Plk1 in vitro, but did not show significant inhibition of active Plk1 and 38 other kinases tested. Computer-based de novo design of screening candidates in combination with ligand- and receptor-based virtual screening generates motivated suggestions for focused library design in hit and lead discovery. Attractive, synthetically accessible compounds can be obtained together with predicted on- and off-target profiles and desired activities.

  2. Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.

    Directory of Open Access Journals (Sweden)

    Xin He

    Full Text Available De novo mutations affect risk for many diseases and disorders, especially those with early-onset. An example is autism spectrum disorders (ASD. Four recent whole-exome sequencing (WES studies of ASD families revealed a handful of novel risk genes, based on independent de novo loss-of-function (LoF mutations falling in the same gene, and found that de novo LoF mutations occurred at a twofold higher rate than expected by chance. However successful these studies were, they used only a small fraction of the data, excluding other types of de novo mutations and inherited rare variants. Moreover, such analyses cannot readily incorporate data from case-control studies. An important research challenge in gene discovery, therefore, is to develop statistical methods that accommodate a broader class of rare variation. We develop methods that can incorporate WES data regarding de novo mutations, inherited variants present, and variants identified within cases and controls. TADA, for Transmission And De novo Association, integrates these data by a gene-based likelihood model involving parameters for allele frequencies and gene-specific penetrances. Inference is based on a Hierarchical Bayes strategy that borrows information across all genes to infer parameters that would be difficult to estimate for individual genes. In addition to theoretical development we validated TADA using realistic simulations mimicking rare, large-effect mutations affecting risk for ASD and show it has dramatically better power than other common methods of analysis. Thus TADA's integration of various kinds of WES data can be a highly effective means of identifying novel risk genes. Indeed, application of TADA to WES data from subjects with ASD and their families, as well as from a study of ASD subjects and controls, revealed several novel and promising ASD candidate genes with strong statistical support.

  3. Os desdobramentos da trama e de seres em admirável mundo novo e rizoma

    OpenAIRE

    Sá, Jussara Bittencourt de

    2010-01-01

    Resumo: Na leitura de Admirável Mundo Novo, de Aldoux Huxley, que apresento, atento para o movimento utópico que advém deste texto articulando-o ao Le principe Espérance, de Ernst Bloch. Um outro aspecto é o agenciamento entre a teoria de reprodução social da obra de Huxley e a teoria do rizoma, desenvolvida em Mil Platôs, de Deleuze e Gattari (1995-1997). Abstract:In this article, I present a study of Admirável Mundo Novo by Aldoux Huxley, intent for the utopian movement that becomes from th...

  4. Diagnosis of Solid Waste Management in The Town of Novo Hamburgo, Rio Grande do Sul

    OpenAIRE

    Karin Luise dos Santos; Roberto Naime

    2010-01-01

    This study is an analysis of the current solid waste management in the municipality of Novo Hamburgo, located in the river basin of the rio dos Sinos, in the metropolitan region of Porto Alegre-RS. Based on data provided by the City Hall, are described and evaluated all the processes involved from generation to final disposal of domestic solid waste from the town. The town of Novo Hamburgo is the largest municipality integral basin of the river valley of the rio dos Sinos. It counts on a form...

  5. Comunidade Novo Horizonte no Lago Janauac? ? AM sob uma ?tica socioecon?mica, ambiental e cultural

    OpenAIRE

    Candido, Priscilla Ribeiro

    2014-01-01

    As popula??es tradicionais da Amaz?nia dentro de um novo contexto mundial assumem um papel de grande relev?ncia para a preserva??o do meio ambiente e para a pr?tica do desenvolvimento sustent?vel. Estas popula??es tradicionais fazem o uso de diversas pr?ticas de agricultura e de pesca transmitidas de gera??o para gera??o. Esta pesquisa consiste em um estudo descritivo explorat?rio, cujo objetivo geral ? caracterizar a comunidade Novo Horizonte no Lago Janauac?, situada no estado do Amazonas, ...

  6. 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...... 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...

  7. De Novo Histoid Leprosy in an Elderly: A Case Report and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Deepak Dimri

    2012-01-01

    Full Text Available Histoid leprosy, an uncommon variant of lepromatous leprosy, develops usually as relapse in lepromatous patients who are on dapsone monotherapy, but uncommonly arises de novo. This rare form of the disease, with unique clinical and histopathological features, may pose a diagnostic challenge even to astute clinicians. We report the case that occurred de novo in an elderly who presented with small to large lesions all over the body. A fresh focus on histoid leprosy is the primary objective of this paper, especially in the context of the postglobal leprosy elimination era.

  8. 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

  9. A mulher trabalhadora em Santa Maria durante o Estado Novo (1937-1945 = The woman worker in Santa Maria during the Estado Novo (1937-1945

    Directory of Open Access Journals (Sweden)

    Fausto, Letícia da Silva

    2014-01-01

    Full Text Available Este trabalho apresenta um estudo sobre a história das mulheres santamarienses no período da Ditadura do Estado Novo, que está sendo desenvolvido no Mestrado em História da Universidade Federal de Santa Maria (UFSM. O tema da pesquisa é a inserção da mulher no mundo do trabalho e sua atuação para a garantia e conquista de direitos sociais e trabalhistas durante o período do Estado Novo (1937-1945, no município de Santa Maria, RS. A escolha do Estado Novo no Brasil se deu em virtude deste ser um período onde muitas conquistas dos trabalhadores estavam sendo objeto de legislação específica e ao mesmo tempo um momento de repressão política, de forte aparato policial e repressivo e do fortalecimento dos sindicatos, sob a tutela do Estado e da luta dos trabalhadores para a garantia destes direitos, historicamente conquistados. As mulheres por séculos passaram despercebidas pela história, reprimidas em uma sociedade machista e autoritária, onde grande parte dos autores insere o homem no palco das lutas por reinvindicações e direitos trabalhistas

  10. 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

    , 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...

  11. Failure of stop and go in de novo Parkinson's disease-a functional magnetic resonance imaging study

    NARCIS (Netherlands)

    Vriend, Chris; Gerrits, Niels J H M; Berendse, Henk W; Veltman, Dick J; van den Heuvel, Odile A; van der Werf, Ysbrand D

    Behavioral impairments in response inhibition and initiation are common in Parkinson's disease (PD) and are associated with reduced impulse control. No prior study, however, has investigated the functional correlates of response inhibition in de novo PD. Twenty-one de novo PD patients and 37 matched

  12. Analysis of Pyrimidine Synthesis "de Novo" Intermediates in Urine and Dried Urine Filter- Paper Strips with HPLC-Electrospray Tandem Mass Spectrometry

    National Research Council Canada - National Science Library

    van Kuilenburg, Andre B.P; van Lenthe, Henk; Loffler, Monika; van Gennip, Albert H

    2004-01-01

    ...: 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...

  13. Predictive Factors of De Novo Overactive Bladder after Artificial Urinary Sphincter Implantation in Men with Post-Prostatectomy Incontinence.

    Science.gov (United States)

    Ko, Kwang Jin; Lee, Chung Un; Kim, Tae Heon; Suh, Yoon Seok; Lee, Kyu-Sung

    2017-10-10

    To investigate the rates and predictive factors associated with the development of de novo overactive bladder (OAB) and assess the effects of de novo OAB on surgical outcomes after artificial urinary sphincter (AUS). We performed a retrospective review of 132 post-prostatectomy incontinence patients who underwent AUS surgery. Urodynamic studies were performed during preoperative visits in all patients, and patients with OAB or neurogenic bladder were excluded. We assessed the development of de novo OAB based on patient symptoms. Treatment success was defined as no need per pads and social continence was defined as need for pad ≤1/day at the end of the follow-up. A multivariate analysis was performed using a logistic regression model to assess predictors of de novo OAB. The rate of development de novo OAB after surgery was 37.5%. The treatment success rate was significantly higher in the no OAB group (72.4%) than the de novo OAB group (55.4%) (p=0.038). Low preoperative cystometric capacity less than 300ml (OR 5.27, CI 1.02-27.28; p=0.048) and pelvic irradiation (OR 3.18, CI 1.01-10.03; p=0.049) were predictive factors of de novo OAB after AUS surgery. De novo OAB occurs commonly after AUS surgery and the presence of de novo OAB adversely impacts treatment success. Low preoperative cystometric capacity of less than 300ml and pelvic irradiation predict the occurrence of de novo OAB after AUS implantation. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Caracterização dos constituintes poliméricos da Maytenus ilicifolia por relaxação nuclear de ¹H por RMN no estado sólido Characterization of Maytenus ilicifolia Samples by ¹H NMR relaxation in the solid state

    Directory of Open Access Journals (Sweden)

    Mônica S. de M. Preto

    2011-01-01

    Full Text Available A Maytenus ilicifolia, conhecida como espinheira-santa, é uma planta popular de uso diverso, como chá é empregada no combate a problemas de doenças gástricas e da diabetes, por exemplo. As plantas possuem em sua constituição polímeros naturais como polissacarídeos, politerpenoides, celulose e fibras. O estudo dos constituintes poliméricos nesse tipo de material tem importância fundamental tanto na identificação, ou seja, qualificação quanto na adulteração da planta. É sabido que podem ser encontrados diversos produtos rotulados como sendo originário da mesma planta, entretanto, muitas das vezes a origem da planta é similar, mas não a mesma, o que pode gerar algum desconforto ou não atividade biológica dos chás quando da ingestão destes. Na literatura não são encontrados muitos trabalhos que envolvam a caracterização comparativa dos constituintes poliméricos, como polissacarídeos e fibras presentes em amostras de origens distintas, para comprovação de adulteração destes produtos. Uma técnica que pode ser promissora para este tipo de estudo é a Ressonância Magnética Nuclear (RMN em estado sólido, já que permite analisar a amostra in natura não sendo um método destrutivo ou invasivo. Esta espectroscopia analisa amostras em campos magnéticos de diferentes potências ou forças. Neste trabalho é apresentado um estudo de caracterização dos constituintes poliméricos majoritários presentes na M. ilicifolia. Três amostras foram estudadas: uma amostra denominada controle e duas comerciais. O estudo envolveu a determinação dos tempos de relaxação spin-rede (T1 do ¹H utilizando a técnica de campo cíclico rápido (FFC, numa gama de frequências que variou de 100 kHz a 10 MHz. Assim, o principal objetivo deste trabalho foi estudar a possibilidade de utilização da RMN de baixo campo magnético na elaboração de um método expedito de análise que permita realizar a caracterização estrutural

  15. 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.

  16. 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...

  17. 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...

  18. 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.

  19. A framework for the detection of de novo mutations in family-based sequencing data

    NARCIS (Netherlands)

    L.C. Francioli (Laurent); M. Cretu-Stancu (Mircea); K.V. Garimella (Kiran); M. Fromer (Menachem); W.P. Kloosterman (Wigard); Genome of the Netherlands Consortium; K. Samocha (Kaitlin); B. Neale (Benjamin); M.J. Daly (Mark); E. Banks (Eric); M.A. DePristo (Mark); P.I.W. de Bakker (Paul)

    2017-01-01

    textabstractGermline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single

  20. A framework for the detection of de novo mutations in family-based sequencing data

    NARCIS (Netherlands)

    Francioli, Laurent C.; Cretu-Stancu, Mircea; Garimella, Kiran V.; Fromer, Menachem; Kloosterman, Wigard P.|info:eu-repo/dai/nl/304076953; Samocha, Kaitlin E.; Neale, Benjamin M.; Daly, Mark J.; Banks, Eric; DePristo, Mark A.; de Bakker, Paul IW|info:eu-repo/dai/nl/342957082

    2016-01-01

    Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants

  1. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

    Science.gov (United States)

    De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol...

  2. 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 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.

  3. 76 FR 61103 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Science.gov (United States)

    2011-10-03

    ... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry and Food and Drug Administration... staff and industry on the process for the submission and review of petitions submitted under the Federal Food, Drug, and Cosmetic Act (FD&C Act), also known as the de novo classification process. FDA is...

  4. 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.

  5. 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

  6. 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...

  7. 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...

  8. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts.

    Science.gov (United States)

    Awadalla, Philip; Gauthier, Julie; Myers, Rachel A; Casals, Ferran; Hamdan, Fadi F; Griffing, Alexander R; Côté, Mélanie; Henrion, Edouard; Spiegelman, Dan; Tarabeux, Julien; Piton, Amélie; Yang, Yan; Boyko, Adam; Bustamante, Carlos; Xiong, Lan; Rapoport, Judith L; Addington, Anjené M; DeLisi, J Lynn E; Krebs, Marie-Odile; Joober, Ridha; Millet, Bruno; Fombonne, Eric; Mottron, Laurent; Zilversmit, Martine; Keebler, Jon; Daoud, Hussein; Marineau, Claude; Roy-Gagnon, Marie-Hélène; Dubé, Marie-Pierre; Eyre-Walker, Adam; Drapeau, Pierre; Stone, Eric A; Lafrenière, Ronald G; Rouleau, Guy A

    2010-09-10

    The role of de novo mutations (DNMs) in common diseases remains largely unknown. Nonetheless, the rate of de novo deleterious mutations and the strength of selection against de novo mutations are critical to understanding the genetic architecture of a disease. Discovery of high-impact DNMs requires substantial high-resolution interrogation of partial or complete genomes of families via resequencing. We hypothesized that deleterious DNMs may play a role in cases of autism spectrum disorders (ASD) and schizophrenia (SCZ), two etiologically heterogeneous disorders with significantly reduced reproductive fitness. We present a direct measure of the de novo mutation rate (μ) and selective constraints from DNMs estimated from a deep resequencing data set generated from a large cohort of ASD and SCZ cases (n = 285) and population control individuals (n = 285) with available parental DNA. A survey of ∼430 Mb of DNA from 401 synapse-expressed genes across all cases and 25 Mb of DNA in controls found 28 candidate DNMs, 13 of which were cell line artifacts. Our calculated direct neutral mutation rate (1.36 × 10(-8)) is similar to previous indirect estimates, but we observed a significant excess of potentially deleterious DNMs in ASD and SCZ individuals. Our results emphasize the importance of DNMs as genetic mechanisms in ASD and SCZ and the limitations of using DNA from archived cell lines to identify functional variants. 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  9. Phenotype and clinical course in a family with a new de novo Twinkle gene mutation

    DEFF Research Database (Denmark)

    Jeppesen, Tina Dysgaard; Schwartz, M.; Colding-Jorgensen, E.

    2008-01-01

    The Twinkle gene product is important for mtDNA replication. Only a few reports have investigated the clinically effect of mutations in this gene. We describe a new de novo mutation (1110C > A) in the PEO1 gene in a mother and her two sons. The mother had progressive ophthalmoplegia, limb weakness...

  10. 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.

  11. De novo synthesis of multisubstituted aryl amines using alkene cross metathesis.

    Science.gov (United States)

    Tatton, Matthew R; Simpson, Iain; Donohoe, Timothy J

    2014-04-04

    The olefin cross-metathesis reaction allows rapid access to 1,5-dicarbonyl intermediates which, upon treatment with a primary or secondary amine, allow the synthesis of a range of multisubstituted carbocyclic aryl amines. This de novo arene synthesis yields nonclassical substitution patterns in a regioselective and predictable approach that is compatible with several functional groups.

  12. Impact of modern chemotherapy on the survival of women presenting with de novo metastatic breast cancer

    Directory of Open Access Journals (Sweden)

    Pal Sumanta K

    2012-09-01

    Full Text Available Abstract Background Data that directly associate utilization of novel systemic therapies with survival trends in metastatic breast cancer (MBC are limited. In the setting of de novo MBC, large registry analyses cite positive temporal trends in survival, but the extent to which advances in systemic therapy have contributed to these gains is not clear. Methods The City of Hope Cancer Registry was used to identify a consecutive series of patients with de novo MBC who received their first line of therapy between 1985 and 2004. Comprehensive clinicopathologic and treatment-related data were collected for each patient. Univariate analyses were conducted via Cox regression to identify factors associated with improved survival. Multivariate analysis was also conducted via Cox regression and the stepwise procedure was used to identify independent predictors of survival. Results A total of 324 patients with de novo MBC were identified. After application of exclusion criteria, including the sole presence of supraclavicular node metastasis, 274 patients were retained in the analysis. The treatment-related characteristics associated with improved survival included: use of endocrine therapy (hazard ratio [HR] 0.60, 95%CI 0.47-0.77; P Conclusions The overall survival of women with de novo metastatic breast cancer has improved over the past 20 years. However, the contribution of conventional cytotoxic agents to this improvement is minimal.

  13. Intravenous glutamine supplementation enhances renal de novo arginine synthesis in humans: a stable isotope study

    NARCIS (Netherlands)

    Buijs, Nikki; Brinkmann, Saskia J. H.; Oosterink, J. Efraim; Luttikhold, Joanna; Schierbeek, Henk; Wisselink, Willem; Beishuizen, Albertus; van Goudoever, Johannes B.; Houdijk, Alexander P. J.; van Leeuwen, Paul A. M.; Vermeulen, Mechteld A. R.

    2014-01-01

    Arginine plays a role in many different pathways in multiple cell types. Consequently, a shortage of arginine, caused by pathologic conditions such as cancer or injury, has the potential to disturb many cellular and organ functions. Glutamine is the ultimate source for de novo synthesis of arginine

  14. Monosaccharide templates for de novo designed 4-alpha-helix bundle proteins: template effects in carboproteins

    DEFF Research Database (Denmark)

    Brask, Jesper; Dideriksen, J.M.; Nielsen, John

    2003-01-01

    De novo design and total chemical synthesis of proteins provide powerful approaches to critically test our understanding of protein folding, structure, and stability. The 4-alpha-helix bundle is a frequently studied structure in which four amphiphilic alpha-helical peptide strands form...

  15. Interaction between Mutations and Regulation of Gene Expression during Development of de novo Antibiotic Resistance

    NARCIS (Netherlands)

    Händel, N.; Schuurmans, J.M.; Feng, Y.; Brul, S.; ter Kuile, B.H.

    2014-01-01

    Bacteria can become resistant not only by horizontal gene transfer or other forms of exchange of genetic information, but also de novo by adaptation at the gene expression level and through DNA mutations. The interrelationship between changes in gene expression and DNA mutations during acquisition

  16. De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

    NARCIS (Netherlands)

    Riviere, Jean-Baptiste; van Bon, Bregje W. M.; Hoischen, Alexander; Kholmanskikh, Stanislav S.; O'Roak, Brian J.; Gilissen, Christian; Gijsen, Sabine; Sullivan, Christopher T.; Christian, Susan L.; Abdul-Rahman, Omar A.; Atkin, Joan F.; Chassaing, Nicolas; Drouin-Garraud, Valerie; Fry, Andrew E.; Fryns, Jean-Pierre; Gripp, Karen W.; Kempers, Marlies; Kleefstra, Tjitske; Mancini, Grazia M. S.; Nowaczyk, Malgorzata J. M.; van Ravenswaaij-Arts, Conny M. A.; Roscioli, Tony; Marble, Michael; Rosenfeld, Jill A.; Siu, Victoria M.; de Vries, Bert B. A.; Shendure, Jay; Verloes, Alain; Veltman, Joris A.; Brunner, Han G.; Ross, M. Elizabeth; Pilz, Daniela T.; Dobyns, William B.

    Brain malformations are individually rare but collectively common causes of developmental disabilities(1-3). Many forms of malformation occur sporadically and are associated with reduced reproductive fitness, pointing to a causative role for de novo mutations(4,5). Here, we report a study of

  17. De novo mutations in the actin genes ACTB and ACTG1 cause Baraitser-Winter syndrome

    NARCIS (Netherlands)

    Riviere, J.B.; Bon, B.W. van; Hoischen, A.; Kholmanskikh, S.S.; O'Roak, B.J.; Gilissen, C.; Gijsen, S.; Sullivan, C.T.; Christian, S.L.; Abdul-Rahman, O.A.; Atkin, J.F.; Chassaing, N.; Drouin-Garraud, V.; Fry, A.E.; Fryns, J.P.; Gripp, K.W.; Kempers, M.; Kleefstra, T.; Mancini, G.M.; Nowaczyk, M.J.; Ravenswaaij-Arts, C.M. van; Roscioli, T.; Marble, M.; Rosenfeld, J.A.; Siu, V.M.; Vries, B.B. de; Shendure, J.; Verloes, A.; Veltman, J.A.; Brunner, H.G.; Ross, M.E.; Pilz, D.T.; Dobyns, W.B.

    2012-01-01

    Brain malformations are individually rare but collectively common causes of developmental disabilities. Many forms of malformation occur sporadically and are associated with reduced reproductive fitness, pointing to a causative role for de novo mutations. Here, we report a study of Baraitser-Winter

  18. Novel de novo nonsense mutation of FBN1 gene in a patient with ...

    Indian Academy of Sciences (India)

    Novel de novo nonsense mutation of FBN1 gene in a patient with Marfan syndrome. YOUNG-HWA SONG1, GU-HWAN KIM2, HAN-WOOK YOO2 and JUNE-BUM KIM3∗. 1Department of Pediatrics, Konyang University Hospital, 685 Gasoowon-Dong, Su-Goo, Daejun 302-718, Republic of Korea. 2Medical Genetics Clinic ...

  19. De novo reconstruction of plant RNA and DNA virus genomes from viral siRNAs

    Science.gov (United States)

    In antiviral defense, plants produce massive quantities of 21-24 nucleotide siRNAs. Here we demonstrate that the complete genomes of DNA and RNA viruses and viroids can be reconstructed by deep sequencing and de novo assembly of viral/viroid siRNAs from experimentally- and naturally-infected plants....

  20. 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...

  1. 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 mutat...

  2. De novo design and synthesis of water-soluble gold(I) compounds ...

    Indian Academy of Sciences (India)

    Administrator

    De novo design and synthesis of water-soluble gold(I) compounds: ... specific transition metal precursors) is central to the design and development of transition metal-based compounds that meet certain ... also brings about kinetic inertness, over a wide range of pH, in aqueous media 1,2. Gold compounds have been ...

  3. 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

  4. SCLLTargeting FGFR1 to suppress leukemogenesis in syndromic and de novo AML in murine models.

    Science.gov (United States)

    Wu, Qing; Bhole, Aaron; Qin, Haiyan; Karp, Judith; Malek, Sami; Cowell, John K; Ren, Mingqiang

    2016-08-02

    Although over expression of chimeric FGFR1 kinase consistently leads to the development of AML in the rare Stem Cell Leukemia and Lymphoma syndrome, we now show that overexpression of FGFR1 is also seen in up to 20% of non-syndromic, de novo AML. To determine whether targeting FGFR1 in both of these AML subtypes can suppress leukemogenesis, we evaluated the effects of different FGFR1 inhibitors in a side-by-side comparison for their ability to affect in vitro proliferation in FGFR1 overexpressing murine and human cells lines. Three newly developed pan-FGFR inhibitors, AZD4547, BGJ398 and JNJ42756493, show a significantly improved efficacy over the more established FGFR inhibitors, PD173074 and TKI258. To examine whether targeting FGFR1 suppresses leukemogenesis in de novo AML in vivo, we created xenografts in immunocompromized mice from primary, de novo AML that showed > 3-fold increased expression of FGFR1. Using BGJ398, the most potent inhibitor identified in the in vitro studies, AML progression in these mice was significantly suppressed compared with vehicle treated animals and overall survival improved. Importantly, no difference in disease course or survival was seen in AML xenografts that did not show overexpression of FGFR1. These observations support the idea that FGFR1 is a driver oncogene in de novo, FGFR1-overexpressing AML and that molecularly targeted therapies using FGFR1 inhibitors may provide a valuable therapeutic regimen for all FGFR1-overexpressing AML.

  5. 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...

  6. De novo Xp terminal deletion in a triple X female with recurrent ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 3. De novo Xp terminal deletion in a triple X female with recurrent spontaneous abortions: a case report. Tahir M. Malla Arshad A. Pandith Fayaz A. Dar Mahrukh H. Zargar Zafar A. Shah. Research Note Volume 93 Issue 3 December 2014 pp 819-822 ...

  7. The present and future of de novo whole-genome assembly.

    Science.gov (United States)

    Sohn, Jang-Il; Nam, Jin-Wu

    2018-01-01

    As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. 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

  9. Increased de novo lipogenesis is a distinct characteristic of individuals with nonalcoholic fatty liver disease.

    Science.gov (United States)

    Lambert, Jennifer E; Ramos-Roman, Maria A; Browning, Jeffrey D; Parks, Elizabeth J

    2014-03-01

    There have been few studies of the role of de novo lipogenesis in the development of nonalcoholic fatty liver disease (NAFLD). We used isotope analyses to compare de novo lipogenesis and fatty acid flux between subjects with NAFLD and those without, matched for metabolic factors (controls). We studied subjects with metabolic syndrome and/or levels of alanine aminotransferase and aspartate aminotransferase >30 mU/L, using magnetic resonance spectroscopy to identify those with high levels (HighLF, n = 13) or low levels (LowLF, n = 11) of liver fat. Clinical and demographic information was collected from all participants, and insulin sensitivity was measured using the insulin-modified intravenous glucose tolerance test. Stable isotopes were administered and gas chromatography with mass spectrometry was used to analyze free (nonesterified) fatty acid (FFA) and triacylglycerol flux and lipogenesis. Subjects with HighLF (18.4% ± 3.6%) had higher plasma levels of FFAs during the nighttime and higher concentrations of insulin than subjects with LowLF (3.1% ± 2.7%; P = .04 and P novo fatty acid synthesis than subjects with LowLF (2.57 ± 1.53 μmol/min vs 0.78 ± 0.42 μmol/min; P = .001). As a percentage of triacylglycerol palmitate, de novo lipogenesis was 2-fold higher in subjects with HighLF (23.2% ± 7.9% vs 10.1% ± 6.7%; P novo lipogenesis on fasting. These findings indicate that lipogenesis might be a therapeutic target for NAFLD. Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

  10. 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

  11. 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.

  12. TRANSPORT OF PATIENTS FOR PRIMARY PTCA FROM GENERAL HOSPITAL NOVO MESTO TO LJUBLJANA

    Directory of Open Access Journals (Sweden)

    Renata Okrajšek

    2003-02-01

    Full Text Available Background. The treatment of acute coronary syndrom (ACS with ST-segment elevation with primary percutaneous transluminal coronary angioplasty (PTCA has been a routine method for treatment of these patients in KC Ljubljana since April 2000. Using this method, mortality due to ACS, reinfarction, total number of death and strokes in comparison to thrombolytic therapy were highly reduced. Since May 2001 primary PTCA has been attainable also for patients from regional hospitals to be transferred quickly enough to Ljubljana.Methods. A retrospective analysis of patients with ACS with ST-segment elevation who have been transferred from General Hospital Novo mesto to KC Ljubljana in the period from Oct. 1, 2001 to March 31, 2002 to have a primary PTCA was performed. The analysis comprised the following: time interval from the chest pain start to the arrival of patient to the General Hospital Novo mesto, handling of patient at Internistic department of General Hospital Novo mesto, transport of patient to Ljubljana and total time interval from the arrival of patient to the first inflation of balloon in Ljubljana.Results. In the upper mentioned period 14 patient (12 males and 2 females were transported from the General Hospital Novo mesto to the KC Ljubljana to perform a primary PTCA. Our patients arrive to hospital very late. Due to problems with transport organisation and patient’s escort and duty, total time interval measured between the patient arrival to the General Hospital Novo mesto to the first inflation of balloon in Ljubljana was 2h and 42 minutes. That was longer that had been stated previously in the literature.Conclusions. In our opinion, primary PTCA is practicable also for patients admitted to a regional hospital because of ACS with ST-segment elevation. The transport of patient is safe. Better organisation of Health Service and patient transportion would shorten the time needed to perform the first inflation of balloon in Ljubljana.

  13. Prenatally diagnosed de novo complex chromosome rearrangements: Two new cases and review of the literature

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz, C.; Grubs, R.E.; Jewett, T. [and others

    1994-09-01

    Complex chromosome rearrangements (CCR) are rare structural rearrangements involving at least three chromosomes with three or more breakpoints. Although there have been numerous reports of individuals with CCR, most have been ascertained through the presence of multiple congenital anomalies, recurrent pregnancy loss, or infertility. Few cases have been ascertained prenatally. We present two new cases of prenatally ascertained CCR. In the first case, an amniocentesis revealed an apparently balanced de novo rearrangement in which chromosomes 5, 6 and 11 were involved in a three-way translocation: 46,XY,t(6;5)(5;11)(q23;p14.3;q15;p13). The pregnancy was unevenful. Recently, at the age of 9 months, a physical and developmental evaluation were normal but, height, weight, and head circumference were below the 5th percentile. In the second case an amniocentesis revealed an unbalanced de novo rearrangement involving separate translocations and an interstitial deletion: 46,XY,del(6)(q25.3q27),t(3;8)(p13;q21.3),t(6;18)(p11.2;q11.2). A meconium plug was present at birth and at 6 months of age surgery for Hirschsprung`s disease was required. Currently, at 10 months of age, the patient has hypotonia and developmental delay. The paucity of information regarding prenatally diagnosed CCR poses a problem in counseling families. Of the four prenatally diagnosed balanced de novo CCR cases, three had abnormal outcomes. In a review of the literature, approximately 70% of the postnatally ascertained balanced de novo CCR cases were associated with congenital anomalies, growth retardation and/or mental retardation. More information regarding the outcome of prenatally ascertained balanced de novo CCR is required for accurate risk assessment.

  14. 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.

  15. Depiction of the martyrdom of Saint Ignatius Theophorus in the prothesis of Novo Hopovo

    Directory of Open Access Journals (Sweden)

    Popović Milica

    2015-01-01

    Full Text Available In the art of the Christian East, the depictions of the martyrdom of Saint Ignatius Theophorus, bishop of Antioch, can usually be found among the illustrations of the Menologion. The scene from the monastery of Novo Hopovo, dated to the 1600s, is one of the rare independent depictions of Saint Ignatius’s martyrdom. The paper discusses the iconography of this scene and possible reasons for placing it in the prothesis of the katholikon of Novo Hopovo. The inclusion of a scene showing the martyrdom of the bishop of Antioch into the thematic repertoire of this compartment is a solitary example in Serbian medieval and Byzantine monumental painting. [Projekat Ministarstva nauke Republike Srbije, br. 177036: Srpska srednjovekovna umetnost i njen evropski kontekst

  16. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

    Science.gov (United States)

    Yassour, Moran; Grabherr, Manfred; Blood, Philip D.; Bowden, Joshua; Couger, Matthew Brian; Eccles, David; Li, Bo; Lieber, Matthias; MacManes, Matthew D.; Ott, Michael; Orvis, Joshua; Pochet, Nathalie; Strozzi, Francesco; Weeks, Nathan; Westerman, Rick; William, Thomas; Dewey, Colin N.; Henschel, Robert; LeDuc, Richard D.; Friedman, Nir; Regev, Aviv

    2013-01-01

    De novo assembly of RNA-Seq data allows us to study transcriptomes without the need for a genome sequence, such as in non-model organisms of ecological and evolutionary importance, cancer samples, or the microbiome. In this protocol, we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms. We also present Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples, and approaches to identify protein coding genes. In an included tutorial we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sf.net. PMID:23845962

  17. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

    DEFF Research Database (Denmark)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo

    2012-01-01

    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....... 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...... 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....

  18. Top-down analysis of protein samples by de novo sequencing techniques

    Energy Technology Data Exchange (ETDEWEB)

    Vyatkina, Kira; Wu, Si; Dekker, Lennard J. M.; VanDuijn, Martijn M.; Liu, Xiaowen; Tolić, Nikola; Luider, Theo M.; Paša-Tolić, Ljiljana; Pevzner, Pavel A.

    2016-05-14

    MOTIVATION: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. RESULTS: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.

  19. Augmenting transcriptome assembly by combining de novo and genome-guided tools

    Directory of Open Access Journals (Sweden)

    Prachi Jain

    2013-08-01

    Full Text Available Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both de novo and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.

  20. Nucleolar development and allocation of key nucleolar proteins require de novo transcription in bovine embryos

    DEFF Research Database (Denmark)

    Svarcova, Olga; Laurincik, Jozef; Avery, Birthe

    2007-01-01

    The goal of the present study was to investigate whether key nucleolar proteins involved in ribosomal RNA (rRNA) transcription and processing are transcribed de novo or from maternally inherited messenger RNAs (mRNA) in bovine embryos, and to which extent de novo transcription of these proteins mRNA...... embryos cultured from the 2-cell stage with or without (control groups) a-amanitin, which blocks the RNA plymerases II and III transcription and, thus the synthesis of mRNA. In the control groups, weak autoradiographic labelling was initially observed in the periphery of few nuclei at the 4-cell...... is required for the development of functional nucleoli during the major activation of the embryonic genome. Immunofluorescence for localization of key nucleolar proteins, autoradiography for detection of transcriptional activity, and transmission electron microscopy were applied to in vitro produc ed bovine...

  1. A strategy to identify de novo mutations in common disorders such as autism and schizophrenia.

    Science.gov (United States)

    Julie, Gauthier; Hamdan, Fadi F; Rouleau, Guy A

    2011-06-15

    There are several lines of evidence supporting the role of de novo mutations as a mechanism for common disorders, such as autism and schizophrenia. First, the de novo mutation rate in humans is relatively high, so new mutations are generated at a high frequency in the population. However, de novo mutations have not been reported in most common diseases. Mutations in genes leading to severe diseases where there is a strong negative selection against the phenotype, such as lethality in embryonic stages or reduced reproductive fitness, will not be transmitted to multiple family members, and therefore will not be detected by linkage gene mapping or association studies. The observation of very high concordance in monozygotic twins and very low concordance in dizygotic twins also strongly supports the hypothesis that a significant fraction of cases may result from new mutations. Such is the case for diseases such as autism and schizophrenia. Second, despite reduced reproductive fitness(1) and extremely variable environmental factors, the incidence of some diseases is maintained worldwide at a relatively high and constant rate. This is the case for autism and schizophrenia, with an incidence of approximately 1% worldwide. Mutational load can be thought of as a balance between selection for or against a deleterious mutation and its production by de novo mutation. Lower rates of reproduction constitute a negative selection factor that should reduce the number of mutant alleles in the population, ultimately leading to decreased disease prevalence. These selective pressures tend to be of different intensity in different environments. Nonetheless, these severe mental disorders have been maintained at a constant relatively high prevalence in the worldwide population across a wide range of cultures and countries despite a strong negative selection against them(2). This is not what one would predict in diseases with reduced reproductive fitness, unless there was a high new

  2. Destabilization of Fatty Acid Synthase by Acetylation Inhibits De Novo Lipogenesis and Tumor Cell Growth.

    Science.gov (United States)

    Lin, Huai-Peng; Cheng, Zhou-Li; He, Ruo-Yu; Song, Lei; Tian, Meng-Xin; Zhou, Li-Sha; Groh, Beezly S; Liu, Wei-Ren; Ji, Min-Biao; Ding, Chen; Shi, Ying-Hong; Guan, Kun-Liang; Ye, Dan; Xiong, Yue

    2016-12-01

    Fatty acid synthase (FASN) is the terminal enzyme in de novo lipogenesis and plays a key role in cell proliferation. Pharmacologic inhibitors of FASN are being evaluated in clinical trials for treatment of cancer, obesity, and other diseases. Here, we report a previously unknown mechanism of FASN regulation involving its acetylation by KAT8 and its deacetylation by HDAC3. FASN acetylation promoted its degradation via the ubiquitin-proteasome pathway. FASN acetylation enhanced its association with the E3 ubiquitin ligase TRIM21. Acetylation destabilized FASN and resulted in decreased de novo lipogenesis and tumor cell growth. FASN acetylation was frequently reduced in human hepatocellular carcinoma samples, which correlated with increased HDAC3 expression and FASN protein levels. Our results suggest opportunities to target FASN acetylation as an anticancer strategy. Cancer Res; 76(23); 6924-36. ©2016 AACR. ©2016 American Association for Cancer Research.

  3. EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

    Science.gov (United States)

    Chu, Hsueh-Ting; Hsiao, William W L; Chen, Jen-Chih; Yeh, Tze-Jung; Tsai, Mong-Hsun; Lin, Han; Liu, Yen-Wenn; Lee, Sheng-An; Chen, Chaur-Chin; Tsao, Theresa T H; Kao, Cheng-Yan

    2013-04-15

    High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data. EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases. EBARDenovo is available at http://ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only. Supplementary data are available at Bioinformatics online.

  4. 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

    .5 years (median) was an overall risk factor for surgical wound complications regardless of treatment group (p=0.025). There was no difference in the EVE versus CyA group with regards to other surgical events. Majority of events were in 1/3 of the patients. CONCLUSION: De novo initiation of EVE and early......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...... (CNI) avoidance (SCHEDULE). The aim of the study was to compare wound complications between EVE and CNI based regimen. MATERIALS AND METHODS: A total of 115 patients (mean age 51 ± 13 years, 73% men) were randomized within five days post-HTx to low dose EVE and reduced dose Cyclosporine (CyA) followed...

  5. Patients with Fanconi anemia and AML have different cytogenetic clones than de novo cases of AML.

    Science.gov (United States)

    Rochowski, Andrzej; Olson, Susan B; Alonzo, Todd A; Gerbing, Robert B; Lange, Beverly J; Alter, Blanche P

    2012-11-01

    Specific cytogenetic clones might distinguish patients with unrecognized Fanconi anemia (FA) who present with acute myeloid leukemia (AML) from those with sporadic AML. Cytogenetic reports in literature cases of FA and AML were compared with de novo cases enrolled on CCG-2961. Gain of 1q, gain of 3q, monosomy 7, deleted 7q, gain of 13q, and deleted 20q were more frequent in FA AML; t(8;21), trisomy 8, t(9;11), t(6;9), and inversion 16 were exclusive to de novo AML cases. Observation of the FA AML cytogenetic clonal patterns should raise suspicion of an underlying leukemia predisposition syndrome and influence management. Copyright © 2012 Wiley Periodicals, Inc. This article is a U.S. Government work and is in the public domain in the USA.

  6. 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.

  7. A trilha de Morales: novo movimento social indígena na Bolívia

    Directory of Open Access Journals (Sweden)

    Carlos Jahnsen Gutierrez

    2007-03-01

    Full Text Available O artigo discute as condições socioeconômicas que possibilitaram a emergência de novos movimentos sociais na Bolívia, sob a liderança dos povos indígenas e plantadores de coca. Esses movimentos sociais apoiaram o presidente Evo Morales nas eleições de dezembro de 2005. Analisa também as dificuldades e contradições enfrentadas pelo novo governo.This paper deals with social and economic conditions which made possible the emergence of new social movements in Bolivia under the leadership of indigenous peoples and coca farmers. These social movements supported the president Evo Morales in December 2005 elections. It also describes hindrances and contradictions faced by this new government.

  8. Dominant transmission of de novo KIF1A motor domain variant underlying pure spastic paraplegia.

    Science.gov (United States)

    Ylikallio, Emil; Kim, Doyoun; Isohanni, Pirjo; Auranen, Mari; Kim, Eunjoon; Lönnqvist, Tuula; Tyynismaa, Henna

    2015-10-01

    Variants in family 1 kinesin (KIF1A), which encodes a kinesin axonal motor protein, have been described to cause variable neurological manifestations. Recessive missense variants have led to spastic paraplegia, and recessive truncations to sensory and autonomic neuropathy. De novo missense variants cause developmental delay or intellectual disability, cerebellar atrophy and variable spasticity. We describe a family with father-to-son transmission of de novo variant in the KIF1A motor domain, in a phenotype of pure spastic paraplegia. Structural modeling of the predicted p.(Ser69Leu) amino acid change suggested that it impairs the stable binding of ATP to the KIF1A protein. Our study reports the first dominantly inherited KIF1A variant and expands the spectrum of phenotypes caused by heterozygous KIF1A motor domain variants to include pure spastic paraplegia. We conclude that KIF1A should be considered a candidate gene for hereditary paraplegias regardless of inheritance pattern.

  9. De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress.

    Science.gov (United States)

    Zhan, Xiangqiang; Yang, Lan; Wang, Dong; Zhu, Jian Kang; Lang, Zhaobo

    2016-03-09

    Ocimum americanum var. pilosum is a chilling-sensitive, widely distributed plant that is consumed as a vegetable in central and southern China. To increase our understanding of cold stress responses in this species, we performed de novo transcriptome assembly for O. americanum var. pilosum and compared the transcriptomes of plants grown under normal and low temperatures. A total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. After isoforms were considered, 42,816 unigenes were generated, 30,748 of which were similar to known proteins as determined by a BLASTx search (E-value stress, respectively. Expression of the 10 most up-regulated and the five most down-regulated unigenes was validated by qRT-PCR. To increase our understanding of these differentially expressed unigenes, we performed Gene ontology and KEGG pathway enrichment analyses. The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome. Our study has generated a genome-wide transcript profile of O. americanum var. pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. This is the first study to assess the cold-responsive transcriptome in an Ocimum species. Our results suggest that cold temperature significantly affects genes related to protein translation and cellular metabolism in this chilling sensitive species. Although most of the CBF pathway genes have orthologs in O. americanum var. pilosum, none of the identified cold responsive (COR) gene orthologs was induced by cold, which is consistent with the lack of cold tolerance in this plant.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Trabalho, precarização e resistências: novos e velhos desafios?

    Directory of Open Access Journals (Sweden)

    Graça Druck

    Full Text Available O artigo discute por que a precarização social do trabalho é um novo e velho fenômeno, é diferente e igual, é passado e presente, um fenômeno de caráter macro e microssocial. Apresenta alguns fetiches presentes nas análises sobre o trabalho no contexto de mundialização do capital, marcado pela hegemonia do capital financeiro, pela reestruturação da produção e do trabalho e por um "novo espírito do capitalismo". São cinco seções: introdução; discussão sobre aspectos metodológicos a partir de reflexões de projetos de pesquisa em andamento; considerações teóricas sobre a caracterização do capitalismo flexível e a centralidade da precarização social do trabalho; contextualização do trabalho na América Latina e no Brasil à luz dos estudos da OIT, indicadores de precarização e de resistências; e debate os velhos e novos desafios trazidos pelas transformações sob a égide da precarização social do trabalho e de um "espírito do capitalismo" reformulado, que, ao mesmo tempo em que reafirma o velho espírito, constitui um novo espírito.

  12. APONTAMENTOS SOBRE O USO DA FOTOGRAFIA PELA POLÍCIA POLÍTICA NO ESTADO NOVO

    OpenAIRE

    Carvalho, Thiago Fabres de; Bisi, Adriana de Oliveira Gonzaga

    2016-01-01

    Academic studies demonstrate the wide use of photography by the Police Policy (DEOPS) in the Estado Novo regime. This article seeks to assert that the photographic image acquires such centrality in police institutional practice. The 'declared ' explanation is that the technical use of photography, given the objectivity and realism to it intrinsic, is a legitimate tool to record and demonstrate the political crime. In addition, the study aims to reveal the functions ' undeclared ' the implemen...

  13. Clinical Implications of Phosphorylated STAT3 Expression in de novo Diffuse Large B-cell Lymphoma

    DEFF Research Database (Denmark)

    Ok, Chi Y; Chen, Jiayu; Xu-Monette, Ziju

    2014-01-01

    of phosphorylated STAT3 (pSTAT3) on prognosis are limited. EXPERIMENTAL DESIGN: We evaluated expression of pSTAT3 in de novo DLBCL using immunohistochemistry, gene expression profiling (GEP), and gene set enrichment analysis (GSEA). Results were analyzed in correlation with cell-of-origin (COO), critical lymphoma...... for the ongoing successful clinical trials targeting the JAK-STAT pathway in DLBCL. Clin Cancer Res; 20(19); 5113-23. ©2014 AACR....

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects

    OpenAIRE

    Liu, Binghang; Shi, Yujian; Yuan, Jianying; Hu, Xuesong; Zhang, Hao; Nan LI.; Li, Zhenyu; Chen, Yanxiang; Mu, Desheng; Fan, Wei

    2013-01-01

    Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the accurate genome size and repeat content. Furthermore, many genomes are highly repetitive or heterozygous, posing problems to current assemblers utilizing short reads. Therefore, it is necessary to develop efficient assembly-independent me...

  16. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.

    Science.gov (United States)

    Cabau, Cédric; Escudié, Frédéric; Djari, Anis; Guiguen, Yann; Bobe, Julien; Klopp, Christophe

    2017-01-01

    De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

  17. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

    Science.gov (United States)

    Li, Heng

    2012-01-01

    Motivation: Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs. Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly can be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we propose FMD-index for forward–backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index. Availability: http://github.com/lh3/fermi Contact: hengli@broadinstitute.org PMID:22569178

  18. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

    Science.gov (United States)

    O'Roak, Brian J; Vives, Laura; Girirajan, Santhosh; Karakoc, Emre; Krumm, Niklas; Coe, Bradley P; Levy, Roie; Ko, Arthur; Lee, Choli; Smith, Joshua D; Turner, Emily H; Stanaway, Ian B; Vernot, Benjamin; Malig, Maika; Baker, Carl; Reilly, Beau; Akey, Joshua M; Borenstein, Elhanan; Rieder, Mark J; Nickerson, Deborah A; Bernier, Raphael; Shendure, Jay; Eichler, Evan E

    2012-04-04

    It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.

  19. [Abnormality of blood coagulation indexes in patients with de novo acute leukemia and its clinical significance].

    Science.gov (United States)

    Xiao, Fang-Fang; Hu, Kai-Xun; Guo, Mei; Qiao, Jian-Hui; Sun, Qi-Yun; Ai, Hui-Sheng; Yu, Chang-Lin

    2013-04-01

    To explore hemorrhage risk and the clinical significance of abnormal change of prothrombin time (PT), activated partial thromboplastin time (APTT), plasma fibrinogen (FIB), plasma thrombin time (TT) and d-dimer (D-D) in de novo acute leukemia (except for APL), the different bleeding manifestations of 114 cases of de novo acute leukemia with different coagulation indexes were analyzed retrospectively. The correlation between these blood coagulation indexes and the possible correlative clinical characteristics were analysed, including age, sex, type of acute leukemia, initial white blood cell(WBC) and platelet(Plt) count, the proportion of blast cells in bone marrow and cytogenetic abnormality of patients at diagnosis. The results indicated that the incidence of abnormal blood coagulation was as high as 78.1% for de novo AL patients. These patients with 5 normal blood coagulation indexes may have mild bleeding manifestation, but the more abnormal indexes, the more severe bleeding. Both PT and D-D were sensitive indexes for diagnosis of level II bleeding. Incidence of abnormal blood coagulation significantly correlates with the proportion of blast cells in bone marrow (χ(2) = 4.184, OR = 1.021, P coagulation. It is concluded that the coagulation and fibrinolysis are abnormal in most patients with de novo acute leukemia. More abnormal indexes indicate more severe bleeding, and both PT and D-D are sensitive indexes for diagnosis of level II bleeding. Higher proportion of blast cells in bone marrow predicts higher incidence of abnormal blood clotting. Acute leukemia with elderly age, high white blood cell count and adverse cytogenetics do not predict severer abnormal blood clotting. Detection of PT, APTT, TT, FIB, and D-D may help to judge whether the patients are in a state of hypercoagulability or disseminated intravenous coagulation, which will provide experiment evidences for early intervention and medication.

  20. De novo cancer-related death in Australian liver and cardiothoracic transplant recipients.

    Science.gov (United States)

    Na, R; Grulich, A E; Meagher, N S; McCaughan, G W; Keogh, A M; Vajdic, C M

    2013-05-01

    Evidence is sparse on the relative mortality risk posed by de novo cancers in liver and cardiothoracic transplant recipients. A retrospective cohort study was conducted in Australia using population-based liver (n = 1926) and cardiothoracic (n = 2718) registries (1984-2006). Standardized mortality ratios (SMRs) were computed by cancer type, transplanted organ, recipient age and sex. During a median 5-year follow-up, de novo cancer-related mortality risk in liver and cardiothoracic recipients was significantly elevated compared to the matched general population (n = 171; SMR = 2.83; 95% confidence interval [95%CI], 2.43-3.27). Excess risk was observed regardless of transplanted organ, recipient age group or sex. Non-Hodgkin lymphoma was the most common cancer-related death (n = 38; SMR = 16.6; 95%CI, 11.87-22.8). The highest relative risk was for nonmelanocytic skin cancer (n = 23; SMR = 49.6, 95%CI, 31.5-74.5), predominantly in males and in recipients of heart and lung transplants. Risk of death from de novo cancer was high in pediatric recipients (n = 5; SMR = 41.3; 95%CI, 13.4-96.5), four of the five deaths were non-Hodgkin lymphoma. De novo cancer was a leading cause of late death, particularly in heart and liver transplantation. These findings support tailored cancer prevention strategies, surveillance to promote early detection, and guidelines for managing immunosuppression once cancer occurs. © Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.

  1. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

    Science.gov (United States)

    Hamdan, Fadi F; Myers, Candace T; Cossette, Patrick; Lemay, Philippe; Spiegelman, Dan; Laporte, Alexandre Dionne; Nassif, Christina; Diallo, Ousmane; Monlong, Jean; Cadieux-Dion, Maxime; Dobrzeniecka, Sylvia; Meloche, Caroline; Retterer, Kyle; Cho, Megan T; Rosenfeld, Jill A; Bi, Weimin; Massicotte, Christine; Miguet, Marguerite; Brunga, Ledia; Regan, Brigid M; Mo, Kelly; Tam, Cory; Schneider, Amy; Hollingsworth, Georgie; FitzPatrick, David R; Donaldson, Alan; Canham, Natalie; Blair, Edward; Kerr, Bronwyn; Fry, Andrew E; Thomas, Rhys H; Shelagh, Joss; Hurst, Jane A; Brittain, Helen; Blyth, Moira; Lebel, Robert Roger; Gerkes, Erica H; Davis-Keppen, Laura; Stein, Quinn; Chung, Wendy K; Dorison, Sara J; Benke, Paul J; Fassi, Emily; Corsten-Janssen, Nicole; Kamsteeg, Erik-Jan; Mau-Them, Frederic T; Bruel, Ange-Line; Verloes, Alain; Õunap, Katrin; Wojcik, Monica H; Albert, Dara V F; Venkateswaran, Sunita; Ware, Tyson; Jones, Dean; Liu, Yu-Chi; Mohammad, Shekeeb S; Bizargity, Peyman; Bacino, Carlos A; Leuzzi, Vincenzo; Martinelli, Simone; Dallapiccola, Bruno; Tartaglia, Marco; Blumkin, Lubov; Wierenga, Klaas J; Purcarin, Gabriela; O'Byrne, James J; Stockler, Sylvia; Lehman, Anna; Keren, Boris; Nougues, Marie-Christine; Mignot, Cyril; Auvin, Stéphane; Nava, Caroline; Hiatt, Susan M; Bebin, Martina; Shao, Yunru; Scaglia, Fernando; Lalani, Seema R; Frye, Richard E; Jarjour, Imad T; Jacques, Stéphanie; Boucher, Renee-Myriam; Riou, Emilie; Srour, Myriam; Carmant, Lionel; Lortie, Anne; Major, Philippe; Diadori, Paola; Dubeau, François; D'Anjou, Guy; Bourque, Guillaume; Berkovic, Samuel F; Sadleir, Lynette G; Campeau, Philippe M; Kibar, Zoha; Lafrenière, Ronald G; Girard, Simon L; Mercimek-Mahmutoglu, Saadet; Boelman, Cyrus; Rouleau, Guy A; Scheffer, Ingrid E; Mefford, Heather C; Andrade, Danielle M; Rossignol, Elsa; Minassian, Berge A; Michaud, Jacques L

    2017-11-02

    Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  2. De novo and recurrent aneurysms in pediatric patients with cerebral aneurysms.

    Science.gov (United States)

    Koroknay-Pál, Päivi; Niemelä, Mika; Lehto, Hanna; Kivisaari, Riku; Numminen, Jussi; Laakso, Aki; Hernesniemi, Juha

    2013-05-01

    Long-term angiographic follow-up studies on pediatric aneurysm patients are scarce. We gathered long-term clinical and angiographic follow-up data on all pediatric aneurysm patients (≤ 18 years at diagnosis) treated at the Department of Neurosurgery, Helsinki University Central Hospital, between 1937 and 2009. Fifty-nine patients with cerebral aneurysms in childhood had long-term clinical and radiological follow-up (median, 34 years; range, 4-56 years). Twenty-four patients (41%) were diagnosed with altogether 25 de novo and 11 recurrent aneurysms, with 9 (25%) of the aneurysms being symptomatic. New subarachnoid hemorrhage occurred in 7 patients; 4 of these patients died. Eight patients (33%) had multiple new aneurysms. The annual rate of hemorrhage was 0.4%, and the annual rate for the development of de novo or recurrent aneurysm was 1.9%. There were no de novo aneurysms in 7 patients with previously unruptured aneurysms. However, 1 recurrent aneurysm was diagnosed. Current and previous smoking (risk ratio, 2.44; 95% confidence interval, 1.07-5.55) was the only statistically significant risk factor for de novo and recurrent aneurysm formation in patients with previous subarachnoid hemorrhage, whereas hypertension, sex, or age at onset had no statistically significant effect. Smoking was also a statistically significant risk factor for new subarachnoid hemorrhage. Patients with ruptured intracranial aneurysms in childhood have a high risk for new aneurysms and new subarachnoid hemorrhage, especially if they start to smoke as adults. Life-long angiographic follow-up is mandatory.

  3. Dispom: a discriminative de-novo motif discovery tool based on the jstacs library.

    Science.gov (United States)

    Grau, Jan; Keilwagen, Jens; Gohr, André; Paponov, Ivan A; Posch, Stefan; Seifert, Michael; Strickert, Marc; Grosse, Ivo

    2013-02-01

    DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions of genomic DNA. However, de-novo discovery of these binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not yet been solved satisfactorily. Here, we present a detailed description and analysis of the de-novo motif discovery tool Dispom, which has been developed for finding binding sites of DNA-binding proteins that are differentially abundant in a set of target regions compared to a set of control regions. Two additional features of Dispom are its capability of modeling positional preferences of binding sites and adjusting the length of the motif in the learning process. Dispom yields an increased prediction accuracy compared to existing tools for de-novo motif discovery, suggesting that the combination of searching for differentially abundant motifs, inferring their positional distributions, and adjusting the motif lengths is beneficial for de-novo motif discovery. When applying Dispom to promoters of auxin-responsive genes and those of ABI3 target genes from Arabidopsis thaliana, we identify relevant binding motifs with pronounced positional distributions. These results suggest that learning motifs, their positional distributions, and their lengths by a discriminative learning principle may aid motif discovery from ChIP-chip and gene expression data. We make Dispom freely available as part of Jstacs, an open-source Java library that is tailored to statistical sequence analysis. To facilitate extensions of Dispom, we describe its implementation using Jstacs in this manuscript. In addition, we provide a stand-alone application of Dispom at http://www.jstacs.de/index.php/Dispom for instant use.

  4. Maturity onset diabetes of young type 2 due to a novel de novo GKC mutation

    OpenAIRE

    Afonso, Paula; Ferraria, Nélia; Carvalho, Alexandre; Castro, Sofia Vidal

    2014-01-01

    Maturity Onset Diabetes of Young (MODY) is a heterogeneous group of monogenic disorders that result in β-cell dysfunction, with an estimated prevalence of 1%-2% in industrialized countries. MODY generally occurs in non-obese patients with negative autoantibodies presenting with mild to moderate hyperglycemia. The clinical features of the patients are heterogeneous, depending on the different genetic subtypes. We pretend to report a case of MODY type 2 caused by a novel de novo CGK mutation, h...

  5. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

    Directory of Open Access Journals (Sweden)

    Cédric Cabau

    2017-02-01

    Full Text Available Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome and their quality (chimera and nucleotide error rates can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP which wraps these two assemblers (Trinity and Oases in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

  6. Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families.

    Science.gov (United States)

    Leppa, Virpi M; Kravitz, Stephanie N; Martin, Christa Lese; Andrieux, Joris; Le Caignec, Cedric; Martin-Coignard, Dominique; DyBuncio, Christina; Sanders, Stephan J; Lowe, Jennifer K; Cantor, Rita M; Geschwind, Daniel H

    2016-09-01

    Rare mutations, including copy-number variants (CNVs), contribute significantly to autism spectrum disorder (ASD) risk. Although their importance has been established in families with only one affected child (simplex families), the contribution of both de novo and inherited CNVs to ASD in families with multiple affected individuals (multiplex families) is less well understood. We analyzed 1,532 families from the Autism Genetic Resource Exchange (AGRE) to assess the impact of de novo and rare CNVs on ASD risk in multiplex families. We observed a higher burden of large, rare CNVs, including inherited events, in individuals with ASD than in their unaffected siblings (odds ratio [OR] = 1.7), but the rate of de novo events was significantly lower than in simplex families. In previously characterized ASD risk loci, we identified 49 CNVs, comprising 24 inherited events, 19 de novo events, and 6 events of unknown inheritance, a significant enrichment in affected versus control individuals (OR = 3.3). In 21 of the 30 families (71%) in whom at least one affected sibling harbored an established ASD major risk CNV, including five families harboring inherited CNVs, the CNV was not shared by all affected siblings, indicating that other risk factors are contributing. We also identified a rare risk locus for ASD and language delay at chromosomal region 2q24 (implicating NR4A2) and another lower-penetrance locus involving inherited deletions and duplications of WWOX. The genetic architecture in multiplex families differs from that in simplex families and is complex, warranting more complete genetic characterization of larger multiplex ASD cohorts. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  7. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).

    Science.gov (United States)

    Larsen, Peter A; Harris, R Alan; Liu, Yue; Murali, Shwetha C; Campbell, C Ryan; Brown, Adam D; Sullivan, Beth A; Shelton, Jennifer; Brown, Susan J; Raveendran, Muthuswamy; Dudchenko, Olga; Machol, Ido; Durand, Neva C; Shamim, Muhammad S; Aiden, Erez Lieberman; Muzny, Donna M; Gibbs, Richard A; Yoder, Anne D; Rogers, Jeffrey; Worley, Kim C

    2017-11-16

    The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly. We used a combination of advanced genomic technologies to iteratively resolve conflicts and super-scaffold the M. murinus genome. We improved the M. murinus genome assembly to a scaffold N50 of 93.32 Mb. Whole genome alignments between our primary super-scaffolds and 23 human chromosomes revealed patterns that are congruent with historical comparative cytogenetic data, thus demonstrating the accuracy of our de novo scaffolding approach and allowing assignment of scaffolds to M. murinus chromosomes. Moreover, we utilized our independent datasets to discover and characterize sequences associated with centromeres across the mouse lemur genome. Quality assessment of the final assembly found 96% of mouse lemur canonical transcripts nearly complete, comparable to other published high-quality reference genome assemblies. We describe a new assembly of the gray mouse lemur (Microcebus murinus) genome with chromosome-scale scaffolds produced using a hybrid bioinformatic and sequencing approach. The approach is cost effective and produces superior results based on metrics of contiguity and completeness. Our results show that emerging genomic technologies can be used in combination to characterize centromeres of non-model species and to produce accurate de novo chromosome-scale genome assemblies of complex mammalian genomes.

  8. Substantia nigra neuromelanin magnetic resonance imaging in de novo Parkinson's disease patients.

    Science.gov (United States)

    Reimão, S; Pita Lobo, P; Neutel, D; Correia Guedes, L; Coelho, M; Rosa, M M; Ferreira, J; Abreu, D; Gonçalves, N; Morgado, C; Nunes, R G; Campos, J; Ferreira, J J

    2015-03-01

    Depigmentation of the substantia nigra (SN) and locus coeruleus (LC) is a conspicuous pathological feature of Parkinson's disease (PD) and is related to the loss of neuromelanin, whose paramagnetic properties result in high signal on specific T1-weighted magnetic resonance imaging (MRI). Recent studies have suggested that neuromelanin decrease in the SN and LC of PD patients may emerge as a possible diagnostic biomarker. The SN neuromelanin signal in de novo and early stage PD patients was studied to assess its diagnostic accuracy. This is the first study based on a semi-automated MRI analysis of the neuromelanin signal in de novo PD patients. The inclusion criteria were untreated de novo PD and a 2-5 year disease duration; in addition, age matched healthy controls were enrolled. These were studied with a high-resolution T1-weighted MRI sequence at 3 T to visualize neuromelanin. The primary outcome was SN high signal area, length and neuromelanin/midbrain ratio obtained with semi-automated methods. A total of 12 de novo PD patients and 10 PD patients with a 2-5 year disease duration were evaluated. The area, length of the SN T1 high signal and the SN neuromelanin/midbrain ratio were markedly decreased in the PD groups compared with age-matched controls, with a substantial overlap between the two PD groups. Neuromelanin-sensitive MRI techniques can discriminate PD patients from healthy individuals with high sensitivity and specificity. Our findings are consistent with recent findings showing that PD neuromelanin changes remain stable during the course of the disease. © 2014 EAN.

  9. De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids

    National Research Council Canada - National Science Library

    Liu, Shaoqun; Li, Wanshun; Wu, Yimin; Chen, Changming; Lei, Jianjun

    2013-01-01

    ... (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data...

  10. 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.

  11. Efeito de dois regimes de suplementação alimentar e dois sistemas de produção, nos constituintes sangüíneos de cabras Saanen durante a lactação Effect of two regimes of alimentary supplementation and two systems of production on blood traits of dairy goats bred

    Directory of Open Access Journals (Sweden)

    Adriana Sampaio Nunes

    2002-06-01

    Full Text Available Foram analisados os constituintes sangüíneos de oito cabras leiteiras cruza Saanen lactantes, entre novembro (1997 e maio (1998, submetidas a dois sistemas de produção ¾ pastagem (S1 e semiconfinamento (S2 ¾ e dois regimes alimentares: 30% das exigências em energia líquida ao longo de toda a lactação (R1 e 60% das exigências diárias em energia líquida da 3ª a 13ª semana de lactação e 15% das exigências em energia líquida da 14ª semana até o final da lactação (R2. Amostras de sangue foram coletadas quinzenalmente de dois animais de cada tratamento para a análise de glicose (Gl, hemoglobina (Hb e hematócrito (Ht. Não foram encontradas diferenças na concentração de GL e Hb e no hematócrito, nos diferentes regimes alimentares. Os animais do sistema de produção S1 apresentaram maiores valores de Hb (7,60 g/100 mL e Ht (22,42% em relação aos animais do sistema de produção S2 (Hb = 6,05 g/100 mL e Ht = 17,71%, não havendo diferença entre os dois sistemas de produção em relação à Gl.Three blood constituents in eight crossbred Saanen goats bred in two systems ¾ pasture (S1 and semi-confinement (S2 ¾ were analyzed. The animals were fed two different diets: 30% of the dairy requirements of net energy supplied by concentrate during all the lactation (R1, and 60% of the requirements from 3rd to 13th week of lactation and 15% from 14th until the end of lactation (R2. Blood samples were taken to evaluate glucose (Gl, hemoglobin (Hb, and hematocrit (Ht levels. The results showed that none of these traits were affected by the feeding systems. Animals in the S1 production system presented higher values of Hb (7,60 g/100 mL and Ht (22,42% than those of S2 animals (Hb = 6,05 g/100 mL and Ht = 17,71%. No significant difference was observed between the two production systems for Gl.

  12. Efeito do sexo e do peso ao abate sobre a produção de carne de cordeiro. Morfometria da carcaça, pesos dos cortes, composição tecidual e componentes não constituintes da carcaça

    Directory of Open Access Journals (Sweden)

    Siqueira Edson Ramos de

    2001-01-01

    Full Text Available Neste experimento, avaliou-se o efeito de sexo (macho e fêmea e de quatro distintos pesos de abate (28, 32, 36, e 40 kg sobre a morfometria da carcaça, os pesos dos cortes, a composição tecidual e os componentes não constituintes da carcaça, em cordeiros mestiços Ile de France x Corriedale, terminados em confinamento. Utilizaram-se 40 animais (20 machos e 20 fêmeas, desmamados aos 60 dias e alimentados, à vontade, com uma ração com 16,46% de PB e 67,63% de NDT. Foram divididos em quatro grupos de machos (G1M, G2M, G3M e G4M, sacrificados, respectivamente, com os pesos supracitados, e, da mesma forma, quatro grupos de fêmeas (G1F, G2F, G3F e G4F. Determinaram-se as medidas da carcaça e, de forma subjetiva, a condição corporal, o grau de conformação e o grau de gordura de cobertura. Calcularam-se os índices de compacidade da carcaça e da perna. Foram registrados os pesos e as porcentagens de sete cortes da meia carcaça, bem como as porcentagens de osso, músculo e tecido adiposo, avaliadas por meio de dissecção do lombo. A espessura da gordura de cobertura foi determinada na região lombar. O estudo morfométrico confirmou maior alongamento ósseo dos machos. De maneira geral, as carcaças apresentaram-se com bom acabamento, segundo os índices de compacidade verificados. Os cortes das carcaças das fêmeas foram mais pesados que os dos machos (exceto para o peso de 28 kg ao abate, principalmente em função dos maiores teores de gordura. Destaca-se a representabilidade dos pesos da pele e do conteúdo gastrintestinal na determinação do rendimento da carcaça. Pelos resultados obtidos, recomenda-se 28 kg como peso referência para sacrifício.

  13. 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

    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 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. PMID:27800169

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

    Directory of Open Access Journals (Sweden)

    Sun-Ju Rhee

    Full Text Available 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.

  15. Monosomal karyotype is not a predictor of dismal outcome in childhood de novo acute myeloid leukemia.

    Science.gov (United States)

    Lee, Na Hee; Choi, Young Bae; Yi, Eun-Sang; Lee, Soo Hyun; Kim, Hee-Jin; Lee, Ji Won; Sung, Ki Woong; Koo, Hong Hoe; Yoo, Keon Hee

    2016-11-01

    Monosomal karyotype (MK) is known as a far end of the unfavorable cytogenetics in adult acute myeloid leukemia (AML), while available data in childhood AML is scarce. In this study, we investigated the prevalence and prognostic value of MK with retrospectively analyzed 119 patients newly diagnosed with childhood de novo AML. Ten patients (8.4%) revealed to have MK. All MK-positive (MK(+)) AML were associated with complex cytogenetic abnormalities and belonged to the cytogenetic adverse-risk group. Nine of MK(+) patients (90%) achieved complete remission. The event-free survival (EFS) and overall survival (OS) of MK(+) adverse group were comparable to the ESF and OS of MK-negative non-adverse group (EFS 60.0±15.5% vs 59.0±5.1%, P=0.925; OS 70.0±14.5% vs 58.1±5.3%, P=0.696). In multivariate analysis, MK was not an independent adverse prognostic factor for EFS (hazard ratio 0.45, 95% C.I. 0.13-1.50, P=0.194). In addition, 7 of 9 MK(+) patients who received allogeneic hematopoietic stem cell transplantation (HSCT) survived event-free, with a median follow-up of 64 months. In conclusion, MK did not act as an adverse prognostic factor in childhood de novo AML. Allogeneic HSCT might have contributed to the excellent outcome of MK(+) childhood de novo AML. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. De novo GTP biosynthesis is critical for virulence of the fungal pathogen Cryptococcus neoformans.

    Directory of Open Access Journals (Sweden)

    Carl A Morrow

    Full Text Available We have investigated the potential of the GTP synthesis pathways as chemotherapeutic targets in the human pathogen Cryptococcus neoformans, a common cause of fatal fungal meningoencephalitis. We find that de novo GTP biosynthesis, but not the alternate salvage pathway, is critical to cryptococcal dissemination and survival in vivo. Loss of inosine monophosphate dehydrogenase (IMPDH in the de novo pathway results in slow growth and virulence factor defects, while loss of the cognate phosphoribosyltransferase in the salvage pathway yielded no phenotypes. Further, the Cryptococcus species complex displays variable sensitivity to the IMPDH inhibitor mycophenolic acid, and we uncover a rare drug-resistant subtype of C. gattii that suggests an adaptive response to microbial IMPDH inhibitors in its environmental niche. We report the structural and functional characterization of IMPDH from Cryptococcus, revealing insights into the basis for drug resistance and suggesting strategies for the development of fungal-specific inhibitors. The crystal structure reveals the position of the IMPDH moveable flap and catalytic arginine in the open conformation for the first time, plus unique, exploitable differences in the highly conserved active site. Treatment with mycophenolic acid led to significantly increased survival times in a nematode model, validating de novo GTP biosynthesis as an antifungal target in Cryptococcus.

  17. 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.

  18. De novo lipogenesis protects cancer cells from free radicals and chemotherapeutics by promoting membrane lipid saturation.

    Science.gov (United States)

    Rysman, Evelien; Brusselmans, Koen; Scheys, Katryn; Timmermans, Leen; Derua, Rita; Munck, Sebastian; Van Veldhoven, Paul P; Waltregny, David; Daniëls, Veerle W; Machiels, Jelle; Vanderhoydonc, Frank; Smans, Karine; Waelkens, Etienne; Verhoeven, Guido; Swinnen, Johannes V

    2010-10-15

    Activation of de novo lipogenesis in cancer cells is increasingly recognized as a hallmark of aggressive cancers and has been implicated in the production of membranes for rapid cell proliferation. In the current report, we provide evidence that this activation has a more profound role. Using a mass spectrometry-based phospholipid analysis approach, we show that clinical tumor tissues that display the lipogenic phenotype show an increase in the degree of lipid saturation compared with nonlipogenic tumors. Reversal of the lipogenic switch in cancer cells by treatment with the lipogenesis inhibitor soraphen A or by targeting lipogenic enzymes with small interfering RNA leads to a marked decrease in saturated and mono-unsaturated phospholipid species and increases the relative degree of polyunsaturation. Because polyunsaturated acyl chains are more susceptible to peroxidation, inhibition of lipogenesis increases the levels of peroxidation end products and renders cells more susceptible to oxidative stress-induced cell death. As saturated lipids pack more densely, modulation of lipogenesis also alters lateral and transversal membrane dynamics as revealed by diffusion of membrane-targeted green fluorescent protein and by the uptake and response to doxorubicin. These data show that shifting lipid acquisition from lipid uptake toward de novo lipogenesis dramatically changes membrane properties and protects cells from both endogenous and exogenous insults. These findings provide important new insights into the role of de novo lipogenesis in cancer cells, and they provide a rationale for the use of lipogenesis inhibitors as antineoplastic agents and as chemotherapeutic sensitizers. ©2010 AACR.

  19. Genetic control of de novo lipogenesis: role in diet-induced obesity.

    Science.gov (United States)

    Strable, Maggie S; Ntambi, James M

    2010-06-01

    De novo lipogenesis (DNL) is a complex yet highly regulated metabolic pathway, and transcription factors such as liver X receptor (LXR), sterol regulatory element-binding protein-1c (SREBP-1c), and carbohydrate response element binding protein (ChREBP) exert significant control over the de novo synthesis of fatty acids. An increase in de novo lipogenesis (DNL) is an important contributor to increased fat mass, while a reduction in lipogenesis may be protective against the development of obesity. In this review, we explore fatty acid synthesis in the context of new insights gleaned from global and tissue-specific gene knockout mouse models of enzymes involved in fatty acid synthesis, namely acetyl-CoA carboxylase, fatty acid synthase, fatty acid elongase 6, and stearoyl-CoA desaturase 1. A disruption in fatty acid synthesis, induced by the deficiency of any one of these enzymes, affects lipid metabolism and in some cases may protect against obesity in a tissue and gene-specific manner, as discussed in detail in this review.

  20. 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.

  1. Engineering Methylobacterium extorquens for de novo synthesis of the sesquiterpenoid α-humulene from methanol.

    Science.gov (United States)

    Sonntag, Frank; Kroner, Cora; Lubuta, Patrice; Peyraud, Rémi; Horst, Angelika; Buchhaupt, Markus; Schrader, Jens

    2015-11-01

    Over the last 10 to 15 years, metabolic engineering of microbes has become a versatile tool for high-level de novo synthesis of terpenoids, with the sesquiterpenoids armopha-1,4-diene, farnesene and artemisinic acid as prime examples. However, almost all cell factory approaches towards terpenoids to date have been based on sugar as the raw material, which is mainly used as a food resource and subject to high price volatilities. In this study we present de novo synthesis of the sesquiterpenoid α-humulene from the abundantly available non-food carbon source methanol by metabolically engineered Methylobacterium extorquens AM1. Expression of α-humulene synthase from Zingiber zerumbet in combination with farnesyl pyrophosphate (FPP) synthase from Saccharomyces cerevisiae led to concentrations of up to 18 mg/L α-humulene. Introduction of a prokaryotic mevalonate pathway from Myxococcus xanthus in combination with ribosome binding site optimization of α-humulene and FPP synthases increased product concentration 3-fold. This value was additionally raised by 30% using a carotenoid synthesis deficient mutant strain. Final product concentrations of up to 1.65 g/L were obtained in methanol limited fed-batch cultivations, which is the highest titer of de novo synthesized α-humulene reported to date. This study demonstrates the potential of M. extorquens as a future platform strain for the production of high-value terpenoids from the alternative carbon source methanol. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  2. Plasma antioxidant status and motor features in de novo Chinese Parkinson's disease patients.

    Science.gov (United States)

    Yuan, Yongsheng; Tong, Qing; Zhang, Li; Jiang, Siming; Zhou, Hong; Zhang, Rui; Zhang, Shu; Xu, Qinrong; Li, Daqian; Zhou, Xiaobin; Ding, Jian; Zhang, Kezhong

    2016-01-01

    This study aimed to explore plasma antioxidant status in de novo Chinese Parkinson's disease (PD) patients and investigate its relationship with specific motor features of PD. Sixty-four de novo Chinese PD patients and 40 age- and sex-matched healthy controls were recruited. Each motor feature of PD patients was assessed by unified Parkinson's disease rating scale. Plasma antioxidant status, including plasma level of glutathione (GSH) and plasma activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), was detected using enzyme-linked immunosorbent assay. The relationship between the plasma antioxidant status and motor features of PD was evaluated by Spearman's coefficient. Plasma GSH level and plasma activities of GSH-Px, CAT and SOD of PD patients were lower than those of healthy controls. Moreover, the declining activity of plasma CAT was related with the increasing mean postural instability and gait disorder (PIGD) score and growing age. In contrast, the severity of tremor was positively correlated with plasma SOD activity. Our study demonstrates that the plasma antioxidant status is impaired in de novo Chinese PD patients. The complex relationship between the plasma antioxidant status and different motor features indicates that the antioxidant mechanisms underlying tremor and PIGD of PD may be different.

  3. Donor-transmitted, donor-derived, and de novo cancer after liver transplant.

    Science.gov (United States)

    Chapman, Jeremy R; Lynch, Stephen V

    2014-03-01

    Cancer is the third most common cause of death (after cardiovascular disease and infection) for patients who have a functioning kidney allograft. Kidney and liver transplant recipients have similar cancer risks because of immunosuppression but different risks because of differences in primary diseases that cause renal and hepatic failure and the inherent behavior of cancers in the liver. There are 4 types of cancer that may develop in liver allograft recipients: (1) recurrent cancer, (2) donor-transmitted cancer, (3) donor-derived cancer, and (4) de novo cancer. Identification of potential donor cancer transmission may occur at postmortem examination of a deceased donor or when a probable donor-transmitted cancer is identified in another recipient. Donor-transmitted cancer after liver transplant is rare in Australia, the United Kingdom, and the United States. Aging of the donor pool may increase the risk of subclinical cancer in donors. Liver transplant recipients have a greater risk of de novo cancer than the general population, and risk factors for de novo cancer in liver transplant recipients include primary sclerosing cholangitis, alcoholic liver disease, smoking, and increased age. Liver transplant recipients may benefit from cancer screening because they have a high risk, are clearly identifiable, and are under continuous medical supervision.

  4. DNA secondary structure is influenced by genetic variation and alters susceptibility to de novo translocation

    Directory of Open Access Journals (Sweden)

    Tsutsumi Makiko

    2011-09-01

    Full Text Available Abstract Background Cumulative evidence suggests that DNA secondary structures impact DNA replication, transcription and genomic rearrangements. One of the best studied examples is the recurrent constitutional t(11;22 in humans that is mediated by potentially cruciform-forming sequences at the breakpoints, palindromic AT-rich repeats (PATRRs. We previously demonstrated that polymorphisms of PATRR sequences affect the frequency of de novo t(11;22s in sperm samples from normal healthy males. These studies were designed to determine whether PATRR polymorphisms affect DNA secondary structure, thus leading to variation in translocation frequency. Methods We studied the potential for DNA cruciform formation for several PATRR11 polymorphic alleles using mobility shift analysis in gel electrophoresis as well as by direct visualization of the DNA by atomic force microscopy. The structural data for various alleles were compared with the frequency of de novo t(11;22s the allele produced. Results The data indicate that the propensity for DNA cruciform structure of each polymorphic allele correlates with the frequency of de novo t(11;22s produced (r = 0.77, P = 0.01. Conclusions Although indirect, our results strongly suggest that the PATRR adopts unstable cruciform structures during spermatogenesis that act as translocation hotspots in humans.

  5. 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.

  6. Most "sporadic" cases of X-linked ichthyosis are not de novo mutations.

    Science.gov (United States)

    Cuevas-Covarrubias, S A; Valdes-Flores, M; Orozco Orozco, E; Díaz-Zagoya, J C; Kofman-Alfaro, S H

    1999-03-01

    X-linked ichthyosis is an inherited disease with dark, regular and adherent scales as clinical characteristics. It is caused by a deficiency of the steroid sulphatase enzyme. Steroid sulphatase assay is a relative easy tool that enables correct diagnosis of X-linked ichthyosis patients and carriers. A large number of X-linked ichthyosis patients correspond to non-familial cases that seem to represent de novo mutations. In this study, we examined the X-linked ichthyosis carrier state of the mothers of 42 non-familial cases to determine whether their children corresponded to de novo mutations. To classify patients and carriers, a steroid sulphatase assay was performed in leukocytes using 7-[3H]-dehydroepiandrosterone sulphate as substrate. In 36 mothers (85%) we found steroid sulphatase activity compatible with the carrier state of X-linked ichthyosis. This data suggest that most of the mothers of these patients present the primary gene defect, excluding de novo mutations in the patients.

  7. De novo inflammatory bowel disease after pediatric kidney or liver transplant.

    Science.gov (United States)

    Fernandes, Melissa A; Braun, Hillary J; Evason, Kim; Rhee, Sue; Perito, Emily R

    2017-02-01

    A subset of children who receive a liver and/or kidney transplant develop de novo inflammatory bowel disease-like chronic intestinal inflammation, not explained by infection or medications, following transplant. We have conducted a single-center, retrospective case series describing the unique clinical and histologic features of this IBD-like chronic intestinal inflammation following solid organ transplant. At our center, nine of 327 kidney or liver recipients developed de novo IBD following transplant (six liver, two kidney, one liver-kidney). Most children presented with prolonged hematochezia and diarrhea and were treated with aminosalicylates. At time of diagnosis, five were not currently using mycophenolate mofetil for transplant immunosuppression. Histologic and endoscopic findings at IBD diagnosis included inflammation, ulcerations, granulomas, and chronic colitis. Since diagnosis, no patients have required surgical intervention, or escalation to biologic therapy, nor developed stricturing or perianal disease. In this case series, de novo post-transplant IBD developed in 4% of pediatric liver and/or kidney recipients; however, it often does not fit the classic patterns of Crohn's disease or ulcerative colitis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.

    Science.gov (United States)

    Gent, Jonathan I; Ellis, Nathanael A; Guo, Lin; Harkess, Alex E; Yao, Yingyin; Zhang, Xiaoyu; Dawe, R Kelly

    2013-04-01

    Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation remain poorly understood. By applying whole-genome bisulfite sequencing to maize, we found that transposons close to cellular genes (particularly within 1 kb of either a gene start or end) are strongly associated with de novo methylation, as evidenced both by 24-nt siRNAs and by methylation specifically in the CHH sequence context. In addition, we found that the major classes of transposons exhibited a gradient of CHH methylation determined by proximity to genes. Our results further indicate that intergenic chromatin in maize exists in two major forms that are distinguished based on proximity to genes-one form marked by dense CG and CHG methylation and lack of transcription, and one marked by CHH methylation and activity of multiple forms of RNA polymerase. The existence of the latter, which we call CHH islands, may have implications for how cellular gene expression could be coordinated with immediately adjacent transposon repression in a large genome with a complex organization of genes interspersed in a landscape of transposons.

  9. Severe clinical course of de novo hepatitis B infection after liver transplantation.

    Science.gov (United States)

    Crespo, J; Fábrega, E; Casafont, F; Rivero, M; Heras, G; de la Peña, J; de la Cruz, F; Pons-Romero, F

    1999-05-01

    The aim of this study is to determine the origin, clinical outcome, allograft histological characteristics, and virological outcome of de novo hepatitis B virus (HBV) infection after orthotopic liver transplantation (OLT). We studied 136 hepatitis B surface antigen (HBsAg)-negative liver transplant recipients. HBV DNA was detected by dot-blot hybridization and polymerase chain reaction (PCR). The S gene was sequenced. Hepatitis C virus (HCV) RNA was assessed by PCR. The long-term clinical and histological outcome was determined. Six of 136 HBsAg-negative patients (4.4%) became HBsAg positive after transplantation. The source of HBV infection was reactivation of latent HBV infection in 2 patients and was not identified in 4 patients. Two donors had isolated core antibody. Two of these 6 patients developed acute liver failure related to hepatitis B. The 4 other patients had severe chronic hepatitis related to hepatitis B. All patients had high-level HBV replication. No significant mutations in the S gene were found. These data suggest that de novo hepatitis B infection is not a mild disease and might represent a significant cause of graft dysfunction. This is the first report of fulminant hepatitis caused by de novo hepatitis B infection after OLT.

  10. A general approach for discriminative de novo motif discovery from high-throughput data.

    Science.gov (United States)

    Grau, Jan; Posch, Stefan; Grosse, Ivo; Keilwagen, Jens

    2013-11-01

    De novo motif discovery has been an important challenge of bioinformatics for the past two decades. Since the emergence of high-throughput techniques like ChIP-seq, ChIP-exo and protein-binding microarrays (PBMs), the focus of de novo motif discovery has shifted to runtime and accuracy on large data sets. For this purpose, specialized algorithms have been designed for discovering motifs in ChIP-seq or PBM data. However, none of the existing approaches work perfectly for all three high-throughput techniques. In this article, we propose Dimont, a general approach for fast and accurate de novo motif discovery from high-throughput data. We demonstrate that Dimont yields a higher number of correct motifs from ChIP-seq data than any of the specialized approaches and achieves a higher accuracy for predicting PBM intensities from probe sequence than any of the approaches specifically designed for that purpose. Dimont also reports the expected motifs for several ChIP-exo data sets. Investigating differences between in vitro and in vivo binding, we find that for most transcription factors, the motifs discovered by Dimont are in good accordance between techniques, but we also find notable exceptions. We also observe that modeling intra-motif dependencies may increase accuracy, which indicates that more complex motif models are a worthwhile field of research.

  11. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae.

    Science.gov (United States)

    Cai, Jing; Zhao, Ruoping; Jiang, Huifeng; Wang, Wen

    2008-05-01

    Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.

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

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    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".

  13. De novo AML exhibits greater microenvironment dysregulation compared to AML with myelodysplasia-related changes.

    Science.gov (United States)

    Lopes, Matheus Rodrigues; Pereira, João Kleber Novais; de Melo Campos, Paula; Machado-Neto, João Agostinho; Traina, Fabiola; Saad, Sara T Olalla; Favaro, Patricia

    2017-01-13

    The interaction between the bone marrow microenvironment and malignant hematopoietic cells can result in the protection of leukemia cells from chemotherapy in both myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). We, herein, characterized the changes in cytokine expression and the function of mesenchymal stromal cells (MSC) in patients with MDS, AML with myelodysplasia-related changes (MRC), a well-recognized clinical subtype of secondary AML, and de novo AML. We observed a significant inhibitory effect of MDS-MSC on T lymphocyte proliferation and no significant differences in any of the cytokines tested. AML-MSC inhibited T-cell proliferation only at a very low MSC/T cell ratio. When compared to the control, AML-MRCderived MSC presented a significant increase in IL6 expression, whereas de novo AML MSC presented a significant increase in the expression levels of VEGFA, CXCL12, RPGE2, IDO, IL1β, IL6 and IL32, followed by a decrease in IL10 expression. Furthermore, data indicate that IL-32 regulates stromal cell proliferation, has a chemotactic potential and participates in stromal cell crosstalk with leukemia cells, which could result in chemoresistance. Our results suggest that the differences between AML-MRC and de novo AML also extend into the leukemic stem cell niche and that IL-32 can participate in the regulation of the bone marrow cytokine milieu.

  14. 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.

  15. De novo deposition of laminin-positive basement membrane in vitro by normal hepatocytes and during hepatocarcinogenesis

    DEFF Research Database (Denmark)

    Albrechtsen, R; Wewer, U M; Thorgeirsson, S S

    1988-01-01

    De novo formation of laminin-positive basement membranes was found to be a distinct morphologic feature of diethylnitrosamine/phenobarbital-induced hepatocellular carcinomas of the rat. The first appearance of extracellularly located laminin occurred in the preneoplastic liver lesions (correspond......De novo formation of laminin-positive basement membranes was found to be a distinct morphologic feature of diethylnitrosamine/phenobarbital-induced hepatocellular carcinomas of the rat. The first appearance of extracellularly located laminin occurred in the preneoplastic liver lesions...

  16. Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses.

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    Angelo Pavesi

    Full Text Available A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or horizontal transfer. In contrast, many viruses generate protein-coding genes de novo, via the overprinting of a new reading frame onto an existing ("ancestral" frame. This mechanism is thought to play an important role in viral pathogenicity, but has been poorly explored, perhaps because identifying the de novo frames is very challenging. Therefore, a new approach to detect them was needed. We assembled a reference set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames. Based on this observation, we designed a method that allowed the identification of de novo frames based on their codon usage with a very good specificity, but intermediate sensitivity. Using our method, we predicted that the Rex gene of deltaretroviruses has originated de novo by overprinting the Tax gene. Intriguingly, several genes in the same genomic region have also originated de novo and encode proteins that regulate the functions of Tax. Such "gene nurseries" may be common in viral genomes. Finally, our results confirm that the genomic GC content is not the only determinant of codon usage in viruses and suggest that a constraint linked to translation must influence codon usage.

  17. 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.

  18. Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers.

    Science.gov (United States)

    Amin, Shorash; Prentis, Peter J; Gilding, Edward K; Pavasovic, Ana

    2014-08-01

    The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.

  19. Prognosis of metastatic breast cancer: are there differences between patients with de novo and recurrent metastatic breast cancer?

    Science.gov (United States)

    Lobbezoo, D J A; van Kampen, R J W; Voogd, A C; Dercksen, M W; van den Berkmortel, F; Smilde, T J; van de Wouw, A J; Peters, F P J; van Riel, J M G H; Peters, N A J B; de Boer, M; Peer, P G M; Tjan-Heijnen, V C G

    2015-04-28

    We aimed to determine the prognostic impact of time between primary breast cancer and diagnosis of distant metastasis (metastatic-free interval, MFI) on the survival of metastatic breast cancer patients. Consecutive patients diagnosed with metastatic breast cancer in 2007-2009 in eight hospitals in the Southeast of the Netherlands were included and categorised based on MFI. Survival curves were estimated using the Kaplan-Meier method. Cox proportional hazards model was used to determine the prognostic impact of de novo metastatic breast cancer vs recurrent metastatic breast cancer (MFI ⩽24 months and >24 months), adjusted for age, hormone receptor and HER2 status, initial site of metastasis and use of prior (neo)adjuvant systemic therapy. Eight hundred and fifteen patients were included and divided in three subgroups based on MFI; 154 patients with de novo metastatic breast cancer, 176 patients with MFI 24 months. Patients with de novo metastatic breast cancer had a prolonged survival compared with patients with recurrent metastatic breast cancer with MFI 24 months (median, 29.4 vs 27.9 months, P=0.73). Adjusting for other prognostic factors, patients with MFI 24 months with de novo metastatic breast cancer no significant difference in mortality risk was found. The association between MFI and survival was seen irrespective of use of (neo)adjuvant systemic therapy. Patients with de novo metastatic breast cancer had a significantly better outcome when compared with patients with MFI 24 months, patients with de novo metastatic breast cancer had similar outcome.

  20. Use of cactus pear (Opuntia ficus indica Mill replacing corn on carcass characteristics and non-carcass components in Santa Inês lambs Utilização da palma forrageira (Opuntia fícus-indica Mill em substituição ao milho sobre as características de carcaça e componentes não constituintes da carcaça de cordeiros da raça Santa Inês

    Directory of Open Access Journals (Sweden)

    Tiago Ferreira Pinto

    2011-06-01

    Full Text Available The objective of this study was to evaluate the biometric and morphometric measures, regional composition, carcass characteristics and non-carcass components of Santa Inês lambs submitted to levels of corn replaced by cactus pear in the diet. It was used 45 Santa Ines non-castrated male lambs, with average initial live weight of 25.50 ± 0.48 kg as a completely randomized block design with five treatments (0; 25; 50; 70 and 100% and nine replicates. There was an effect of the diet on slaughter weight, empty body weight, hot and cold carcass, cold carcass weight, shoulder weight and loin weight. Cactus pear can replace up to 75% of corn in diets for feedlot Santa Inês lambs, without compromising production, carcass characteristics and production of non-carcass components.O objetivo neste trabalho foi avaliar as medidas biométricas e morfométricas, a composição regional, as características de carcaça e os componentes não constituintes da carcaça de cordeiros Santa Inês, submetidos a níveis de substituição do milho por palma forrageira na dieta. Foram utilizados 45 cordeiros não-castrados da raça Santa Inês com peso vivo inicial de 25,0 ± 0,48 kg, distribuídos em delineamento de blocos ao acaso com cinco tratamentos (0; 25; 50; 75 e 100% e nove repetições. Houve efeito da dieta sobre o peso ao abate, peso do corpo vazio, peso de carcaça quente e fria, peso da paleta e peso do lombo. A palma forrageira pode substituir até 75% do milho em dietas para cordeiros da raça santa Inês em confinamento, sem comprometer a produção, as características da carcaça e a produção de componentes não constituintes da carcaça.

  1. Identification of novel candidate disease genes from de novo exonic copy number variants.

    Science.gov (United States)

    Gambin, Tomasz; Yuan, Bo; Bi, Weimin; Liu, Pengfei; Rosenfeld, Jill A; Coban-Akdemir, Zeynep; Pursley, Amber N; Nagamani, Sandesh C S; Marom, Ronit; Golla, Sailaja; Dengle, Lauren; Petrie, Heather G; Matalon, Reuben; Emrick, Lisa; Proud, Monica B; Treadwell-Deering, Diane; Chao, Hsiao-Tuan; Koillinen, Hannele; Brown, Chester; Urraca, Nora; Mostafavi, Roya; Bernes, Saunder; Roeder, Elizabeth R; Nugent, Kimberly M; Bader, Patricia I; Bellus, Gary; Cummings, Michael; Northrup, Hope; Ashfaq, Myla; Westman, Rachel; Wildin, Robert; Beck, Anita E; Immken, LaDonna; Elton, Lindsay; Varghese, Shaun; Buchanan, Edward; Faivre, Laurence; Lefebvre, Mathilde; Schaaf, Christian P; Walkiewicz, Magdalena; Yang, Yaping; Kang, Sung-Hae L; Lalani, Seema R; Bacino, Carlos A; Beaudet, Arthur L; Breman, Amy M; Smith, Janice L; Cheung, Sau Wai; Lupski, James R; Patel, Ankita; Shaw, Chad A; Stankiewicz, Paweł

    2017-09-21

    Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation

  2. 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

  3. 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

  4. Cerambycidae (Coleoptera da Colômbia: VII. Novos táxons, novos registros, nova sinonímia, nova combinação e novo nome

    Directory of Open Access Journals (Sweden)

    Ubirajara R. Martins

    2005-03-01

    Full Text Available Novos táxons descritos da Colômbia, Amazonas: Xenofrea triangularis sp. nov. (Xenofreini; Boyaca: Neoclytus canescens sp. nov. (Clytini; Epropetes variabile sp. nov. (Tillomorphini; Oreodera advena sp. nov.; Irundisa gen. nov, type species I. ocularis sp. nov. (Acanthoderini; Cauca: Ischiocentra punctata sp. nov. (Onciderini; Caquetá: Oreodera adornata sp. nov. (Acanthoderini; Chocó: Oreodera nivea sp. nov. (Acanthoderini; Magdalena: Mecometopus arixi sp. nov. (Clytini; Nariño: Carterica rubra sp. nov. (Colobotheini; Putumayo: Eburodacrys guttata sp. nov. (Eburiini; Valle del Cauca: Blabia bicolor sp. nov. (Desmiphorini. Novos registros: Colômbia, Amazonas: Criodion cinereum (Olivier, 1795; Coleoxestia atrata (Gounelle, 1909; Eburodacrys quadridens (Fabricius, 1801; E. rufispinis Bates, 1870; E. sulphureosignata (Erichson, 1847; Rhomboidederes minutus Napp & Martins, 1984; Aneuthetochorus conjunctus Napp & Martins, 1984; Lissozodes basalis White, 1855; Mecometopus latecinctus Bates, 1870; Chrysoprasis aureicollis White, 1853; Oreodera curvata Martins & Monné, 1993; Carterica cincticornis Bates, 1865; Magdalena: Atenizus castaneus Martins, 1981; Vichada: Eusapia guyanensis Huedepohl, 1988; Gnomidolon biarcuatum (White, 1855; Tropidion subcruciatum (White, 1855; Sthelenus ichneumoneus Buquet, 1859; Putumayo: Hemilissa opaca Martins, 1976; H. sulcicollis Bates, 1870; Glyptoscapus flaveolus (Bates, 1870; Orthostoma abdominale (Gyllenhal, 1817; Oreodera melzeri Monné & Fragoso, 1988; Caquetá: Gnomidolon conjugatum (White, 1855; Cauca: Mecometopus macilentus Bates, 1872; Tolima: Cherentes niveilateris (Thomson, 1868. Nova sininímia: Necalphus maranduba Galileo &Martins, 2003 = Myoxomorpha decorata Monné & Magno, 1992 e proposta a nova combinação: Necalphus decoratus (Monné & Magno, 1992 comb. nov. Cotyadesmus, novo nome, é dado para Paradesmus Galileo & Martins, 2003 pré-ocupado em Myriapoda.New taxa described from Colombia, Amazonas

  5. De Novo Donor-Specific Antibody Formation in Tacrolimus-Based, Mycophenolate Versus Mammalian Target of Rapamycin Immunosuppressive Regimens.

    Science.gov (United States)

    Mithani, Zain; Gralla, Jane; Adebiyi, Oluwafisayo; Klem, Patrick; Cooper, James E; Wiseman, Alexander C

    2017-03-22

    De novo donor-specific antibody formation posttransplant is associated with decreased graft survival. It is not known whether mammalian target of rapamycin inhibitors may be advantageous or detrimental compared with mycophenolate in the prevention of de novo donor-specific antibody formation. We compared 66 kidney and kidney-pancreas transplant recipients who received tacrolimus, mammalian target of rapamycin inhibitor, and prednisone (group 1; 36 of whom received everolimus and 30 of whom received sirolimus) versus 132 patients who received tacrolimus, mycophenolate, and prednisone (group 2) matched for age, sex, race, and type/timing of transplant from 2007 to 2012. Rates of de novo donor-specific antibody formation were comparable between groups at 1, 6, and 12 months (16.7%, 25.8%, and 28.8% for group 1 vs 9.8%, 15.2%, and 22.0% for group 2). There were no significant differences in class (I, II, or mixed), strength (mean fluorescence intensity) of de novo donor-specific antibody, glomerular filtration rate, proteinuria levels, or acute rejection between the groups. In those with de novo donor-specific antibody by 6 months, acute rejection was more common versus those without de novo donor-specific antibody formation (24.3% vs 5.6% at 6 mo; P = .002), with rates of 27.0% versus 6.8% at 1 year (P = .001) and 40.7% versus 11.3% at 2 years (P < .001). An associated reduction in glomerular filtration rate also occurred. Mammalian target of rapamycin inhibitors were neither protective nor permissive for de novo donor-specific antibody formation versus mycophenolate when used with clinically relevant tacrolimus dosing regimens.

  6. Constituents of Moquinia kingii Constituintes de Moquinia kingii

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    Elisandra Cristina Schinor

    2005-03-01

    Full Text Available Extraction of the constituents of total plant (aerial parts and roots of Moquinia kingii afforded three flavonoids described for the first time in the tribe Moquinieae. In addition sesquiterpene lactone and triterpenes were isolated. Structures were established by spectroscopic studies.A extração da planta total (partes aéreas e raiz de Moquinia kingii forneceu três flavonóides, descritos pela primeira vez na tribo Moquinieae, além de lactona sesquiterpênica e triterpenos. As estruturas foram determinadas por estudos espectroscópicos.

  7. Constituintes químicos de Arrabidaea samydoides (Bignoniaceae

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    Pauletti Patrícia Mendonça

    2003-01-01

    Full Text Available Chemical investigation of Arrabidaea samydoides resulted in the isolation of the flavone chrysin; five triterpenes: lupeol, ursolic acid, 3b,16a-dihydroxy-urs-12-ene, uvaol, and erythrodiol; and two sterols: sitosterol and stigmasterol. The structures of these compounds were established by spectroscopic analysis. This paper deal with the first phytochemical study of Arrabidaea samydoides.

  8. Da disciplina ao controle: novos processos de subjetivação no mundo do trabalho

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    Attila Magno e Silva Barbosa

    2012-12-01

    Full Text Available http://dx.doi.org/10.5007/2175-7984.2012v11n22p75 Partindo do pressuposto de que as relações de poder são contextuais, históricas e em constante transformação, este artigo tem como objetivo refletir sobre a passagem da chamada sociedade disciplinar para a sociedade de controle. Tomaremos como referência o “mundo do trabalho” por entendermos que nele testemunhamos a constituição de um novo processo de subjetivação em que a disciplina, antes circunscrita em um sistema fechado – no caso em questão, a fábrica –, deu lugar a formas de controle que se estendem por todas as esferas da vida social. Para nós, o suporte discursivo desse novo dispositivo de poder seria o discurso do trabalhador como  empreendedor de si mesmo”. Iniciaremos nossa discussão versando sobre a analítica do poder de Foucault, mais precisamente sobre a noção de sociedade disciplinar que teria tido seu apogeu no início do século XX e desde então teria perdido força e cedido lugar à sociedade de controle, esta noção melhor desenvolvida por Deleuze. Nesse sentido, refletiremos sobre a ocorrência de um novo processo de subjetivação e como novas formas de controle passam a ser exercidas no mundo do trabalho.

  9. A subtle interplay between three Pex11 proteins shapes de novo formation and fission of peroxisomes.

    Science.gov (United States)

    Huber, Anja; Koch, Johannes; Kragler, Friedrich; Brocard, Cécile; Hartig, Andreas

    2012-01-01

    The organization of eukaryotic cells into membrane-bound compartments must be faithfully sustained for survival of the cell. A subtle equilibrium exists between the degradation and the proliferation of organelles. Commonly, proliferation is initiated by a membrane remodeling process. Here, we dissect the function of proteins driving organelle proliferation in the particular case of peroxisomes. These organelles are formed either through a growth and division process from existing peroxisomes or de novo from the endoplasmic reticulum (ER). Among the proteins involved in the biogenesis of peroxisomes, peroxins, members of the Pex11 protein family participate in peroxisomal membrane alterations. In the yeast Saccharomyces cerevisiae, the Pex11 family consists of three proteins, Pex11p, Pex25p and Pex27p. Here we demonstrate that yeast mutants lacking peroxisomes require the presence of Pex25p to regenerate this organelle de novo. We also provide evidence showing that Pex27p inhibits peroxisomal function and illustrate that Pex25p initiates elongation of the peroxisomal membrane. Our data establish that although structurally conserved each of the three Pex11 protein family members plays a distinct role. While ScPex11p promotes the proliferation of peroxisomes already present in the cell, ScPex25p initiates remodeling at the peroxisomal membrane and ScPex27p acts to counter this activity. In addition, we reveal that ScPex25p acts in concert with Pex3p in the initiation of de novo peroxisome biogenesis from the ER. © 2011 John Wiley & Sons A/S.

  10. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei.

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    Christopher Leija

    2016-11-01

    Full Text Available The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD, which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA, which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5'-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5'-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug.

  11. 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.

  12. De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits.

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    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

  13. 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.

  14. Whole Exome Sequencing Identifies de Novo Mutations in GATA6 Associated with Congenital Diaphragmatic Hernia

    Science.gov (United States)

    Yu, Lan; Bennett, James T.; Wynn, Julia; Carvill, Gemma L.; Cheung, Yee Him; Shen, Yufeng; Mychaliska, George B.; Azarow, Kenneth S.; Crombleholme, Timothy M.; Chung, Dai H.; Potoka, Douglas; Warner, Brad W.; Bucher, Brian; Lim, Foong-Yen; Pietsch, John; Stolar, Charles; Aspelund, Gudrun; Arkovitz, Marc S.; Mefford, Heather; Chung, Wendy K.

    2014-01-01

    Background Congenital diaphragmatic hernia (CDH) is a common birth defect affecting 1 in 3,000 births. It is characterized by herniation of abdominal viscera through an incompletely formed diaphragm. Although chromosomal anomalies and mutations in several genes have been implicated, the cause for most patients is unknown. Methods We used whole exome sequencing in two families with CDH and congenital heart disease, and identified mutations in GATA6 in both. Results In the first family, we identified a de novo missense mutation (c.1366C>T, p.R456C) in a sporadic CDH patient with tetralogy of Fallot. In the second, a nonsense mutation (c.712G>T, p.G238*) was identified in two siblings with CDH and a large ventricular septal defect. The G238* mutation was inherited from their mother, who was clinically affected with congenital absence of the pericardium, patent ductus arteriosus, and intestinal malrotation. Deep sequencing of blood and saliva derived DNA from the mother suggested somatic mosaicism as an explanation for her milder phenotype, with only approximately 15% mutant alleles. To determine the frequency of GATA6 mutations in CDH, we sequenced the gene in 378 patients with CDH. We identified one additional de novo mutation (c.1071delG, p.V358Cfs34*). Conclusions Mutations in GATA6 have been previously associated with pancreatic agenesis and congenital heart disease. We conclude that, in addition to the heart and the pancreas, GATA6 is involved in development of two additional organs, the diaphragm and the pericardium. In addition we have shown that de novo mutations can contribute to the development of CDH, a common birth defect. PMID:24385578

  15. Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia.

    Science.gov (United States)

    Yu, Lan; Bennett, James T; Wynn, Julia; Carvill, Gemma L; Cheung, Yee Him; Shen, Yufeng; Mychaliska, George B; Azarow, Kenneth S; Crombleholme, Timothy M; Chung, Dai H; Potoka, Douglas; Warner, Brad W; Bucher, Brian; Lim, Foong-Yen; Pietsch, John; Stolar, Charles; Aspelund, Gudrun; Arkovitz, Marc S; Mefford, Heather; Chung, Wendy K

    2014-03-01

    Congenital diaphragmatic hernia (CDH) is a common birth defect affecting 1 in 3000 births. It is characterised by herniation of abdominal viscera through an incompletely formed diaphragm. Although chromosomal anomalies and mutations in several genes have been implicated, the cause for most patients is unknown. We used whole exome sequencing in two families with CDH and congenital heart disease, and identified mutations in GATA6 in both. In the first family, we identified a de novo missense mutation (c.1366C>T, p.R456C) in a sporadic CDH patient with tetralogy of Fallot. In the second, a nonsense mutation (c.712G>T, p.G238*) was identified in two siblings with CDH and a large ventricular septal defect. The G238* mutation was inherited from their mother, who was clinically affected with congenital absence of the pericardium, patent ductus arteriosus and intestinal malrotation. Deep sequencing of blood and saliva-derived DNA from the mother suggested somatic mosaicism as an explanation for her milder phenotype, with only approximately 15% mutant alleles. To determine the frequency of GATA6 mutations in CDH, we sequenced the gene in 378 patients with CDH. We identified one additional de novo mutation (c.1071delG, p.V358Cfs34*). Mutations in GATA6 have been previously associated with pancreatic agenesis and congenital heart disease. We conclude that, in addition to the heart and the pancreas, GATA6 is involved in development of two additional organs, the diaphragm and the pericardium. In addition, we have shown that de novo mutations can contribute to the development of CDH, a common birth defect.

  16. 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

  17. Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline.

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    Mark Davids

    Full Text Available Metatranscriptomic landscapes can provide insights in functional relationships within natural microbial communities. Analysis of complex metatranscriptome datasets of these communities poses a considerable bioinformatic challenge since they are non-restricted with a varying number of participating strains and species. For RNA-Seq data a standard approach is to align the generated reads to a set of closely related reference genomes. This only works well for microbial communities for which a near complete catalogue of reference genomes is available at a small evolutionary distance. In this study, we focus on the design of a validated de novo metatranscriptome assembly pipeline for single-end Illumina RNA-Seq data to obtain functional and taxonomic profiles of murine microbial communities.The here developed de novo assembly metatranscriptome pipeline combined rRNA removal, IDBA-UD assembler, functional annotation and taxonomic classification. Different assemblers were tested and validated using RNA-Seq data from an in silico generated mock community and in vivo RNA-Seq data from a restricted microbial community taken from a mouse model colonized with Altered Schaedler Flora (ASF. Precision and recall of resulting gene expression, functional and taxonomic profiles were compared to those obtained with a standard alignment method. The validated pipeline was subsequently used to generate expression profiles from non-restricted cecal communities of four C57BL/6J mice fed on a high-fat high-protein diet spiked with an RNA-Seq data set from a well-characterized human sample. The spike in control was used to estimate precision and recall at assembly, functional and taxonomic level of non-restricted communities.A generic de novo assembly pipeline for metatranscriptome data analysis was designed for microbial ecosystems, which can be applied for microbial metatranscriptome analysis in any chosen niche.

  18. Repeated quantitative measurements of De Novo synthesis of albumin and fibrinogen.

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    Gabriel Dumitrescu

    Full Text Available The possibility of using two different isotopomers, for the incorporation of isotopically labeled amino acids, was explored to enable longitudinal studies of de novo synthesis of two export liver proteins, albumin and fibrinogen. The agreement of the synthesis rates between the two different labels was evaluated along with the reproducibility of repeated experiments using different time intervals. Healthy volunteers were studied in a standardized fed state. Protocol A (n = 10 involved two measurements 48 hours apart. Protocol B (n = 6 involved three measurements at baseline and five hours and then seven days after the initial measurement. De novo synthesis of albumin and fibrinogen by the incorporation of D5-phenylalanine or D8-phenylalanine were measured using the flooding dose technique. Albumin and fibrinogen were isolated from plasma using standard techniques. Fractional and absolute synthesis rates were calculated. Repeated measurements employing the two isotoptomers showed good agreement for albumin fractional synthesis rate after 48 hours (p = 0.92 and after 7 days (p = 0.99, with a coefficient of variation of 5.9% when using the same isotopic label. For fibrinogen, the coefficient of variation for the fractional synthesis rate employing the same isotopic label was 16.6%. Repeated measurements after 48 hours and seven days showed less agreement although there was no statistical difference (P = 0.32 and P = 0.30 respectively. Repeated measurement after five hours showed a statistical significant difference for the fractional synthesis rate of fibrinogen (p = 0.008 but not for albumin (p = 0.12. Repeated measurements of albumin de novo synthesis more than 48 hours apart show acceptable agreement using either one or two different isotopic labels. For fibrinogen the larger intra-individual scatter necessitates larger study groups to detect changes in longitudinal studies. Repeated measurements within 48 hours need to be validated further.

  19. 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.

  20. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

    Science.gov (United States)

    Kajitani, Rei; Toshimoto, Kouta; Noguchi, Hideki; Toyoda, Atsushi; Ogura, Yoshitoshi; Okuno, Miki; Yabana, Mitsuru; Harada, Masayuki; Nagayasu, Eiji; Maruyama, Haruhiko; Kohara, Yuji; Fujiyama, Asao; Hayashi, Tetsuya; Itoh, Takehiko

    2014-08-01

    Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity. © 2014 Kajitani et al.; Published by Cold Spring Harbor Laboratory Press.

  1. Subtypes of postnatal depression? A comparison of women with recurrent and de novo postnatal depression.

    Science.gov (United States)

    Phillips, Jane; Sharpe, Louise; Matthey, Stephen; Charles, Margaret

    2010-01-01

    It has been suggested that there may be two groups of women with postnatal depression (PND) - one who have a history of depression and whose depression is etiologically similar to depression experienced at other times of life, and another who develop depression de novo in the postnatal period and whose depression is uniquely 'postnatal'. The primary aim of this study was to clarify the role of negative attitudes (general and maternal-specific) for these proposed subtypes, whilst also considering the role of a range of other potentially relevant etiological factors. 157 postnatal women were classified into four groups: (i) 'recurrent depression', (ii) 'de novo PND', (iii) 'prior (but not current) depression', (iv) 'healthy control'. Groups were compared on known vulnerability and situational risk factors for depression including negative attitudes (general and maternal-specific), personality style vulnerability, relationship insecurity, low social support, stressful life events and difficult infant behaviour. Hierarchical regressions were conducted to examine the role of general and maternal-specific negative attitudes in mediating the relationship between previous depression and PND. Women with recurrent depression had more personality vulnerability and maternal-specific negative attitudes than women with de novo PND, but there were no differences in general negative attitudes or relationship insecurity. Non-depressed women with a history of prior depression were characterized by elevated general depression vulnerability but lower maternal-specific negative attitudes. General negative attitudes mediated the relationship between previous depression and PND. All participants had unsettled infants and the generalizability of results to general postpartum samples is not known. Although these results do not provide support for the proposed subtypes of PND, they highlight encouraging new avenues for cognitively based preventative interventions.

  2. Long-term probability of and mortality from de novo malignancy after liver transplantation.

    Science.gov (United States)

    Watt, Kymberly D S; Pedersen, Rachel A; Kremers, Walter K; Heimbach, Julie K; Sanchez, William; Gores, Gregory J

    2009-12-01

    Information about malignancies that arise in patients after liver transplantation comes from volunteer registry databases and single-center retrospective studies. We analyzed a multicenter, prospectively obtained database to assess the probabilities of and risk factors for de novo malignancies in patients after liver transplantation. We analyzed the National Institute of Diabetes and Digestive and Kidney Diseases' liver transplantation database of 798 adults who received transplants from April 1990 to June 1994 and long-term follow-up data through January 2003. In this patient population, 171 adult patients developed 271 de novo malignancies. Of these malignancies, 147 were skin-related, 29 were hematologic, and 95 were solid organ cancers; we focused on nonskin malignancies. The probability of developing any nonskin malignancy was highest in patients with primary sclerosing cholangitis (PSC; 22% at 10 years) or alcohol-related liver disease (ALD; 18% at 10 years); all other diagnoses had a 10% probability. Multivariate analysis indicated that increased age by decade (hazard ratio [HR] = 1.33, P = .01), a history of smoking (HR = 1.6, P = .046), PSC (HR = 2.5, P = .001), and ALD (HR = 2.1, P = .01) were associated with development of solid malignancies after liver transplantation. The probabilities of death after diagnosis of hematologic and solid malignancy were 44.0% and 38.0% at 1 year and 57.6% and 53.1% at 5 years, respectively. De novo malignancy primarily affects patients with PSC or ALD, compared to other transplant recipients, with a significant impact on long-term survival.

  3. Rare de novo copy number variants in patients with congenital pulmonary atresia.

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    Li Xie

    Full Text Available BACKGROUND: Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA. METHODS AND RESULTS: Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%, and eight of these CNVs (9.8% are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD loci (16p13.1 and 22q11.2. Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. CONCLUSIONS: Rare CNVs contribute to the pathogenesis of PA (9.8%, suggesting that the causes of PA are heterogeneous and pleiotropic. Together with previous data from animal models, our results might help identify a link between CHD and folate-mediated one-carbon metabolism (FOCM. With the accumulation of high-resolution SNP array data, these previously undescribed rare CNVs may help reveal critical gene(s in CHD and may provide novel insights about CHD pathogenesis.

  4. Movimento estudantil brasileiro: Práticas militantes na ótica dos Novos Movimentos Sociais

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    Marcos Ribeiro Mesquita

    2012-10-01

    Full Text Available Este artigo visa identificar na estrutura e organização do movimento estudantil conteúdos e formas organizativas que nos indiquem o surgimento de uma nova sociabilidade militante. Para tanto, foi necessário analisar as relações entre os diversos grupos organizados do movimento estudantil, desde os mais institucionalizados, àqueles que empreendem outras formas de fazer política. A pluralidade de expressões estudantis, de novos formatos, metodologias e pautas parecem apontar para esta sociabilidade, apesar do forte caráter tradicional que a política estudantil institucional ainda possui.

  5. Novos sedativos hipnóticos The newer sedative-hypnotics

    OpenAIRE

    Lucia Sukys-Claudino; Walter André dos Santos Moraes; Sergio Tufik; Dalva Poyares

    2010-01-01

    Nas últimas décadas houve um esforço para o desenvolvimento de hipnóticos mais seguros e eficazes. Zolpidem, zaleplona, zopiclona, eszopiclona (drogas-z) e indiplona são moduladores do receptor GABA-A, os quais agem de forma seletiva na subunidade α1, exibindo, desta forma, mecanismos similares de ação, embora evidências recentes sugiram que a eszopiclona não seja tão seletiva para a subunidade α1 quanto o zolpidem. Ramelteon e tasimelteon são novos agentes crono-hipnóticos seletivo...

  6. De novo interstitial deletion q16.2q21 on chromosome 6

    Energy Technology Data Exchange (ETDEWEB)

    Villa, A.; Urioste, M.; Luisa, M. [Universidad Complutense, Madrid (Spain)] [and others

    1995-01-30

    A de novo interstitial deletion of 6q16.2q21 was observed in a 23-month-old boy with mental and psychomotor delay, obese appearance, minor craniofacial anomalies, and brain anomalies. We compare clinical manifestations of this patient with those observed in previously reported cases with similar 6q interstitial deletions. It is interesting to note the clinical similarities between some patients with interstitial deletions of 6q16 or q21 bands and patients with Prader-Willi syndrome (PWS) and it may help to keep in mind cytogenetic studies of patients with some PWS findings. 24 refs., 3 figs., 2 tabs.

  7. 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.

  8. 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.

  9. Recent Advances Towards The Discovery Of Drug-Like Peptides De Novo

    Directory of Open Access Journals (Sweden)

    Michael eGoldflam

    2015-12-01

    Full Text Available Peptides are important natural molecules that possess functions as diverse as antibiotics, toxins, venoms and hormones, for example. However, whilst these peptides have useful properties, there are many targets and pathways that are not addressed through the activities of natural peptidic compounds. In these circumstances, directed evolution techniques, such as phage display, have been developed to sample the diverse chemical and structural repertoire of small peptides for useful means. In this review, we consider recent concepts that relate peptide structure to drug-like attributes and how these are incorporated within display technologies to deliver peptides de novo with valuable pharmaceutical properties.

  10. Novos aspectos sobre a intoxicação por Trema micrantha (Cannabaceae) em equideos

    OpenAIRE

    Pavarini, Saulo Petinatti; Bandinelli,Marcele Bettim; Bassuino,Daniele Mariath; Correa,Gabriel Laizola Frainer; Bandarra, Paulo Mota; Driemeier, David; Hohendorff,Raquel Von; Both,Maria do Carmo

    2013-01-01

    Trema micrantha é uma planta arbórea distribuída amplamente no Brasil. Descrevem-se nesse trabalho novos aspectos epidemiológicos e patológicos relacionados com a intoxicação por essa planta em equídeos. Dois equinos adultos da raça Crioula e dois asininos, de localidades distintas, foram intoxicados naturalmente por Trema micrantha, após consumirem grande quantidade da planta que ficou disponível a eles após uma poda. Além disso, um cavalo adulto, de outra propriedade, que estava passando po...

  11. De novo assembly of the perennial ryegrass transcriptome using an RNA-seq strategy

    DEFF Research Database (Denmark)

    Farrell, Jacqueline Danielle; Byrne, Stephen; Paina, Cristiana

    2014-01-01

    Background Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from...... a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype...... has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping....

  12. SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome.

    Science.gov (United States)

    Stadermann, Kai Bernd; Weisshaar, Bernd; Holtgräwe, Daniela

    2015-09-16

    Third generation sequencing methods, like SMRT (Single Molecule, Real-Time) sequencing developed by Pacific Biosciences, offer much longer read length in comparison to Next Generation Sequencing (NGS) methods. Hence, they are well suited for de novo- or re-sequencing projects. Sequences generated for these purposes will not only contain reads originating from the nuclear genome, but also a significant amount of reads originating from the organelles of the target organism. These reads are usually discarded but they can also be used for an assembly of organellar replicons. The long read length supports resolution of repetitive regions and repeats within the organelles genome which might be problematic when just using short read data. Additionally, SMRT sequencing is less influenced by GC rich areas and by long stretches of the same base. We describe a workflow for a de novo assembly of the sugar beet (Beta vulgaris ssp. vulgaris) chloroplast genome sequence only based on data originating from a SMRT sequencing dataset targeted on its nuclear genome. We show that the data obtained from such an experiment are sufficient to create a high quality assembly with a higher reliability than assemblies derived from e.g. Illumina reads only. The chloroplast genome is especially challenging for de novo assembling as it contains two large inverted repeat (IR) regions. We also describe some limitations that still apply even though long reads are used for the assembly. SMRT sequencing reads extracted from a dataset created for nuclear genome (re)sequencing can be used to obtain a high quality de novo assembly of the chloroplast of the sequenced organism. Even with a relatively small overall coverage for the nuclear genome it is possible to collect more than enough reads to generate a high quality assembly that outperforms short read based assemblies. However, even with long reads it is not always possible to clarify the order of elements of a chloroplast genome sequence reliantly

  13. 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.

  14. 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...... 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...

  15. Effects of dietary nutrient composition on de novo lipogenesis in gilthead sea bream (Sparus aurata)

    DEFF Research Database (Denmark)

    Ekmann, Kim Schøn

    substantiate that considerable de novo lipogenesis was taking place and apparently subject to nutritional control, while apparent retention of poly unsaturated fatty acids (PUFA) appeared to be un-affected by dietary treatment. Combined, this caused the SAFA and MUFA content of the fish to increase...... to rigorously maintain a certain whole body energy status under a wide variety of dietary DP/DE ratios, energy densities and nutrient compositions, even if substantial amounts of dietary protein is sacrificed to achieve this. This may indicate that this species has evolved to maximise energy storage in the from...

  16. De novo production of the monoterpenoid geranic acid by metabolically engineered Pseudomonas putida.

    Science.gov (United States)

    Mi, Jia; Becher, Daniela; Lubuta, Patrice; Dany, Sarah; Tusch, Kerstin; Schewe, Hendrik; Buchhaupt, Markus; Schrader, Jens

    2014-12-04

    Production of monoterpenoids as valuable chemicals using recombinant microbes is a growing field of interest. Unfortunately, antimicrobial activity of most monoterpenoids hampers a wide application of microorganisms for their production. Strains of Pseudomonas putida, a fast growing and metabolically versatile bacterium, often show an outstanding high tolerance towards organic solvents and other toxic compounds. Therefore, Pseudomonas putida constitutes an attractive alternative host in comparison to conventionally used microorganisms. Here, metabolic engineering of solvent tolerant Pseudomonas putida as a novel microbial cell factory for de novo production of monoterpenoids is reported for the first time, exemplified by geranic acid production from glycerol as carbon source. The monoterpenoic acid is an attractive compound for application in the flavor, fragrance, cosmetics and agro industries. A comparison between Escherichia coli, Saccharomyces cerevisiae and Pseudomonas putida concerning the ability to grow in the presence of geranic acid revealed that the pseudomonad bears a superior resilience compared to the conventionally used microbes. Moreover, Pseudomonas putida DSM 12264 wildtype strain efficiently oxidized externally added geraniol to geranic acid with no further degradation. Omitting external dosage of geraniol but functionally expressing geraniol synthase (GES) from Ocimum basilicum, a first proof-of-concept for de novo biosynthesis of 1.35 mg/L geranic acid in P. putida DSM 12264 was achieved. Doubling the amount of glycerol resulted in twice the amount of product. Co-expression of the six genes of the mevalonate pathway from Myxococcus xanthus to establish flux from acetyl-CoA to the universal terpenoid precursor isopentenylpyrophosphate yielded 36 mg/L geranic acid in shake flask experiments. In the bioreactor, the recombinant strain produced 193 mg/L of geranic acid under fed-batch conditions within 48 h. Metabolic engineering turned Pseudomonas

  17. 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.......2 mL/min (SD 17.4 mL/min) in the everolimus and CNI groups, respectively, a difference of 18.3 mL/min (95% CI 11.1-25.6 mL/min; p independent determinant of mGFR at month 36. Coronary intravascular...

  18. 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.

  19. 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

  20. 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

  1. 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

    -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...... of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y...

  2. A Novel De Novo EFNB1 Gene Mutation in a Mexican Patient with Craniofrontonasal Syndrome

    Science.gov (United States)

    Ramirez-Garcia, M. A.; Chacon-Camacho, O. F.; Leyva-Hernandez, C.; Cardenas-Conejo, A.; Zenteno, J. C.

    2013-01-01

    Craniofrontonasal syndrome (CNFS) is an X-linked disorder caused by mutations in the EFNB1 gene in which, paradoxically, heterozygous females are more severely affected than hemizygous males. In this paper, the clinical and molecular studies of a female subject with CFNS are described. A novel de novo c.473T>C (p.M158T) mutation in exon 3 of EFNB1 was demonstrated in this patient. The M158 residue of the Ephrin-B1 protein is highly conserved between species. Our results expand the mutational spectrum exposed by CNFS. PMID:23509643

  3. A Novel De Novo EFNB1 Gene Mutation in a Mexican Patient with Craniofrontonasal Syndrome

    Directory of Open Access Journals (Sweden)

    M. A. Ramirez-Garcia

    2013-01-01

    Full Text Available Craniofrontonasal syndrome (CNFS is an X-linked disorder caused by mutations in the EFNB1 gene in which, paradoxically, heterozygous females are more severely affected than hemizygous males. In this paper, the clinical and molecular studies of a female subject with CFNS are described. A novel de novo c.473T>C (p.M158T mutation in exon 3 of EFNB1 was demonstrated in this patient. The M158 residue of the Ephrin-B1 protein is highly conserved between species. Our results expand the mutational spectrum exposed by CNFS.

  4. Parental origin of de novo chromosome 9 deletions in del(9p) syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Micale, M.A.; Haren, J.M.; Conroy, J.M. [Case Western University School of Medicine, Clevelend, OH (United States)

    1995-05-22

    Parental origin of de novo deletions in the short arm of chromosome 9 in patients with a clinical diagnosis of del(9p) syndrome was assessed in 13 patients using polymerase chain reaction (PCR) analysis of highly polymorphic dinucleotide repeat microsatellite markers located in the putative deleted region. The deletion was found to be of paternal origin in 9 cases and of maternal origin in the remaining 4 cases, suggesting that the molecular event resulting in the deletion occurs in both male and female gametogenesis and that genomic imprinting does not appear to play a role in the pathogenesis of del(9p) syndrome. 22 refs., 1 fig.

  5. de novo interstitial deletions at the 11q23.3-q24.2 region

    OpenAIRE

    Su, Jiasun; Chen, Rongyu; Luo, Jingsi; Fan, Xin; Fu, Chunyun; Wang, Jin; He, Sheng; Hu, Xuyun; Zhang, ShuJie; Yi, Shang; Chen, Shaoke; Shen, Yiping

    2016-01-01

    Background Jacobsen syndrome (JBS) is a contiguous gene deletion syndrome involving 11q terminal deletion. Interstitial deletions at distal 11q are rare and their contributions to the clinical phenotype of JBS are unknown. Case presentation We presented the chromosome microarray (CMA) data and the clinical features of two individuals carrying a non-overlapping de novo deletion each at the 11q23.3-q24.2 region in an effort to analyze the correlation between region of deletion at 11q and phenot...

  6. 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

    in coronary de novo lesions, either as part of a DEB-only strategy or in combination with another device, mainly a bare metal stent (BMS). By searching Pubmed and Embase we were able to identify 52 relevant studies, differing in design, intervention, and clinical setting, including patients with small vessel...... compared with DES is not evident from the current studies. In conclusion, the main indication for DEB seems to be small vessel disease, especially in clinical scenarios in which a contraindication to dual antiplatelet therapy exists. The main approach should be a DEB-only strategy with only provisional...

  7. Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus.

    Science.gov (United States)

    Rana, Satshil B; Zadlock, Frank J; Zhang, Ziping; Murphy, Wyatt R; Bentivegna, Carolyn S

    2016-01-01

    De novo assembly of non-model organism's transcriptomes has recently been on the rise in concert with the number of de novo transcriptome assembly software programs. There is a knowledge gap as to what assembler software or k-mer strategy is best for construction of an optimal de novo assembly. Additionally, there is a lack of consensus on which evaluation metrics should be used to assess the quality of de novo transcriptome assemblies. Six different assembly strategies were evaluated from four different assemblers. The Trinity assembly was used in its default 25 single k-mer value while Bridger, Oases, and SOAPdenovo-Trans were performed with multiple k-mer strategies. Bridger, Oases, and SOAPdenovo-Trans used a small multiple k-mer (SMK) strategy consisting of the k-mer lengths of 21, 25, 27, 29, 31, and 33. Additionally, Oases and SOAPdenovo-Trans were performed using a large multiple k-mer (LMK) strategy consisting of k-mer lengths of 25, 35, 45, 55, 65, 75, and 85. Eleven metrics were used to evaluate each assembly strategy including three genome related evaluation metrics (contig number, N50 length, Contigs >1 kb, reads) and eight transcriptome evaluation metrics (mapped back to transcripts (RMBT), number of full length transcripts, number of open reading frames, Detonate RSEM-EVAL score, and percent alignment to the southern platyfish, Amazon molly, BUSCO and CEGMA databases). The assembly strategy that performed the best, that is it was within the top three of each evaluation metric, was the Bridger assembly (10 of 11) followed by the Oases SMK assembly (8 of 11), the Oases LMK assembly (6 of 11), the Trinity assembly (4 of 11), the SOAP LMK assembly (4 of 11), and the SOAP SMK assembly (3 of 11). This study provides an in-depth multi k-mer strategy investigation concluding that the assembler itself had a greater impact than k-mer size regardless of the strategy employed. Additionally, the comprehensive performance transcriptome evaluation metrics utilized

  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. Um novo modelo de implementação de serviços partilhados

    OpenAIRE

    Pinto, José Agostinho de Sousa

    2009-01-01

    Dissertação de mestrado em Sistemas de Informação O sucesso das organizações, entidades de natureza sistémica, depende da sua capacidade de interacção com o meio envolvente, ou seja, da sua capacidade de operar globalmente. Os Sistemas de Informação assumem um papel central, tanto no planeamento estratégico e táctico quanto no seu funcionamento operacional. Neste contexto, as organizações vêem-se na necessidade de alterar estratégias, pensar novos modelos de negócio e adapta...

  10. 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

  11. Efeito das lojas vazias, sôbre o rendimento do café mundo novo Influence of the empty seeds on the outturn of mundo novo coffee

    Directory of Open Access Journals (Sweden)

    L. C. Mônaco

    1960-01-01

    Full Text Available O rendimento do café, isto é, a relação entre o pêso de café maduro para o de beneficiado, é influenciado, entre outros fatôres, pela ocorrência de frutos com lojas sem sementes, os quais flutuam quando colocados no água. Procurando avaliar o efeito de quantidades variáveis dêste tipo de frutos sôbre o rendimento do café Mundo Novo, foram preparados quatro grupos de cinco amostras, contendo 0, 25, 50, 75 e 100 por cento de frutos dessa natureza. Nestas amostras realizaram-se observações sôbre as quantidades de sementes moca, concha e chato, tamanho, densidade e pêso dos sementes. Os dados obtidos mostraram que o abôrto do endosperma em uma das lojas do fruto não afetou as características de pêso, densidade e tamanho das sementes desenvolvidas no outra loja do fruto. Verificou-se, também, que as sementes moca diminuíram à medida que aumentaram nas amostras as quantidades de frutos com lojas sem sementes, sendo êste fato atribuído ao número reduzido de frutos moca que flutuam no água. As sementes concha, ao contrário, aumentaram com as crescentes porções de frutos que boiam nas amostras preparadas, o que talvez possa ser atribuível a um efeito pleiotrópico do fator genético responsável pelo abôrto do endosperma. O rendimento apresentou uma forte tendência de piorar com o aumento do quantidade de lojas sem sementes nas amostras e a análise estatística levou à conclusão de que se trata de um efeito linear. Os resultados dêste ensaio vieram mostrar que o processo de seleção que vem sendo adotado para o café Nundo Novo, eliminando a maioria das plantas com alta quantidade de lojas vazias, é eficiente e assim dsve ser prosseguido.The major factor that has notable influence on the outturn of the coffee (the berry to clean coffee weight relation is the occurrence of fruits with empty seed, which float when put in water. In order to have information on the effect of this kind of fruits on the outturn of the

  12. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

    Directory of Open Access Journals (Sweden)

    Banfield Jillian F

    2010-03-01

    Full Text Available Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

  13. 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.

  14. De novo melanoma and melanoma arising from pre-existing nevus: in vivo morphologic differences as evaluated by confocal microscopy.

    Science.gov (United States)

    Longo, Caterina; Rito, Cintia; Beretti, Francesca; Cesinaro, Anna Maria; Piñeiro-Maceira, Juan; Seidenari, Stefania; Pellacani, Giovanni

    2011-09-01

    Although in the majority of melanomas there is no evidence of pre-existing melanocytic nevus, it is believed that malignant transformation may sometimes occur within a benign precursor. We sought to describe the morphologic features of de novo melanoma and melanoma arising from nevi by means of in vivo confocal microscopy, and to correlate them with their corresponding histopathologic features. A total of 113 consecutive, histopathologically proven melanoma cases, 33 arising from a nevus and 80 occurring de novo, were imaged by confocal microscopy and retrospectively evaluated. Cyto-architectural features preferentially expressed in melanomas arising from nevi and in de novo melanomas were defined. By confocal microscopy, abrupt transition, localized distribution of junctional atypical cells, and the presence of dense dermal nests were the most helpful criteria for categorizing a melanoma as arising from a nevus. Melanomas arising from common and congenital nevi were predominantly composed of roundish, monomorphous cells, whereas melanomas arising either de novo or from dysplastic nevi were characterized by markedly pleomorphic cells. The study is retrospective. Confocal microscopy is effective in identifying melanoma even when a nevus is simultaneously present, confirming the clinical usefulness of this methodology. Moreover, distinctive features were observed in de novo melanomas and melanomas arising from nevi, permitting accurate distinction between the two groups. Finally, differences in cell morphology, easily detectable by confocal microscopy, seemed to characterize different melanoma types. Copyright © 2010 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

  15. De novo lipogenesis in human fat and liver is linked to ChREBP-β and metabolic health.

    Science.gov (United States)

    Eissing, Leah; Scherer, Thomas; Tödter, Klaus; Knippschild, Uwe; Greve, Jan Willem; Buurman, Wim A; Pinnschmidt, Hans O; Rensen, Sander S; Wolf, Anna M; Bartelt, Alexander; Heeren, Joerg; Buettner, Christoph; Scheja, Ludger

    2013-01-01

    Clinical interest in de novo lipogenesis has been sparked by recent studies in rodents demonstrating that de novo lipogenesis specifically in white adipose tissue produces the insulin-sensitizing fatty acid palmitoleate. By contrast, hepatic lipogenesis is thought to contribute to metabolic disease. How de novo lipogenesis in white adipose tissue versus liver is altered in human obesity and insulin resistance is poorly understood. Here we show that lipogenic enzymes and the glucose transporter-4 are markedly decreased in white adipose tissue of insulin-resistant obese individuals compared with non-obese controls. By contrast, lipogenic enzymes are substantially upregulated in the liver of obese subjects. Bariatric weight loss restored de novo lipogenesis and glucose transporter-4 gene expression in white adipose tissue. Notably, lipogenic gene expression in both white adipose tissue and liver was strongly linked to the expression of carbohydrate-responsive element-binding protein-β and to metabolic risk markers. Thus, de novo lipogenesis predicts metabolic health in humans in a tissue-specific manner and is likely regulated by glucose-dependent carbohydrate-responsive element-binding protein activation.

  16. Increased hepatic de novo lipogenesis and mitochondrial efficiency in a model of obesity induced by diets rich in fructose.

    Science.gov (United States)

    Crescenzo, Raffaella; Bianco, Francesca; Falcone, Italia; Coppola, Paola; Liverini, Giovanna; Iossa, Susanna

    2013-03-01

    To assess hepatic de novo lipogenesis and mitochondrial energetics as well as whole-body energy homeostasis in sedentary rats fed a fructose-rich diet. Male rats of 90 days of age were fed a high-fructose or control diet for 8 weeks. Body composition, energy balance, oxygen consumption, carbon dioxide production, non-protein respiratory quotient, de novo lipogenesis and insulin resistance were measured. Determination of specific activity of hepatic enzymes of de novo lipogenesis, mitochondrial mass, oxidative capacity and degree of coupling, together with parameters of oxidative stress and antioxidant defence, was also carried out. Body energy and lipid content as well as plasma insulin and non-esterified fatty acids were significantly higher in fructose-fed than in control rats. Significantly higher rates of net de novo lipogenesis and activities of hepatic lipogenic enzymes fatty acid synthase and stearoyl CoA desaturase-1 were found in fructose-fed rats compared to controls. Mitochondrial protein mass and degree of coupling were significantly higher in fructose-fed rats compared to controls. Hepatic mitochondria showed oxidative damage, both in the lipid and in the protein component, together with decreased activity of antioxidant defence. Liver mitochondrial compartment is highly affected by fructose feeding. The increased mitochondrial efficiency allows liver cells to burn less substrates to produce ATP for de novo lipogenesis and gluconeogenesis. In addition, increased lipogenesis gives rise to whole body and ectopic lipid deposition, and higher mitochondrial coupling causes mitochondrial oxidative stress.

  17. Origin of monoterpene emissions from boreal tree species: Determination of de novo and pool emissions by 13CO2 labeling

    Science.gov (United States)

    Rinne, J.; Ghirardo, A.; Koch, K.; Taipale, R.; Zimmer, I.; Schnitzler, J.

    2009-12-01

    Boreal forests emit a large amount of monoterpenes into the atmosphere. Traditionally these emissions are assumed to originate as evaporation from large storage pools. Thus their diurnal cycle would depend mostly on temperature. However, there is indication that a significant part of the monoterpene emission would originate directly from de novo synthesis. By applying 13CO2 fumigation and analyzing the isotope fractions with proton transfer reaction mass spectrometry (PTR-MS) and classical GC-MS we studied the origin of monoterpene emissions from some major Eurasian boreal and alpine tree species. We determined the fractions originating from de novo biosynthesis and from large internal monoterpene storages for three coniferous tree species with specialized monoterpene storage structures and one dicotyledon species without such structures. The emission from dicotyledon species Betula pendula originated solely from the de novo synthesis. The origin of the emissions from coniferous species was mixed with varying fraction originating from de novo synthesis (Pinus sylvestris 58%, Picea abies 33.5%, Larix decidua 9.8%) and the rest from large internal monoterpene storage pools. Application of the observed fractions of emission originating from de novo synthesis and large storage pools in a hybrid emission algorithm resulted in a better description of ecosystem scale monoterpene emissions from a boreal Scots pine forest stand.

  18. 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.

  19. Critical importance of the de novo pyrimidine biosynthesis pathway for Trypanosoma cruzi growth in the mammalian host cell cytoplasm

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, Muneaki, E-mail: muneaki@juntendo.ac.jp [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Morales, Jorge; Fukai, Yoshihisa; Suzuki, Shigeo; Takamiya, Shinzaburo; Tsubouchi, Akiko; Inoue, Syou [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Inoue, Masayuki [Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kita, Kiyoshi [Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harada, Shigeharu [Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585 (Japan); Tanaka, Akiko [Systems and Structural Biology Center, RIKEN, Tsurumi, Yokohama 230-0045 (Japan); Aoki, Takashi [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Nara, Takeshi, E-mail: tnara@juntendo.ac.jp [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan)

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer We established Trypanosoma cruzi lacking the gene for carbamoyl phosphate synthetase II. Black-Right-Pointing-Pointer Disruption of the cpsII gene significantly reduced the growth of epimastigotes. Black-Right-Pointing-Pointer In particular, the CPSII-null mutant severely retarded intracellular growth. Black-Right-Pointing-Pointer 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.

  20. Association between kinetics of ruminal degradation parameters and cell wall constituents of four tropical grasses Associações entre parâmetros da cinética de degradação ruminal e os constituintes da parede celular de quatro gramíneas tropicais

    Directory of Open Access Journals (Sweden)

    Hernan Maldonado Vásquez

    2010-09-01

    Full Text Available The association of digestible and indigestible cell wall contents, the in vitro dry mater digestibility, the digestion rate, lag phase and the relative gas volume produced from neutral detergent fiber potentially digestible were evaluated in tropical grasses samples. The samples were from setaria grass, hemarthria grass, angola grass and acroceres grass fertilized with 0, 100, 200, 300 and 400kg of N/ha and in the cutting ages of 28, 42, 56 and 70 days. The results were submitted to a factor analysis. It was opted for the adoption of three factors comprising 73,81% % of the total variation, where the first factor was strongly associated with the in vitro dry matter digestibility, neutral detergent fiber potentially digestible, lag and with relative gas volume. The second factor was connected to the indigestible neutral detergent fiber and with digestion rate, and the third factor was related to lignin. The neutral potentially digestible detergent fiber showed positive correlation (0.5294 with in vitro dry matter digestibility (P<0.01, for hermarthria grass at 42 days old. This grass showed better results when compared to the other grasses, and it presented higher values for in vitro dry matter digestibility (69.39% and neutral detergent fiber potentially digestible (57.89% and smaller production of relative gas volume (0,186mL/mg, that means better fermentation characteristics and utilization of carbon for energy production.Objetivou-se avaliar a associação entre constituintes digestíveis e indigestíveis da parede celular, a digestibilidade in vitro da matéria seca e a taxa de digestão, latência e volume relativo de gás produzido a partir da fibra em detergente neutro potencialmente digestível de amostras obtidas de capins setária, hemarthria, angola e acroceres, adubados com 0, 100, 200, 300 e 400kg de N/ha e colhidos aos 28, 42, 56 e 70 dias de idade. Os resultados foram avaliados através de análise de fatores. Optou-se pela ado

  1. Avaliação das estruturas secretoras de Ocimum gratissimum var. macrophyllum Briq. (Lamiaceae após extração dos constituintes voláteis Evaluation of secretory structures of Ocimum gratissimum var. macrophyllum Briq. (Lamiaceae after extraction of volatile compounds

    Directory of Open Access Journals (Sweden)

    A.S. Alvarez

    2013-01-01

    Full Text Available O impacto provocado nas estruturas secretoras de folhas adultas de Ocimum gratissimum var. macrophyllum após extração dos componentes voláteis utilizando-se diferentes métodos de extração foi investigado através de microscopia eletrônica de varredura (MEV. Secções transversais do ápice, da nervura central, e da margem mostraram superfície com cutícula estriada, estômatos diacíticos, tricomas tectores simples, filiformes, e glandulares peltados. Os peltados, com estrutura envolta por uma cutícula contendo o exsudado celular, variaram de 60 a 80µm de diâmetro sendo formados por uma porção apical multicelular com disposição radial formada por dois círculos concêntricos com 9 a 16 células. Na região central do ápice do tricoma peltado se identificou a presença de 4 células em forma de vértice dispostas sobre o pedúnculo, sendo esta a região mais externa formada por número variável de células. Os componentes voláteis das folhas adultas foram extraídos por hidrodestilação (HD, destilação-extração simultânea (DES, e solvente (SO. Os dados obtidos evidenciaram que o maior impacto nas estruturas secretoras ocorreu após extração por hidrodestilação quando comparado aos outros métodos utilizados. A porcentagem dos principais constituintes químicos, timol e γ-terpineno variaram de acordo com o método de extração: timol (HD = 25,4%, SO = 18,2%, DES = 54,8% e γ-terpineno (HD = 38,2%, SO = ausente, DES = 13,7%.The impact on the secretory structures of mature leaves of Ocimum gratissimum var. macrophyllum, after extraction of the volatile compounds using different extraction methods, was investigated by scanning electron microscopy (SEM. Cross-sections of the apex, the midrib and the margin showed surface with striated cuticle, diacitic stomata, single tector, filiform and glandular peltate trichomes. The peltate trichomes with a structure surrounded by cuticle containing the celllular exudate ranged from

  2. Immunosuppressant-driven de novo malignant neoplasms after solid-organ transplant.

    Science.gov (United States)

    Billups, Kelsey; Neal, Jennifer; Salyer, Jeanne

    2015-06-01

    Solid-organ transplant recipients are at a 3- to 5-fold increased risk of a de novo malignant neoplasm developing compared with the general population. The most frequently developed virus-associated malignant neoplasms are Kaposi sarcoma (standardized incidence ratio [SIR], 208.0), nonmelanoma skin cancer (SIR, 28.6), and posttransplant lymphoproliferative disorder, primarily non-Hodgkin lymphoma (SIR, 8.1). Immunosuppressive agents such as corticosteroids, antimetabolites, calcineurin inhibitors, and mammalian target of rapamycin (mTOR) inhibitors play a key role in either causing or preventing this complication. It is hypothesized that some of these regimens can impair cancer surveillance, facilitate the action of oncogenic viruses, and promote direct oncogenic activity. Evolving research has shown promising dual antitumor and immunosuppressive properties of the mTOR inhibitor class. The effective management of posttransplant neoplasms most likely involves the use of these medications among other preventative options. These measures include monitoring certain viral loads as well as immunosuppressant drug levels. Reducing these levels to as low as possible for healthy engraftment and altering regimens when appropriate are management strategies that could lessen this complication of solid-organ transplant. More studies examining the effects of therapeutic drug monitoring are needed to determine specific plasma drug concentrations that will ensure organ engraftment without the development of de novo malignant neoplasms.

  3. Arginine Methylation of SREBP1a via PRMT5 Promotes De Novo Lipogenesis and Tumor Growth.

    Science.gov (United States)

    Liu, Liu; Zhao, Xiaoping; Zhao, Li; Li, Jiajin; Yang, Hao; Zhu, Zongping; Liu, Jianjun; Huang, Gang

    2016-03-01

    Dysregulation of the sterol regulatory element-binding transcription factors sterol regulatory element-binding protein (SREBP) and SREBF activates de novo lipogenesis to high levels in cancer cells, a critical event in driving malignant growth. In this study, we identified an important posttranslational mechanism by which SREBP1a is regulated during metabolic reprogramming in cancer cells. Mass spectrometry revealed protein arginine methyltransferase 5 (PRMT5) as a binding partner of SREBP1a that symmetrically dimethylated it on R321, thereby promoting transcriptional activity. Furthermore, PRMT5-induced methylation prevented phosphorylation of SREBP1a on S430 by GSK3β, leading to its disassociation from Fbw7 (FBXW7) and its evasion from degradation through the ubiquitin-proteasome pathway. Consequently, methylation-stabilized SREBP1a increased de novo lipogenesis and accelerated the growth of cancer cells in vivo and in vitro. Clinically, R321 symmetric dimethylation status was associated with malignant progression of human hepatocellular carcinoma, where it served as an independent risk factor of poor prognosis. By showing how PRMT5-induced methylation of SREBP1a triggers hyperactivation of lipid biosynthesis, a key event in tumorigenesis, our findings suggest a new generalized strategy to selectively attack tumor metabolism. ©2016 American Association for Cancer Research.

  4. Asystole in alternating hemiplegia with de novo ATP1A3 mutation.

    Science.gov (United States)

    Novy, Jan; McWilliams, Eric; Sisodiya, Sanjay M

    2014-01-01

    Alternating hemiplegia is a rare condition presenting with episodes of hemiplegia, epileptic seizures and, at times, dysautonomic attacks. De novo ATP1A3 (Na(+)/K(+) ATPase subunit) mutations were recently found to be the most common cause. We report a patient with alternating hemiplegia with de novo ATP1A3 mutation who experienced new-onset episodes of collapse in early adulthood unrelated to seizures. An implantable cardiac loop recorder documented episodes of asystole up to 5 s long. Subsequently a permanent pacemaker was implanted. ATP1A3 heart expression may be the explanation for the association of alternating hemiplegia and asystole episodes. Alternating hemiplegia has been associated with an increased risk of sudden death and lethal cardiac arrhythmias may be causative. Patients may need referral for appropriate cardiac investigations, especially if there is a change in symptoms. This case highlights the importance of clinical vigilance in patients with alternating hemiplegia. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  5. Adrenoleukodystrophy in Norway: high rate of de novo mutations and age-dependent penetrance.

    Science.gov (United States)

    Horn, Morten A; Retterstøl, Lars; Abdelnoor, Michael; Skjeldal, Ola H; Tallaksen, Chantal M E

    2013-03-01

    To investigate X-linked adrenoleukodystrophy in an unselected population, we performed a population based, cross-sectional prevalence study, supplemented by a retrospective study of deceased subjects. Sixty-three subjects (34 males, 29 females) belonging to 22 kindreds were included. Thirty-nine subjects (13 males, 26 females) were alive, and 24 (21 males, 3 females) were deceased on the prevalence day. The point prevalence of X-linked adrenoleukodystrophy in Norway on July 1, 2011, was 0.8 per 100,000 inhabitants. The incidence at birth in the period 1956-1995 was 1.6 per 100,000 inhabitants. An age-dependent penetrance was observed among males and females, with more severe phenotypes appearing with rising age. Only 5% of deceased males had not developed cerebral leukodystrophy. No female older than 50 years was neurologically intact. Sixteen mutations in the ABCD1 gene were identified. De novo mutations were found in 19% of probands. The frequency of X-linked adrenoleukodystrophy was lower in Norway than reported in the literature. A more severe natural course than previously reported was observed, indicating a need for better follow-up of both male and female patients. Given the high rate of de novo mutations, identification programs such as newborn screening may be required to offer timely treatment to all patients. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. 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

  7. X-linked deafness: De novo deletion of a cosmid using dosage studies

    Energy Technology Data Exchange (ETDEWEB)

    Bitner-Glindzicz, M.; Pembrey, M.E. [Institute of Child Health, London (United Kingdom); deKok, Y. [University Hospital of Nijmegen (Netherlands)] [and others

    1994-09-01

    We have used three polymorphic microsatellite repeats at Xq21, (DXS986, DXS995 and DXS1002) to test for linkage in families with X-linked deafness. Close linkage was demonstrated between all three markers and the disease locus in families with and without a bony abnormality on the CT scan. DXS995 gave a maximum two point lod score of l0.37 with no recombinations. This marker was used to type an additional small sibship. Analysis showed that the two brothers, one deaf and one hearing, both inherited the same maternal allele indicating either the first recombination seen to date or a de novo mutation in the proband. Using a cosmid from the critical region, a deletion was detected in the proband of this sibship. By using a phoshorimager, dosage of an EcoR1 fragment from this cosmid and a control probe was compared to normal subjects and obligate carriers from another family with a similar deletion. Results show that the mother of this isolated case does not carry the deletion, confirming that it is de novo. These markers may be useful for carrier ascertainment in families with a radiological change on CT scan or a pedigree which is linked to Xq21.

  8. Contribuições de Angel Pino para pensar o Homem Novo em Vigotski

    Directory of Open Access Journals (Sweden)

    Anna Maria Lunardi Padilha*

    Full Text Available Resumo Este texto tem por objetivo apontar algumas contribuições de Angel Pino para a compreensão do conceito de homem novo proposto por Lev Vigotski. Esse conceito está estreitamente vinculado ao pensamento de K. Marx e F. Engels e dele deriva. Vigotski propõe que a cultura é produção humana, de modo que o homem produz a própria vida e a modifica conforme as suas necessidades e as condições históricas. Em várias obras, Angel Pino retoma e explicita, com rigor teórico e aprofundamento em vários campos do conhecimento, que as condições de existência, de onde origina a consciência dos homens, são transformadas pelo homem e, para isso, ele inventa e utiliza instrumentos e signos. O esforço de Angel Pino em direção à compreensão da teoria de Vigotski sobre a passagem da ordem do desenvolvimento natural para o cultural é inspiração para pensar a passagem de uma sociedade que explora e priva seus membros dos bens materiais e culturais para uma nova sociedade constitutiva de um novo homem.

  9. 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.

  10. Assemblathon 1: A competitive assessment of de novo short read assembly methods

    Science.gov (United States)

    Earl, Dent; Bradnam, Keith; St. John, John; Darling, Aaron; Lin, Dawei; Fass, Joseph; Yu, Hung On Ken; Buffalo, Vince; Zerbino, Daniel R.; Diekhans, Mark; Nguyen, Ngan; Ariyaratne, Pramila Nuwantha; Sung, Wing-Kin; Ning, Zemin; Haimel, Matthias; Simpson, Jared T.; Fonseca, Nuno A.; Birol, İnanç; Docking, T. Roderick; Ho, Isaac Y.; Rokhsar, Daniel S.; Chikhi, Rayan; Lavenier, Dominique; Chapuis, Guillaume; Naquin, Delphine; Maillet, Nicolas; Schatz, Michael C.; Kelley, David R.; Phillippy, Adam M.; Koren, Sergey; Yang, Shiaw-Pyng; Wu, Wei; Chou, Wen-Chi; Srivastava, Anuj; Shaw, Timothy I.; Ruby, J. Graham; Skewes-Cox, Peter; Betegon, Miguel; Dimon, Michelle T.; Solovyev, Victor; Seledtsov, Igor; Kosarev, Petr; Vorobyev, Denis; Ramirez-Gonzalez, Ricardo; Leggett, Richard; MacLean, Dan; Xia, Fangfang; Luo, Ruibang; Li, Zhenyu; Xie, Yinlong; Liu, Binghang; Gnerre, Sante; MacCallum, Iain; Przybylski, Dariusz; Ribeiro, Filipe J.; Yin, Shuangye; Sharpe, Ted; Hall, Giles; Kersey, Paul J.; Durbin, Richard; Jackman, Shaun D.; Chapman, Jarrod A.; Huang, Xiaoqiu; DeRisi, Joseph L.; Caccamo, Mario; Li, Yingrui; Jaffe, David B.; Green, Richard E.; Haussler, David; Korf, Ian; Paten, Benedict

    2011-01-01

    Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/. PMID:21926179

  11. 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.

  12. De Novo Assembly of the Transcriptome of Turritopsis, a Jellyfish that Repeatedly Rejuvenates.

    Science.gov (United States)

    Hasegawa, Yoshinori; Watanabe, Takashi; Takazawa, Masaki; Ohara, Osamu; Kubota, Shin

    2016-08-01

    In most animals, aging is an irreversible process; however the species Turritopsis sp. has been observed to undergo a rejuvenation process as many as 14 times. In the present study, we used multiplexed RNA libraries to obtain the transcriptome from four developmental stages (St) of Turritopsis sp., including (I) immature medusa, (II) dumpling, (III) dumpling with a short stolon, and (IV) polyp, which had recently rejuvenated. A total of 4.02 billion paired-end reads were assembled de novo, yielding 90,327 contigs. Our analyses revealed that significant blast hits were recovered for 74% of the assembled contigs, and 19% were successfully annotated with gene ontology (GO) terms. A BLAST search demonstrated that 32% of the contigs were most similar to Hydra vulgarissequences. Raw reads from each sample were mapped against the contigs to find St-specific genes. This represents the first comprehensive set of de novo transcriptome data for this species, which may provide clues toward a better understanding of cyclical rejuvenation in multicellular animals.

  13. Polymorphisms, de novo lipogenesis, and plasma triglyceride response following fish oil supplementation.

    Science.gov (United States)

    Bouchard-Mercier, Annie; Rudkowska, Iwona; Lemieux, Simone; Couture, Patrick; Vohl, Marie-Claude

    2013-10-01

    Interindividual variability in the response of plasma triglyceride concentrations (TG) following fish oil consumption has been observed. Our objective was to examine the associations between single-nucleotide polymorphisms (SNPs) within genes encoding proteins involved in de novo lipogenesis and the relative change in plasma TG levels following a fish oil supplementation. Two hundred and eight participants were recruited in the greater Quebec City area. The participants completed a six-week fish oil supplementation (5 g fish oil/day: 1.9-2.2 g eicosapentaenoic acid and 1.1 g docosahexaenoic acid. SNPs within SREBF1, ACLY, and ACACA genes were genotyped using TAQMAN methodology. After correction for multiple comparison, only two SNPs, rs8071753 (ACLY) and rs1714987 (ACACA), were associated with the relative change in plasma TG concentrations (P = 0.004 and P = 0.005, respectively). These two SNPs explained 7.73% of the variance in plasma TG relative change following fish oil consumption. Genotype frequencies of rs8071753 according to the TG response groups (responders versus nonresponders) were different (P = 0.02). We conclude that the presence of certain SNPs within genes, such as ACLY and ACACA, encoding proteins involved in de novo lipogenesis seem to influence the plasma TG response following fish oil consumption.

  14. Nicotinamide phosphoribosyl transferase (Nampt) is required for de novo lipogenesis in tumor cells.

    Science.gov (United States)

    Bowlby, Sarah C; Thomas, Michael J; D'Agostino, Ralph B; Kridel, Steven J

    2012-01-01

    Tumor cells have increased metabolic requirements to maintain rapid growth. In particular, a highly lipogenic phenotype is a hallmark of many tumor types, including prostate. Cancer cells also have increased turnover of nicotinamide adenine dinucleotide (NAD(+)), a coenzyme involved in multiple metabolic pathways. However, a specific role for NAD(+) in tumor cell lipogenesis has yet to be described. Our studies demonstrate a novel role for the NAD(+)-biosynthetic enzyme Nicotinamide phosphoribosyltransferase (Nampt) in maintaining de novo lipogenesis in prostate cancer (PCa) cells. Inhibition of Nampt reduces fatty acid and phospholipid synthesis. In particular, short chain saturated fatty acids and the phosphatidylcholine (PC) lipids into which these fatty acids are incorporated were specifically reduced by Nampt inhibition. Nampt blockade resulted in reduced ATP levels and concomitant activation of AMP-activated protein kinase (AMPK) and phosphorylation of acetyl-CoA carboxylase (ACC). In spite of this, pharmacological inhibition of AMPK was not sufficient to fully restore fatty acid synthesis. Rather, Nampt blockade also induced protein hyperacetylation in PC-3, DU145, and LNCaP cells, which correlated with the observed decreases in lipid synthesis. Moreover, the sirtuin inhibitor Sirtinol, and the simultaneous knockdown of SIRT1 and SIRT3, phenocopied the effects of Nampt inhibition on fatty acid synthesis. Altogether, these data reveal a novel role for Nampt in the regulation of de novo lipogenesis through the modulation of sirtuin activity in PCa cells.

  15. The Glucose Sensor ChREBP Links De Novo Lipogenesis to PPARγ Activity and Adipocyte Differentiation.

    Science.gov (United States)

    Witte, Nicole; Muenzner, Matthias; Rietscher, Janita; Knauer, Miriam; Heidenreich, Steffi; Nuotio-Antar, Alli M; Graef, Franziska A; Fedders, Ronja; Tolkachov, Alexander; Goehring, Isabel; Schupp, Michael

    2015-11-01

    Reduced de novo lipogenesis in adipose tissue, often observed in obese individuals, is thought to contribute to insulin resistance. Besides trapping excess glucose and providing for triglycerides and energy storage, endogenously synthesized lipids can function as potent signaling molecules. Indeed, several specific lipids and their molecular targets that mediate insulin sensitivity have been recently identified. Here, we report that carbohydrate-response element-binding protein (ChREBP), a transcriptional inducer of glucose use and de novo lipogenesis, controls the activity of the adipogenic master regulator peroxisome proliferator-activated receptor (PPAR)γ. Expression of constitutive-active ChREBP in precursor cells activated endogenous PPARγ and promoted adipocyte differentiation. Intriguingly, ChREBP-constitutive-active ChREBP expression induced PPARγ activity in a fatty acid synthase-dependent manner and by trans-activating the PPARγ ligand-binding domain. Reducing endogenous ChREBP activity by either small interfering RNA-mediated depletion, exposure to low-glucose concentrations, or expressing a dominant-negative ChREBP impaired differentiation. In adipocytes, ChREBP regulated the expression of PPARγ target genes, in particular those involved in thermogenesis, similar to synthetic PPARγ ligands. In summary, our data suggest that ChREBP controls the generation of endogenous fatty acid species that activate PPARγ. Thus, increasing ChREBP activity in adipose tissue by therapeutic interventions may promote insulin sensitivity through PPARγ.

  16. Um fungo novo do caeté Bilboque, a new genus of hyphomycetes on calathea

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    A. P. Viégas

    1960-01-01

    Full Text Available Um fungo hifomicete, ocasionando lesões em folhas de Calathea sp., da família Marantaceae, vulgarmente chamada caeté e tido como novo à micologia brasileira é agora descrito pela primeira vez. Êsse organismo foi constatado também em fôlhas de Canna sp., da família Cannaceae, no Estado do Rio de Janeiro. Ao gênero novo deu-se o nome de Bilboque. À espécie, magnificum. A etimologia do gênero é apresentada e discutida, assim como a posição taxonômica do hifomicete, amparando-as na morfologia. Vai ilustrada com séries de figuras a bico de pena pelo próprio autor.A new genus of the Hyphomycetes is described on living leaves of Calathea sp., caeté in Tupi and Portuguese, a plant belonging to the family Marantaceae. The new erected genus has been called Bilboque, and the specific name magnificum: The implications which this genus have when compared to other well known genera, like Polythrincium, Cordana and Piricularia are focussed, and in order to clear problems dealing with morphological features of the new genus its characteristics have been shown in four serial sequences of figures by Indian ink, all them by the hand of the writer.

  17. CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids.

    Science.gov (United States)

    Manolova, Vania; Hirabayashi, Yoshio; Mori, Lucia; De Libero, Gennaro

    2003-01-01

    CD1 molecules resemble classical MHC molecules in structure, bind self and bacterial glycolipids and present them to T cells. Whether the CD1 antigen-binding groove becomes filled during maturation and traffic to the cell surface is an important and still unsolved biological question. As most cell types synthesize complex glycosphingolipids (GSL), which also stimulate CD1-restricted T cells, it could be possible that these ligands associate with nascent CD1 molecules. Here, we show that treatment of cells with drugs blocking at different levels the de novo and salvage pathways of GSL synthesis does not prevent surface expression of CD1a and CD1b. Furthermore, transfection of CD1A and CD1B genes in a mutant cell line unable to synthesize glucosylceramides and galactosylceramides showed normal surface expression of both CD1 molecules. Lack of GSL did not induce intracellular CD1 accumulation as indicated by confocal microscopy. The same results were obtained by transfecting the Lec series of mutants, which are deficient in sugar addition to glycolipids and glycoproteins. These findings demonstrate that endogenous de novo synthesized GSL are not mandatory for CD1a and CD1b negotiating surface expression.

  18. Effects of GC bias in next-generation-sequencing data on de novo genome assembly.

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    Yen-Chun Chen

    Full Text Available Next-generation-sequencing (NGS has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

  19. Effects of GC bias in next-generation-sequencing data on de novo genome assembly.

    Science.gov (United States)

    Chen, Yen-Chun; Liu, Tsunglin; Yu, Chun-Hui; Chiang, Tzen-Yuh; Hwang, Chi-Chuan

    2013-01-01

    Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

  20. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.

    Science.gov (United States)

    Chino, Marco; Maglio, Ornella; Nastri, Flavia; Pavone, Vincenzo; DeGrado, William F; Lombardi, Angela

    2015-07-01

    A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.

  1. Spectrum of genetic mutations in de novo PUNLMP of the urinary bladder.

    Science.gov (United States)

    Rodriguez Pena, Maria Del Carmen; Tregnago, Aline C; Eich, Marie-Lisa; Springer, Simeon; Wang, Yuxuan; Taheri, Diana; Ertoy, Dilek; Fujita, Kazutoshi; Bezerra, Stephania M; Cunha, Isabela W; Raspollini, Maria Rosaria; Yu, Lijia; Bivalacqua, Trinity J; Papadopoulos, Nickolas; Kinzler, Kenneth W; Vogelstein, Bert; Netto, George J

    2017-06-08

    Our group and others have previously demonstrated the presence of TERT promoter mutations (TERT-mut) in 60-80% of urothelial carcinomas and some of their histologic variants. Five other genes have been frequently implicated in bladder cancer: FGRF3, TP53, PIK3CA, HRAS, and CDKN2A. In the current study, we sought to determine the prevalence of mutations in TERT and these five other genes in de novo papillary urothelial neoplasms of low malignant potential (PUNLMP) of the urinary bladder. A retrospective search of our archives for PUNLMP was performed and 30 de novo cases were identified and included in the study. We found mutations in TERT (TERT-mut) and FGFR3 (FGFR3-mut) to be the most common alterations in the cohort (63 and 60%, respectively). The majority of the TERT-mut-positive tumors (84%) had a g.1295228C > T alteration with the remaining tumors demonstrating g.1295250C > T. Approximately one fourth of tumors had TP53 mutations. These findings support the potential utility of a uniform genetic mutation panel to detect bladder cancers of various subtypes.

  2. GIS and Green Spaces' Management in Porto Novo Town in Benin

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    Osseni, AA.

    2015-01-01

    Full Text Available SIG et gestion des espaces verts dans la ville de Porto-Novo au Bénin. Porto­Novo town has for a long time neglected to take in account ecological parameters in its process of development, in favor of uncontrolled expansion of constructed areas. The aim of this study is to analyze the attractiveness of public green spaces in the city for their efficient management. GPS, survey questionnaire and GIS were the main tools used for this purpose. Fourteen green spaces, distributed into eight public squares, four gardens and two wooded esplanades were identified in the town. The numbers of trees available in each site and their species diversity are relatively weak. The area of green space per inhabitant is very low and difficult to improve because of the lack of available areas. A strong frequentation of the spaces (61.4% of surveyed was noted on a radius of 300 m, against respectively 30% and 8.6% of frequentation on radii of 600 and 900 m. Finally, maps of attractiveness and spatial coverage of green areas were developed. A model of optimal management of green spaces in the town is proposed based on identified sociological and technical constraints.

  3. Karyomapping allows preimplantation genetic diagnosis of a de-novo deletion undetectable using conventional PGD technology.

    Science.gov (United States)

    Giménez, Carles; Sarasa, Jonás; Arjona, César; Vilamajó, Ester; Martínez-Pasarell, Olga; Wheeler, Kenny; Valls, Gemma; Garcia-Guixé, Elena; Wells, Dagan

    2015-12-01

    Preimplantation genetic diagnosis (PGD) was carried out for a couple carrying a de-novo deletion in the TSC2 gene, responsible for tuberous sclerosis. Karyomapping, a method employing genome-wide analysis of single nucleotide polymorphisms (SNP), was used as PGD protocol. Analysis of DNA from the affected parent using karyomapping confirmed the region covered by the deletion and revealed more than 30 SNP located within the affected region. These SNP were subsequently used for embryo diagnosis (deletion revealed by hemizygosity and/or reduced probe intensity). Seven blastocyst embryos underwent trophectoderm biopsy followed by vitrification. Biopsied cells were subjected to comprehensive aneuploidy screening using microarray comparative genomic hybridization (aCGH), with karyomapping for the detection of embryos carrying the mutant TSC2 gene carried out in tandem. Two embryo transfers were performed, the second of which resulted in the birth of a child. This study highlights that karyomapping may be applicable to a subset of de-novo mutations undetectable using standard PGD strategies. Additionally, karyomapping results were in complete concordance with aCGH, both methods revealing the same aneuploidies in the embryos tested. It was concluded that karyomapping may represent a valuable advance in cases of PGD for monogenic diseases. Copyright © 2015 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  4. Observation of de novo bladder dysfunction under treatment with Her2-neu antibodies.

    Science.gov (United States)

    Hinkel, Andreas; Strumberg, Dirk; Noldus, Joachim; Pannek, Jürgen

    2011-01-01

    We diagnosed de novo bladder dysfunction in several breast cancer patients under cancer-specific therapy with trastuzumab. The goal of this retrospective analysis was to investigate whether bladder dysfunction is common in a larger population of breast cancer patients receiving trastuzumab therapy. We identified 93 patients who received at least two doses of trastuzumab at our institution in the years 2003-2006. 57 of those patients were still alive at the time of this analysis. We mailed a validated global questionnaire for the assessment of incontinence (King's Health Questionnaire, KHQ) to them, additionally asking for bladder dysfunction observed under trastuzumab therapy. 43 (75%) of the patients returned the questionnaire, 11 (25%) of them reporting severe de novo bladder dysfunction under therapy. Significant differences between symptomatic and asymptomatic patients were detected in all KHQ subscales. Previous conditions and surgeries as well as medications, especially hormonal therapy, were excluded as underlying causes. However, there were more patients under taxane-based chemotherapy in the symptomatic group. The epidermal growth factor receptor is involved in the cellular response to mechanical stretch in the urinary bladder. Based on our findings, we hypothesize that interfering with this pathway may well be the cause of symptomatic bladder dysfunction in patients under trastuzumab medication. A prospective study is required to further elucidate this hypothesis. Copyright © 2010 S. Karger AG, Basel.

  5. Selection of gait parameters for differential diagnostics of patients with de novo Parkinson's disease.

    Science.gov (United States)

    Djurić-Jovičić, Milica; Belić, Minja; Stanković, Iva; Radovanović, Saša; Kostić, Vladimir S

    2017-10-01

    Gait disturbances are an integral part of clinical manifestations of Parkinson's disease (PD), even in the initial stages of the disease. Our goal was to identify the set of spatio-temporal gait parameters that bear the highest relevance for characterizing de novo PD patients. Forty patients with de novo PD and forty healthy controls were recorded while walking over an electronic walkway in three different conditions: (1) base walking, (2) walking with an additional motor task, (3) walking with an additional mental task. Both groups were well balanced concerning age and gender. To select a smaller number of relevant parameters, affinity propagation clustering was applied on parameter pairwise correlation. The exemplars were then sorted by importance using the random forest algorithm. Classification accuracy of a support vector machine was tested using the selected parameters and compared to the accuracy of the model using a set of parameters derived from literature. Final selection of parameters included: stride length and stride length coefficient of variation (CV), stride time and stride time CV, swing time and swing time CV, step time asymmetry, and heel-to-heel base support CV. Classification performed using these parameters showed higher overall accuracy (85%) than classification using the common parameter set containing: stride time, stride length, swing time and double support time, along with their CVs (78%). In early stages of PD, double support time and its CV appear to be weak indicators of the disease. We instead found step time asymmetry and support base CV to significantly contribute to classification accuracy.

  6. Increase in de novo allergies after paediatric liver transplantation: the Brisbane experience.

    Science.gov (United States)

    Noble, C; Peake, J; Lewindon, P J

    2011-08-01

      Pediatric liver transplantation is a successful procedure with 10-yr survival rate of 70%; following transplantation, the emphasis on promoting good quality of life is important. The increasing prevalence of allergic disorders in the general population and an increase in food allergy following solid organ transplantation are described in patients, especially in children, but the contribution to morbidity post-OLT has not been addressed. Identifying the incidence de novo allergies post-OLT performed by QLTS over 11 yr. Comprehensive medical record review of OLT recipients during study period. From 1st July 1998 to 1st August 2009, 78 children received 85 cadaveric OLT; 60 children survived. Allergic disease was documented in 24/60 (40%) survivors. De novo food allergies were diagnosed in 12/60 (20%) (Table 2), 9/12 occurred in children who were infants at time of transplant. Ten of 12 had severe allergies, six anaphylactic; 6/60 (10%) carry an EpiPen. Only 31/60 (51%) diagnosed are followed in Queensland, suggesting severe allergic disease in our cohort is an underestimate. Serious allergic disease post-OLT is clinically important, especially in infants at time of transplant, and should be targeted for specialist allergist referral and risk management. [Table: see text]. © 2011 John Wiley & Sons A/S.

  7. 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.

  8. 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.

  9. Hirschsprung-like disease is exacerbated by reduced de novo GMP synthesis.

    Science.gov (United States)

    Lake, Jonathan I; Tusheva, Olga A; Graham, Brittany L; Heuckeroth, Robert O

    2013-11-01

    Hirschsprung disease (HSCR) is a partially penetrant oligogenic birth defect that occurs when enteric nervous system (ENS) precursors fail to colonize the distal bowel during early pregnancy. Genetic defects underlie HSCR, but much of the variability in the occurrence and severity of the birth defect remain unexplained. We hypothesized that nongenetic factors might contribute to disease development. Here we found that mycophenolate, an inhibitor of de novo guanine nucleotide biosynthesis, and 8 other drugs identified in a zebrafish screen impaired ENS development. In mice, mycophenolate treatment selectively impaired ENS precursor proliferation, delayed precursor migration, and induced bowel aganglionosis. In 2 different mouse models of HSCR, addition of mycophenolate increased the penetrance and severity of Hirschsprung-like pathology. Mycophenolate treatment also reduced ENS precursor migration as well as lamellipodia formation, proliferation, and survival in cultured enteric neural crest–derived cells. Using X-inactivation mosaicism for the purine salvage gene Hprt, we found that reduced ENS precursor proliferation most likely causes mycophenolate-induced migration defects and aganglionosis. To the best of our knowledge, mycophenolate is the first medicine identified that causes major ENS malformations and Hirschsprung-like pathology in a mammalian model. These studies demonstrate a critical role for de novo guanine nucleotide biosynthesis in ENS development and suggest that some cases of HSCR may be preventable.

  10. CYCLONE--a utility for de novo sequencing of microbial cyclic peptides.

    Science.gov (United States)

    Kavan, Daniel; Kuzma, Marek; Lemr, Karel; Schug, Kevin A; Havlicek, Vladimir

    2013-08-01

    We have developed a de novo sequencing software tool (CYCLONE) and applied it for determination of cyclic peptides. The program uses a non-redundant database of 312 nonribosomal building blocks identified to date in bacteria and fungi (more than 230 additional residues in the database list were isobaric). The software was used to fully characterize the tandem mass spectrum of several cyclic peptides and provide sequence tags. The general strategy of the script was based on fragment ion pre-characterization to accomplish unambiguous b-ion series assignments. Showcase examples were a cyclic tetradepsipeptide beauverolide, a cyclic hexadepsipeptide roseotoxin A, a lasso-like hexapeptide pseudacyclin A, and a cyclic undecapeptide cyclosporin A. The extent of ion scrambling in smaller peptides was as low as 5 % of total ion current; this demonstrated the feasibility of CYCLONE de novo sequencing. The robustness of the script was also tested against database sets of various sizes and isotope-containing data. It can be downloaded from the http://ms.biomed.cas.cz/MSTools/ website. ᅟ

  11. Comparative genomic analysis reveals a critical role of de novo nucleotide biosynthesis for Saccharomyces cerevisiae virulence.

    Science.gov (United States)

    Pérez-Torrado, Roberto; Llopis, Silvia; Perrone, Benedetta; Gómez-Pastor, Rocío; Hube, Bernhard; Querol, Amparo

    2015-01-01

    In recent years, the number of human infection cases produced by the food related species Saccharomyces cerevisiae has increased. Whereas many strains of this species are considered safe, other 'opportunistic' strains show a high degree of potential virulence attributes and can cause infections in immunocompromised patients. Here we studied the genetic characteristics of selected opportunistic strains isolated from dietary supplements and also from patients by array comparative genomic hybridization. Our results show increased copy numbers of IMD genes in opportunistic strains, which are implicated in the de novo biosynthesis of the purine nucleotides pathway. The importance of this pathway for virulence of S. cerevisiae was confirmed by infections in immunodeficient murine models using a GUA1 mutant, a key gene of this pathway. We show that exogenous guanine, an end product of this pathway in its triphosphorylated form, increases the survival of yeast strains in ex vivo blood infections. Finally, we show the importance of the DNA damage response that activates dNTP biosynthesis in yeast cells during ex vivo blood infections. We conclude that opportunistic yeasts may use an enhanced de novo biosynthesis of the purine nucleotides pathway to increase survival and favor infections in the host.

  12. 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.

  13. The mutational oncoprint of recurrent cytogenetic abnormalities in adult patients with de novo acute myeloid leukemia.

    Science.gov (United States)

    Eisfeld, A-K; Mrózek, K; Kohlschmidt, J; Nicolet, D; Orwick, S; Walker, C J; Kroll, K W; Blachly, J S; Carroll, A J; Kolitz, J E; Powell, B L; Wang, E S; Stone, R M; de la Chapelle, A; Byrd, J C; Bloomfield, C D

    2017-10-01

    Recurrent chromosomal abnormalities and gene mutations detected at the time of diagnosis of acute myeloid leukemia (AML) are associated with particular disease features, treatment response and survival of AML patients, and are used to denote specific disease entities in the World Health Organization classification of myeloid neoplasms and acute leukemia. However, large studies that integrate cytogenetic and comprehensive mutational information are scarce. We created a comprehensive oncoprint of mutations associated with recurrent cytogenetic findings by combining the information on mutational patterns of 80 cancer- and leukemia-associated genes with cytogenetic findings in 1603 adult patients with de novo AML. We show unique differences in the mutational profiles among major cytogenetic subsets, identify novel associations between recurrent cytogenetic abnormalities and both specific gene mutations and gene functional groups, and reveal differences in cytogenetic and mutational features between patients younger than 60 years and those aged 60 years or older. The identified associations between cytogenetic and molecular genetic data may help guide mutation testing in AML, and result in more focused application of targeted therapy in patients with de novo AML.

  14. De novo cerebral arteriovenous malformation: Pink Floyd's song "Brick in the Wall" as a warning sign.

    Science.gov (United States)

    Ozsarac, Murat; Aksay, Ersin; Kiyan, Selahattin; Unek, Orkun; Gulec, F Feray

    2012-07-01

    Arteriovenous malformations are shunts between an artery and the venous system that lie within a nidus without an intervening capillary bed. These lesions are thought to be congenital, but recent reports have challenged this assumption. A 50-year-old man presented to the emergency department with a generalized tonic-clonic seizure. Before the onset of his seizure, he experienced a vivid auditory hallucination of his favorite song by the band Pink Floyd, "A Brick in the Wall." He had been diagnosed with epilepsy 25 years previously. On presentation, his neurological examination was normal, but a computed tomography scan of the brain revealed a large arteriovenous malformation (AVM) occupying the left temporal lobe. Upon more detailed questioning, he recalled that a brain angiogram had been performed 25 years before and was reported to be normal. Neurosurgery was not performed in view of the size of the malformation. The patient is being followed-up as an outpatient. AVMs may arise de novo and then spontaneously become symptomatic. Cerebral de novo AVM should be considered in the differential diagnosis in patients with complex auditory musical hallucinations or any new neuropsychiatric symptoms. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. A framework for the detection of de novo mutations in family-based sequencing data

    Science.gov (United States)

    Francioli, Laurent C; Cretu-Stancu, Mircea; Garimella, Kiran V; Fromer, Menachem; Kloosterman, Wigard P; Wijmenga, Cisca; Investigator, Principal; Swertz, Morris A; van Duijn, Cornelia M; Boomsma, Dorret I; Slagboom, PEline; van Ommen, Gertjan B; de Bakker, Paul IW; Swertz, Morris A; Francioli, Laurent C; van Dijk, Freerk; Menelaou, Androniki; Neerincx, Pieter BT; Pulit, Sara L; Deelen, Patrick; Elbers, Clara C; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen FJ; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H; van den Berg, Leonard H; Byelas, Heorhiy; den Dunnen, Johan T; Dijkstra, Martijn; Amin, Najaf; van der Velde, K Joeri; Hottenga, Jouke Jan; van Setten, Jessica; van Leeuwen, Elisabeth M; Kanterakis, Alexandros; Kattenberg, Mathijs; Karssen, Lennart C; van Schaik, Barbera DC; Bot, Jan; Nijman, Isaäc J; Renkens, Ivo; van Enckevort, David; Mei, Hailiang; Koval, Vyacheslav; Estrada, Karol; Medina-Gomez, Carolina; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H; Hehir-Kwa, Jayne Y; Handsaker, Robert E; McCarroll, Steven A; Sunyaev, Shamil R; Polak, Paz; Vuzman, Dana; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; de Bakker, Paul IW; Slagboom, P Eline; Beekman, Marian B; de Craen, Anton JM; Suchiman, H Eka D; Hofman, Albert; van Duijn, Cornelia M; Oostra, Ben; Isaacs, Aaron; Amin, Najaf; Rivadeneira, Fernando; Uitterlinden, André G; Boomsma, Dorret I; Willemsen, Gonneke; Platteel, Mathieu; Pitts, Steven J; Potluri, Shobha; Sundar, Purnima; Cox, David R; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A; Brandsma, Margreet; Samocha, Kaitlin E; Neale, Benjamin M; Daly, Mark J; Banks, Eric; DePristo, Mark A; de Bakker, Paul IW

    2017-01-01

    Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father's age at conception and the number of DNMs in female offspring's X chromosome, consistent with previous literature reports. PMID:27876817

  16. 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.

  17. De novo biosynthesis of trans-cinnamic acid derivatives in Saccharomyces cerevisiae.

    Science.gov (United States)

    Gottardi, Manuela; Knudsen, Jan Dines; Prado, Lydie; Oreb, Mislav; Branduardi, Paola; Boles, Eckhard

    2017-06-01

    The production of natural aroma compounds is an expanding field within the branch of white biotechnology. Three aromatic compounds of interest are cinnamaldehyde, the typical cinnamon aroma that has applications in agriculture and medical sciences, as well as cinnamyl alcohol and hydrocinnamyl alcohol, which have applications in the cosmetic industry. Current production methods, which rely on extraction from plant materials or chemical synthesis, are associated with drawbacks regarding scalability, production time, and environmental impact. These considerations make the development of a sustainable microbial-based production highly desirable. Through steps of rational metabolic engineering, we engineered the yeast Saccharomyces cerevisiae as a microbial host to produce trans-cinnamic acid derivatives cinnamaldehyde, cinnamyl alcohol, and hydrocinnamyl alcohol, from externally added trans-cinnamic acid or de novo from glucose as a carbon source. We show that the desired products can be de novo synthesized in S. cerevisiae via the heterologous overexpression of the genes encoding phenylalanine ammonia lyase 2 from Arabidopsis thaliana (AtPAL2), aryl carboxylic acid reductase (acar) from Nocardia sp., and phosphopantetheinyl transferase (entD) from Escherichia coli, together with endogenous alcohol dehydrogenases. This study provides a proof of concept and a strain that can be further optimized for production of high-value aromatic compounds.

  18. De novo KCNH1 mutations in four patients with syndromic developmental delay, hypotonia and seizures.

    Science.gov (United States)

    Fukai, Ryoko; Saitsu, Hirotomo; Tsurusaki, Yoshinori; Sakai, Yasunari; Haginoya, Kazuhiro; Takahashi, Kazumasa; Hubshman, Monika Weisz; Okamoto, Nobuhiko; Nakashima, Mitsuko; Tanaka, Fumiaki; Miyake, Noriko; Matsumoto, Naomichi

    2016-05-01

    The voltage-gated Kv10.1 potassium channel, also known as ether-a-go-go-related gene 1, encoded by KCNH1 (potassium voltage-gated channel, subfamily H (eag related), member 1) is predominantly expressed in the central nervous system. Recently, de novo missense KCNH1 mutations have been identified in six patients with Zimmermann-Laband syndrome and in four patients with Temple-Baraitser syndrome. These syndromes were historically considered distinct. Here we report three de novo missense KCNH1 mutations in four patients with syndromic developmental delay and epilepsy. Two novel KCNH1 mutations (p.R357Q and p.R357P), found in three patients, were located at the evolutionally highly conserved arginine in the channel voltage-sensor domain (S4). Another mutation (p.G496E) was found in the channel pore domain (S6) helix, which acts as a hinge in activation gating and mainly conducts non-inactivating outward potassium current. A previously reported p.G496R mutation was shown to produce no voltage-dependent outward current in CHO cells, suggesting that p.G496E may also disrupt the proper function of the Kv channel pore. Our report confirms that KCNH1 mutations are associated with syndromic neurodevelopmental disorder, and also support the functional importance of the S4 domain.

  19. A LÓGICA DOMINANTE DO SERVIÇO EM MARKETING – UM NOVO PARADIGMA?

    Directory of Open Access Journals (Sweden)

    Clara Isabel Koetz

    2013-01-01

    Full Text Available As diversas mudanças que vêm ocorrendo na disciplina de marketing têm sido consideradas, por diversos estudiosos da área, como um novo paradigma. Vargo e Lusch (2004 apontam a emergência de uma nova lógica, cuja ênfase está nos aspectos intangíveis, como habilidades, informação e conhecimento e na interatividade e conectividade dos relacionamentos, o qual poderia vir a substituir o modelo tradicional. O objetivo deste ensaio teórico é propor uma reflexão acerca da Service Dominant Logic (SDL, proposta por Vargo e Lusch (2004, a fim de identificar se, de fato, ela pode ser considerada um novo paradigma em marketing. Para tal, é realizado um exame do desenvolvimento teórico da disciplina, bem como da estrutura teórica proposta pelos autores, com base na perspectiva filosófico-científica e no conceito de paradigma de Kuhn (2006. A análise demonstra que o marketing evoluiu, por um lado, orientado pelas alterações impostas pelo ambiente; por outro lado, por meio de discussões teóricas que permitiram o avanço da disciplina. Não houve, ao logo deste processo, nem mesmo com a lógica dominante dos serviços, uma ruptura drástica que possa ser considerada uma troca de paradigmas.

  20. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

    Science.gov (United States)

    Wang, Moye; Hu, Jie; Zhang, Zhuqing

    2016-04-26

    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.

  1. 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.

  2. A de novo dominant mutation in KIF1A associated with axonal neuropathy, spasticity and autism spectrum disorder.

    Science.gov (United States)

    Tomaselli, Pedro J; Rossor, Alexander M; Horga, Alejandro; Laura, Matilde; Blake, Julian C; Houlden, Henry; Reilly, Mary M

    2017-08-23

    Mutations in the kinesin family member 1A (KIF1A) gene have been associated with a wide range of phenotypes including recessive mutations causing hereditary sensory neuropathy and hereditary spastic paraplegia and de novo dominant mutations causing a more complex neurological disorder affecting both the central and peripheral nervous system. We identified by exome sequencing a de novo dominant missense variant, (c.38G>A, p.R13H), within an ATP binding site of the kinesin motor domain in a patient manifesting a complex phenotype characterized by autism spectrum disorder (ASD), spastic paraplegia and axonal neuropathy. The presence of ASD distinguishes this case from previously reported patients with de novo dominant mutations in KIF1A. © 2017 The Authors. Journal of the Peripheral Nervous System published by Wiley Periodicals, Inc. on behalf of Peripheral Nerve Society.

  3. 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.

  4. De Novo Vertebral Artery Dissection after Endovascular Trapping for Ruptured Dissecting Internal Carotid Artery Aneurysm: Case Report

    Science.gov (United States)

    HORIE, Nobutaka; SADAKATA, Eisaku; IZUMO, Tsuyoshi; HAYASHI, Kentaro; MORIKAWA, Minoru; NAGATA, Izumi

    The authors present an extremely rare case of a 54-year-old female patient with subarachnoid hemorrhage due to a rupture of a dissecting internal carotid artery (ICA) aneurysm, who developed de novo vertebral artery dissection in the spasm period after endovascular trapping of the ICA. Interestingly, postoperative cardiopulmonary monitoring showed high global end-diastolic volume index and mean arterial pressure, which could contribute to this de novo dissection via hemodynamic stress in the cerebral circulation. Spontaneous intracranial artery dissection of more than two arteries is rare, and we believe this is the first case of de novo dissection occurring on a circulating vessel different from that of the initial dissection. The clinical implications are discussed in relation to postoperative hemodynamic stress with a review of the literature. PMID:24418785

  5. Curva de Phillips novo keynesiana, custo marginal e expectativas de inflação no Brasil

    OpenAIRE

    Carvalho, Bruno Silva

    2009-01-01

    A importância deste trabalho será analisar a dinâmica inflacionária brasileira de acordo com um modelo híbrido de curva de Phillips baseado nos estudos sobre a curva de Phillips “Novo-Keynesiana”. Através deste estudo será possível avaliar a inflação passada e as expectativas de inflação como determinantes à inflação corrente e a aplicabilidade da curva de Phillips “Novo-Keynesiana” para o caso brasileiro. As conclusões do estudo darão uma indicação mais concreta do novo dinami...

  6. The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen De Novo.

    Science.gov (United States)

    Gubala, Anna M; Schmitz, Jonathan F; Kearns, Michael J; Vinh, Tery T; Bornberg-Bauer, Erich; Wolfner, Mariana F; Findlay, Geoffrey D

    2017-05-01

    New genes arise through a variety of mechanisms, including the duplication of existing genes and the de novo birth of genes from noncoding DNA sequences. While there are numerous examples of duplicated genes with important functional roles, the functions of de novo genes remain largely unexplored. Many newly evolved genes are expressed in the male reproductive tract, suggesting that these evolutionary innovations may provide advantages to males experiencing sexual selection. Using testis-specific RNA interference, we screened 11 putative de novo genes in Drosophila melanogaster for effects on male fertility and identified two, goddard and saturn, that are essential for spermatogenesis and sperm function. Goddard knockdown (KD) males fail to produce mature sperm, while saturn KD males produce few sperm, and these function inefficiently once transferred to females. Consistent with a de novo origin, both genes are identifiable only in Drosophila and are predicted to encode proteins with no sequence similarity to any annotated protein. However, since high levels of divergence prevented the unambiguous identification of the noncoding sequences from which each gene arose, we consider goddard and saturn to be putative de novo genes. Within Drosophila, both genes have been lost in certain lineages, but show conserved, male-specific patterns of expression in the species in which they are found. Goddard is consistently found in single-copy and evolves under purifying selection. In contrast, saturn has diversified through gene duplication and positive selection. These data suggest that de novo genes can acquire essential roles in male reproduction. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Environmental risk factors for autism: do they help cause de novo genetic mutations that contribute to the disorder?

    Science.gov (United States)

    Kinney, Dennis K; Barch, Daniel H; Chayka, Bogdan; Napoleon, Siena; Munir, Kerim M

    2010-01-01

    Recent research has discovered that a number of genetic risk factors for autism are de novo mutations. Advanced parental age at the time of conception is associated with increased risk for both autism and de novo mutations. We investigated the hypothesis that other environmental factors associated with increased risk for autism might also be mutagenic and contribute to autism by causing de novo mutations. A survey of the research literature identified 9 environmental factors for which increased pre-conceptual exposure appears to be associated with increased risk for autism. Five of these factors--mercury, cadmium, nickel, trichloroethylene, and vinyl chloride--are established mutagens. Another four--including residence in regions that are urbanized, located at higher latitudes, or experience high levels of precipitation--are associated with decreased sun exposure and increased risk for vitamin D deficiency. Vitamin D plays important roles in repairing DNA damage and protecting against oxidative stress--a key cause of DNA damage. Factors associated with vitamin D deficiency will thus contribute to higher mutation rates and impaired repair of DNA. We note how de novo mutations may also help explain why the concordance rate for autism is so markedly higher in monozygotic than dizygotic twins. De novo mutations may also explain in part why the prevalence of autism is so remarkably high, given the evidence for a strong role of genetic factors and the low fertility of individuals with autism--and resultant selection pressure against autism susceptibility genes. These several lines of evidence provide support for the hypothesis, and warrant new research approaches--which we suggest--to address limitations in existing studies. The hypothesis has implications for understanding possible etiologic roles of de novo mutations in autism, and it suggests possible approaches to primary prevention of the disorder, such as addressing widespread vitamin D deficiency and exposure to

  8. Mudanças da prática docente a partir do desenvolvimento de um novo projeto na escola

    OpenAIRE

    Fontenele, Thais Regina Cunha Ventura Fernandes

    2016-01-01

    O presente trabalho tem como contexto de estudo duas escolas municipais de Guarulhos e tem o objetivo de investigar o significado da experiência de um novo projeto pedagógico na escola para os professores nele envolvidos, especialmente com relação às alterações da sua prática docente. Os objetivos específicos voltam-se para a identificação de mudanças na prática das professoras, que foram possibilitadas pela vivência do novo projeto, analisando suas compreensões a respeito do trabalho coletiv...

  9. The Computer Code NOVO for the Calculation of Wake Potentials of the Very Short Ultra-relativistic Bunches

    Energy Technology Data Exchange (ETDEWEB)

    Novokhatski, Alexander; /SLAC

    2005-12-01

    The problem of electromagnetic interaction of a beam and accelerator elements is very important for linear colliders, electron-positron factories, and free electron lasers. Precise calculation of wake fields is required for beam dynamics study in these machines. We describe a method which allows computation of wake fields of the very short bunches. Computer code NOVO was developed based on this method. This method is free of unphysical solutions like ''self-acceleration'' of a bunch head, which is common to well known wake field codes. Code NOVO was used for the wake fields study for many accelerator projects all over the world.

  10. A Swedish family with de novo alpha-synuclein A53T mutation: evidence for early cortical dysfunction

    DEFF Research Database (Denmark)

    Puschmann, Andreas; Ross, Owen A; Vilariño-Güell, Carles

    2009-01-01

    A de novo alpha-synuclein A53T (p.Ala53 Th; c.209G > A) mutation has been identified in a Swedish family with autosomal dominant Parkinson's disease (PD). Two affected individuals had early-onset (before 31 and 40 years), severe levodopa-responsive PD with prominent dysphasia, dysarthria, and cog......A de novo alpha-synuclein A53T (p.Ala53 Th; c.209G > A) mutation has been identified in a Swedish family with autosomal dominant Parkinson's disease (PD). Two affected individuals had early-onset (before 31 and 40 years), severe levodopa-responsive PD with prominent dysphasia, dysarthria...

  11. 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 ...

  12. Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

    Science.gov (United States)

    Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

    2017-01-01

    Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

  13. 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

  14. 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)

  15. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jonathan F Schmitz

    2017-01-01

    Full Text Available Over the last few years, there has been an increasing amount of evidence for the de novo emergence of protein-coding genes, i.e. out of non-coding DNA. Here, we review the current literature and summarize the state of the field. We focus specifically on open questions and challenges in the study of de novo protein-coding genes such as the identification and verification of de novo-emerged genes. The greatest obstacle to date is the lack of high-quality genomic data with very short divergence times which could help precisely pin down the location of origin of a de novo gene. We conclude that, while there is plenty of evidence from a genetics perspective, there is a lack of functional studies of bona fide de novo genes and almost no knowledge about protein structures and how they come about during the emergence of de novo protein-coding genes. We suggest that future studies should concentrate on the functional and structural characterization of de novo protein-coding genes as well as the detailed study of the emergence of functional de novo protein-coding genes.

  16. De Novo Loss-of-Function Mutations in USP9X Cause a Female-Specific Recognizable Syndrome with Developmental Delay and Congenital Malformations

    NARCIS (Netherlands)

    Reijnders, Margot R. F.; Zachariadis, Vasilios; Latour, Brooke; Jolly, Lachlan; Mancini, Grazia M.; Pfundt, Rolph; Wu, Ka Man; van Ravenswaaij-Arts, Conny M. A.; Veenstra-Knol, Hermine E.; Anderlid, Britt-Marie M.; Wood, Stephen A.; Cheung, Sau Wai; Barnicoat, Angela; Probst, Frank; Magoulas, Pilar; Brooks, Alice S.; Malmgren, Helena; Harila-Saari, Arja; Marcelis, Carlo M.; Vreeburg, Maaike; Hobson, Emma; Sutton, V. Reid; Stark, Zornitza; Vogt, Julie; Cooper, Nicola; Lim, Jiin Ying; Price, Sue; Lai, Angeline Hwei Meeng; Domingo, Deepti; Reversade, Bruno; Gecz, Jozef; Gilissen, Christian; Brunner, Han G.; Kini, Usha; Roepman, Ronald; Nordgren, Ann; Kleefstra, Tjitske

    2016-01-01

    Mutations in more than a hundred genes have been reported to cause X-linked recessive intellectual disability (ID) mainly in males. In contrast, the number of identified X-linked genes in which de novo mutations specifically cause ID in females is limited. Here, we report 17 females with de novo

  17. Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale

    DEFF Research Database (Denmark)

    Liu, Siyang; Huang, Shujia; Rao, Junhua

    2015-01-01

    present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome...

  18. Some effects of mouthrinses containing salifluor on de novo plaque formation and developing gingivitis.

    Science.gov (United States)

    Furuichi, Y; Ramberg, P; Lindhe, J; Nabi, N; Gaffar, A

    1996-08-01

    Three clinical trials were carried out to evaluate the effects of mouthrinses containing 5n-octanoyl-3'-trifluormethylsalicylanilide (salifluor) on plaque and gingivitis. Each trial was performed as a double-blind, randomised and cross-over designed study (studies 1, 2 and 3). In each study, 10 young individuals with healthy gingiva abolished all means of mechanical plaque control during the course of the experimental period including 6 x 4 days (study 1), 3 x 18 days (study 2) and 3 x 14 days (study 3). They rinsed, 2 x daily, with various mouthwash preparations for 4 days (study 1), for the last 4 days of a 18 day period (study 2) or for 14 days (study 3). 6 (control, vehicle control, 0.08%, 0.12% and 0.2% salifluor and 0.12% chlorhexidine), 3 (control, 0.12% salifluor and 0.12% chlorhexidine) and 3 (control, 0.12% salifluor and 0.12% chlorhexidine) mouthwash preparations were tested in studies 1, 2 and 3, respectively. The findings of study 1 indicated that (i) mouthrinses containing salifluor were significantly more effective than control rinses and that (ii) the salifluor mouthrinses were equally effective as the 0.12% chlorhexidine mouthrinse, in retarding 4-day de novo plaque formation. The findings of study 2 indicated that (i) the mouthrinse containing 0.12% salifluor retarded de novo plaque formation to the same extent as the 0.12% chlorhexidine mouthrinse at healthy as well as at inflamed sites but that (ii) the anti-plaque effects of the salifluor and chlorhexidine mouthrinses were significantly smaller at sites with inflamed than with healthy gingiva. In study 3, it was observed that there was no significant difference between the 0.12% salifluor and 0.12% chlorhexidine mouthrinses in retarding de novo plaque formation and the development of gingivitis during a 14-day period of no mechanical plaque control. Thus, the results of the 3 clinical trials demonstrated the potential of salifluor as an effective anti-plaque and anti-inflammatory agent.

  19. De novo transcriptome analysis of petal senescence in Gardenia jasminoides Ellis.

    Science.gov (United States)

    Tsanakas, Georgios F; Manioudaki, Maria E; Economou, Athanasios S; Kalaitzis, Panagiotis

    2014-07-04

    The petal senescence of ethylene insensitive species has not been investigated thoroughly while little is known about the temporal and tissue specific expression patterns of transcription factors (TFs) in this developmental process. Even less is known on flower senescence of the ornamental pot plant Gardenia jasminoides, a non climacteric flower with significant commercial value. We initiated a de novo transcriptome study to investigate the petal senescence in four developmental stages of cut gardenia flowers considering that the visible symptoms of senescence appear within 4 days of flower opening. De novo assembly of transcriptome sequencing resulted in 102,263 contigs with mean length of 360 nucleotides that generated 57,503 unigenes. These were further clustered into 20,970 clusters and 36,533 singletons. The comparison of the consecutive developmental stages resulted in 180 common, differentially expressed unigenes. A large number of Simple Sequence Repeats were also identified comprising a large number of dinucleotides and trinucleotides. The prevailing families of differentially expressed TFs comprise the AP2/EREBP, WRKY and the bHLH. There are 81 differentially expressed TFs when the symptoms of flower senescence become visible with the most prevailing being the WRKY family with 19 unigenes. No other WRKY TFs had been identified up to now in petal senescence of ethylene insensitive species. A large number of differentially expressed genes were identified at the initiation of visible symptoms of senescence compared to the open flower stage indicating a significant shift in the expression profiles which might be coordinated by up-regulated and/or down-regulated TFs. The expression of 16 genes that belong to the TF families of WRKY, bHLH and the ethylene sensing pathway was validated using qRT--PCR. This de novo transcriptome analysis resulted in the identification of TFs with specific temporal expression patterns such as two WRKYs and one bHLH, which might

  20. De Novo Origin of VCY2 from Autosome to Y-Transposed Amplicon

    Science.gov (United States)

    Cao, Peng-Rong; Wang, Lei; Jiang, Yu-Chao; Yi, Yin-Sha; Qu, Fang; Liu, Tao-Cheng; Lv, Yuan

    2015-01-01

    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 (VCY)2, 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 VCY2cannot 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 chromosome. PMID

  1. Morphologic and Molecular Characteristics of De Novo AML With JAK2 V617F Mutation.

    Science.gov (United States)

    Hidalgo-López, Juliana E; Kanagal-Shamanna, Rashmi; Medeiros, L Jeffrey; Estrov, Zeev; Yin, C Cameron; Verstovsek, Srdan; Konoplev, Sergej; Jorgensen, Jeffrey L; Mohammad, Mohammad M; Miranda, Roberto N; Zhao, Chong; Lee, John; Zuo, Zhuang; Bueso-Ramos, Carlos E

    2017-06-01

    Background:JAK2 V617F mutation (mut) in acute myeloid leukemia (AML) is rare. We describe the clinicopathologic findings of a single-institution series of 11 de novo AML cases with JAK2 V617. Methods: We identified cases of de novo AML with JAK2 V617F over a 10-year period. We reviewed diagnostic peripheral blood and bone marrow (BM) morphologic, cytogenetic, and molecular studies, including next-generation sequencing. The control group consisted of 12 patients with JAK2 wild-type (wt) AML matched for age, sex, and diagnosis. Results: We identified 11 patients (0.5%) with JAK2 V617F, with a median age at diagnosis of 72.5 years (range, 36-90 years). Ten neoplasms were classified as AML with myelodysplasia-related changes and 1 as AML with t(8;21)(q22;q22). All JAK2mut AML cases showed at least bilineage dysplasia, 7 of 11 showed fibrosis, 8 of 11 had an abnormal karyotype, and 5 had deletions or monosomy of chromosomes 5 and 7. Using the European LeukemiaNet (ELN) classification, 9 patients (82%) with JAK2mut AML were intermediate-2 and adverse risk. Cases of JAK2mut AML did not have mutations in other activating signaling pathways (P=.013); 7 (64%) showed additional mutations in at least one gene involving DNA methylation and/or epigenetic modification. Patients with JAK2mut AML had a significantly higher median BM granulocyte percentage (12% vs 3.5%; P=.006) and a higher frequency of ELN intermediate-2 and adverse risk cytogenetics (P=.04) compared with those with JAK2wt AML. JAK2mut AML showed higher circulating blasts, but this difference was not significant (17% vs 5.5%; P=not significant). No difference was seen in the median overall survival rate of patients with JAK2mut AML versus those with JAK2wt AML (14 vs 13.5 months, respectively). Conclusions: De novo JAK2mut AML is rare and frequently found in patients with dysplasia, BM fibrosis, and abnormal karyotype with intermediate- or high-risk features; gene mutations in DNA methylation and epigenetic

  2. 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.

  3. [Men of the sugarcane fields and their hospitals: the architecture of health under the Estado Novo].

    Science.gov (United States)

    Monteiro, Marcia Rocha

    2011-12-01

    The article explores the emergence of an architectural heritage in the realm of healthcare assistance for workers in the sugarcane agroindustry in Brazil following enactment of the law known as the Estatuto da Lavoura Canavieira (1941), under the auspices of the Instituto do Açúcar e do Álcool and as part of Estado Novo policies (1937-1945). The institute proposed solutions based on surveys conducted at sugarcane mills in cane-producing states and on the medical and hospital system adopted by the institute's enlightened bureaucracy in the 1940s, which took the U.S. system as its model. Special focus is given to the central hospitals in Pernambuco and especially in Alagoas, which opposed institute guidelines.

  4. De novo REEP2 missense mutation in pure hereditary spastic paraplegia.

    Science.gov (United States)

    Roda, Ricardo H; Schindler, Alice B; Blackstone, Craig

    2017-05-01

    Alterations in proteins that regulate endoplasmic reticulum morphology are common causes of hereditary spastic paraplegia (SPG1-78, plus others). Mutations in the REEP1 gene that encodes an endoplasmic reticulum-shaping protein are well-known causes of SPG31, a common autosomal dominant spastic paraplegia. A closely-related gene, REEP2, is mutated in SPG72, with both autosomal and recessive inheritances. Here, we report a patient with a pure hereditary spastic paraplegia due to a de novo missense mutation (c.119T > G, p.Met40Arg) in REEP2 at a highly-conserved residue very close to another known pathogenic missense change. This represents only the second autosomal dominant SPG72 missense mutation reported.

  5. 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.

  6. 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 intellectual disability and epilepsy. METHODS: Reported females were selected for genetic testing because of substantial developmental problems and/or epilepsy. X-inactivation and expression studies were performed when possible. RESULTS: All mutations were predicted to result in a frameshift or premature stop....... 12 out of 14 patients had intractable epilepsy with myoclonic and/or absence seizures, and generalised in 11. Thirteen patients had mild to severe intellectual disability. This female phenotype partially overlaps with the reported male phenotype which consists of more severe intellectual disability...

  7. 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.

  8. Acampomelic campomelic syndrome and sex reversal associated with de novo t(12;17) translocation

    Energy Technology Data Exchange (ETDEWEB)

    Ninomiya, Shinsuke; Narahara, Kouji; Tsuji, Kazushiro [Okayama Univ. Medical School (Japan)] [and others

    1995-03-13

    The association of rare chromosomal rearrangements involving a specific 17q breakpoint with campomelic syndrome (CMPS) and/or sex reversal (SR) has led to an assignment of the CMPS1/SRA1 locus to 17q24.3 {yields} q25.1. We describe a patient with multiple anomalies and SR, who had a de novo t(12;17) translocation. The phenotype was consistent with that of CMPS except for the lack of lower limb bowing and talipes equinovarus. Chromosome painting indicated that the breakpoints appeared to have occurred at 12q21.32 and 17q24.3 or q25.1. CMPD with SR represents a variant of the CMPS1/SRA1 locus disorder. We emphasize the likelihood that CMPS may be a contiguous gene syndrome. 18 refs., 4 figs., 1 tab.

  9. 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.

  10. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae

    Science.gov (United States)

    Sachdeva, Himani; Barma, Mustansir; Rao, Madan

    2016-12-01

    A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.

  11. 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...

  12. Clinical assessment of hepatic de novo lipogenesis in non-alcoholic fatty liver disease.

    Science.gov (United States)

    Paglialunga, Sabina; Dehn, Clayton A

    2016-09-17

    Non-alcoholic fatty liver disease (NAFLD) is heralded as the next big global epidemic. Hepatic de novo lipogenesis (DNL), the synthesis of new fatty acids from non-lipid sources, is thought to play a pivotal role in the development of NAFLD. While there is currently no NAFLD-specific therapeutic agent available, pharmaceutical drugs aimed at reducing hepatic fat accretion may prove to be a powerful ally in the treatment and management of this disease. With a focus on NAFLD, the present review summarizes current techniques examining DNL from a clinical perspective, and describes the merits and limitations of three commonly used assays; stable-label isotope tracer studies, fatty acid indexes and indirect calorimetry as non-invasive measures of hepatic DNL. Finally, the application of DNL assessments in the pharmacological and nutraceutical treatment of NAFLD/NASH is summarized. In a clinical research setting, measures of DNL are an important marker in the development of anti-NAFLD treatments.

  13. Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

    DEFF Research Database (Denmark)

    Gallie, Jenna; Libby, Eric; Bertels, Frederic

    2015-01-01

    in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results......Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical...... insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed...

  14. 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.

  15. 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

    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......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...

  16. EM-Fold: De novo atomic-detail protein structure determination from medium resolution density maps

    Science.gov (United States)

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L.; Meiler, Jens

    2012-01-01

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy (cryoEM) or X-ray crystallography. In these density maps the general arrangement of secondary structure elements is revealed while their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the secondary structure elements de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins the protocol consistently and reproducibly achieves models with RMSD values smaller than 3 Å. PMID:22405005

  17. 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

  18. Daunting but Worthy Goal: Reducing the De Novo Cancer Incidence After Transplantation.

    Science.gov (United States)

    Dantal, Jacques; Campone, Mario

    2016-12-01

    Solid-organ transplant recipients are at increased risk of developing de novo malignancies compared with the general population, and malignancies become a major limitation in achieving optimal outcomes. The prevention and the management of posttransplant malignancies must be considered as a main goal in our transplant programs. For these patients, immunosuppression plays a major role in oncogenesis by both impairement of immunosurveillance, enhancement of chronic viral infection, and by direct prooncogenic effects. It is essential to manage the recipient with a long-term adapted screening program beginning before transplantation to use a prophylaxis to decrease infection-related cancer, to propose a viral monitoring, and to modulate the immunosuppression toward lower doses especially for calcineurin inhibitors. Indeed, strategies to induce tolerance or to allow a dramatic reduction of the immunosuppression burden are the more promising approaches for the reduction of the posttransplant malignancies.

  19. Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways.

    Science.gov (United States)

    Hadadi, Noushin; Hatzimanikatis, Vassily

    2015-10-01

    Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs from renewable resources and natural or engineered enzymes. The best candidate pathways are then engineered within a metabolic network of microorganisms that serve as synthetic platforms for synthetic biology. The complexity of biological chemistry and metabolism requires computational approaches to explore the full possibilities of engineering synthetic pathways towards target compounds. Herein, we discuss recent developments in the design of computational tools for retrosynthetic biochemistry and outline the workflow and design elements for such tools. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Downregulation of Hepatic De Novo Lipogenesis and Adipogenesis in Adipocytes by Pinus densiflora Bark Extract.

    Science.gov (United States)

    Ahn, Hyemyoung; Jeong, Jeongho; Moyo, Knowledge; Ryu, Yungsun; Min, Bokkee; Yun, Seong Ho; Kim, Hwa Yeon; Kim, Wooki; Go, Gwang-Woong

    2017-11-28

    Korean red pine (Pinus densiflora) bark extract, PineXol (PX), was investigated for its potential antioxidant and anti-inflammation effects in vitro. It was hypothesized that PX treatment (25-150 μg/ml) would reduce the lipid synthesis in HepG2 hepatocytes as well as lipid accumulation in 3T3-L1 adipocytes. Hepatocytes' intracellular triglycerides and cholesterol were decreased in the PX 150 μg/ml treatment group compared with the control (p novo lipogenic proteins (acetyl-CoA carboxylase 1, stearoyl-CoA desaturase 1, elongase of very long chain fatty acids 6, glycerol-3-phosphate acyltransferase 1, and sterol regulatory element-binding protein 1) were significantly decreased in hepatocytes by PX 150 μg/ml treatment compared with the control (p lipogenesis and by inhibiting adipogenesis in adipocytes.

  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. Paternal Age Explains a Major Portion of De Novo Germline Mutation Rate Variability in Healthy Individuals

    Science.gov (United States)

    Bourassa, Cynthia V.; Lemieux Perreault, Louis-Philippe; Legault, Marc-André; Barhdadi, Amina; Ambalavanan, Amirthagowri; Brendgen, Mara; Vitaro, Frank; Noreau, Anne; Dionne, Ginette; Tremblay, Richard E.; Dion, Patrick A.; Boivin, Michel; Dubé, Marie-Pierre; Rouleau, Guy A.

    2016-01-01

    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. PMID:27723766

  4. De novo loss- or gain-of-function mutations in KCNA2 cause epileptic encephalopathy

    DEFF Research Database (Denmark)

    Syrbe, Steffen; Hedrich, Ulrike B S; Riesch, Erik

    2015-01-01

    Epileptic encephalopathies are a phenotypically and genetically heterogeneous group of severe epilepsies accompanied by intellectual disability and other neurodevelopmental features. Using next-generation sequencing, we identified four different de novo mutations in KCNA2, encoding the potassium...... disability, delayed speech development and sometimes ataxia. Functional studies of the two mutations associated with this phenotype showed almost complete loss of function with a dominant-negative effect. Two further individuals presented with a different and more severe epileptic encephalopathy phenotype....... They carried mutations inducing a drastic gain-of-function effect leading to permanently open channels. These results establish KCNA2 as a new gene involved in human neurodevelopmental disorders through two different mechanisms, predicting either hyperexcitability or electrical silencing of KV1.2-expressing...

  5. 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.

  6. CONCERTS: dynamic connection of fragments as an approach to de novo ligand design.

    Science.gov (United States)

    Pearlman, D A; Murcko, M A

    1996-04-12

    We have implemented and tested a new approach to de novo ligand design, CONCERTS (creation of novel compounds by evaluation of residues at target sites). In this method, each member of a user-defined set of fragments is allowed to move independently about a target active site during a molecular dynamics simulation. This allows the fragments to sample various low-energy orientations. When the geometry between proximal fragments is appropriate, bonds can be formed between the fragments. In this fashion, larger molecules can be built. The bonding arrangement can subsequently be changed-breaking bonds between chosen fragment pairs and forming them between other pairs-if the overall process creates lower energy molecules. We have tested this method with various mixes of fragments against the active sites of the FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In several cases, CONCERTS suggests ligands which are in surprisingly good agreement with known inhibitors of these proteins.

  7. 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.

  8. Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks.

    Science.gov (United States)

    Kalender Atak, Zeynep; Imrichova, Hana; Svetlichnyy, Dmitry; Hulselmans, Gert; Christiaens, Valerie; Reumers, Joke; Ceulemans, Hugo; Aerts, Stein

    2017-08-30

    The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying "personal" gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genomes of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers. μ-cisTarget is available from http://mucistarget.aertslab.org .

  9. 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

    investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents. Mutation rates varied widely throughout the genome (by 100-fold) and could be explained by intrinsic characteristics of DNA sequence and chromatin structure. Dense clusters...... of mutations within individual genomes were attributable to compound mutation or gene conversion. Hypermutability was a characteristic of genes involved in ASD and other diseases. In addition, genes impacted by mutations in this study were associated with ASD in independent exome-sequencing data sets. Our......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...

  10. De novo deletion in MECP2 in a monozygotic twin pair: a case report

    Directory of Open Access Journals (Sweden)

    Juyal Ramesh

    2011-08-01

    Full Text Available Abstract Background Rett syndrome (RTT is a severe, progressive, neurodevelopmental disorder predominantly observed in females that leads to intellectual disability. Mutations and gross rearrangements in MECP2 account for a large proportion of cases with RTT. A limited number of twin pairs with RTT have also been reported in literature. Case Presentation We investigated 13 year old, monozygotic twin females with RTT and some noticeable differences in development using a combinatorial approach of sequencing and Taqman assay. Monozygosity status of the twins was confirmed by informative microsatellite markers. Conclusions The twins shared a de novo deletion in exon 3 in the MBD domain of MECP2. To the best of our knowledge, this is only the second report of genetic analysis of a monozygotic twin pair.

  11. De Novo Assembly, Characterization and Functional Annotation of Southern Hake (Merluccius australis Transcriptome

    Directory of Open Access Journals (Sweden)

    Daniela Reyes

    2016-11-01

    Full Text Available Southern hake (Merluccius australis is an ecological and economically important demersal fish in Chile and Argentina. Notwithstanding, genetic resource for genetic or ecological studies on this species are scarce. Consequently, here we present transcriptome sequencing results (RNA-Seq for spleen and liver tissues with the 454 FLX titanium platform. The de novo transcriptome assembly generated 10,314 unigenes, with an average length of 510 bp, N50 of 572 bp and 3,171 annotated sequences. A specific Gadiform BLAST search, with focus on immune genes, showed 186 (56% genes homologous to those of Atlantic cod. A total of 2,302 microsatellites were detected in 1,687 unigenes and 741 presented adequate flanking sequences for primer design. In total, these potential molecular markers and transcriptome characterization represent an important resource for genetic and ecological studies on southern hake.

  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. Indomethacin-induced de novo headache in hemicrania continua--fighting fire with fire?

    Science.gov (United States)

    Jürgens, Tim P; Schulte, Laura H; May, Arne

    2013-10-01

    The response to indomethacin is an important feature for the diagnosis of hemicrania continua. We report the case of a 34-year-old female patient with a one-year history of strictly unilateral continuous headache with accompanying ipsilateral autonomic symptoms. As diagnostic testing was unremarkable, hemicrania continua was suspected. A dose of 150 mg of indomethacin/day reduced the headache by 80%. Although an increase to 225 mg/day led to a further reduction of headaches, a new onset of moderate to severe pulsating migrainous bilateral headache developed. As shown in older studies, indomethacin can induce de novo headaches in a presumably dose-related fashion although the exact mechanism in uncertain. A treatable secondary origin of the indomethacin-induced headaches in patients with hemicrania continua or paroxysmal hemicrania (such as reversible cerebral vasoconstriction syndrome or aseptic meningitis) should be considered and excluded by further diagnostic testing if headaches persist after discontinuation of indomethacin.

  14. A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation.

    Science.gov (United States)

    Hu, Yuanqi; Georgiou, Pantelis

    2016-01-01

    This paper presents an FPGA based DNA comparison platform which can be run concurrently with the sensing phase of DNA sequencing and shortens the overall time needed for de novo DNA assembly. A hybrid overlap searching algorithm is applied which is scalable and can deal with incremental detection of new bases. To handle the incomplete data set which gradually increases during sequencing time, all-against-all comparisons are broken down into successive window-against-window comparison phases and executed using a novel dynamic suffix comparison algorithm combined with a partitioned dynamic programming method. The complete system has been designed to facilitate parallel processing in hardware, which allows real-time comparison and full scalability as well as a decrease in the number of computations required. A base pair comparison rate of 51.2 G/s is achieved when implemented on an FPGA with successful DNA comparison when using data sets from real genomes.

  15. De novo design and synthesis of a 30-cistron translation-factor module.

    Science.gov (United States)

    Shepherd, Tyson R; Du, Liping; Liljeruhm, Josefine; Samudyata; Wang, Jinfan; Sjödin, Marcus O D; Wetterhall, Magnus; Yomo, Tetsuya; Forster, Anthony C

    2017-10-13

    Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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.

  17. 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.

  18. 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.

  19. Transformações no mundo laboral e novos desafios do sindicalismo português

    Directory of Open Access Journals (Sweden)

    Elísio Estanque

    2012-10-01

    Full Text Available O problema da transformação das relações laborais tem necessariamente de ser discutido à luz do actual contexto de globalização económica para que se compreendam as consequências deste processo para o movimento sindical e os novos desafios que este tem hoje pela frente. Como se sabe, a economia mundial assentou desde sempre em múltiplos desequilíbrios entre centros e periferias. Mas, hoje, os contrastes entre pólos de desenvolvimento e zonas de exclusão e de miséria não só assumem contornos ...

  20. Todos os desafios do mundo: a geração de 1964 no Cinema Novo

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo Pinto de Pinto

    2011-06-01

    Full Text Available The aim of this article is eliciting the concepts of generation and youth to approach the creative scenario of young directors stylistically linked to the Cinema Novo as well as the young movement represented in their movies. Two very different movies regarding their youth representation are analyzed: Paulo César Saraceni‟s O Desafio (1965 and Domingos de Oliveira‟s Todas as mulheres do mundo (1967. Both of them are about love stories but show the respective relationships on different ways. The main characteristics of 1960‟s Brazilian young people are analyzed not only through the characters and the way their lives are told, but also through both directors‟ generation marks and creative impulses.

  1. De novo partial deletion in GRID2 presenting with complicated spastic paraplegia.

    Science.gov (United States)

    Maier, André; Klopocki, Eva; Horn, Denise; Tzschach, Andreas; Holm, Teresa; Meyer, Robert; Meyer, Thomas

    2014-02-01

    Complex forms of spastic paraplegia (SPG) are rare and genetically heterogeneous. In apparently sporadic cases, analysis of known SPG genes often fails to reveal a mutation. We report a 24-year-old patient with a syndrome of spastic paraplegia, ataxia, frontotemporal dementia, and lower motor neuron involvement. Screening of the patient's genome for copy number variation identified a novel 276 kb deletion spanning the first exon of the GRID2 gene. MRI scan showed atrophy of the cerebellum, and electromyography revealed a chronic disorder of motor neurons or their axons. A deletion in GRID2, coding for the glutamate receptor delta-2 subunit precursor protein, was excluded in either parent, suggesting that the deletion in the index patient occurred de novo. We hypothesize that the deletion identified here is the cause of our patient's clinical presentation, due to the resemblance to the GRID2 mutation phenotype in mouse models. Copyright © 2013 Wiley Periodicals, Inc.

  2. 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.

  3. Educação popular na América Latina no novo milênio: impactos do novo paradigma

    Directory of Open Access Journals (Sweden)

    Maria da Glória Gohn

    2002-01-01

    Full Text Available O trabalho objetiva realizar um balanço da trajetória das ações, práticas e políticas pedagógicas da educação popular na América Latina, nas últimas décadas. Destacam-se as novas tendências, seus fundamentos, as novas áreas temáticas, suas práticas e inovações. Destacam-se também suas inovações no campo da educação não-formal e as articulações com a educação formal. Analisa-se a contribuição e o papel do método de Paulo Freire nesta trajetória. As questões básicas abordadas são: o que mudou no novo paradigma? Como tem interferido, na área da educação popular, as mudanças na economia globalizada e a conjuntura sociopolítica do país e suas políticas sociais de corte neoliberal? Como tem atuado, na educação popular, o setor organizado da sociedade civil, portador de novas formas de associativismo, expressas em Ongs do Terceiro Setor e em novíssimos movimentos sociais? Qual foi o papel do processo de conscientização, previsto na método freireano, no desenvolvimento atual da educação popular na América Latina? Quais são as contribuições e perspectivas para a educação popular para o novo milênio? This paper work to carry setting the trajectory of the actions, pratical and pedagogical politics of the popular education in Latin America, the last decades. The new trands, its beddings, the new pratical thematic areas, its and innovations are distinguished. Its innovations in the field of the education non-formal of division and the joints with the formal education are also distinguished. The contribuition and the paper of the method Paulo Freire in this trajetory is analysed. The boarded basic questions are: what it moved in the new paradigm? How it has intervened, in the area of the popular education, the changes in the globalized economy and the sociopolitic conjuncture of the coutry and its social politics of neoliberal cut? How it has acted, in the popular education, the organized sector of the

  4. 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....

  5. 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 Impact factor: 2.773, year: 2016

  6. Clinical and biological significance of de novo CD5+ diffuse large B-cell lymphoma in Western countries

    NARCIS (Netherlands)

    Xu-Monette, Z.Y.; Tu, M.; Jabbar, K.J.; Cao, X.; Tzankov, A.; Visco, C.; Cai, Q.; Montes-Moreno, S.; An, Y.; Dybkaer, K.; Chiu, A.; Orazi, A.; Zu, Y.; Bhagat, G.; Richards, K.L.; Hsi, E.D.; Choi, W.W.; Krieken, J.H.J.M. van; Huh, J.; Ponzoni, M.; Ferreri, A.J.; Zhao, X.; Moller, M.B.; Farnen, J.P.; Winter, J.N.; Piris, M.A.; Miranda, R.N.; Medeiros, L.J.; Young, K.H.

    2015-01-01

    CD5 is a pan-T-cell surface marker and is rarely expressed in diffuse large B-cell lymphoma (DLBCL). Large-scale studies of de novo CD5+ DLBCL are lacking in Western countries. In this study by the DLBCL Rituximab-CHOP Consortium, CD5 was expressed in 5.5% of 879 DLBCL patients from Western

  7. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

    Science.gov (United States)

    Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and ma...

  8. Projector or projection screen? The Portuguese Estado Novo and ‘renewal’ in the Netherlands (1933-1946)

    NARCIS (Netherlands)

    de Bruin, R.

    2014-01-01

    In the 1930s and during the first year after the Nazi invasion of the Netherlands in May 1940, the basic principles of Salazar's authoritarian Estado Novo were widely discussed and cheered in the Netherlands. Influential Dutch newspapers featured articles about the 'lessons' for Dutch politics and

  9. 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)....

  10. LANA-Mediated Recruitment of Host Polycomb Repressive Complexes onto the KSHV Genome during De Novo Infection.

    Directory of Open Access Journals (Sweden)

    Zsolt Toth

    2016-09-01

    Full Text Available One of the hallmarks of the latent phase of Kaposi's sarcoma-associated herpesvirus (KSHV infection is the global repression of lytic viral gene expression. Following de novo KSHV infection, the establishment of latency involves the chromatinization of the incoming viral genomes and recruitment of the host Polycomb repressive complexes (PRC1 and PRC2 to the promoters of lytic genes, which is accompanied by the inhibition of lytic genes. However, the mechanism of how PRCs are recruited to the KSHV episome is still unknown. Utilizing a genetic screen of latent genes in the context of KSHV genome, we identified the latency-associated nuclear antigen (LANA to be responsible for the genome-wide recruitment of PRCs onto the lytic promoters following infection. We found that LANA initially bound to the KSHV genome right after infection and subsequently recruited PRCs onto the viral lytic promoters, thereby repressing lytic gene expression. Furthermore, both the DNA and chromatin binding activities of LANA were required for the binding of LANA to the KSHV promoters, which was necessary for the recruitment of PRC2 to the lytic promoters during de novo KSHV infection. Consequently, the LANA-knockout KSHV could not recruit PRCs to its viral genome upon de novo infection, resulting in aberrant lytic gene expression and dysregulation of expression of host genes involved in cell cycle and proliferation pathways. In this report, we demonstrate that KSHV LANA recruits host PRCs onto the lytic promoters to suppress lytic gene expression following de novo infection.

  11. Identification and functional characterization of de novo FOXP1 variants provides novel insights into the etiology of neurodevelopmental disorder

    NARCIS (Netherlands)

    Sollis, E; Graham, S.A.; Vino, A.; Froehlich, H.; Vreeburg, M.; Dimitropoulou, D.; Gilissen, C.; Pfundt, R.; Rappold, G.A.; Brunner, H.G; Deriziotis, P.; Fisher, S.E.

    2016-01-01

    De novo disruptions of the neural transcription factor FOXP1 are a recently discovered, rare cause of sporadic intellectual disability (ID). We report three new cases of FOXP1-related disorder identified through clinical whole-exome sequencing. Detailed phenotypic assessment confirmed that global

  12. The role of superficial femoral artery endoluminal bypass in long de novo lesions and in-stent restenosis.

    NARCIS (Netherlands)

    Doomernik, D.E.; Golchehr, B.; Lensvelt, M.M.A.; Reijnen, M.M.P.J.

    2012-01-01

    AIM: Results of endovascular treatment for long de novo lesions of the superficial femoral artery (SFA) are limited by in-stent restenosis (ISR). Polytetrafluoroethylene (PTFE) covered stents are developed to reduce the incidence of ISR. This study was conducted to summarize available data on the

  13. 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 preci...

  14. Molecular analysis of "de novo" purine biosynthesis in solanaceous species and in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    van der Graaff, Eric; Hooykaas, Paul; Lein, Wolfgang

    2004-01-01

    Purine nucleotides are essential components to sustain plant growth and development. In plants they are either synthesized "de novo" during the process of purine biosynthesis or are recycled from purine bases and purine nucleosides throughout the salvage pathway. Comparison between animals, micro...

  15. 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

  16. De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs

    Science.gov (United States)

    In antiviral defense, plants produce massive quantities of 21-24 nucleotide siRNAs. Here we demonstrate that the complete genomes of DNA and RNA viruses and viroids can be reconstructed by deep sequencing and de novo assembly of viral/viroid siRNAs from experimentally- and naturally-infected plants....

  17. De novo SCN1A mutations in Dravet syndrome and related epileptic encephalopathies are largely of paternal origin.

    Science.gov (United States)

    Heron, Sarah E; Scheffer, Ingrid E; Iona, Xenia; Zuberi, Sameer M; Birch, Rachael; McMahon, Jacinta M; Bruce, Carla M; Berkovic, Samuel F; Mulley, John C

    2010-02-01

    Dravet syndrome is a severe infantile epileptic encephalopathy caused in approximately 80% of cases by mutations in the voltage gated sodium channel subunit gene SCN1A. The majority of these mutations are de novo. The parental origin of de novo mutations varies widely among genetic disorders and the aim of this study was to determine this for Dravet syndrome. 91 patients with de novo SCN1A mutations and their parents were genotyped for single nucleotide polymorphisms (SNPs) in the region surrounding their mutation. Allele specific polymerase chain reaction (PCR) based on informative SNPs was used to separately amplify and sequence the paternal and maternal alleles to determine in which parental chromosome the mutation arose. The parental origin of SCN1A mutations was established in 44 patients for whom both parents were available and SNPs were informative. The mutations were of paternal origin in 33 cases and of maternal origin in the remaining 11 cases. De novo mutation of SCN1A most commonly, but not exclusively, originates from the paternal chromosome. The average age of parents originating mutations did not differ from that of the general population. The greater frequency of paternally derived mutations in SCN1A is likely to be due to the greater chance of mutational events during the increased number of mitoses which occur during spermatogenesis compared to oogenesis, and the greater susceptibility to mutagenesis of the methylated DNA characteristic of sperm cells.

  18. An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind.

    Science.gov (United States)

    London, Nir; Ambroggio, Xavier

    2014-02-01

    Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Psychological Stress and Changes of Hypothalamic-Pituitary-Adrenal Axis in Patients with "De Novo" Parkinson's Disease.

    Science.gov (United States)

    Ibrahimagic, Omer C; Jakubovic, Amra Cickusic; Smajlovic, Dzevdet; Dostovic, Zikrija; Kunic, Suljo; Iljazovic, Amra

    2016-12-01

    Psychological stress and changes in hypothalamic-pituitary-adrenal (HPA) axis in period after diagnosis of "de novo" Parkinson disease (PD) could be a big problem for patients. We measured psychological stress and changes in hypothalamic-pituitary-adrenal axis (HPA) in thirty patients (15:15) with "de novo" Parkinson's disease, average age 64.17 ± 13.19 (28-82) years (Department of Neurology, University Clinical Center Tuzla). We used Impact of events scale (with 15 questions) to evaluate psychological stress. Normal level of morning cortisol was 201-681 nmol/l, and morning adrenocorticotropic hormone (ACTH) up to 50 pg/ml. Almost 55% patients suffered from mild or serious psychological stress according to IES testing (Horowitz et al.). Non-iatrogenic changes in HPA axis were noticed at 30% patients. The differences between female and male patients regarding to the age (p=0.561), value of cortisol (p=0.745), value of ACTH (p=0.886) and IES testing (p=0.318) were not noticed. The value of cortisol was the predictor of value of ACTH (r=0.427). Psychological stress and changes in hypothalamic-pituitary-adrenal axis are present in patients with "de novo" PD. There is significant relation between values of cortisol and ACTH. Psychological stress is frequent problem for "de novo" PD patients.

  20. Novo algodoeiro de origem interespecífica New cotton of interspecific origin

    Directory of Open Access Journals (Sweden)

    Imre Lajos Gridi-Papp

    1975-01-01

    Full Text Available Um novo tipo de algodoeiro foi isolado de uma população híbrida originada por cruzamento entre as espécies alotetraplóides Gossypium hirsutum L. v. latifolium Hutch, e G. barbadense L. v. brasiliense Hutch. A metodologia empregada e as principais características econômicas e morfológicas do novo algodoeiro são descritas e discutidas. Um ciclo de cruzamentos "intra", realizados na segunda geração após o retrocruzamento, seguido de seleção individual nas progenies desses cruzamentos, levou à obtenção de heptalobatum. O material não apresentou sinais de esterilidade, nem tendência a degenerar na descendência. Seu nome se deve às folhas, que, no estádio de completo desenvolvimento, apresentam sete lóbulos delgados. £ intermediário entre os pais para vários caracteres, aproxima-se de um ou outro ou representa um caso de segregação transgressiva para os demais.The selection of a new type of cotton in a population originated by crossing Gossypium hirsutum L. v. latifoliumHutch, and G. barbadenseL. v. brasiliense Hutch., is reported and the underlying methods and procedures described. One backcross to hirsutumfollowed by one cycle of crossing plants within populations and individual selection, led to the obterition of heptalobatum.Its fully developped leaves normally have seven narrow lobes. It is fully fertile and no sign of degeneration was observed in subsequent generations. The means of several economical and morphological characters are presented and discussed. The new cotton showed to be intermediary between the parental types for various characters, to be like one of the parents or a case of transgression for the others.