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  1. As bases moleculares da hemofilia A

    Directory of Open Access Journals (Sweden)

    Simone Ferreira Pio

    2009-01-01

    Full Text Available As hemofilias são doenças hemorrágicas resultantes da deficiência de fator VIII (hemofilia A ou de fator IX (hemofilia B da coagulação, decorrentes de mutações nos genes que codificam os fatores VIII ou IX, respectivamente. A hemofilia A é mais frequente que a hemofilia B e acomete aproximadamente 1:10.000 nascimentos masculinos. A gravidade e frequência dos episódios hemorrágicos está relacionado ao nível residual de atividade de fator VIII presente no plasma e este relaciona-se ao tipo de mutação associada à doença. A clonagem do gene do fator VIII tornou possível o conhecimento das bases moleculares da hemofilia A, sendo hoje conhecidas mais de 1.000 mutações associadas à doença. O conhecimento das bases moleculares da hemofilia A permite uma melhor compreensão da relação genótipo-fenótipo da doença, tomada de condutas clínicas diferenciadas em casos de mutações associadas a um maior risco de desenvolvimento de inibidor, determinação da condição de portadora de hemofilia em mulheres relacionadas aos pacientes, implementação de programa de aconselhamento genético/orientação familiar e melhor compreensão das relações estruturais-funcionais do gene-proteína. Este artigo propõe revisar as bases moleculares da hemofilia A, os métodos laboratoriais utilizados para a caracterização das mutações e as implicações clínicas envolvidas no diagnóstico molecular da hemofilia A.Hemophilias are bleeding disorders due to deficiency of the blood coagulation factor VIII (hemophilia A or factor IX (hemophilia B, resulting from mutation on the gene coding for factor VIII or factor IX. Hemophilia A is more frequent than hemophilia B and affects 1:10,000 male newborns. The severity and frequency of hemorrhagic episodes is related to residual activity of factor VIII present in the plasma and relates to the type of mutation associated with the disorder. Cloning of the factor VIII gene has enabled researchers to

  2. BASES MOLECULARES DA ABSORÇÃO DO FERRO

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    A. A. MACHADO

    2009-03-01

    Full Text Available

    O ferro é um elemento essencial a todos os organismos vivos e alterações em sua homeostase resultam em quadro de deficiência ou acúmulo, ambos com alta prevalência e relevância clínica. A última década foi marcada pela geração de conhecimentos importantes, que estão contribuindo para a elucidação dos mecanismos moleculares da homeostase do ferro. Foram identificadas proteínas, envolvidas na absorção intestinal do ferro não-heme, e progressos significativos foram feitos no entendimento da regulação da absorção intestinal do ferro, sendo identificadas várias moléculas candidatas. As bases moleculares da homeostase do ferro ainda não foram totalmente elucidadas, porém as informações já existentes sugerem que, em condições fisiológicas, a absorção, o transporte e o armazenamento sejam feitos por moléculas altamente especializadas e, em especial, a absorção, com mecanismos saturáveis em baixa concentração. No entanto, a absorção pode ocorrer por vias menos sujeitas ao controle, dependendo da sobrecarga e da natureza química do composto utilizado. Estas informações advogam a favor de uma revisão nas estratégias de combate à anemia ferropriva. PALAVRAS-CHAVE: Absorção do ferro; DMT-1; hepahestina; ceruloplasmina; ferroportina; hepcidina.

  3. Molecular basis of Acute Myelogenous Leukemia As bases moleculares da leucemia mielóide aguda

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    Eduardo M. Rego

    2002-01-01

    Full Text Available Acute Myelogenous Leukemia (AML is frequently associated with recurring chromosomal translocations, which lead to the fusion of two genes encoding transcription factors. As the moieties of these fusion proteins retain part of the functional domains of the wild-type proteins, they may interfere directly or indirectly with the transcriptional regulation of the leukemic cell, conferring survival advantage. The majority of the transcription factors commonly involved in recurring chromosomal translocations may be grouped in one of the following families: core binding factor (CBF, retinoic acid receptor alpha (RARalpha, homeobox (HOX family, and mixed lineage leukemia (MLL. In vivo analysis of the molecular basis of leukemogenesis through the generation of transgenic mouse models revealed that a common theme is the recruitment of transcriptional co-activators and co-repressors by these fusion proteins. However, the expression of the fusion protein is not sufficient to induce full blown leukemia, as evidenced in part by the long latencies required for disease development in the transgenic models of leukemia, and therefore, second mutagenic events may contribute to AML pathogenesis.A leucemia mielóide aguda (LMA está freqüentemente associada a translocações cromossômicas recorrentes. Em muitos casos, os genes presentes nos pontos de quebra cromossômica são conhecidos e, quase todos codificam para fatores de transcrição. O gene híbrido, resultante da justaposição de exons de genes distintos, codifica para proteínas de fusão. Como estas retêm a maior parte dos domínios funcionais das proteínas selvagens, elas interferem direta ou indiretamente com regulação da transcrição gênica, conferindo vantagem à sobrevivência das células leucêmicas. A maioria dos fatores de transcrição afetados pelas translocações cromossômicas associadas a LMA pode ser agrupada numa das seguintes famílias: dos core binding factors (CBF, do receptor

  4. Aspectos moleculares da anemia falciforme

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    Galiza Neto Gentil Claudino de

    2003-01-01

    Full Text Available No presente artigo abordaram-se vários aspectos relacionados à natureza molecular da anemia falciforme, desordem hematológica de caráter hereditário que acomete expressivo número de indivíduos em várias regiões do mundo. As pesquisas realizadas em torno desta patologia da hemácia, ao longo de quase um século, a partir de 1910, cooperaram para a criação de um novo e importante segmento da ciência, denominado biologia molecular. A descoberta dos polimorfismos da mutação (GAT->GTG no gene que codifica a cadeia beta da hemoglobina, originando diferentes haplótipos da doença, permitiu um melhor e mais amplo conhecimento em torno da heterogeneidade clínica nos pacientes falcêmicos. Analisando a hemoglobina na sua estrutura normal e mutante, sua produção e evolução, pode-se ter um entendimento mais completo da fisiopatologia desta doença e da sua complexidade clínica.

  5. Nanoplatform-based molecular imaging

    National Research Council Canada - National Science Library

    Chen, Xiaoyuan

    2011-01-01

    "Nanoplathform-Based Molecular Imaging provides rationale for using nanoparticle-based probes for molecular imaging, then discusses general strategies for this underutilized, yet promising, technology...

  6. Molecular differentiation and phylogenetic relationships of three Angiostrongylus species and Angiostrongylus cantonensis geographical isolates based on a 66-kDa protein gene of A. cantonensis (Nematoda: Angiostrongylidae).

    Science.gov (United States)

    Eamsobhana, Praphathip; Lim, Phaik Eem; Zhang, Hongman; Gan, Xiaoxian; Yong, Hoi Sen

    2010-12-01

    The phylogenetic relationships and molecular differentiation of three species of angiostrongylid nematodes (Angiostrongylus cantonensis, Angiostrongylus costaricensis and Angiostrongylus malaysiensis) were studied using the AC primers for a 66-kDa protein gene of A. cantonensis. The AC primers successfully amplified the genomic DNA of these angiostrongylid nematodes. No amplification was detected for the DNA of Ascaris lumbricoides, Ascaris suum, Anisakis simplex, Gnathostoma spinigerum, Toxocara canis, and Trichinella spiralis. The maximum-parsimony (MP) consensus tree and the maximum-likelihood (ML) tree both showed that the Angiostrongylus taxa could be divided into two major clades - Clade 1 (A. costaricensis) and Clade 2 (A. cantonensis and A. malaysiensis) with a full support bootstrap value. A. costaricensis is the most distant taxon. A. cantonensis is a sister group to A. malaysiensis; these two taxa (species) are clearly separated. There is no clear distinction between the A. cantonensis samples from four different geographical localities (Thailand, China, Japan and Hawaii); only some of the samples are grouped ranging from no support or low support to moderate support of bootstrap values. The published nucleotide sequences of A. cantonensis adult-specific native 66kDa protein mRNA, clone L5-400 from Taiwan (U17585) appear to be very distant from the A. cantonensis samples from Thailand, China, Japan and Hawaii, with the uncorrected p-distance values ranging from 26.87% to 29.92%.

  7. Aspectos moleculares da anemia falciforme Molecular aspects for sickle cell anemia

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    Gentil Claudino de Galiza Neto

    2003-01-01

    Full Text Available No presente artigo abordaram-se vários aspectos relacionados à natureza molecular da anemia falciforme, desordem hematológica de caráter hereditário que acomete expressivo número de indivíduos em várias regiões do mundo. As pesquisas realizadas em torno desta patologia da hemácia, ao longo de quase um século, a partir de 1910, cooperaram para a criação de um novo e importante segmento da ciência, denominado biologia molecular. A descoberta dos polimorfismos da mutação (GAT->GTG no gene que codifica a cadeia beta da hemoglobina, originando diferentes haplótipos da doença, permitiu um melhor e mais amplo conhecimento em torno da heterogeneidade clínica nos pacientes falcêmicos. Analisando a hemoglobina na sua estrutura normal e mutante, sua produção e evolução, pode-se ter um entendimento mais completo da fisiopatologia desta doença e da sua complexidade clínica.The present article dealt with various aspects related to molecular nature of sickle cell disease (SCD, a heritable hematology disorder that attacks a great number of people in different regions of the world. Researches done on red cell patology, in approximately half a century, starting since 1910, cooperated to gave origin a new branch of science called molecular biology. The discovery of mutation polymorphism (GAT -> GTC in the gene that codifies beta globin chain, give origin to different illness haplotypes, permitted a better and great knowledge about the clinic heterogeneity of the patients. Analysing hemoglobin in its normal and mutation structure as well as in its productions and evolution, one can have a complete understanding of the illness phisiopathology and its clinical complexity.

  8. Modelo para sistemas da qualidade como base da estrategia competitiva

    OpenAIRE

    Marco Antonio Silveira

    1999-01-01

    Resumo: Vários autores propõem a empresa como um sistema em transformação, sendo que esse enfoque sistêmico parece oferecer um meio efetivo de prover as capacidades estratégicas que são valorizadas pelos mercados atuais. Por outro lado, vem crescendo a consciência para o enfoque da qualidade como base da estratégia competitiva, onde esta é associada à lucratividade e incluída no processo de planejamento estratégico, tornando-se um instrumento eficaz de concorrência que, para fazer frente à di...

  9. Polypeptides Based Molecular Electronics

    National Research Council Canada - National Science Library

    Lam, Yeng M; Mhaisalkar, Subodh; Li, Lain-Jong; Dravid, Vinayak P; Shekhawat, Gajendra S; Suri, Raman

    2008-01-01

    ... the formation of molecular devices such as transistors, diodes, and sensors. We have designed the peptides, arranged them on substrates using self-assembly, Dip-PEN nanolithography, and also e-beam assisted lithography...

  10. Efeitos do exercicio físico em parâmetros moleculares da via de sinalização da insulina e obesidade

    Directory of Open Access Journals (Sweden)

    Joni Marcio de Farias

    2014-08-01

    Full Text Available http://dx.doi.org/10.5007/1980-0037.2014v16n5p588 A prevalência da obesidade e diabetes mellitus tem aumentado significativamente nos últimos anos e o conhecimento de que o tecido adiposo tem atividade endócrina e desempenha funções importantes na regulação da inflamação e no metabolismo energético por meio de mecanismos moleculares entre outros é fonte de novas pesquisas. Este trabalho versa sobre os mecanismos moleculares envolvidos na obesidade e diabetes principalmente em tecidos periféricos bem como a relação do exercício físico neste contexto, em forma de revisão bibliográfica. A metodologia foi levantamento bibliográfico nas principais bases de dados: Scielo e PubMed, publicados no período de 1998 a 2012. Os estudos tem demonstrado uma inter-relação entre os mecanismos moleculares envolvidos no desenvolvimento da obesidade e diabetes em tecidos periféricos e centrais. Do ponto de vista do exercício físico, vários estudos demonstram uma contribuição muito grande na diminuição da prevalência, no controle e até mesmo no tratamento da obesidade e diabetes. No entanto há necessidade de estudos mais aprofundados relacionando diversos tipos de exercício físico, em volumes e intensidades diferentes e preferencialmente com humanos, bem como o modelo de estudo, que quando utilizado animais, os programas de exercício devem ser desenvolvidos concomitantemente com alimentação rica em gordura, verificando mais intensamente o exercício físico e o seu real papel na prevenção destas doenças.

  11. Carbon Nanotube Based Molecular Electronics

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1998-01-01

    Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

  12. ESTUDO DOS COMPRIMENTOS DE LIGAÇÃO DA FORMA CETÔNICA DA CURCUMINA NO VÁCUO USANDO DINÂMICA MOLECULAR DE CAR-PARRINELLO

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    Eduardo MartinsToledo

    2015-03-01

    Full Text Available A curcumina é um pigmento amarelo-laranja extraído do rizoma da planta Curcuma longa L. Tem-se destacado por apresentar um amplo potencial terapêutico, com atividade antibacteriana, anti-inflamatória, antioxidante, pró-apoptótica, quimiopreventiva, anticarcinogênica entre outras. Apesar das diversas propriedades biológicas identificadas, existem poucos estudos teóricos sobre este candidato a fármaco. Nesse sentido, o presente trabalho objetivou-se no estudo dos comprimentos de ligação da forma cetônica da curcumina no vácuo, utilizando o método de Dinâmica Molecular de Car-Parrinello. Para os cálculos, a molécula foi disposta em uma caixa cúbica, com dimensões de 23 Å. O funcional de energia de troca e correlação foi modelado usando o funcional do gradiente corrigido PBE. Os elétrons do núcleo foram tratados com pseudopotenciais ultrasolf de Vanderbilt, e os de valência foram representados pelo conjunto de funções de base em ondas planas, truncadas em energia cinética de corte de 20 Ry. As simulações de DMCP foram realizadas a 300 K, com um passo de integração de 6,0 a.t.u. e massa fictícia de 500 a.u. Os resultados mostram uma boa concordância com as propriedades estruturais da forma cetônica da curcumina determinadas por outros métodos teóricos. Este estudo contribui para a compreensão inicial das propriedades estruturais da forma cetônica da curcumina.

  13. Revisiting shape selectivity in liquid chromatography for polycyclic aromatic hydrocarbons (PAHs) - six-ring and seven-ring Cata-condensed PAH isomers of molecular mass 328 Da and 378 Da.

    Science.gov (United States)

    Oña-Ruales, Jorge O; Sander, Lane C; Wilson, Walter B; Wise, Stephen A

    2018-01-01

    The relationship of reversed-phase liquid chromatography (RPLC) retention on a polymeric C 18 stationary phase and the shape of polycyclic aromatic hydrocarbons (PAHs) was investigated for three-ring to seven-ring cata-condensed isomers. We report the first RPLC separation for six-ring and seven-ring cata-condensed PAH isomers. Correlations of LC retention and shape parameters (length-to-breath ratio, L/B and thickness, T) were investigated for 2 three-ring isomers (molecular mass 178 Da), 5 four-ring isomers (molecular mass 228 Da), 11 five-ring isomers (molecular mass 278 Da), 17 six-ring isomers (molecular mass 328 Da), and 20 seven-ring isomers (molecular mass 378 Da). Significant linear correlations were found for all isomer groups (r = 0.71 to 0.94). Nonplanarity of the PAH isomers was found to influence retention (i.e., nonplanar isomers eluting earlier than expected based on L/B) and linear correlations of retention vs. T for isomer groups containing nonplanar isomers were significant (r = 0.71 to 0.86). Graphical abstract.

  14. Bases moleculares de las leucemias agudas

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    G. Martínez Antuña

    2006-04-01

    Full Text Available El gran desarrollo de la biología molecular en los últimos años ha contribuido a un importante avance en los conocimientos relacionados con las bases moleculares de las leucemias agudas (LA. Ademas de profundizar en la biología de estas enfermedades y conocer las bases moleculares, ha renido también gran impacto en mejorar el resultado de los tratamientos y disminuir la toxicidad de las terapias.

  15. Bases moleculares da ação anti-inflamatória dos ácidos oleanólico e ursólico sobre as isoformas da ciclo-oxigenase por docking e dinâmica molecular

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    Wendell Santos Magalhães

    2012-01-01

    Full Text Available The triterpenoids oleanolic (OA and ursolic (UA acids show non-selective antiinflamatory activity in vitro for cyclooxygenase (COX isoforms. 3D conformations of OA and UA, with three possible orientations (1, 1' and 2 in the active site of isoforms COX, obtained by docking, were submitted to molecular dynamics. The results show that orientation 2 of the OA in COX-2 is more favorable because orientation 1 moved away from the active site. The carboxylate group of OA interact by hydrogen bonds with Ser353 and with Phe357 and Leu359, mediated by water, while hydroxyl in C-3 interact by hydrogen bond, mediated by water, with Tyr385.

  16. On the Da Vinci size effect in tensile strengths of nanowires: A molecular dynamics study

    Science.gov (United States)

    Zhao, Ziyu; Liu, Jinxing; Soh, Ai Kah

    2018-01-01

    In recent decades, size effects caused by grain size, strain gradient, typical defects etc., have been widely investigated. Nevertheless, the dependence of tensile strength on the specimen length, addressed by Da Vinci around 500 hundred years ago, has received rather limited attention, even though it is one unavoidable question to answer if people attempt to bring materials' amazing nano-scale strengths up to macro-level. Therefore, we make efforts to study tensile behaviors of copper nanowires with a common cross-section and various lengths by employing the molecular dynamics simulations. Surprisingly, a strong size effect of Da Vinci type indeed arises. We have shown the influences of lattice orientation, temperature and prescribed notch on such a Da Vinci size effect. Two different theoretical explanations are briefly proposed for a qualitative understanding. Finally, a simple scaling rule is summarized to cover the tendencies observed.

  17. On the Da Vinci size effect in tensile strengths of nanowires: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Ziyu Zhao

    2018-01-01

    Full Text Available In recent decades, size effects caused by grain size, strain gradient, typical defects etc., have been widely investigated. Nevertheless, the dependence of tensile strength on the specimen length, addressed by Da Vinci around 500 hundred years ago, has received rather limited attention, even though it is one unavoidable question to answer if people attempt to bring materials’ amazing nano-scale strengths up to macro-level. Therefore, we make efforts to study tensile behaviors of copper nanowires with a common cross-section and various lengths by employing the molecular dynamics simulations. Surprisingly, a strong size effect of Da Vinci type indeed arises. We have shown the influences of lattice orientation, temperature and prescribed notch on such a Da Vinci size effect. Two different theoretical explanations are briefly proposed for a qualitative understanding. Finally, a simple scaling rule is summarized to cover the tendencies observed.

  18. PET molecular imaging of peripheral and central inflammatory processes targeting the TSPO 18 kDa

    International Nuclear Information System (INIS)

    Bernards, Nicholas

    2014-01-01

    The purpose of this study was to determine the in vivo potential of the TSPO 18 kDa as a bio-marker of inflammation, with the use of its radioligand [ 18 F]DPA-714, to non-invasively quantify the inflammatory state within the scope of various pathologies. Multiple animal models of various inflammatory diseases, to include: inflammatory bowel disease, neuro-inflammation, and septic shock, were developed and put in place by adapted measures. The animals well-being and the subsequent inflammation was evaluated. The inflammatory state was measured using quantitative PET imaging with the TSPO radioligand [ 18 F]DPA-714 and correlated to the expression of conventional inflammatory markers using microscopy. Based on the observed data, we were able to distinguish control groups from treated groups when using [ 18 F]DPA-714. This TSPO radioligand permitted us to quantify the inflammatory level and to observe evolutionary changes in the inflammatory state of the disease in multiple models. The PET results, using the [ 18 F]DPA-714 signal was correlated with an increased TSPO expression at cellular level. Results indicate that [ 18 F]DPA-714 is a suitable tracer for studying inflammation of multiple diseases. [ 18 F]DPA-714 could be a good molecular probe to non-invasively evaluate the level and localization of inflammation. Moreover, in vivo imaging using this TSPO ligand is potentially a powerful tool to stage and certainly to follow the evolution and therapeutic efficiency at molecular level in inflammatory diseases. (author) [fr

  19. Bases históricas da Epidemiologia

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    Naomar de Almeida Filho

    1986-09-01

    Full Text Available O presente ensaio tenta sistematizar uma série de informações esquemáticas sobre a história da Epidemiologia, a fim de compreender a sua evolução enquanto disciplina articulada ao desenvolvimento histórico dos principais movimentos sociais na área da saúde. Discute-se as raízes da Epidemiologia a partir do tripé Clínica-Estatística-Medicina Social, o seu desenvolvimento inicial subsidiário à Saúde Pública, a sua constituição ideológica e o seu avanço técnico no bojo do projeto preventivista. Finalmente, a Epidemiologia moderna é vista como uma disciplina que retorna às suas raízes históricas e políticas no movimento da Saúde Coletiva, opondo-se, a nível teórico, às pressões para torná-la um mero instrumento "método-lógico " da pesquisa clínica.The present article is an attempt to organize some information about the history of Epidemiology, in order to understand its evolution as a scientific discipline connected with the historical development of major social movements in the health fields. The roots of Epidemiology from the triad Clinics-Statistics-Social Medicine, its initial development depending on the Public Health, its Technical advancement and ideological constitution within the preventive project, are all discussed. Finnally, modem Epidemiology is seen as a discipline that recovers its historical and roots through the movement of Collective Health, in opposition, at a theoretical level, to pressures to make it a mere "methodological" tool for clinical research.

  20. Bases epistemológicas da psicologia cognitiva experimental

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    Carmem Beatriz Neufeld

    Full Text Available O presente artigo tem como objetivo analisar as bases epistemológicas da Psicologia Cognitiva Experimental. Inicialmente serão traçados alguns dos pressupostos da Psicologia Cognitiva, dentro da abrangência da Ciência Cognitiva e sua relação com o Cognitivismo. Serão retomados alguns aspectos históricos que serão relacionados com os pressupostos das teorias e suas influências na aplicação das mesmas. A partir destes aspectos, serão levantados alguns dos pressupostos filosóficos que marcaram a transição de modelos em ciência, enfocando por fim a emergência da Ciência Cognitiva. O presente trabalho conclui enfocando os argumentos pró e contra a revolução cognitiva enquanto quebra de paradigma com o Behaviorismo.

  1. Gas Sensors Based on Molecular Imprinting Technology.

    Science.gov (United States)

    Zhang, Yumin; Zhang, Jin; Liu, Qingju

    2017-07-04

    Molecular imprinting technology (MIT); often described as a method of designing a material to remember a target molecular structure (template); is a technique for the creation of molecularly imprinted polymers (MIPs) with custom-made binding sites complementary to the target molecules in shape; size and functional groups. MIT has been successfully applied to analyze; separate and detect macromolecular organic compounds. Furthermore; it has been increasingly applied in assays of biological macromolecules. Owing to its unique features of structure specificity; predictability; recognition and universal application; there has been exploration of the possible application of MIPs in the field of highly selective gas sensors. In this present study; we outline the recent advances in gas sensors based on MIT; classify and introduce the existing molecularly imprinted gas sensors; summarize their advantages and disadvantages; and analyze further research directions.

  2. Molecular characterization of ruminal bacterial diversity in vitro = Caracterização molecular da diversidade bacteriana ruminal in vitro

    Directory of Open Access Journals (Sweden)

    Humberto Maciel França Madeira

    2008-04-01

    Full Text Available PCR analysis is a sensitive and specific tool to detect and monitormicroorganisms in complex environmental samples. The amplification of 16S ribosomal DNA sequences followed by gel electrophoresis under denaturing gradient (DGGE has been a powerful technique to genetically evaluate microbial ecosystems. Changes in rumenmicrobial populations were investigated in vitro using a basal diet with different lipid sources. PCRs were performed with two different sets of primers in order to amplify 16S rRNA sequences, and the amplified fragments were submitted to DGGE analysis. The findings presented in this study show that distinct microbial communities were present in each treatment. The presence of soybean oil seems to maximize growth of bacterial population, whereas fish oil appears to reduce growth. We demonstrated the successful application of molecular ecological techniques to analyze the structure and composition of bacterial communities in rumen ecosystems.A análise por PCR fornece um meio sensível e específico para detectar e monitorar microrganismos em amostras ambientais complexas. Desde sua aplicação inicial, o DNA ribossomal 16S (rRNA em eletroforese com gel com gradiente desnaturante (DGGE, tem sido uma técnica atrativa para a ecologia molecular microbiana. Foram investigadas mudanças na população microbiana no rúmen, a partir de alterações da dieta com tratamentos in vitro de diferentes fontes de lipídeos. ODGGE foi testado com dois pares de primers para o rRNA 16S. O uso do fragmento de 200 pb gerou um perfil de bandas mais discriminatório, mostrando que diferentes comunidades microbianas estavam presentes entre os tratamentos in vitro analisados. A presença de óleo de sojapotencializou o crescimento da população bacteriana, enquanto que óleo de peixe parece ter reduzido esse crescimento. Foi possível demonstrar o sucesso da aplicação de técnicas moleculares para analisar a estrutura e a composição de comunidades

  3. Fluorescence based molecular in vivo imaging

    International Nuclear Information System (INIS)

    Ebert, Bernd

    2008-01-01

    Molecular imaging represents a modern research area that allows the in vivo study of molecular biological process kinetics using appropriate probes and visualization methods. This methodology may be defined- apart from the contrast media injection - as non-abrasive. In order to reach an in vivo molecular process imaging as accurate as possible the effects of the used probes on the biological should not be too large. The contrast media as important part of the molecular imaging can significantly contribute to the understanding of molecular processes and to the development of tailored diagnostics and therapy. Since more than 15 years PTB is developing optic imaging systems that may be used for fluorescence based visualization of tissue phantoms, small animal models and the localization of tumors and their predecessors, and for the early recognition of inflammatory processes in clinical trials. Cellular changes occur during many diseases, thus the molecular imaging might be of importance for the early diagnosis of chronic inflammatory diseases. Fluorescent dyes can be used as unspecific or also as specific contrast media, which allow enhanced detection sensitivity

  4. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic analysis of 92 ...

  5. M S MOLECULARES Rumo aos limites da miniaturiza o - (Molecular Magnets - towards the limits of miniaturization)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-01-01

    Por s culos, acreditou-se que o magnetismo s se manifestava em metais, como aqueles contendo ferro; hoje, a imagem mais comum de um m talvez seja a daquelas plaquinhas flex veis coladas geladeira com propagandas dos mais diversos tipos. O leitor conseguiria imaginar um material puramente org nico daqueles que formam os seres vivos como magn tico? E m s do tamanho de mol culas? fato: ambos existem. Esses novos materiais, conhecidos como magnetos moleculares, descobertos e desenvolvidos em v rios laborat rios do mundo, j re nem longa lista de aplica es, do tratamento do c ncer a refrigeradores ecol gicos, passando pela transmiss o de eletricidade sem perda de calor e a fabrica o de computadores extremamente velozes.

  6. Graphene-based nanoprobes for molecular diagnostics.

    Science.gov (United States)

    Chen, Shixing; Li, Fuwu; Fan, Chunhai; Song, Shiping

    2015-10-07

    In recent years, graphene has received widespread attention owing to its extraordinary electrical, chemical, optical, mechanical and structural properties. Lately, considerable interest has been focused on exploring the potential applications of graphene in life sciences, particularly in disease-related molecular diagnostics. In particular, the coupling of functional molecules with graphene as a nanoprobe offers an excellent platform to realize the detection of biomarkers, such as nucleic acids, proteins and other bioactive molecules, with high performance. This article reviews emerging graphene-based nanoprobes in electrical, optical and other assay methods and their application in various strategies of molecular diagnostics. In particular, this review focuses on the construction of graphene-based nanoprobes and their special advantages for the detection of various bioactive molecules. Properties of graphene-based materials and their functionalization are also comprehensively discussed in view of the development of nanoprobes. Finally, future challenges and perspectives of graphene-based nanoprobes are discussed.

  7. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  8. A nanoplasmonic switch based on molecular machines

    KAUST Repository

    Zheng, Yue Bing

    2009-06-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental data show that an Au nanodisk array, coated with rotaxane molecular machines, switches its localized surface plasmon resonances (LSPR) reversibly when it is exposed to chemical oxidants and reductants. Conversely, bare Au nanodisks and disks coated with mechanically inert control compounds, do not display the same switching behavior. Along with calculations based on time-dependent density functional theory (TDDFT), these observations suggest that the nanoscale movements within surface-bound "molecular machines" can be used as the active components in plasmonic devices. ©2009 IEEE.

  9. Broadening of molecular weight distribution of polymers synthesized by metallocene-based dual-site catalysts; Alargamento da distribuicao de massa molar de polimeros sintetizados com catalisadores metalocenicos dual-site

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Joao H.Z. dos [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Inst. de Quimica]. E-mail: jhzds@iq.ufrgs.br; Fisch, Adriano G.; Cardozo, Nilo S.M.; Secchi, Argimiro R. [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Dept. de Engenharia Quimica

    2008-07-01

    The main topics related to the use of dual-site catalysts in the production of polymers with broad molecular weight distribution are reviewed. The polymerization using dual-site catalysts is more economical and allows to produce a higher quality product than other processes, such as polymer blend and multistage reactors. However, the formulation of these catalysts is quite complicated since the same catalyst must produce distinct polymer grades. In addition, the release of patents concerning the combination of metallocenes and new technologies for polymerization shows that polymerization processes using dual-site catalysts are of current industrial interest. (author)

  10. A patogênese genética e molecular da síndrome de Angelman

    Directory of Open Access Journals (Sweden)

    Angelica Francesca Maris

    2011-01-01

    Full Text Available Objetivo: Fornecer uma revisão atualizada em língua portuguesa sobre a síndrome de Angelman, com ênfase nos mecanismos genéticos e moleculares dessa patologia, uma causa de deficiência mental severa que em alguns casos pode apresentar recorrência familiar. Método: Foi feita uma revisão bibliográfica utilizando a base de dados do PubMed, tendo como critérios de busca o termo "Angelman syndrome" isoladamente e combinado com "UBE3A", "clinical", "genetics" e "molecular" no título dos artigos. Dentre esses, foram selecionados artigos de revisão e artigos originais sobre a fisiopatologia da síndrome, com ênfase nos últimos dez anos. Resultados: Utilizando-se "Angelman syndrome" na busca, apareceram cerca de 1.100 artigos, incluindo 240 de revisão. Nos últimos dez anos são mais de 600 artigos, aproximadamente 120 de revisão, 50% dos quais publicados nos últimos cinco anos. Na base de dados SciELO, são apenas nove artigos sobre a síndrome, dos quais três em português e nenhum artigo atual de revisão. Conclusão: Após ter sido uma das principais causas que atraíram atenção ao estudo e ao entendimento dos mecanismos do imprinting genômico, a síndrome de Angelman está agora se revelando como uma patologia das sinapses. Apesar de o entendimento da fisiopatologia molecular da síndrome de Angelman ainda estar longe de ser compreendida, seu estudo está fornecendo uma visão extraordinária sobre os mecanismos que regem a plasticidade sináptica, novamente atraindo a atenção de pesquisadores que trabalham na fronteira do conhecimento.

  11. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  12. Progress on RNAi-based molecular medicines

    OpenAIRE

    Chen, Jing; Xie, Jianping

    2012-01-01

    Jing Chen, Jianping XieInstitute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, ChinaAbstract: RNA interference (RNAi) is a promising strategy to suppress the expression of disease-relevant genes and induce post-transcriptional gene silencing. Their simplicity and stability endow RNAi with great advantages in molecular medicine. Several RNA...

  13. Avaliação da composição molecular da cápsula anterior da lente de cães idosos com catarata de alto risco

    Directory of Open Access Journals (Sweden)

    Ana Paula Hvenegaard

    Full Text Available Resumo: Atualmente, a cápsula anterior e o epitélio da lente tem sido cada vez mais estudados, com o intuito de reduzir as possíveis complicações do pós-operatório da remoção da catarata, tal como a opacidade da cápsula posterior, alteração ocasionada principalmente pela diferenciação e migração das células do epitélio lenticular para a cápsula posterior da lente. O objetivo deste estudo foi analisar a composição molecular da cápsula anterior da lente pela técnica histoquímica de PAS (avaliação de proteoglicanos e picrosirius red (avaliação de colágeno IV, em cães idosos com catarata diabética e não diabética do tipo hipermadura, submetidos ao uso ou não de azul de tripano a 0,1 % durante a facoemulsificação. Vinte e sete cães foram estudados, incluindo 21 fêmeas e 6 machos, de 8 a 12 anos de idade (média = 9,6 anos, de diversas raças e divididos em 2 grupos: GC (catarata hipermadura e GCD (catarata diabética. Os resultados das análises realizadas mostraram que ambas as amostras, tanto as provenientes das cataratas hipermaduras, quanto das diabéticas, apresentam semelhante composição molecular de proteoglicanos e colágeno IV e isto independente da utilização de azul de tripano a 0,1 %. Conclui-se, portanto, que se os resultados obtidos forem decorrentes de alterações provocadas pelo rápido metabolismo da catarata diabética e pela cronicidade da catarata hipermadura sugere-se que o comprometimento da estrutura capsular seja de intensidade equivalente e, por consequência, que isto também possa prejudicar o metabolismo das células do epitélio anterior da lente, diminuindo assim a incidência da opacidade da cápsula posterior de cães com catarata diabética e hipermadura submetidos à facoemulsificação.

  14. ANÁLISE DA PAISAGEM DA BACIA HIDROGRÁFICA DO RIO ALMADA (BA COM BASE NA FRAGMENTAÇÃO DA VEGETAÇÃO

    Directory of Open Access Journals (Sweden)

    Maria Eugênia Bruck de Moraes

    2012-04-01

    Full Text Available O estudo da fragmentação da paisagem em uma bacia é de extrema importância por avaliar o status de conservação da vegetação, um recurso essencial para a manutenção da qualidade da água. O presente trabalho apresenta uma análise da fragmentação da paisagem na Bacia Hidrográfica do Rio Almada, localizada no sul da Bahia, abrangendo 9 municípios parcialmente abastecidos pela água desta bacia. Foi realizado o mapeamento dos fragmentos florestais que apresentaram área mínima de 3ha, com base na interpretação da Carta de Uso e Cobertura do Solo elaborada através da classificação supervisionada de imagens Landsat. Para a análise dos fragmentos foram adotadas 5 métricas da paisagem: tamanho, formato, efeito de borda, isolamento e conectividade. Os resultados obtidos demonstram que a BHRA ainda abriga fragmentos bastante representativos, visto que dos 58 fragmentos identificados, 8 têm área acima de 300ha, 20 entre 100 e 300ha, 21 entre 30 e 100ha e 9 entre 3 e 30ha. Com relação ao formato dos fragmentos, constatou-se que apenas 10% dos mesmos apresentam forma circular, indicando que os 90% restantes encontram-se susceptíveis ao efeito de borda, sendo que os mais alongados estão localizados no interior da bacia, provavelmente em função do avanço da pecuária extensiva nessa direção. E quanto ao isolamento dos fragmentos, a análise da conectividade com borda expandida, através de simulações, permitiu identificar que a partir da distância de 200m, 31 dos fragmentos poderiam ser conectados. Assim, pôde-se concluir que o somatório destes fragmentos, caso fossem devidamente conectados, representaria uma área de significativo valor para a conservação de espécies típicas da mata atlântica e, consequentemente, para a manutenção da qualidade da água desta bacia.

  15. Organic-based molecular switches for molecular electronics.

    Science.gov (United States)

    Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

    2011-10-05

    In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

  16. Advanced molecular devices based on light-driven molecular motors

    NARCIS (Netherlands)

    Chen, Jiawen

    2015-01-01

    Nature has provided a large collection of molecular machines and devices that are among the most amazing nanostructures on this planet. These machines are able to operate complex biological processes which are of great importance in our organisms. Inspired by these natural devices, artificial

  17. Evidência molecular da ocorrência de um fitoplasma associado ao lenho mole da macieira

    OpenAIRE

    Ribeiro,Luiz Fernando Caldeira; Bedendo,Ivan Paulo; Sanhueza,Rosa Maria Valdebenito

    2007-01-01

    O lenho mole da macieira é uma doença relevante em diversas partes do mundo. Sintomas típicos desta doença têm sido observados em pomares instalados em estados do sul do território brasileiro desde a década de oitenta. Enxertia tem revelado a natureza infecciosa da doença e a observação de corpúsculos filamentosos no floema tem evidenciado possível associação com fitoplasma. No presente trabalho plantas com sintomas de lenho mole foram coletadas em pomar comercial, visando demonstrar a presen...

  18. Can thiolation render a low molecular weight polymer of just 20-kDa mucoadhesive?

    Science.gov (United States)

    Mahmood, Arshad; Bonengel, Sonja; Laffleur, Flavia; Ijaz, Muhammad; Idrees, Muneeb Ahmad; Hussain, Shah; Huck, Christian W; Matuszczak, Barbara; Bernkop-Schnürch, Andreas

    2016-01-01

    The objective was to investigate whether even low-molecular weight polymers (LMWPs) can be rendered mucoadhesive due to thiolation. Interceded by the double catalytic system carbodiimide/N-hydroxysuccinimide, cysteamine was covalently attached to a copolymer, poly(4-styrenesulfonic acid-co-maleic acid) (PSSA-MA) exhibiting a molecular weight of just 20 kDa. Depending on the amount of added N-hydroxysuccinimide and cysteamine, the resulting PSSA-MA-cysteamine (PC) conjugates exhibited increasing degree of thiolation, highest being "PC 2300" exhibiting 2300.16 ± 149.86 μmol thiol groups per gram of polymer (mean ± SD; n = 3). This newly developed thiolated polymer was evaluated regarding mucoadhesive, rheological and drug release properties as well from the toxicological point of view. Swelling behavior in 100 mM phosphate buffer pH 6.8 was improved up to 180-fold. Furthermore, due to thiolation, the mucoadhesive properties of the polymer were 240-fold improved. Rheological measurements of polymer/mucus mixtures confirmed results obtained by mucoadhesion studies. In comparison to unmodified polymer, PC 2300 showed 2.3-, 2.3- and 2.4-fold increase in dynamic viscosity, elastic modulus and viscous modulus, respectively. Sustained release of the model drug codeine HCl out of the thiomer was provided for 2.5 h (p polymer. Moreover, the thiomer was found non-toxic over Caco-2 cells for a period of 6- and 24-h exposure. Findings of the present study provide evidence that due to thiolation LMWPs can be rendered highly mucoadhesive as well as cohesive and that a controlled drug release out of such polymers can be provided.

  19. Abstracts of the 26. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 26. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-07-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

  20. Abstracts of the 27. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 27. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-07-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

  1. Molecular heterogeneity of Malassezia pachydermatis through RAPD-PCR = Heterogeneidade molecular da Malassezia pachydermatis através de RAPD-PCR

    Directory of Open Access Journals (Sweden)

    Patrícia da Silva Nascente

    2010-04-01

    Full Text Available Several methodologies in molecular biology have been used in theinvestigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiologicalstudy of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands among the 49 studied isolates, grouped into nine patterns. Isolate groupings were not found to be related to animal breed, age or sex. It was concluded that M. pachydermatis has differences in its molecular profile, as shown by the molecular technique (RAPD – PCR, which allows isolates to be classified into nine subtypes.Várias metodologias em biologia molecular têm sido aplicadas para estudar a M. pachydermatis diferenciando-a em subgrupos. Recentemente utiliza-se a investigação molecular desta espécie isolada de otite externa e dermatite, e também de isolados da mesma de animais hígidos, para um estudo epidemiológico da levedura. O objetivo deste trabalho foi identificar diferenças moleculares entre isolados de M. pachydermatis obtidos de casos de otite externa canina. Para isto, amostras da levedura provenientes de cães com esta enfermidade foram estudadas através da técnica de Polimorfismo de DNA Amplificado aoAcaso - Reação da Polimerase em Cadeia (RAPD–PCR para pesquisa de heterogeneidade molecular. A extração de DNA foi realizada no processo fenol-cloroformio e a técnica de RAPD foi estudada com o primer

  2. Gas Sensors Based on Molecular Imprinting Technology

    OpenAIRE

    Zhang, Yumin; Zhang, Jin; Liu, Qingju

    2017-01-01

    Molecular imprinting technology (MIT); often described as a method of designing a material to remember a target molecular structure (template); is a technique for the creation of molecularly imprinted polymers (MIPs) with custom-made binding sites complementary to the target molecules in shape; size and functional groups. MIT has been successfully applied to analyze; separate and detect macromolecular organic compounds. Furthermore; it has been increasingly applied in assays of biological mac...

  3. Identidade molecular dos fitoplasmas associados aos enfezamentos do tomateiro e da berinjela com base na análise do gene 16S rDNA Molecular identity of the phytoplasma associated to stunting of tomato and eggplant on the basis of analyses of the 16S rDNA

    Directory of Open Access Journals (Sweden)

    Ana Paula de Oliveira Amaral Mello

    2007-09-01

    Full Text Available Doenças de hortaliças de ocorrência no território brasileiro e em outras áreas do mundo têm sido associadas a diversos fitoplasmas. Na região de Piracicaba-SP e Bragança Paulista-SP, em plantas de tomate e berinjela foram observados sintomas típicos de enfezamento caracterizados por porte reduzido, clorose foliar, superbrotamento de ramos, desenvolvimento anormal do cálice, encurtamento de entre-nós, redução no tamanho de folhas, flores e frutos. Através de duplo PCR, utilizando os iniciadores R16 mF1/mR2 e R16 F2n/R2, fragmentos de DNA de 1,2 kb foram amplificados de amostras sintomáticas, demonstrando a presença de fitoplasma nos tecidos das plantas. O uso de iniciadores específicos demonstrou que estes fitoplasmas eram afiliados ao grupo 16SrIII. Análises de RFLP, usando as enzimas de restrição AluI, HpaII, KpnI, MboI, MseI e RsaI confirmaram que os fitoplasmas detectados eram representantes do grupo 16SrIII. Os fragmentos de DNA amplificados foram clonados em Escherichia coli, sequenciados e comparados, por homologia de seqüência, entre si e com outros fitoplasmas do grupo 16SrIII. Um índice de similaridade de seqüência acima de 95% foi encontrado quando seqüências dos fitoplasmas detectados em tomate e berinjela foram comparadas com aquelas de outros representantes do grupo 16SrIII. Um índice de 98-99% foi obtido quando seqüências dos fitoplasmas encontrados em tomate e berinjela foram comparadas entre si. Estes resultados evidenciaram que o enfezamento do tomateiro e da berinjela podem estar associados a um mesmo fitoplasma, com base na análise de seqüências do gene do 16S rDNA.Vegetable diseases occurring in the Brazilian territory and around the world have been associated with various phytoplasmas. In the region of Piracicaba-SP and Bragança-SP, in eggplant and tomato plants typical symptoms of stunting characterized by reduced canopy, leaf yellowing, proliferation of shoots, calix malformation

  4. PET-based molecular imaging in neuroscience

    International Nuclear Information System (INIS)

    Jacobs, A.H.; Heiss, W.D.; Li, H.; Knoess, C.; Schaller, B.; Kracht, L.; Monfared, P.; Vollmar, S.; Bauer, B.; Wagner, R.; Graf, R.; Wienhard, K.; Winkeler, A.; Rueger, A.; Klein, M.; Hilker, R.; Galldiks, N.; Herholz, K.; Sobesky, J.

    2003-01-01

    Positron emission tomography (PET) allows non-invasive assessment of physiological, metabolic and molecular processes in humans and animals in vivo. Advances in detector technology have led to a considerable improvement in the spatial resolution of PET (1-2 mm), enabling for the first time investigations in small experimental animals such as mice. With the developments in radiochemistry and tracer technology, a variety of endogenously expressed and exogenously introduced genes can be analysed by PET. This opens up the exciting and rapidly evolving field of molecular imaging, aiming at the non-invasive localisation of a biological process of interest in normal and diseased cells in animal models and humans in vivo. The main and most intriguing advantage of molecular imaging is the kinetic analysis of a given molecular event in the same experimental subject over time. This will allow non-invasive characterisation and ''phenotyping'' of animal models of human disease at various disease stages, under certain pathophysiological stimuli and after therapeutic intervention. The potential broad applications of imaging molecular events in vivo lie in the study of cell biology, biochemistry, gene/protein function and regulation, signal transduction, transcriptional regulation and characterisation of transgenic animals. Most importantly, molecular imaging will have great implications for the identification of potential molecular therapeutic targets, in the development of new treatment strategies, and in their successful implementation into clinical application. Here, the potential impact of molecular imaging by PET in applications in neuroscience research with a special focus on neurodegeneration and neuro-oncology is reviewed. (orig.)

  5. Molecularly Imprinted Polymer/Metal Organic Framework Based Chemical Sensors

    Directory of Open Access Journals (Sweden)

    Zhenzhong Guo

    2016-10-01

    Full Text Available The present review describes recent advances in the concept of molecular imprinting using metal organic frameworks (MOF for development of chemical sensors. Two main strategies regarding the fabrication, performance and applications of recent sensors based on molecularly imprinted polymers associated with MOF are presented: molecularly imprinted MOF films and molecularly imprinted core-shell nanoparticles using MOF as core. The associated transduction modes are also discussed. A brief conclusion and future expectations are described herein.

  6. Bases neurofisiológicas da dependência do tabaco Neurophysiological basis of tobacco dependence

    Directory of Open Access Journals (Sweden)

    Cleopatra S. Planeta

    2005-10-01

    Full Text Available A maioria dos estudos pré-clínicos e clínicos aponta a nicotina como o principal agente responsável pelo desenvolvimento da dependência ao tabaco. Muitos trabalhos têm demonstrado que as bases neurais da dependência à nicotina são semelhantes àquelas das outras drogas de abuso. A nicotina induz preferência condicionada por lugar e auto-administração e, portanto, atua como reforçador positivo, esse efeito parece ser mediado pelo sistema dopaminérgico mesolímbico. A nicotina também induz à sensibilização comportamental que é provavelmente resultante de alterações da expressão gênica do núcleo acumbens induzidas pela exposição prolongada a essa substância. A suspensão do uso de nicotina resulta em síndrome de abstinência. As evidências indicam que esses sinais e sintomas sejam mediados por receptores colinérgicos nicotínicos centrais e periféricos. Outros neurotransmissores, como por exemplo a serotonina e os peptídeos opióides, também podem estar envolvidos na mediação da dependência e síndrome de abstinência à nicotina. A revisão da literatura mostra a complexidade dos efeitos da nicotina no organismo. A integração entre as abordagens comportamental, neuroquímica e molecular possibilitará a compreensão dos mecanismos neurais da dependência ao tabaco e fornecerá as bases para o desenvolvimento racional de agentes terapêuticos que possam ser utilizados para o tratamento da dependência e síndrome de abstinência ao tabaco.It is generally accepted that nicotine is the major component in tobacco smoke responsible for addiction. Several studies have demonstrated that the neural mechanisms underlying nicotine addiction have much in common with those underlying the mechanisms of addiction to other drugs. Thus, it has been shown that nicotine induces conditioning place preference and self-administration across many species. Repeated treatment with nicotine also induces behavioral sensitization in

  7. A nanoplasmonic switch based on molecular machines

    KAUST Repository

    Zheng, Yue Bing; Yang, Ying-Wei; Jensen, Lasse; Fang, Lei; Juluri, Bala Krishna; Weiss, Paul S.; Stoddart, J. Fraser; Huang, Tony Jun

    2009-01-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental

  8. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... evidence regarding the systematic classification of Ranunculaceae plants, we used molecular ... Ranunculaceae is a family of flowering plants known as ... and in the analysis of the evolutionary rate for lower level phylogeny ...

  9. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  10. Piezoelectric sensors based on molecular imprinted polymers for detection of low molecular mass analytes.

    Science.gov (United States)

    Uludağ, Yildiz; Piletsky, Sergey A; Turner, Anthony P F; Cooper, Matthew A

    2007-11-01

    Biomimetic recognition elements employed for the detection of analytes are commonly based on proteinaceous affibodies, immunoglobulins, single-chain and single-domain antibody fragments or aptamers. The alternative supra-molecular approach using a molecularly imprinted polymer now has proven utility in numerous applications ranging from liquid chromatography to bioassays. Despite inherent advantages compared with biochemical/biological recognition (which include robustness, storage endurance and lower costs) there are few contributions that describe quantitative analytical applications of molecularly imprinted polymers for relevant small molecular mass compounds in real-world samples. There is, however, significant literature describing the use of low-power, portable piezoelectric transducers to detect analytes in environmental monitoring and other application areas. Here we review the combination of molecularly imprinted polymers as recognition elements with piezoelectric biosensors for quantitative detection of small molecules. Analytes are classified by type and sample matrix presentation and various molecularly imprinted polymer synthetic fabrication strategies are also reviewed.

  11. Comprehensive characterization of molecular interactions based on nanomechanics.

    Directory of Open Access Journals (Sweden)

    Murali Krishna Ghatkesar

    Full Text Available Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6 Da adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.

  12. [Department of the molecular bases of semiotics].

    Science.gov (United States)

    Ternovyĭ, K S

    1995-01-01

    Department of molecular basis of semiotics was organized in 1986. The main task of the department was to work out new approaches in estimation of the state of immune and blood system at the tissue, cell and molecular levels, using biochemical, biophysical and molecular biology techniques. There are several main directions of scientific investigations at the department. Most informational methods were collected in "immunological portrait" for differential diagnostic and complex investigation of the immune system of autoimmune patients. This group of techniques was used to study changes in the immune system of Kievites after the Chernobyl disaster. A decrease of complement and thymic serum activity was detected. Antibodies against nuclear components appeared in 20% of donors. And a higher of circulating immune complex of low molecular weight was observed. Low level of thymic serum activity in blood of autoimmune patients with rheumatoid arthritis, lupus erythematosus, diabetes, herpes and other depends on the appearance of zinc-independent timuline inhibitor less then 2000 D. Another kind of thymic hormone inhibitors was detected in thymectomized adult mice. Its effect disappears when zinc added in blood rather due to competition for lymphocyte surface receptors timuline and its inactive analogue than other mechanism. Therapeutic effect of UV irradiation of patients' blood was shown to be closely connected with the changes in thymic serum activity in respect to stabilization of thymic hormone/inhibitor ratio. The immunochemical techniques were used to detect and investigate tumor-associated chromatin antigens in human and animal tumor cells. Antigens not found in normal tissues were detected when using rabbit antibodies against chromatin of rat hepatocarcinoma and human colon and carcinoma.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

    Science.gov (United States)

    Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

    2018-03-06

    Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. A conservative region of the mercuric reductase gene (merA) as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA) como marcador molecular da resistência bacteriana ao mercúrio

    OpenAIRE

    Adriana Sotero-Martins; Michele Silva de Jesus; Michele Lacerda; Josino Costa Moreira; Ana Luzia Lauria Filgueiras; Paulo Rubens Guimarães Barrocas

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II) a Hg0, através da ativida...

  15. Base de linhas moleculares para síntese espectral estelar

    Science.gov (United States)

    Milone, A.; Sanzovo, G.

    2003-08-01

    A análise das abundâncias quí micas fotosféricas em estrelas do tipo solar ou tardia, através do cálculo teórico de seus espectros, emprega a espectroscopia de alta resolução e necessita de uma base representativa de linhas atômicas e moleculares com suas respectivas constantes bem determinadas. Nesse trabalho, utilizamos como ponto de partida as extensas listas de linhas espectrais de sistemas eletrônicos de algumas moléculas diatômicas compiladas por Kurucz para a construção de uma base de linhas moleculares para a sí ntese espectral estelar. Revisamos as determinações dos fatores rotacionais de Honl-London das forças de oscilador das linhas moleculares, para cada banda vibracional de alguns sistemas eletrônicos, seguindo a regra usual de normalização. Usamos as forças de oscilador eletrônicas da literatura. Os fatores vibracionais de Franck-Condon de cada banda foram especialmente recalculados empregando-se novas constantes moleculares. Reproduzimos, com êxito, as absorções espectrais de determinadas bandas eletrônicas-vibracionais das espécies moleculares C12C12, C12N14 e Mg24H em espectros de estrelas de referência como o Sol e Arcturus.

  16. Molecular bases of methamphetamine-induced neurodegeneration.

    Science.gov (United States)

    Cadet, Jean Lud; Krasnova, Irina N

    2009-01-01

    Methamphetamine (METH) is a highly addictive psychostimulant drug, whose abuse has reached epidemic proportions worldwide. The addiction to METH is a major public concern because its chronic abuse is associated with serious health complications including deficits in attention, memory, and executive functions in humans. These neuropsychiatric complications might, in part, be related to drug-induced neurotoxic effects, which include damage to dopaminergic and serotonergic terminals, neuronal apoptosis, as well as activated astroglial and microglial cells in the brain. Thus, the purpose of the present paper is to review cellular and molecular mechanisms that might be responsible for METH neurotoxicity. These include oxidative stress, activation of transcription factors, DNA damage, excitotoxicity, blood-brain barrier breakdown, microglial activation, and various apoptotic pathways. Several approaches that allow protection against METH-induced neurotoxic effects are also discussed. Better understanding of the cellular and molecular mechanisms involved in METH toxicity should help to generate modern therapeutic approaches to prevent or attenuate the long-term consequences of psychostimulant use disorders in humans.

  17. Controlling charge current through a DNA based molecular transistor

    Energy Technology Data Exchange (ETDEWEB)

    Behnia, S., E-mail: s.behnia@sci.uut.ac.ir; Fathizadeh, S.; Ziaei, J.

    2017-01-05

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I–V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive. - Highlights: • Modeling a DNA based molecular transistor and studying its transport properties. • Choosing the appropriate DNA sequence using the quantum chaos tools. • Choosing the functional interval for voltages via the inverse participation ratio tool. • Detecting the rectifier and negative differential resistance behavior of DNA.

  18. Bibliographic data base on atomic and molecular data

    International Nuclear Information System (INIS)

    Itikawa, Yukikazu.

    1983-03-01

    A comparative study is made on three bibliographic data bases: INSPEC, ORNL - AMPIC, GAPHYOR. An on - line retrieval is carried out for searching a number of specific atomic and molecular data. Characteristics of each data base are clarified and suggestions are given for use of those data bases. (author)

  19. BASES EPISTEMOLÓGICAS DA TEORIA DE CRIAÇÃO DE CONHECIMENTO ORGANIZACIONAL

    OpenAIRE

    Juliana Leonardi; Rogério Cid Bastos

    2014-01-01

    A passagem da era industrial para era do conhecimento alavancou estudos científicos organizacionais no campo da Ciência da Administração, ao longo do século XX. Estudos sobre a criação do conhecimento organizacional fazem parte deste arcabouço teórico contemporâneo. Este artigo objetiva investigar as bases epistemológicas da teoria de criação do conhecimento organizacional, desenvolvida por Ikujiro Nonaka. Foi realizado um levantamento de suas obras (artigos e livros) que tratam sobre o tema ...

  20. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  1. Optimal separable bases and molecular collisions

    International Nuclear Information System (INIS)

    Poirier, L.W.

    1997-12-01

    A new methodology is proposed for the efficient determination of Green's functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. The primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR's) and iterative sparse matrix methods commonly employed in such calculations. State to state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H 2 → H 2 + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes

  2. Docking molecular de derivados de 2-fenilindano-1,3-dionas inibidores da enzima HMG-CoA

    Directory of Open Access Journals (Sweden)

    R. Q. Pordeus

    2014-11-01

    Full Text Available As doenças cardiovasculares constituem uma das principais causas de mortes em todo o mundo. Estudos mostram que a enzima HMG-CoA é considerada uma precursora da via metabólica hipolipidêmica no soro sanguíneo. Na busca por uma nova classe de compostos aptos a inibir esta enzima e consequentemente reduzir os níveis de colesterol, as 2-fenilindano-1,3-dionas apresentam resultados promissores. Uma das maneiras de avaliar o poder farmacológico destes compostos e predizer análogos ainda mais potentes consiste na avaliação da interação entre fármaco (2-fenilindano-1,3-diona e enzima (HMG-CoA, em que se utiliza da técnica de modelagem molecular docking. Neste estudo, o procedimento computacional para obtenção dos resultados de docking foi feito através do software AutoDock 1.5.6. Para avaliar a interação no sítio ativo da HMG-CoA, utilizamos, dentre a série de congêneres, o composto 2-(2-clorofenilindano-1,3-diona. De acordo com os resultados obtidos, foi identificada uma interação hidrofílica importante, do tipo ligação de hidrogênio C=O∙∙∙H–N, a qual apresenta uma distância de 1.62 Å entre os grupos carbonila do anel diona e o aminoácido metionina da HMG-CoA. Outra ligação de hidrogênio p∙∙∙H–N com distância de 3.10 Å formada entre o anel aromático do grupo indano-1,3-diona e o aminoácido glicina também foi identificada.

  3. Electrochemical sensor for dopamine based on a novel graphene-molecular imprinted polymers composite recognition element

    DEFF Research Database (Denmark)

    Mao, Yan; Bao, Yu; Gan, Shiyu

    2011-01-01

    A novel composite of graphene sheets/Congo red-molecular imprinted polymers (GSCR-MIPs) was synthesized through free radical polymerization (FRP) and applied as a molecular recognition element to construct dopamine (DA) electrochemical sensor. The template molecules (DA) were firstly absorbed...... at the GSCR surface due to their excellent affinity, and subsequently, selective copolymerization of methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) was further achieved at the GSCR surface. Potential scanning was presented to extract DA molecules from the imprinted polymers film...

  4. Environmental Phosphorus Recovery Based on Molecular Bioscavengers

    DEFF Research Database (Denmark)

    Gruber, Mathias Felix

    Phosphorus is a ubiquitous element of all known life and as such it is found throughout numerous key molecules related to various cellular functions. The supply of phosphorus is tightly linked to global food security, since phosphorus is used to produce agricultural fertilizers, without which...... it would not be possible to feed the world population. Sadly, the current supply of phosphorus is based on the gradual depletion of limited fossil reserves, and some estimates predict that within 15-25 years we will consume more phosphorus than we can produce. There is therefore a strong international...... pressure to develop sustainable phosphorus practices as well as new technologies for phosphorus recovery. Nature has spent billions of years refining proteins that interact with phosphates. This has inspired the present work where the overall ambitions are: to facilitate the development of a recovery...

  5. Progress in molecular-based management of differentiated thyroid cancer

    Science.gov (United States)

    Xing, Mingzhao; Haugen, Bryan R; Schlumberger, Martin

    2014-01-01

    Substantial developments have occurred in the past 5–10 years in clinical translational research of thyroid cancer. Diagnostic molecular markers, such as RET-PTC, RAS, and BRAFV600E mutations; galectin 3; and a new gene expression classifier, are outstanding examples that have improved diagnosis of thyroid nodules. BRAF mutation is a prognostic genetic marker that has improved risk stratification and hence tailored management of patients with thyroid cancer, including those with conventionally low risks. Novel molecular-targeted treatments hold great promise for radioiodine-refractory and surgically inoperable thyroid cancers as shown in clinical trials; such treatments are likely to become a component of the standard treatment regimen for patients with thyroid cancer in the near future. These novel molecular-based management strategies for thyroid nodules and thyroid cancer are the most exciting developments in this unprecedented era of molecular thyroid-cancer medicine. PMID:23668556

  6. A conservative region of the mercuric reductase gene (merA as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA como marcador molecular da resistência bacteriana ao mercúrio

    Directory of Open Access Journals (Sweden)

    Adriana Sotero-Martins

    2008-06-01

    Full Text Available The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II to Hg0, which is dependent of the mercuric reductase enzyme (MerA activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II a Hg0, através da atividade da enzima mercúrio redutase (MerA. O uso do fragmento de 431 pb amplificado de uma região conservada do gene merA, que codifica a enzima MerA,foi utilizado como marcador molecular deste mecanismo, permitindo a identificação de bactérias resistentes ao mercúrio.

  7. Molecular diagnosis of Huntington disease in Brazilian patients Diagnóstico molecular da doença de Huntington em pacientes brasileiros

    Directory of Open Access Journals (Sweden)

    TEREZA C. LIMA E SILVA

    2000-03-01

    ós o início da doença. A HD está associada a uma expansão trinucleotídica CAG presente na porção 5' do gene IT15. Nós investigamos a repetição CAG no gene IT15 em 44 indivíduos brasileiros (42 pacientes e 2 membros não afetados de uma família pertencentes a 34 famílias não relacionadas com diagnóstico provável de HD. Um alelo CAG expandido foi encontrado em 32 indivíduos (76% pertencentes a 25 famílias não relacionadas. Nos pacientes com a mutação HD, os alelos expandidos variaram de 43 a 73 unidades de repetição CAG e os alelos normais apresentaram variação de 18 a 26 CAGs. Correlação negativa significativa foi encontrada entre a idade de início dos sintomas e o tamanho da expansão trinucleotídica CAG (r=0,6; p=0,0001; no entanto, o tamanho da repetição CAG expandida foi capaz de explicar somente 40% da variação encontrada na idade de início da doença (r2=0,4. Além disso, nós genotipamos um total de 25 indivíduos pertencentes a um grupo controle da população brasileira (total de 50 alelos, sendo que o alelo normal apresentou variação de 16 a 33 unidades de repetição CAG. A porcentagem de heterozigozidade do alelo normal na população brasileira controle foi 88%. Em conclusão, nossos resultados mostraram que nem todos os pacientes com fenótipo ``HD'' possuíam a expansão CAG no gene IT15. O diagnóstico molecular foi possível em todos os indivíduos analisados nesse estudo, não sendo encontrada em nossa amostra nenhum alelo de tamanho intermediário. Portanto, nós recomendamos que a confirmação molecular do diagnóstico na HD deva ser realizada em todos os casos suspeitos, a fim de proporcionar subsídios para um aconselhamento genético adequado.

  8. Study of the molecular structure and dynamics of bakelite with neutron cross section measurements; Estudo da estrutura e da dinamica moleculares da baquelite atraves de medidas de secoes de choque para neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Voi, D L

    1990-06-01

    The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 800{sup 0} C. (F.E.). 65 refs, 31 figs, 5 tabs.

  9. The glyoxysomal and plastid molecular chaperones (70-kDa heat shock protein) of watermelon cotyledons are encoded by a single gene

    NARCIS (Netherlands)

    Wimmer, Bernhard; Lottspeich, Friedrich; Klei, Ida van der; Veenhuis, Marten; Gietl, Christine

    1997-01-01

    The monoclonal a-70-kDa heat shock protein (hsp70) antibody recognizes in crude extracts from watermelon (Citrullus vulgaris) cotyledons with molecular masses of 70 and 72 KDa, Immunocytochemistry on watermelon cotyledon tissue and on isolated glyoxysomes identified hsp70s in the matrix of

  10. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  11. Optical materials based on molecular nano/microcrystals and ...

    Indian Academy of Sciences (India)

    Wintec

    generation capability of these ultrathin films are dimini- shed due to aggregation. The efficient solution to this problem based on polyelectrolyte templating is described. Current efforts in our laboratory are focused on the ex- ploitation of these molecular nanostructures for potential applications in sensors and photonics.

  12. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

  13. Fullerene-based Anchoring Groups for Molecular Electronics

    DEFF Research Database (Denmark)

    Martin, Christian A.; Ding, Dapeng; Sørensen, Jakob Kryger

    2008-01-01

    We present results on a new fullerene-based anchoring group for molecular electronics. Using lithographic mechanically controllable break junctions in vacuum we have determined the conductance and stability of single-molecule junctions of 1,4-bis(fullero[c]pyrrolidin-1-yl)benzene. The compound can...

  14. Molecular Recognition: Detection of Colorless Compounds Based on Color Change

    Science.gov (United States)

    Khalafi, Lida; Kashani, Samira; Karimi, Javad

    2016-01-01

    A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

  15. Intelligent DNA-based molecular diagnostics using linked genetic markers

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  16. Chemical sensors based on molecularly modified metallic nanoparticles

    International Nuclear Information System (INIS)

    Haick, Hossam

    2007-01-01

    This paper presents a concise, although admittedly non-exhaustive, didactic review of some of the main concepts and approaches related to the use of molecularly modified metal nanoparticles in or as chemical sensors. This paper attempts to pull together different views and terminologies used in sensors based on molecularly modified metal nanoparticles, including those established upon electrochemical, optical, surface Plasmon resonance, piezoelectric and electrical transduction approaches. Finally, this paper discusses briefly the main advantages and disadvantages of each of the presented class of sensors. (review article)

  17. A molecular shift register based on electron transfer

    Science.gov (United States)

    Hopfield, J. J.; Onuchic, Josenelson; Beratan, David N.

    1988-01-01

    An electronic shift-register memory at the molecular level is described. The memory elements are based on a chain of electron-transfer molecules and the information is shifted by photoinduced electron-transfer reactions. This device integrates designed electronic molecules onto a very large scale integrated (silicon microelectronic) substrate, providing an example of a 'molecular electronic device' that could actually be made. The design requirements for such a device and possible synthetic strategies are discussed. Devices along these lines should have lower energy usage and enhanced storage density.

  18. NEW MOLECULAR MEDICINE-BASED SCAR MANAGEMENT STRATEGIES

    Science.gov (United States)

    Arno, Anna I; Gauglitz, Gerd G; Barret, Juan P; Jeschke, Marc G

    2014-01-01

    Keloids and hypertrophic scars are prevalent disabling conditions with still suboptimal treatments. Basic science and molecular-based medicine research has contributed to unravel new bench-to-bedside scar therapies, and to dissect the complex signaling pathways involved. Peptides such as transforming growth factor beta (TGF-β) superfamily, with SMADs, Ski, SnoN, Fussels, endoglin, DS-Sily, Cav-1p, AZX100, thymosin-β4 and other related molecules may emerge as targets to prevent and treat keloids and hypertrophic scars. The aim of this review is to describe the basic complexity of these new molecular scar management strategies, and point out new fibrosis research lines. PMID:24438742

  19. Evidência molecular da ocorrência de um fitoplasma associado ao lenho mole da macieira Molecular evidence for an association of a phytoplasma with apple rubbery wood

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Caldeira Ribeiro

    2007-03-01

    Full Text Available O lenho mole da macieira é uma doença relevante em diversas partes do mundo. Sintomas típicos desta doença têm sido observados em pomares instalados em estados do sul do território brasileiro desde a década de oitenta. Enxertia tem revelado a natureza infecciosa da doença e a observação de corpúsculos filamentosos no floema tem evidenciado possível associação com fitoplasma. No presente trabalho plantas com sintomas de lenho mole foram coletadas em pomar comercial, visando demonstrar a presença de fitoplasma em tecido doente, bem como identificar molecularmente este fitoplasma. Através do emprego de duplo PCR com iniciadores universais R16mF2/R1 e R16F2n/R2, fitoplasma foi consistentemente detectado em plantas sintomáticas. A identificação conduzida com duplo PCR usando-se iniciadores específicos R16(IIIF2/R demonstrou que o fitoplasma detectado pertencia ao grupo 16SrIII. Análises de RFLP conduzidas com as endonucleases AluI, KpnI, HinfI, HpaII, MseI, RsaI e SauIIIA confirmaram que o fitoplasma era um representante típico do grupo 16SrIII. A detecção e identificação molecular se constitui numa forte evidência que um fitoplasma está associado ao lenho mole da macieira no Brasil, complementando os trabalhos realizados anteriormente com transmissão por enxertia e observação por microscopia eletrônica .Apple rubbery wood is an important disease occurring worldwide. Typical symptoms have been observed since 80' decade in orchards located in the South part of Brazil. In previous studies, grafting has evidenciated that the disease had infeccious etiology and visualization of filamentous bodies inside phloem had indicated that a phytoplasma could be associated with the disease. In the present study, plants with symptoms of rubbery wood were sampled in a commercial orchard in order to demonstrate the presence of phytoplasma in infected tissue and to identify molecularly that the organism. Using nested PCR with universal

  20. Gesture Interaction Browser-Based 3D Molecular Viewer.

    Science.gov (United States)

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

  1. Clustering the Orion B giant molecular cloud based on its molecular emission.

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. A clustering analysis based only on the J = 1 - 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes ( n H ~ 100 cm -3 , ~ 500 cm -3 , and > 1000 cm -3 ), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 - 0 line of HCO + and the N = 1 - 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO + and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO + intensity ratio in UV-illuminated regions. Finer distinctions in density classes ( n H ~ 7 × 10 3 cm -3 ~ 4 × 10 4 cm -3 ) for the densest regions are also

  2. Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

    Science.gov (United States)

    Algieri, Catia; Drioli, Enrico; Guzzo, Laura; Donato, Laura

    2014-01-01

    An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported. PMID:25196110

  3. Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

    Directory of Open Access Journals (Sweden)

    Catia Algieri

    2014-07-01

    Full Text Available An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported.

  4. A patogênese genética e molecular da síndrome de Angelman

    OpenAIRE

    Maris,Angelica Francesca; Trott,Alexis

    2011-01-01

    Objetivo: Fornecer uma revisão atualizada em língua portuguesa sobre a síndrome de Angelman, com ênfase nos mecanismos genéticos e moleculares dessa patologia, uma causa de deficiência mental severa que em alguns casos pode apresentar recorrência familiar. Método: Foi feita uma revisão bibliográfica utilizando a base de dados do PubMed, tendo como critérios de busca o termo "Angelman syndrome" isoladamente e combinado com "UBE3A", "clinical", "genetics" e "molecular" no título dos artigos. De...

  5. Molecular characterization of 45 kDa aspartic protease of Trichinella spiralis.

    Science.gov (United States)

    Park, Jong Nam; Park, Sang Kyun; Cho, Min Kyoung; Park, Mi-Kyung; Kang, Shin Ae; Kim, Dong-Hee; Yu, Hak Sun

    2012-12-21

    In a previous study, we identified an aspartic protease gene (Ts-Asp) from the Trichinella spiralis muscle stage larva cDNA library. The gene sequence of Ts-Asp was 1281 bp long and was found to encode a protein consisting of 405 amino acids, with a molecular mass of 45.248 kD and a pI of 5.95. The deduced Ts-Asp has a conserved catalytic motif with catalytic aspartic acid residues in the active site, a common characteristic of aspartic proteases. In addition, the deduced amino acid sequence of Ts-Asp was found to possess significant homology (above 50%) with aspartic proteases from nematode parasites. Results of phylogenetic analysis indicated a close relationship of Ts-Asp with cathepsin D aspartic proteases. For production of recombinant Ts-Asp (rTs-Asp), the pGEX4T expression system was used. Like other proteases, the purified rTs-Asp was able to digest collagen matrix in vitro. Abundant expression of Ts-Asp was observed in muscle stage larva. Ts-Asp was detected in ES proteins, and was able to elicit the production of specific antibodies. It is the first report of molecular characterization of aspartic protease isolated from T. spiralis. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Arthropod phylogeny based on eight molecular loci and morphology

    Science.gov (United States)

    Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

    2001-01-01

    The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

  7. Forcefields based molecular modeling on the mechanical and physical properties of emeraldine base polyaniline

    NARCIS (Netherlands)

    Chen, X.; Yuan, C.A.; Wong, K.Y.; Zhang, G.Q.

    2010-01-01

    Molecular dynamics (MD) and molecular mechanical (MM) analysis are carried out to provide reliable and accurate model for emeraldine base polyaniline. This study validate the forcefields and model with the physical and mechanical properties of the polyaniline. The temperature effects on non-bond

  8. Organization of a radioisotope based molecular biology laboratory

    International Nuclear Information System (INIS)

    2006-12-01

    Polymerase chain reaction (PCR) has revolutionized the application of molecular techniques to medicine. Together with other molecular biology techniques it is being increasingly applied to human health for identifying prognostic markers and drug resistant profiles, developing diagnostic tests and genotyping systems and for treatment follow-up of certain diseases in developed countries. Developing Member States have expressed their need to also benefit from the dissemination of molecular advances. The use of radioisotopes, as a step in the detection process or for increased sensitivity and specificity is well established, making it ideally suitable for technology transfer. Many molecular based projects using isotopes for detecting and studying micro organisms, hereditary and neoplastic diseases are received for approval every year. In keeping with the IAEA's programme, several training activities and seminars have been organized to enhance the capabilities of developing Member States to employ in vitro nuclear medicine technologies for managing their important health problems and for undertaking related basic and clinical research. The background material for this publication was collected at training activities and from feedback received from participants at research and coordination meetings. In addition, a consultants' meeting was held in June 2004 to compile the first draft of this report. Previous IAEA TECDOCS, namely IAEA-TECDOC-748 and IAEA-TECDOC-1001, focused on molecular techniques and their application to medicine while the present publication provides information on organization of the laboratory, quality assurance and radio-safety. The technology has specific requirements of the way the laboratory is organized (e.g. for avoiding contamination and false positives in PCR) and of quality assurance in order to provide accurate information to decision makers. In addition while users of the technology accept the scientific rationale of using radio

  9. Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons.

    Science.gov (United States)

    Lin, Jia-Hui; Tseng, Wei-Lung

    2014-03-21

    This study presents a single, resettable, and sensitive molecular beacon (MB) used to operate molecular-scale logic gates. The MB consists of a random DNA sequence, a fluorophore at the 5'-end, and a quencher at the 3'-end. The presence of Hg(2+), Ag(+), and coralyne promoted the formation of stable T-Hg(2+)-T, C-Ag(+)-C, and A2-coralyne-A2 coordination in the MB probe, respectively, thereby driving its conformational change. The metal ion or small molecule-mediated coordination of mismatched DNA brought the fluorophore and the quencher into close proximity, resulting in collisional quenching of fluorescence between the two organic dyes. Because thiol can bind Hg(2+) and remove it from the T-Hg(2+)-T-based MB, adding thiol to a solution of the T-Hg(2+)-T-based MB allowed the fluorophore and the quencher to be widely separated. A similar phenomenon was observed when replacing Hg(2+) with Ag(+). Because Ag(+) strongly binds to iodide, cyanide, and cysteine, they were capable of removing Ag(+) from the C-Ag(+)-C-based MB, restoring the fluorescence of the MB. Moreover, the fluorescence of the A2-coralyne-A2-based MB could be switched on by adding polyadenosine. Using these analytes as inputs and the MB as a signal transducer, we successfully developed a series of two-input, three-input, and set-reset logic gates at the molecular level.

  10. DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

    Science.gov (United States)

    Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2017-07-01

    Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/. © 2017 Wiley Periodicals, Inc.

  11. Molecular polarization potential maps of the nucleic acid bases

    International Nuclear Information System (INIS)

    Alkorta, I.; Perez, J.J.

    1996-01-01

    Ab initio calculations at the SCF level were carried out to compute the polarization potential map NM of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning's 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (MPP) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that point. MEPS and MPPS for the different molecules were computed with a density of 5 points/Angstrom 2 on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine. The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases. 23 refs., 5 figs., 1 tab

  12. Programmable molecular recognition based on the geometry of DNA nanostructures.

    Science.gov (United States)

    Woo, Sungwook; Rothemund, Paul W K

    2011-07-10

    From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

  13. Clustering the Orion B giant molecular cloud based on its molecular emission

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    Context. Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods: We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional probability density function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results: A clustering analysis based only on the J = 1-0 lines of three isotopologues of CO proves sufficient to reveal distinct density/column density regimes (nH 100 cm-3, 500 cm-3, and >1000 cm-3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1-0 line of HCO+ and the N = 1-0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH 7 × 103 cm-3, 4 × 104 cm-3) for the densest regions are also

  14. Análise da produção em auditoria e saúde pública a partir da base de dados da Biblioteca Virtual da Saúde

    Directory of Open Access Journals (Sweden)

    Fábio Solon Tajra

    Full Text Available Trata-se de revisão da literatura de base a partir de pesquisa bibliográfica realizada na plataforma da Biblioteca Virtual em Saúde com o objetivo de caracterizar as pesquisas produzidas sobre auditoria no SUS. O levantamento bibliográfico abrangeu as publicações nacionais em auditoria de 2000 a 2010, sendo identificados quatorze documentos para compor a amostra do estudo. Os achados das pesquisas foram classificados de acordo com o tema investigado e os aspectos metodológicos categorizados. Os resultados ressaltam a insuficiência de estudos voltados para essa temática e a necessidade de divulgação dos relatos como fator de consolidação do processo de trabalho em saúde pública.

  15. Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials.

    Science.gov (United States)

    Le Tourneau, Christophe; Kamal, Maud; Tsimberidou, Apostolia-Maria; Bedard, Philippe; Pierron, Gaëlle; Callens, Céline; Rouleau, Etienne; Vincent-Salomon, Anne; Servant, Nicolas; Alt, Marie; Rouzier, Roman; Paoletti, Xavier; Delattre, Olivier; Bièche, Ivan

    2016-04-01

    With the advent of high-throughput molecular technologies, several precision medicine (PM) studies are currently ongoing that include molecular screening programs and PM clinical trials. Molecular profiling programs establish the molecular profile of patients' tumors with the aim to guide therapy based on identified molecular alterations. The aim of prospective PM clinical trials is to assess the clinical utility of tumor molecular profiling and to determine whether treatment selection based on molecular alterations produces superior outcomes compared with unselected treatment. These trials use treatment algorithms to assign patients to specific targeted therapies based on tumor molecular alterations. These algorithms should be governed by fixed rules to ensure standardization and reproducibility. Here, we summarize key molecular, biological, and technical criteria that, in our view, should be addressed when establishing treatment algorithms based on tumor molecular profiling for PM trials. © The Author 2015. Published by Oxford University Press.

  16. Identification and molecular characterization of 48 kDa calcium binding protein as calreticulin from finger millet (Eleusine coracana) using peptide mass fingerprinting and transcript profiling.

    Science.gov (United States)

    Singh, Manoj; Metwal, Mamta; Kumar, Vandana A; Kumar, Anil

    2016-01-30

    Attempts were made to identify and characterize the calcium binding proteins (CaBPs) in grain filling stages of finger millet using proteomics, bioinformatics and molecular approaches. A distinctly observed blue color band of 48 kDa stained by Stains-all was eluted and analyzed as calreticulin (CRT) using nano liquid chromatography-tandem mass spectrometry (nano LC-MS). Based on the top hits of peptide mass fingerprinting results, conserved primers were designed for isolation of the CRT gene from finger millet using calreticulin sequences of different cereals. The deduced nucleotide sequence analysis of 600 bp amplicon showed up to 91% similarity with CRT gene(s) of rice and other plant species and designated as EcCRT1. Transcript profiling of EcCRT1 showed different levels of relative expression at different stages of developing spikes. The higher expression of EcCRT1 transcripts and protein were observed in later stages of developing spikes which might be due to greater translational synthesis of EcCRT1 protein during seed maturation in finger millet. Preferentially higher synthesis of this CaBP during later stages of grain filling may be responsible for the sequestration of calcium in endoplasmic reticulum of finger millet grains. © 2015 Society of Chemical Industry.

  17. Effect of furan n-bridge on the photovoltaic performance of D-A copolymers based on bi(alkylthio-thienyl)benzodithiophene and fluorobenzotriazole

    Institute of Scientific and Technical Information of China (English)

    Tinghai Yan; Haijun Bin; Yankang Yang; Lingwei Xue; Zhi-Guo Zhang; Yongfang Li

    2017-01-01

    The medium band gap donor-acceptor (D-A) copolymer J61 based on bi(alkylthio-thienyl)benzodithiophene as donor unit and fluorobenzotriazole as acceptor unit and thiophene as π-bridge has demonstrated excellent photovoltaic performance as donor material in nonfullerene polymer solar cells (PSCs) with narrow bandgap n-type organic semiconductor ITIC as acceptor.For studying the effect of π-bridges on the photovoltaic performance of the D-A copolymers,here we synthesized a new D-A copolymer J61-F based on the same donor and acceptor units as J61 but with furan π-bridges instead ofthiophene.J61-F possesses a deeper the highest occupied molecular orbital (HOMO) level at-5.45 eV in comparison with that (-5.32 eV) of J61.The non-fullerene PSCs based on J61-F:ITIC exhibited a maximum power conversion efficiency (PCE) of 8.24% with a higher open-circuit voltage (Voo) of 0.95 V,which is benefitted from the lower-lying HOMO energy level of J61-F donor material.The results indicate that main chain engineering by changing π-bridges is another effective way to tune the electronic energy levels of the conjugated D-A copolymers for the application as donor materials in non-fullerene PSCs.

  18. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

    Science.gov (United States)

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W

    2011-10-11

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

  19. Molecular Bases Underlying the Hepatoprotective Effects of Coffee

    Directory of Open Access Journals (Sweden)

    Federico Salomone

    2017-01-01

    Full Text Available Coffee is the most consumed beverage worldwide. Epidemiological studies with prospective cohorts showed that coffee intake is associated with reduced cardiovascular and all-cause mortality independently of caffeine content. Cohort and case-control studies reported an inverse association between coffee consumption and the degree of liver fibrosis as well as the development of liver cancer. Furthermore, the beneficial effects of coffee have been recently confirmed by large meta-analyses. In the last two decades, various in vitro and in vivo studies evaluated the molecular determinants for the hepatoprotective effects of coffee. In the present article, we aimed to critically review experimental evidence regarding the active components and the molecular bases underlying the beneficial role of coffee against chronic liver diseases. Almost all studies highlighted the beneficial effects of this beverage against liver fibrosis with the most solid results indicating a pivot role for both caffeine and chlorogenic acids. In particular, in experimental models of fibrosis, caffeine was shown to inhibit hepatic stellate cell activation by blocking adenosine receptors, and emerging evidence indicated that caffeine may also favorably impact angiogenesis and hepatic hemodynamics. On the other side, chlorogenic acids, potent phenolic antioxidants, suppress liver fibrogenesis and carcinogenesis by reducing oxidative stress and counteract steatogenesis through the modulation of glucose and lipid homeostasis in the liver. Overall, these molecular insights may have translational significance and suggest that coffee components need clinical evaluation.

  20. Avaliação da coleta de sangue em papel de filtro para diagnóstico molecular da dengue

    OpenAIRE

    Célia Luiza de Lima Rodrigues

    2010-01-01

    O diagnóstico rotineiro da dengue é realizado com amostra de sangue dos casos suspeitos. A coleta tradicional de sangue (por punção venosa) é um procedimento que dificulta a realização de exames e pesquisas por ser um procedimento invasivo que nem sempre é prático para crianças e bebês, requer pessoal especializado e necessita de um local para armazenamento da amostra sob refrigeração ou congelamento. O propósito deste estudo foi coletar amostras por punção digital com uma nova tecnologia (FT...

  1. DNA barcode-based molecular identification system for fish species.

    Science.gov (United States)

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

  2. Molecular neuron based on the Franck–Condon blockade

    International Nuclear Information System (INIS)

    Timm, C; Di Ventra, M

    2013-01-01

    Electronic realizations of neurons are of great interest as building blocks for neuromorphic computation. Electronic neurons should send signals into the input and output lines when subject to an input signal exceeding a given threshold, in such a way that they may affect all other parts of a neural network. Here, we propose a design for a neuron that is based on molecular-electronics components and thus promises a very high level of integration. We employ the Monte Carlo technique to simulate typical time evolutions of this system and thereby show that it indeed functions as a neuron. (paper)

  3. Molecular tools for the construction of peptide-based materials.

    Science.gov (United States)

    Ramakers, B E I; van Hest, J C M; Löwik, D W P M

    2014-04-21

    Proteins and peptides are fundamental components of living systems where they play crucial roles at both functional and structural level. The versatile biological properties of these molecules make them interesting building blocks for the construction of bio-active and biocompatible materials. A variety of molecular tools can be used to fashion the peptides necessary for the assembly of these materials. In this tutorial review we shall describe five of the main techniques, namely solid phase peptide synthesis, native chemical ligation, Staudinger ligation, NCA polymerisation, and genetic engineering, that have been used to great effect for the construction of a host of peptide-based materials.

  4. Acidity constants from DFT-based molecular dynamics simulations

    International Nuclear Information System (INIS)

    Sulpizi, Marialore; Sprik, Michiel

    2010-01-01

    In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Broensted pK a when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK a values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.

  5. Nitrogen-doped graphene quantum dots-based fluorescence molecularly imprinted sensor for thiacloprid detection.

    Science.gov (United States)

    Liu, Yang; Cao, Nan; Gui, Wenying; Ma, Qiang

    2018-06-01

    In this paper, a test strip-based sensor was developed for thiacloprid quantitative detection based on PDA molecularly imprinted polymer (MIP) and nitrogen-doped graphene quantum dots (N-GQDs). Thiacloprid is a new type of nicotine insecticide, which can block the normal neurotransmitter delivery process in insects. In the sensing system, N-GQDs were immersed into filter paper at first. Then, dopamine (DA) with thiacloprid can be self-polymerized on test strip surface to form the uniform PDA film. After removed thiacloprid template, the established poly dopamine (PDA) MIP can selectively recognize thiacloprid. As a result, captured thiacloprid can enhance the fluorescence intensity of N-GQDs into the test strip. As a result, the fluorescence intensity of N-GQDs can be linearly related within a certain range of thiacloprid concentration. Under the optimum conditions, the proposed sensor for thiacloprid detection exhibited a linear ranging from 0.1 mg/L to 10 mg/L with a low detection limit of 0.03 mg/L. The N-GQDs based test strip-based sensor for thiaclopridis reported for the first time. The sensing system has high selectivity to thiacloprid and provides new opportunities in the pesticide detection. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Stable Molecular Diodes Based on π-π Interactions of the Molecular Frontier Orbitals with Graphene Electrodes.

    Science.gov (United States)

    Song, Peng; Guerin, Sarah; Tan, Sherman Jun Rong; Annadata, Harshini Venkata; Yu, Xiaojiang; Scully, Micheál; Han, Ying Mei; Roemer, Max; Loh, Kian Ping; Thompson, Damien; Nijhuis, Christian A

    2018-03-01

    In molecular electronics, it is important to control the strength of the molecule-electrode interaction to balance the trade-off between electronic coupling strength and broadening of the molecular frontier orbitals: too strong coupling results in severe broadening of the molecular orbitals while the molecular orbitals cannot follow the changes in the Fermi levels under applied bias when the coupling is too weak. Here, a platform based on graphene bottom electrodes to which molecules can bind via π-π interactions is reported. These interactions are strong enough to induce electronic function (rectification) while minimizing broadening of the molecular frontier orbitals. Molecular tunnel junctions are fabricated based on self-assembled monolayers (SAMs) of Fc(CH 2 ) 11 X (Fc = ferrocenyl, X = NH 2 , Br, or H) on graphene bottom electrodes contacted to eutectic alloy of gallium and indium top electrodes. The Fc units interact more strongly with graphene than the X units resulting in SAMs with the Fc at the bottom of the SAM. The molecular diodes perform well with rectification ratios of 30-40, and they are stable against bias stressing under ambient conditions. Thus, tunnel junctions based on graphene with π-π molecule-electrode coupling are promising platforms to fabricate stable and well-performing molecular diodes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Plasmon-Based Colorimetric Nanosensors for Ultrasensitive Molecular Diagnostics.

    Science.gov (United States)

    Tang, Longhua; Li, Jinghong

    2017-07-28

    Colorimetric detection of target analytes with high specificity and sensitivity is of fundamental importance to clinical and personalized point-of-care diagnostics. Because of their extraordinary optical properties, plasmonic nanomaterials have been introduced into colorimetric sensing systems, which provide significantly improved sensitivity in various biosensing applications. Here we review the recent progress on these plasmonic nanoparticles-based colorimetric nanosensors for ultrasensitive molecular diagnostics. According to their different colorimetric signal generation mechanisms, these plasmonic nanosensors are classified into two categories: (1) interparticle distance-dependent colorimetric assay based on target-induced forming cross-linking assembly/aggregate of plasmonic nanoparticles; and (2) size/morphology-dependent colorimetric assay by target-controlled growth/etching of the plasmonic nanoparticles. The sensing fundamentals and cutting-edge applications will be provided for each of them, particularly focusing on signal generation and/or amplification mechanisms that realize ultrasensitive molecular detection. Finally, we also discuss the challenge and give our future perspective in this emerging field.

  8. Mesoporous Silica Molecular Sieve based Nanocarriers: Transpiring Drug Dissolution Research.

    Science.gov (United States)

    Pattnaik, Satyanarayan; Pathak, Kamla

    2017-01-01

    Improvement of oral bioavailability through enhancement of dissolution for poorly soluble drugs has been a very promising approach. Recently, mesoporous silica based molecular sieves have demonstrated excellent properties to enhance the dissolution velocity of poorly water-soluble drugs. Current research in this area is focused on investigating the factors influencing the drug release from these carriers, the kinetics of drug release and manufacturing approaches to scale-up production for commercial manufacture. This comprehensive review provides an overview of different methods adopted for synthesis of mesoporous materials, influence of processing factors on properties of these materials and drug loading methods. The drug release kinetics from mesoporous silica systems, the manufacturability and stability of these formulations are reviewed. Finally, the safety and biocompatibility issues related to these silica based materials are discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. Selective interface transparency in graphene nanoribbon based molecular junctions.

    Science.gov (United States)

    Dou, K P; Kaun, C C; Zhang, R Q

    2018-03-08

    A clear understanding of electrode-molecule interfaces is a prerequisite for the rational engineering of future generations of nanodevices that will rely on single-molecule coupling between components. With a model system, we reveal a peculiar dependence on interfaces in all graphene nanoribbon-based carbon molecular junctions. The effect can be classified into two types depending on the intrinsic feature of the embedded core graphene nanoflake (GNF). For metallic GNFs with |N A - N B | = 1, good/poor contact transparency occurs when the core device aligns with the center/edge of the electrode. The situation is reversed when a semiconducting GNF is the device, where N A = N B . These results may shed light on the design of real connecting components in graphene-based nanocircuits.

  10. Molecular medicine of fragile X syndrome: based on known molecular mechanisms.

    Science.gov (United States)

    Luo, Shi-Yu; Wu, Ling-Qian; Duan, Ran-Hui

    2016-02-01

    Extensive research on fragile X mental retardation gene knockout mice and mutant Drosophila models has largely expanded our knowledge on mechanism-based treatment of fragile X syndrome (FXS). In light of these findings, several clinical trials are now underway for therapeutic translation to humans. Electronic literature searches were conducted using the PubMed database and ClinicalTrials.gov. The search terms included "fragile X syndrome", "FXS and medication", "FXS and therapeutics" and "FXS and treatment". Based on the publications identified in this search, we reviewed the neuroanatomical abnormalities in FXS patients and the potential pathogenic mechanisms to monitor the progress of FXS research, from basic studies to clinical trials. The pathological mechanisms of FXS were categorized on the basis of neuroanatomy, synaptic structure, synaptic transmission and fragile X mental retardation protein (FMRP) loss of function. The neuroanatomical abnormalities in FXS were described to motivate extensive research into the region-specific pathologies in the brain responsible for FXS behavioural manifestations. Mechanism-directed molecular medicines were classified according to their target pathological mechanisms, and the most recent progress in clinical trials was discussed. Current mechanism-based studies and clinical trials have greatly contributed to the development of FXS pharmacological therapeutics. Research examining the extent to which these treatments provided a rescue effect or FMRP compensation for the developmental impairments in FXS patients may help to improve the efficacy of treatments.

  11. A low molecular weight zinc2+-dipicolylamine-based probe detects apoptosis during tumour treatment better than an annexin V-based probe

    International Nuclear Information System (INIS)

    Palmowski, Karin; Rix, Anne; Lederle, Wiltrud; Kiessling, Fabian; Behrendt, Florian F.; Mottaghy, Felix M.; Gray, Brian D.; Pak, Koon Y.; Palmowski, Moritz

    2014-01-01

    Molecular imaging of apoptosis is frequently discussed for monitoring cancer therapies. Here, we compare the low molecular weight phosphatidylserine-targeting ligand zinc 2+ -dipicolylamine (Zn 2+ -DPA) with the established but reasonably larger protein annexin V. Molecular apoptosis imaging with the fluorescently labelled probes annexin V (750 nm, 36 kDa) and Zn 2+ -DPA (794 nm, 1.84 kDa) was performed in tumour-bearing mice (A431). Three animal groups were investigated: untreated controls and treated tumours after 1 or 4 days of anti-angiogenic therapy (SU11248). Additionally, μPET with 18 F-FDG was performed. Imaging data were displayed as tumour-to-muscle ratio (TMR) and validated by quantitative immunohistochemistry. Compared with untreated control tumours, TUNEL staining indicated significant apoptosis after 1 day (P 2+ -DPA uptake increased significantly after 1 day (P 2+ -DPA, 18 F-FDG tumour uptake decreased significantly at days 1 (P 2+ -DPA than with the annexin V-based probe. Additionally, significant treatment effects were detectable as early using Zn 2+ -DPA as with measurements of the glucose metabolism using 18 F-FDG. (orig.)

  12. Photoredox-Based Actuation of an Artificial Molecular Muscle.

    Science.gov (United States)

    Liles, Kevin P; Greene, Angelique F; Danielson, Mary K; Colley, Nathan D; Wellen, Andrew; Fisher, Jeremy M; Barnes, Jonathan C

    2018-01-24

    The use of light to actuate materials is advantageous because it represents a cost-effective and operationally straightforward way to introduce energy into a stimuli-responsive system. Common strategies for photoinduced actuation of materials typically rely on light irradiation to isomerize azobenzene or spiropyran derivatives, or to induce unidirectional rotation of molecular motors incorporated into a 3D polymer network. Although interest in photoredox catalysis has risen exponentially in the past decade, there are far fewer examples where photoinduced electron transfer (PET) processes are employed to actuate materials. Here, a novel mode of actuation in a series of redox-responsive hydrogels doped with a visible-light-absorbing ruthenium-based photocatalyst is reported. The hydrogels are composed primarily of polyethylene glycol and low molar concentrations of a unimolecular electroactive polyviologen that is activated through a PET mechanism. The rate and degree of contraction of the hydrogels are measured over several hours while irradiating with blue light. Likewise, the change in mechanical properties-determined through oscillatory shear rheology experiments-is assessed as a function of polyviologen concentration. Finally, an artificial molecular muscle is fabricated using the best-performing hydrogel composition, and its ability to perform work, while irradiated, is demonstrated by lifting a small weight. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Bases moleculares de alfa-talasemia en la Argentina

    Directory of Open Access Journals (Sweden)

    Karen G Scheps

    2015-04-01

    Full Text Available La α-talasemia, es uno de los desórdenes hereditarios más frecuentes mundialmente. Al presente, el diagnóstico molecular es la única herramienta que permite el diagnóstico certero. El propósito de este trabajo fue caracterizar las bases moleculares de estos síndromes en nuestro medio, y establecer relaciones genotipo-fenotipo. Mediante la complementación de distintas técnicas de biología molecular e hibridación fluorescente in situ (FISH, se logró poner en evidencia la presencia de mutaciones α-talasémicas en 145 de 184 (78.8% pacientes estudiados con perfil hematológico compatible con α-talasemia. Dentro de este grupo, las deleciones correspondieron al defecto genético más frecuente, prevaleciendo la mutación -α3.7 en genotipos heterocigotas y homocigotas. Asimismo, en pacientes con fenotipo α0 las deleciones prevalentes fueron -MED y -CAL/CAMP. Este estudio permitió también describir una deleción de la región sub-telomérica en un paciente con α-talasemia y retraso mental. En el 7.6% de los pacientes caracterizados clínicamente como posibles α-talasémicos (microcitosis con valores de Hb A2 inferiores al 3.5%, se hallaron mutaciones β-talasémicas en estado heterocigota. Se lograron establecer perfiles hematológicos asociados a los genotipos α+ y α0 para pacientes adultos y niños. Esperamos que este trabajo pueda servir como guía para reconocer posibles portadores α-talasémicos. También permite destacar el trabajo en conjunto de médicos hematólogos, el laboratorio (bioquímico y de biología molecular y de los médicos genetistas, con el fin de proporcionar adecuado consejo genético.

  14. dK/da effects on the SCC growth rates of nickel base alloys in high-temperature water

    Science.gov (United States)

    Chen, Kai; Wang, Jiamei; Du, Donghai; Andresen, Peter L.; Zhang, Lefu

    2018-05-01

    The effect of dK/da on crack growth behavior of nickel base alloys has been studied by conducting stress corrosion cracking tests under positive and negative dK/da loading conditions on Alloys 690, 600 and X-750 in high temperature water. Results indicate that positive dK/da accelerates the SCC growth rates, and the accelerating effect increases with dK/da and the initial CGR. The FRI model was found to underestimate the dK/da effect by ∼100X, especially for strain hardening materials, and this underscores the need for improved insight and models for crack tip strain rate. The effect of crack tip strain rate and dK/dt in particular can explain the dK/da accelerating effect.

  15. Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

    Science.gov (United States)

    Lee, Jonghwan; Kim, Soonhag

    2016-01-01

    The fluorescence monitoring system for examining endogenous microRNA (miRNA) activity in cellular level provides crucial information on not only understanding a critical role of miRNA involving a variety of biological processes, but also evaluating miRNA expression patterns in a noninvasive manner. In this protocol, we report the details of a new procedure for a molecular beacon-based miRNA monitoring system, which includes the illustration scheme for miRNA detection strategy, exogenous miRNA detection, and measurement of endogenous miRNA expression level during neurogenesis. The fluorescence signal of miR-124a beacon quenched by BHQ2 was gradually recovered as increasing concentration of the miR-124a in tube. The functional work of miR-124a beacon was examined in intracellular environment, allowing for the internalization of the miR-124a beacon by lipofectamine, which resulted in activated fluorescent signals of the miR-124a beacon in the HeLa cells after the addition of synthetic miR-124a. The endogenous miR-124a expression level was detected by miR-124a beacon system during neurogenesis, showing brighter fluorescence intensity in cytoplasmic area of P19 cells after induction of neuronal differentiation by retinoic acid. The molecular beacon based-miRNA detection technique could be applicable to the simultaneous visualization of a variety of miRNA expression patterns using different fluorescence dyes. For the study of examining endogenous miRNA expression level using miRNA-beacon system, if cellular differentiation step is already prepared, transfection step of miR-124a beacon into P19 cells, and acquisition of activated fluorescence signal measured by confocal microscope can be conducted approximately within 6 h.

  16. [Applicability of the da Vinci robotic system in the skull base surgical approach. Preclinical investigation].

    Science.gov (United States)

    Fernandez-Nogueras Jimenez, Francisco J; Segura Fernandez-Nogueras, Miguel; Jouma Katati, Majed; Arraez Sanchez, Miguel Ángel; Roda Murillo, Olga; Sánchez Montesinos, Indalecio

    2015-01-01

    The role of robotic surgery is well established in various specialties such as urology and general surgery, but not in others such as neurosurgery and otolaryngology. In the case of surgery of the skull base, it has just emerged from an experimental phase. To investigate possible applications of the da Vinci surgical robot in transoral skull base surgery, comparing it with the authors' experience using conventional endoscopic transnasal surgery in the same region. A transoral transpalatal approach to the nasopharynx and medial skull base was performed on 4 cryopreserved cadaver heads. We used the da Vinci robot, a 30° standard endoscope 12mm thick, dual camera and dual illumination, Maryland forceps on the left terminal and curved scissors on the right, both 8mm thick. Bone drilling was performed manually. For the anatomical study of this region, we used 0.5cm axial slices from a plastinated cadaver head. Various skull base structures at different depths were reached with relative ease with the robot terminals Transoral robotic surgery with the da Vinci system provides potential advantages over conventional endoscopic transnasal surgery in the surgical approach to this region. Copyright © 2014 Sociedad Española de Neurocirugía. Published by Elsevier España. All rights reserved.

  17. Light-operated machines based on threaded molecular structures.

    Science.gov (United States)

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  18. Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Maria Françoise Bayer

    2013-01-01

    Full Text Available In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma plays pivotal roles in the orchestration of development, defence responses and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialised domains of the endoplasmic reticulum and the plasma membrane. PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalisation or screening of random cDNAs, only few PD proteins had been conclusively identified and characterised. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on free PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD associated proteins.

  19. Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

    Science.gov (United States)

    Salmon, Magali S; Bayer, Emmanuelle M F

    2012-01-01

    In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma) plays pivotal roles in the orchestration of development, defence responses, and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialized domains of the endoplasmic reticulum (ER) and the plasma membrane (PM). PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalization, or screening of random cDNAs, only few PD proteins had been conclusively identified and characterized. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on "free" PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic-based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD-associated proteins.

  20. POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

    Science.gov (United States)

    Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

    2015-12-01

    We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

  1. Photoacoustic-based approach to surgical guidance performed with and without a da Vinci robot

    Science.gov (United States)

    Gandhi, Neeraj; Allard, Margaret; Kim, Sungmin; Kazanzides, Peter; Lediju Bell, Muyinatu A.

    2017-12-01

    Death and paralysis are significant risks of modern surgeries, caused by injury to blood vessels and nerves hidden by bone and other tissue. We propose an approach to surgical guidance that relies on photoacoustic (PA) imaging to determine the separation between these critical anatomical features and to assess the extent of safety zones during surgical procedures. Images were acquired as an optical fiber was swept across vessel-mimicking targets, in the absence and presence of teleoperation with a research da Vinci Surgical System. Vessel separation distances were measured directly from PA images. Vessel positions were additionally recorded based on the fiber position (calculated from the da Vinci robot kinematics) that corresponded to an observed PA signal, and these recordings were used to indirectly measure vessel separation distances. Amplitude- and coherence-based beamforming were used to estimate vessel separations, resulting in 0.52- to 0.56-mm mean absolute errors, 0.66- to 0.71-mm root-mean-square errors, and 65% to 68% more accuracy compared to fiber position measurements obtained through the da Vinci robot kinematics. Similar accuracy was achieved in the presence of up to 4.5-mm-thick ex vivo tissue. Results indicate that PA image-based measurements of the separation among anatomical landmarks could be a viable method for real-time path planning in multiple interventional PA applications.

  2. A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

    Science.gov (United States)

    Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

    2016-02-01

    Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. The influence of different PAST-based subspace trackers on DaPT parameter estimation

    Science.gov (United States)

    Lechtenberg, M.; Götze, J.

    2012-09-01

    In the context of parameter estimation, subspace-based methods like ESPRIT have become common. They require a subspace separation e.g. based on eigenvalue/-vector decomposition. In time-varying environments, this can be done by subspace trackers. One class of these is based on the PAST algorithm. Our non-linear parameter estimation algorithm DaPT builds on-top of the ESPRIT algorithm. Evaluation of the different variants of the PAST algorithm shows which variant of the PAST algorithm is worthwhile in the context of frequency estimation.

  4. Molecular biology-based diagnosis and therapy for pancreatic cancer

    International Nuclear Information System (INIS)

    Fujita, Hayato; Ohuchida, Kenoki; Mizumoto, Kazuhiro; Tanaka, Masao

    2011-01-01

    Mainly described are author's investigations of the title subject through clinical and basic diagnosis/therapeutic approach. Based on their consideration of carcinogenesis and pathological features of pancreatic cancer (PC), analysis of expression of cancer-related genes in clinically available samples like pancreatic juice and cells biopsied can result in attaining their purposes. Desmoplasia, a pathological feature of PC, possibly induces resistance to therapy and one of strategies is probably its suppression. Targeting stem cells of the mesenchyma as well as those of PC is also a strategy in future. Authors' studies have revealed that quantitation of hTERT (coding teromerase) mRNA levels in PC cells micro-dissected from cytological specimens is an accurate molecular biological diagnostic method applicable clinically. Other cancer-related genes are also useful for the diagnosis and mucin (MUC) family genes are shown to be typical ones for differentiating the precancerous PC, PC and chronic pancreatisis. Efficacy of standard gemcitabine chemotherapy can be individualized with molecular markers concerned to metabolism of the drug like dCK. Radiotherapy/radio-chemotherapy are not so satisfactory for PC treatment now. Authors have found elevated MMP-2 expression and HGF/c-Met signal activation in irradiated PC cells, which can increase the invasive capability; and stimulation of phosphorylation and activation of c-Met/MARK in co-culture of irradiated PC cells with messenchymal cells from PC, which possibly leads to progression of malignancy of PC through their interaction, of which suppression, therefore, can be a new approach to increase the efficacy of radiotherapy. Authors are making effort to introducing adenovirus therapy in clinic; exempli gratia (e.g.), the virus carrying wild type p53, a cancer-suppressive gene, induces apoptosis of PC cells often having its mutated gene. (T.T.)

  5. Effect of furan π-bridge on the photovoltaic performance of D-A copolymers based on bi(alkylthio-thienyl)benzodithiophene and fluorobenzotriazole

    Institute of Scientific and Technical Information of China (English)

    Tinghai Yan; Haijun Bin; Yankang Yang; Lingwei Xue; Zhi-Guo Zhang; Yongfang Li

    2017-01-01

    The medium band gap donor-acceptor(D-A) copolymer J61 based on bi(alkylthio-thienyl)benzodithiophene as donor unit and fluorobenzotriazole as acceptor unit and thiophene as π-bridge has demonstrated excellent photovoltaic performance as donor material in nonfullerene polymer solar cells(PSCs) with narrow bandgap n-type organic semiconductor ITIC as acceptor.For studying the effect of π-bridges on the photovoltaic performance of the D-A copolymers,here we synthesized a new D-A copolymer J61-F based on the same donor and acceptor units as J61 but with furan π-bridges instead of thiophene.J61-F possesses a deeper the highest occupied molecular orbital(HOMO) level at-5.45 eV in comparison with that(-5.32 eV) of J61.The non-fullerene PSCs based on J61-F:ITIC exhibited a maximum power conversion efficiency(PCE) of 8.24%with a higher open-circuit voltage(Voc) of 0.95 V,which is benefitted from the lower-lying HOMO energy level of J61-F donor material.The results indicate that main chain engineering by changing π-bridges is another effective way to tune the electronic energy levels of the conjugated D-A copolymers for the application as donor materials in non-fullerene PSCs.

  6. Molecular dosimetry based on radiation induced degradation of polyisobutylene

    International Nuclear Information System (INIS)

    Joerkov Thomsen, Kristina

    1999-01-01

    This project investigates the possibility of qualitative measurement of radiation doses through detection of changes in the average molecular weight in the polymer Polyisobutylene (PIB). Changes in molecular weight and molecular weight distribution is detected by Gel Permeation Chromatography (GPC). The aim of the project is to decide whether or not it is possible to determine a quality difference between α-radiation ( 241 Am, 5,5 MeV) and γ-radiation ( 60 Co, 1,25 MeV) in the dose range 0,5 to 10 kGy by irradiation of PIB. Irradiation with 60 Co changes the average number molecular weight M n by 12% per kGy and the average weight molecular weight M w by 23% per kGy. The presence of antioxidant in the irradiated sample inhibits a change in average molecular weight by 5% and 16% for M n and M w respectively. (au)

  7. Determinação dos multiplicadores da matriz de contabilidade social, da indústria de base florestal paranaense - 1998

    Directory of Open Access Journals (Sweden)

    Ricardo Kureski

    2006-12-01

    Full Text Available Este artigo tem como objetivo mensurar o impacto do aumento da demanda final da indústria de base florestal. Como instrumento de análise utiliza-se a matriz de contabilidade social do Estado do Paraná de 1998. Foi necessário calcular o multiplicares da matriz. Os efeitos de uma injeção nas variáveis exógenas sobre os segmentos de Madeira e Mobiliário e de Papel e Papelão resultaram em choques de demanda mais intensos dentro do próprio setor. Observa-se que o ramo de Madeira e Mobiliário tem maiores ligações com as atividades relativas ao setor terciário; já o segmento de Papel e Papelão, com atividades que necessitam embalagem. Conclui-se que, apesar da agregação das atividades econômicas da matriz de contabilidade social paranaense, foi possível identificar os principais impactos decorrentes do aumento da demanda final.The present article aims at measuring the final demand impact on the forest-based industry by using the 1998 State of Paraná social accounting matrix as the analysis tool. We also had to calculate the matrix multipliers. The increased effects of exogenous activity on the Wood/Furniture and Paper/Pulp activities brought a more intense demand shock to that sector. We noticed that the Wood and Furniture activity is mostly connected with the tertiary sector activities, while the Paper and Pulp activity is mostly connected with activities that need packing. Finally, we could identify the main impacts originated by an increased final demand in spite of the reduction in the number of Paraná Social Accounting Matrix economic activities.

  8. Molecularly Imprinted Polypyrrole Based Impedimentric Sensor for Theophylline Determination

    International Nuclear Information System (INIS)

    Ratautaite, Vilma; Janssens, Stoffel D.; Haenen, Ken; Nesládek, Milos; Ramanaviciene, Almira; Baleviciute, Ieva; Ramanavicius, Arunas

    2014-01-01

    Highlights: • Sensor based on polypyrrole imprinted by theophylline (MIP) deposited on oxygen terminated boron-doped nanocrystalline diamond was developed. • This structure was applied as impedimetric sensor sensitive for theophylline. • Optimal polymer formation conditions suitable for MIP formation were elaborated. • Some analytical parameters were determined and evaluated. - Abstract: In this study development of impedimetric sensor based on oxygen terminated boron-doped nanocrystalline diamond (B:NCD:O) modified with theophylline imprinted polypyrrole is described. Hydrogen peroxide induced chemical formation of polypyrrole molecularly imprinted by theophylline was applied for the modification of conducting silicon substrate covered by B:NCD:O film. Non-imprinted polypyrrole layer was formed on similar substrate in order to prove efficiency of imprinted polypyrrole. Electrochemical impedance spectroscopy was applied for the evaluation of analyte-induced changes in electrochemical capacitance/resistance. The impact of polymerization duration on the capacitance of impedimetric sensor was estimated. A different impedance behavior was observed at different ratio of polymerized monomer and template molecule in the polymerization media. The influence of ethanol as additive to polymerization media on registered changes in capacitance/resistance was evaluated. Degradation of sensor stored in buffer solution was evaluated

  9. Pathological Bases for a Robust Application of Cancer Molecular Classification

    Directory of Open Access Journals (Sweden)

    Salvador J. Diaz-Cano

    2015-04-01

    Full Text Available Any robust classification system depends on its purpose and must refer to accepted standards, its strength relying on predictive values and a careful consideration of known factors that can affect its reliability. In this context, a molecular classification of human cancer must refer to the current gold standard (histological classification and try to improve it with key prognosticators for metastatic potential, staging and grading. Although organ-specific examples have been published based on proteomics, transcriptomics and genomics evaluations, the most popular approach uses gene expression analysis as a direct correlate of cellular differentiation, which represents the key feature of the histological classification. RNA is a labile molecule that varies significantly according with the preservation protocol, its transcription reflect the adaptation of the tumor cells to the microenvironment, it can be passed through mechanisms of intercellular transference of genetic information (exosomes, and it is exposed to epigenetic modifications. More robust classifications should be based on stable molecules, at the genetic level represented by DNA to improve reliability, and its analysis must deal with the concept of intratumoral heterogeneity, which is at the origin of tumor progression and is the byproduct of the selection process during the clonal expansion and progression of neoplasms. The simultaneous analysis of multiple DNA targets and next generation sequencing offer the best practical approach for an analytical genomic classification of tumors.

  10. Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer

    Directory of Open Access Journals (Sweden)

    Stobiecki Maciej

    2009-07-01

    Full Text Available Abstract Background Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry. Methods Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women. Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves. Results We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity. Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0

  11. Avaliação de marcadores moleculares associados à qualidade da carne de bovinos Simental Sul Africano x Nelore

    OpenAIRE

    Roberta Doriguello Fonseca

    2016-01-01

    No Brasil, a perspectiva de aumento do volume de exportações e a exigência dos diferentes mercados faz com que a adaptação da cadeia produtiva da carne seja necessária, assim como a mudança de conceitos e critérios de seleção dos animais, de forma a melhorar as características consideradas pelo consumidor como de primeira importância: aparência e a palatabilidade. Porém existem diversos fatores que podem influenciar na qualidade da carne: sexo, raça (genética), idade, nutrição e estresse dura...

  12. Molecular clips based on propanediurea : synthesis and physical properties

    NARCIS (Netherlands)

    Jansen, Robertus Johannes

    2002-01-01

    This thesis describes the synthesis and physical properties of a series of molecular clips derived from the concave molecule propanediurea. These molecular clips are cavity-containing receptors that can bind a variety of aromatic guests. This binding is a result of hydrogen bonding and pi-pi

  13. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  14. A low molecular weight zinc{sup 2+}-dipicolylamine-based probe detects apoptosis during tumour treatment better than an annexin V-based probe

    Energy Technology Data Exchange (ETDEWEB)

    Palmowski, Karin [RWTH-Aachen University, Department of Experimental Molecular Imaging, Aachen (Germany); University of Heidelberg, Department of Pneumology, Thoraxklinik Heidelberg, Heidelberg (Germany); Rix, Anne; Lederle, Wiltrud; Kiessling, Fabian [RWTH-Aachen University, Department of Experimental Molecular Imaging, Aachen (Germany); Behrendt, Florian F. [RWTH-Aachen University, Department of Nuclear Medicine, Aachen (Germany); Mottaghy, Felix M. [RWTH-Aachen University, Department of Nuclear Medicine, Aachen (Germany); Maastricht University Medical Center, Department of Nuclear Medicine, Maastricht (Netherlands); Gray, Brian D. [Molecular Targeting Technologies, Inc., West Chester, PA (United States); Pak, Koon Y. [University Medical Center Heidelberg, Academic Radiology Baden-Baden, Diagnostic and Interventional Radiology, Heidelberg (Germany); Palmowski, Moritz [RWTH-Aachen University, Department of Experimental Molecular Imaging, Aachen (Germany); RWTH-Aachen University, Department of Nuclear Medicine, Aachen (Germany); University Medical Center Heidelberg, Academic Radiology Baden-Baden, Diagnostic and Interventional Radiology, Heidelberg (Germany)

    2014-02-15

    Molecular imaging of apoptosis is frequently discussed for monitoring cancer therapies. Here, we compare the low molecular weight phosphatidylserine-targeting ligand zinc{sup 2+}-dipicolylamine (Zn{sup 2+}-DPA) with the established but reasonably larger protein annexin V. Molecular apoptosis imaging with the fluorescently labelled probes annexin V (750 nm, 36 kDa) and Zn{sup 2+}-DPA (794 nm, 1.84 kDa) was performed in tumour-bearing mice (A431). Three animal groups were investigated: untreated controls and treated tumours after 1 or 4 days of anti-angiogenic therapy (SU11248). Additionally, μPET with {sup 18} F-FDG was performed. Imaging data were displayed as tumour-to-muscle ratio (TMR) and validated by quantitative immunohistochemistry. Compared with untreated control tumours, TUNEL staining indicated significant apoptosis after 1 day (P < 0.05) and 4 days (P < 0.01) of treatment. Concordantly, Zn{sup 2+}-DPA uptake increased significantly after 1 day (P < 0.05) and 4 days (P < 0.01). Surprisingly, annexin V failed to detect significant differences between control and treated animals. Contrary to the increasing uptake of Zn{sup 2+}-DPA, {sup 18} F-FDG tumour uptake decreased significantly at days 1 (P < 0.05) and 4 (P < 0.01). Increase in apoptosis during anti-angiogenic therapy was detected significantly better with the low molecular weight probe Zn{sup 2+}-DPA than with the annexin V-based probe. Additionally, significant treatment effects were detectable as early using Zn{sup 2+}-DPA as with measurements of the glucose metabolism using {sup 18} F-FDG. (orig.)

  15. UPAR targeted molecular imaging of cancers with small molecule-based probes.

    Science.gov (United States)

    Ding, Feng; Chen, Seng; Zhang, Wanshu; Tu, Yufeng; Sun, Yao

    2017-10-15

    Molecular imaging can allow the non-invasive characterization and measurement of biological and biochemical processes at the molecular and cellular levels in living subjects. The imaging of specific molecular targets that are associated with cancers could allow for the earlier diagnosis and better treatment of diseases. Small molecule-based probes play prominent roles in biomedical research and have high clinical translation ability. Here, with an emphasis on small molecule-based probes, we review some recent developments in biomarkers, imaging techniques and multimodal imaging in molecular imaging and highlight the successful applications for molecular imaging of cancers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Sensitive determination of citrinin based on molecular imprinted electrochemical sensor

    Energy Technology Data Exchange (ETDEWEB)

    Atar, Necip [Department of Chemical Engineering, Faculty of Engineering, Pamukkale University, Denizli (Turkey); Yola, Mehmet Lütfi, E-mail: mehmetyola@gmail.com [Department of Metallurgical and Materials Engineering, Faculty of Engineering, Sinop University, Sinop (Turkey); Eren, Tanju [Department of Chemical Engineering, Faculty of Engineering, Pamukkale University, Denizli (Turkey)

    2016-01-30

    Graphical abstract: - Highlights: • Citrinin-imprinted electrochemical sensor is developed for the sensitive detection of citrinin. • The nanomaterial and citrinin-imprinted surfaces were characterized by several methods. • Citrinin-imprinted electrochemical sensor is sensitive and selective in analysis of food. • Citrinin-imprinted electrochemical sensor is preferred to the other methods. - Abstract: In this report, a novel molecular imprinted voltammetric sensor based on glassy carbon electrode (GCE) modified with platinum nanoparticles (PtNPs) involved in a polyoxometalate (H{sub 3}PW{sub 12}O{sub 40}, POM) functionalized reduced graphene oxide (rGO) was prepared for the determination of citrinin (CIT). The developed surfaces were characterized by using scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) method. CIT imprinted GCE was prepared via electropolymerization process of 80.0 mM pyrrole as monomer in the presence of phosphate buffer solution (pH 6.0) containing 20.0 mM CIT. The linearity range and the detection limit of the developed method were calculated as 1.0 × 10{sup −12}–1.0 × 10{sup −10} M and 2.0 × 10{sup −13} M, respectively. In addition, the voltammetric sensor was applied to rye samples. The stability and selectivity of the voltammetric sensor were also reported.

  17. Sensitive determination of citrinin based on molecular imprinted electrochemical sensor

    International Nuclear Information System (INIS)

    Atar, Necip; Yola, Mehmet Lütfi; Eren, Tanju

    2016-01-01

    Graphical abstract: - Highlights: • Citrinin-imprinted electrochemical sensor is developed for the sensitive detection of citrinin. • The nanomaterial and citrinin-imprinted surfaces were characterized by several methods. • Citrinin-imprinted electrochemical sensor is sensitive and selective in analysis of food. • Citrinin-imprinted electrochemical sensor is preferred to the other methods. - Abstract: In this report, a novel molecular imprinted voltammetric sensor based on glassy carbon electrode (GCE) modified with platinum nanoparticles (PtNPs) involved in a polyoxometalate (H_3PW_1_2O_4_0, POM) functionalized reduced graphene oxide (rGO) was prepared for the determination of citrinin (CIT). The developed surfaces were characterized by using scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) method. CIT imprinted GCE was prepared via electropolymerization process of 80.0 mM pyrrole as monomer in the presence of phosphate buffer solution (pH 6.0) containing 20.0 mM CIT. The linearity range and the detection limit of the developed method were calculated as 1.0 × 10"−"1"2–1.0 × 10"−"1"0 M and 2.0 × 10"−"1"3 M, respectively. In addition, the voltammetric sensor was applied to rye samples. The stability and selectivity of the voltammetric sensor were also reported.

  18. Sensitive determination of citrinin based on molecular imprinted electrochemical sensor

    Science.gov (United States)

    Atar, Necip; Yola, Mehmet Lütfi; Eren, Tanju

    2016-01-01

    In this report, a novel molecular imprinted voltammetric sensor based on glassy carbon electrode (GCE) modified with platinum nanoparticles (PtNPs) involved in a polyoxometalate (H3PW12O40, POM) functionalized reduced graphene oxide (rGO) was prepared for the determination of citrinin (CIT). The developed surfaces were characterized by using scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) method. CIT imprinted GCE was prepared via electropolymerization process of 80.0 mM pyrrole as monomer in the presence of phosphate buffer solution (pH 6.0) containing 20.0 mM CIT. The linearity range and the detection limit of the developed method were calculated as 1.0 × 10-12-1.0 × 10-10 M and 2.0 × 10-13 M, respectively. In addition, the voltammetric sensor was applied to rye samples. The stability and selectivity of the voltammetric sensor were also reported.

  19. MrGrid: a portable grid based molecular replacement pipeline.

    Directory of Open Access Journals (Sweden)

    Jason W Schmidberger

    Full Text Available BACKGROUND: The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. METHODOLOGY/PRINCIPAL FINDINGS: MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. CONCLUSIONS: MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success.

  20. A CZT-based blood counter for quantitative molecular imaging.

    Science.gov (United States)

    Espagnet, Romain; Frezza, Andrea; Martin, Jean-Pierre; Hamel, Louis-André; Lechippey, Laëtitia; Beauregard, Jean-Mathieu; Després, Philippe

    2017-12-01

    Robust quantitative analysis in positron emission tomography (PET) and in single-photon emission computed tomography (SPECT) typically requires the time-activity curve as an input function for the pharmacokinetic modeling of tracer uptake. For this purpose, a new automated tool for the determination of blood activity as a function of time is presented. The device, compact enough to be used on the patient bed, relies on a peristaltic pump for continuous blood withdrawal at user-defined rates. Gamma detection is based on a 20 × 20 × 15 mm 3 cadmium zinc telluride (CZT) detector, read by custom-made electronics and a field-programmable gate array-based signal processing unit. A graphical user interface (GUI) allows users to select parameters and easily perform acquisitions. This paper presents the overall design of the device as well as the results related to the detector performance in terms of stability, sensitivity and energy resolution. Results from a patient study are also reported. The device achieved a sensitivity of 7.1 cps/(kBq/mL) and a minimum detectable activity of 2.5 kBq/ml for 18 F. The gamma counter also demonstrated an excellent stability with a deviation in count rates inferior to 0.05% over 6 h. An energy resolution of 8% was achieved at 662 keV. The patient study was conclusive and demonstrated that the compact gamma blood counter developed has the sensitivity and the stability required to conduct quantitative molecular imaging studies in PET and SPECT.

  1. Symbol Synchronization for Diffusion-Based Molecular Communications.

    Science.gov (United States)

    Jamali, Vahid; Ahmadzadeh, Arman; Schober, Robert

    2017-12-01

    Symbol synchronization refers to the estimation of the start of a symbol interval and is needed for reliable detection. In this paper, we develop several symbol synchronization schemes for molecular communication (MC) systems where we consider some practical challenges, which have not been addressed in the literature yet. In particular, we take into account that in MC systems, the transmitter may not be equipped with an internal clock and may not be able to emit molecules with a fixed release frequency. Such restrictions hold for practical nanotransmitters, e.g., modified cells, where the lengths of the symbol intervals may vary due to the inherent randomness in the availability of food and energy for molecule generation, the process for molecule production, and the release process. To address this issue, we develop two synchronization-detection frameworks which both employ two types of molecule. In the first framework, one type of molecule is used for symbol synchronization and the other one is used for data detection, whereas in the second framework, both types of molecule are used for joint symbol synchronization and data detection. For both frameworks, we first derive the optimal maximum likelihood (ML) symbol synchronization schemes as performance upper bounds. Since ML synchronization entails high complexity, for each framework, we also propose three low-complexity suboptimal schemes, namely a linear filter-based scheme, a peak observation-based scheme, and a threshold-trigger scheme, which are suitable for MC systems with limited computational capabilities. Furthermore, we study the relative complexity and the constraints associated with the proposed schemes and the impact of the insertion and deletion errors that arise due to imperfect synchronization. Our simulation results reveal the effectiveness of the proposed synchronization schemes and suggest that the end-to-end performance of MC systems significantly depends on the accuracy of the symbol

  2. Program and abstracts of the 25. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Programa e resumos da 25. Reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    The meeting was about biochemistry and molecular biology.In this meeting it was also discussed the following subjects: biotechnology, metabolism, enzymes, proteins, immunology, drugs and others related topics.

  3. Uso da bioinformática na diferenciação molecular da Entamoeba histolytica e Entamoeba díspar - DOI: 10.4025/actascihealthsci.v30i2.2375 Molecular discrimination of Entamoeba histolytica and Entamoeba dispar by bioinformatics resources - DOI: 10.4025/actascihealthsci.v30i2.2375

    Directory of Open Access Journals (Sweden)

    Débora Sommer

    2008-12-01

    Full Text Available Amebíase invasiva, causada por Entamoeba histolytica, é microscopicamente indistinguível da espécie não-patogênica Entamoeba dispar. Com auxílio de ferramentas de bioinformática, objetivou-se diferenciar Entamoeba histolytica e Entamoeba dispar por técnicas moleculares. A análise foi realizada a partir do banco de dados da National Center for Biotechnology Information; pela pesquisa de similaridade de sequências, elegeu-se o gene da cisteína sintase. Um par de primer foi desenhado (programa Web Primer e foi selecionada a enzima de restrição TaqI (programa Web Cutter. Após a atuação da enzima, o fragmento foi dividido em dois, um com 255 pb e outro com 554 pb, padrão característico da E. histolytica. Na ausência de corte, o fragmento apresentou o tamanho de 809 pb, referente à E. dispar.Under microscopic conditions, the invasive Entamoeba histolytica is indistinguishable from the non-pathogenic species Entamoeba dispar. In this way, the present study was carried out to determine a molecular strategy for discriminating both species by the mechanisms of bioinformatics. The gene cysteine synthetase was considered for such a purpose by using the resources of the National Center for Biotechnology Information data bank in the search for similarities in the gene sequence. In this way, a primer pair was designed by the Web Primer program and the restriction enzyme TaqI was selected by the Web Cutter software program. The DNA fragment had a size of 809 bp before cutting, which is consistent with E. dispar. The gene fragment was partitioned in a first fragment with 255 bp and a second one with 554 bp, which is similar to the genetic characteristics of E. histolytica.

  4. O Programa Inovativo da Pequena Empresa (PIPE da FAPESP como indutor do desenvolvimento de micro e pequenas empresas de base tecnológica

    Directory of Open Access Journals (Sweden)

    Victor Wolowski Kenski

    2017-09-01

    Full Text Available Resumo Este texto analisa a relevância do apoio ao desenvolvimento de micro e pequenas empresas de base tecnológica na forma de um “pacote” de recursos e capacidades estratégicos incorporados em um curto espaço de tempo, por meio do programa PIPE da FAPESP. A abordagem adotada foi a da Visão Baseada em Recursos (VBR dado o foco do estudo. Adotou-se a metodologia qualitativa com a aplicação da análise de conteúdo. Os dados foram levantados com base em entrevistas com um roteiro estruturado com perguntas abertas junto aos sócios/gestores de 10 empresas de base tecnológica divididas em dois grupos, um deles constituído por empresas beneficiadas pelo PIPE e o outro por aquelas que utilizaram recursos próprios. A intenção foi comparar a sua evolução. Os resultados do estudo indicaram que o apoio do PIPE foi decisivo para favorecer o desenvolvimento das empresas beneficiadas por ele. Um dos ganhos relevantes foi o encurtamento do tempo do caminho percorrido para a disponibilização dos recursos complementares, como decorrência da combinação produtiva dos recursos e capacidades pré-existentes nas empresas com aqueles obtidos por meio do programa. Uma constatação importante foi que, para as empresas terem crescido no mercado de base tecnológica, independentemente da ajuda do PIPE, foi decisivo possuírem inicialmente uma tecnologia diferenciada, os sócios/gestores terem uma visão clara dos seus mercados e voltados à criação de valor para os seus produtos e serviços. A limitação da pesquisa está na seleção de pequenas empresas de base tecnológica com produtos muito distintos dificultando comparações sobre sucessos.

  5. Determinants of molecular marker based classification of rice (Oryza ...

    African Journals Online (AJOL)

    mr devi singh

    2015-01-07

    Jan 7, 2015 ... 1Molecular Biology Laboratory, Department of Genetics and Plant Breeding, SVP University of Agriculture and ... Basmati and non-Basmati rice adapted to different agro- ecological ..... acid soils in southern New South Wales?

  6. Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target

    Directory of Open Access Journals (Sweden)

    Yu-Jung Kim

    2017-03-01

    Full Text Available The tegument, representing the membrane-bound outer surface of platyhelminth parasites, plays an important role for the regulation of the host immune response and parasite survival. A comprehensive understanding of tegumental proteins can provide drug candidates for use against helminth-associated diseases, such as clonorchiasis caused by the liver fluke Clonorchis sinensis. However, little is known regarding the physicochemical properties of C. sinensis teguments. In this study, a novel 20.6-kDa tegumental protein of the C. sinensis adult worm (CsTegu20.6 was identified and characterized by molecular and in silico methods. The complete coding sequence of 525 bp was derived from cDNA clones and encodes a protein of 175 amino acids. Homology search using BLASTX showed CsTegu20.6 identity ranging from 29% to 39% with previously-known tegumental proteins in C. sinensis. Domain analysis indicated the presence of a calcium-binding EF-hand domain containing a basic helix-loop-helix structure and a dynein light chain domain exhibiting a ferredoxin fold. We used a modified method to obtain the accurate tertiary structure of the CsTegu20.6 protein because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. A refined CsTegu20.6 structure was used to identify a potential CsTegu20.6 inhibitor based on protein structure-compound interaction analysis. The recombinant proteins were expressed in Escherichia coli and purified by nickel-nitrilotriacetic acid affinity chromatography. In C. sinensis, CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. Immunohistochemistry revealed that CsTegu20.6 localized to the surface of the tegument in the adult fluke. Collectively, our results

  7. Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target.

    Science.gov (United States)

    Kim, Yu-Jung; Yoo, Won Gi; Lee, Myoung-Ro; Kang, Jung-Mi; Na, Byoung-Kuk; Cho, Shin-Hyeong; Park, Mi-Yeoun; Ju, Jung-Won

    2017-03-04

    The tegument, representing the membrane-bound outer surface of platyhelminth parasites, plays an important role for the regulation of the host immune response and parasite survival. A comprehensive understanding of tegumental proteins can provide drug candidates for use against helminth-associated diseases, such as clonorchiasis caused by the liver fluke Clonorchis sinensis . However, little is known regarding the physicochemical properties of C. sinensis teguments. In this study, a novel 20.6-kDa tegumental protein of the C. sinensis adult worm (CsTegu20.6) was identified and characterized by molecular and in silico methods. The complete coding sequence of 525 bp was derived from cDNA clones and encodes a protein of 175 amino acids. Homology search using BLASTX showed CsTegu20.6 identity ranging from 29% to 39% with previously-known tegumental proteins in C. sinensis . Domain analysis indicated the presence of a calcium-binding EF-hand domain containing a basic helix-loop-helix structure and a dynein light chain domain exhibiting a ferredoxin fold. We used a modified method to obtain the accurate tertiary structure of the CsTegu20.6 protein because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. A refined CsTegu20.6 structure was used to identify a potential CsTegu20.6 inhibitor based on protein structure-compound interaction analysis. The recombinant proteins were expressed in Escherichia coli and purified by nickel-nitrilotriacetic acid affinity chromatography. In C. sinensis , CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. Immunohistochemistry revealed that CsTegu20.6 localized to the surface of the tegument in the adult fluke. Collectively, our results contribute to a

  8. Análise comparativa da base social da Medicina e Enfermagem no Brasil entre os anos de 2000 e 2010

    Directory of Open Access Journals (Sweden)

    Lucas Wan Der Maas

    2018-03-01

    Full Text Available O objetivo deste artigo é analisar as alterações ocorridas durante os anos 2000 na base social das profissões da Medicina e Enfermagem no Brasil, como resultado da expansão do Ensino Superior iniciada na segunda metade dos anos 1990. De um lado, analisa descritivamente a base social de recrutamento valendo-se dos dados do questionário socioeconômico do Exame Nacional de Desempenho dos Estudantes de 2004 e 2010, referentes aos ingressantes e concluintes dos cursos de Medicina e Enfermagem. De outro, analisa a base social dos habilitados nas profissões valendo-se dos dados do Censo Demográfico do Instituto Brasileiro de Geografia e Estatística de 2000 e 2010. Os resultados mostram que ocorreu ampliação da base social de recrutamento das duas profissões, sobretudo pelo crescimento do alunado proveniente de famílias de baixa renda e que se declararam negros/as, pardos/as e mulato/as. Já a base social dos habilitados passou por uma reconfiguração, caracterizada pelo rejuvenescimento da população e pela diminuição das recompensas no mercado de trabalho. Ambos os processos foram vivenciados de forma distinta entre e dentro das profissões, destacando a existência de diferenças na capacidade de cada grupo profissional em mobilizar recursos que são próprios do mundo profissional e que lhes podem garantir posições especiais no mercado de trabalho e na estrutura social.

  9. Identificação molecular da uva 'Goethe' de Urussanga - SC por marcadores microssatélites Molecular identification of the grapevine 'Goethe' from Urussanga (SC with microsatellite markers

    Directory of Open Access Journals (Sweden)

    Mariane Ruzza Schuck

    2010-09-01

    Full Text Available A variedade Goethe é símbolo da vitivinicultura da região de Urussanga, sul do Estado de Santa Catarina, a qual, atualmente, busca a Indicação Geográfica da Uva e do Vinho Goethe. Para isto, um dos requisitos necessários é a identificação precisa do material genético. Os marcadores microssatélites constituem a ferramenta molecular mais utilizada para a identificação varietal de videira em todo o mundo e têm a capacidade de produzir um perfil genético único para cada material vitícola. O objetivo deste trabalho foi caracterizar duas seleções de uva 'Goethe', presentes no município de Urussanga, por meio de marcadores moleculares microssatélites, visando a atender aos requisitos de denominação de origem e indicação de procedência controlada. A extração do DNA genômico foi realizada a partir de folhas jovens e ramos de nove acessos de cada seleção de 'Goethe Classica' e 'Goethe Primo' provenientes de uma coleção pública e de oito coleções privadas da região de Urussanga. Dez loci microssatélites VVS2, VVMD5, VVMD7, VVMD27, VrZAG62, VrZAG79, VVMD25, VVMD28, VVMD31 e VVMD32 foram genotipados através de eletroforese capilar. As análises realizadas mostraram que as duas variantes da uva 'Goethe' apresentaram um perfil molecular idêntico e único, isto é, representam a mesma variedade e sem nenhuma correspondência com variedades descritas anteriormente na literatura e nos bancos de dados consultados. As diferenças fenotípicas observadas provavelmente são devidas a mutações somáticas em regiões funcionais do genoma, fenômeno que dá origem aos clones em videira.'Goethe' grape is a symbol of the viticulture of Urussanga region, South of Santa Catarina State, which is currently claiming the geographical indication of the grape and wine Goethe. Microsatellite markers are the biotechnological tool most used for molecular identification of grapevine varieties worldwide. These markers have the potential of

  10. Congenital neutropenia: diagnosis, molecular bases and patient management

    Directory of Open Access Journals (Sweden)

    Chantelot Christine

    2011-05-01

    Full Text Available Abstract The term congenital neutropenia encompasses a family of neutropenic disorders, both permanent and intermittent, severe ( When neutropenia is detected, an attempt should be made to establish the etiology, distinguishing between acquired forms (the most frequent, including post viral neutropenia and auto immune neutropenia and congenital forms that may either be isolated or part of a complex genetic disease. Except for ethnic neutropenia, which is a frequent but mild congenital form, probably with polygenic inheritance, all other forms of congenital neutropenia are extremely rare and have monogenic inheritance, which may be X-linked or autosomal, recessive or dominant. About half the forms of congenital neutropenia with no extra-hematopoetic manifestations and normal adaptive immunity are due to neutrophil elastase (ELANE mutations. Some patients have severe permanent neutropenia and frequent infections early in life, while others have mild intermittent neutropenia. Congenital neutropenia may also be associated with a wide range of organ dysfunctions, as for example in Shwachman-Diamond syndrome (associated with pancreatic insufficiency and glycogen storage disease type Ib (associated with a glycogen storage syndrome. So far, the molecular bases of 12 neutropenic disorders have been identified. Treatment of severe chronic neutropenia should focus on prevention of infections. It includes antimicrobial prophylaxis, generally with trimethoprim-sulfamethoxazole, and also granulocyte-colony-stimulating factor (G-CSF. G-CSF has considerably improved these patients' outlook. It is usually well tolerated, but potential adverse effects include thrombocytopenia, glomerulonephritis, vasculitis and osteoporosis. Long-term treatment with G-CSF, especially at high doses, augments the spontaneous risk of leukemia in patients with congenital neutropenia.

  11. Influence of incorporation method of sulfated zirconia in MCM-41 molecular sieve; Influencia do metodo de incorporacao da zirconia sulfatada na peneira molecular MCM-41

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, C.E.; Santos, J.S.B.; Cavalcante, J.N.A.; Andrade, M.R.A.; Sousa, B.V., E-mail: eduardopereira.eq@gmail.com [Universidade Federal de Campina Grande (UFCG), PB (Brazil). Centro de Ciencia e Tecnologia

    2016-07-01

    Sulfated metal oxides and sulfated zirconia have attracted great attention in recent years due to its high catalytic activity. The sulfated zirconia has the function of assigning the acidic material, through the formation of Bronsted acids and Lewis sites. The incorporation of sulfated zirconia in MCM-41 molecular sieve was carried out through the techniques: dry and wet. The wet process involves the use of an excess of solution on the volume of the support pores. Therefore, the concentration of the metal precursor on the support depends on the solution concentration and the pore volume of the support. In the process of incorporating by dry, the volume of the solution containing the precursor does not exceed the pore volume of the support. After either procedure, the impregnated support must be dried in order to allow the precursor compound can be converted into a catalytically active phase. This study aims to evaluate two methods of incorporation of sulfated zirconia in the mesoporous molecular sieve MCM-41. The process of merger took for wet and dry impregnation. Through the XRD patterns it was possible to identify the presence of the hexagonal structure of the molecular sieve, as well as the tetragonal and monoclinic phases of zirconia. From the spectroscopic analysis in the infrared region to the method the wet, it was possible to identify the vibrational frequencies related to the merger of sulfated zirconia in the MCM-41 structure of the molecular sieve. (author)

  12. Estudos QSAR e Ancoragem Molecular de Inibidores da Atividade Biológica do Fator de Inibição da Migração dos Macrófagos (MIF

    Directory of Open Access Journals (Sweden)

    Alex Gutterres Taranto

    2012-08-01

    Full Text Available Cumarina e 4-Cromonas são promissores inibidores de fator inibição da migração de macrófagos (MIF, uma proteína envolvida em doenças inflamatórias, como artrite reumatóide e outras patologias. Estudos teóricos de QSAR e ancoragem molecular de um conjunto de compostos mostraram correlação com estudos experimentais. Os descritores doadores de ligação hidrogênio e momento dipolo total foram capazes de prever atividade inibitória de compostos contra o MIF (MIFi . Paralelamente, estudos de ancoragem molecular também foram capazes de identificar ligações hidrogênio e hidrofóbicas entre os ligantes e o MIF. Como resultado, ambas as metodologias mostraram as contribuições de ligação de hidrogênio e interações hidrofóbicas para explicar a atividade de compostos inibidores de MIF, descrevendo os grupos farmacofóricos destes compostos. Adicionalmente, um conjunto de cumarinas naturais e sintéticas foi submetido aos modelos QSAR e de ancoragem molecular a fim de que as suas atividades contra MIF fossem preditas. Ambas as metodologias de modelagem molecular puderam estimar as interações intermoleculares entre inibidores e a enzima, os quais foram muito similares a compostos descritos previamente. Estes resultados podem ser úteis para o desenho de novos compostos contra doenças inflamatórias como artrite reumatóide.

  13. APROVEITAMENTO DA SEMENTE DE AÇAÍ PARA PRODUÇÃO DE BEBIDA À BASE DE CAFÉ

    OpenAIRE

    Lara Santana Fernandes; UFV; Bruna Giaretta Martins; UFV; Juliana Lane Paixão; UFV; Lara Stela Mendes Lustoza; UFV; Daniel Mariano Leite; UFV

    2011-01-01

    O aproveitamento da semente de açaí em bebida à base de café é uma alternativa para a redução do impacto ambiental e para a agregação de valor ao resíduo da agroindústria de açaí. Objetivou–se com a condução do presente trabalho avaliar o aproveitamento da semente de açaí, subproduto do beneficiamento dos frutos, para a produção de uma bebida à base de café e semente de açaí. Foram feitas a torrefação e moagem da semente de açaí e de grãos de café, tendo sido analisada sensorialmente a beb...

  14. The mitochondrial 60-kDa heat shock protein in marine invertebrates: biochemical purification and molecular characterization.

    Science.gov (United States)

    Choresh, Omer; Loya, Yossi; Müller, Werner E G; Wiedenmann, Jörg; Azem, Abdussalam

    2004-03-01

    Sessile marine invertebrates undergo constant direct exposure to the surrounding environmental conditions, including local and global environmental fluctuations that may lead to fatal protein damage. Induction of heat shock proteins (Hsps) constitutes an important defense mechanism that protects these organisms from deleterious stress conditions. In a previous study, we reported the immunological detection of a 60-kDa Hsp (Hsp60) in the sea anemone Anemonia viridis (formerly called Anemonia sulcata) and studied its expression under a variety of stress conditions. In the present study, we show that the sponge Tetilla sp. from tidal habitats with a highly variable temperature regime is characterized by an increased level of Hsp60. Moreover, we show the expression of Hsp60 in various species among Porifera and Cnidaria, suggesting a general importance of this protein among marine invertebrates. We further cloned the hsp60 gene from A viridis, using a combination of conventional protein isolation methods and screening of a complementary deoxyribonucleic acid library by polymerase chain reaction. The cloned sequence (1764 bp) encodes for a protein of 62.8 kDa (588 amino acids). The 62.8-kDa protein, which contains an amino terminal extension that may serve as a mitochondrial targeting signal, shares a significant identity with mitochondrial Hsp60s from several animals but less identity with Hsp60s from either bacteria or plants.

  15. Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

    Science.gov (United States)

    Aksela, Maija; Lundell, Jan

    2008-01-01

    Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…

  16. Molecular materials and devices: developing new functional systems based on the coordination chemistry approach

    Directory of Open Access Journals (Sweden)

    Toma Henrique E.

    2003-01-01

    Full Text Available At the onset of the nanotechnology age, molecular designing of materials and single molecule studies are opening wide possibilities of using molecular systems in electronic and photonic devices, as well as in technological applications based on molecular switching or molecular recognition. In this sense, inorganic chemists are privileged by the possibility of using the basic strategies of coordination chemistry to build up functional supramolecular materials, conveying the remarkable chemical properties of the metal centers and the characteristics of the ancillary ligands. Coordination chemistry also provides effective self-assembly strategies based on specific metal-ligand affinity and stereochemistry. Several molecular based materials, derived from inorganic and metal-organic compounds are focused on this article, with emphasis on new supramolecular porphyrins and porphyrazines, metal-clusters and metal-polyimine complexes. Such systems are also discussed in terms of their applications in catalysis, sensors and molecular devices.

  17. Nanohashtag structures based on carbon nanotubes and molecular linkers

    Science.gov (United States)

    Frye, Connor W.; Rybolt, Thomas R.

    2018-03-01

    Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

  18. Effects of molecular weight on the glass transition temperature in Durolon polycarbonate; Os efeitos da massa molecular sobre a temperatura de transicao vitrea (Tg) para o policarbonato Durolon

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, Adelina; Sciani, Valdir [Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, SP (Brazil)

    1995-12-31

    The effect of variation of the dose rate on degradation mechanism of PC Durolon irradiated with gamma rays was determined trough out intrinsic viscosity and thermal analysis of DSC-type measurements. The results showed a linear relationship between the glass transition temperature and the viscosimetric average molecular weight. From the results it`s shown that with an increased of the dose rate it also increases the degradation of the material. (author). 12 refs., 3 figs.

  19. Bases moleculares del hipotiroidismo congénito

    OpenAIRE

    Pinzón-Serrano, Estefanía; Morán-Barroso, Verónica; Coyote-Estrada, Ninel

    2006-01-01

    Las alteraciones endocrinológicas constituyen parte importante de la consulta pediátrica, la más frecuente es el hipotiroidismo congénito, grave problema de salud pública que requiere de diagnóstico neonatal. Los avances en el estudio molecular han permitido discernir las alteraciones en los procesos de organogénesis y hormonogénesis que lo producen. Se describen las principales alteraciones moleculares relacionadas con: diferenciación tiroidea, síntesis hormonal, hipotiroidismo central y con...

  20. Do paradigma molecular ao impacto no prognóstico: uma visão da leucemia promielocítica aguda From the molecular model to the impact on prognosis: an overview on acute promyelocytic leukemia

    Directory of Open Access Journals (Sweden)

    Rafael Henriques Jácomo

    2008-02-01

    Full Text Available A leucemia promielocítica aguda (LPA é um modelo da aplicabilidade clínica dos conhecimentos moleculares fisiopatológicos. Caracteriza-se por alterações genéticas recorrentes que envolvem o gene do receptor alfa do ácido retinóico. A conseqüência é uma proteína com sensibilidade reduzida ao ligante, com bloqueio da diferenciação mielóide. Entretanto, doses suprafisiológicas do ácido all-trans-retinóico (ATRA são capazes de suplantar esta deficiência, e este é o princípio fundamental do tratamento da LPA, permitindo uma sobrevida livre de doença acima de 80% quando adequadamente tratada. Epidemiologicamente, difere dos demais subtipos de leucemia mielóide aguda por apresentar incidência predominante em adultos jovens e, aparentemente, maior incidência em países de colonização "latina". Contrastando com os excelentes resultados observados em países desenvolvidos, a mortalidade por LPA no Brasil ainda é alta, apesar da ampla disponibilidade das medicações no país.Acute promyelocytic leukemia (APL is a model of clinical applicability of the knowledge of molecular physiopathology. It is characterized by recurrent genetic involvement of the retinoic acid alpha receptor. The consequence is a protein with low sensibility to its ligand and a myeloid maturation arrest. However, higher doses of all-trans-retinoic acid (ATRA are able to supersede this deficiency and this is the mainstay of APL treatment leading to over 80% disease free survival, when adequately treated. Epidemiologically, it differs from other acute myeloid leukemia due to a higher incidence in young adults and in countries of "Latin" colonization. Differing from excellent results observed in developed countries, APL mortality in Brazil is still high, despite the wide availability of drugs.

  1. Full Length Research Paper LTR-retrotransposons-based molecular ...

    African Journals Online (AJOL)

    LTR-retrotransposons possess unique properties that make them appropriate for investigating relationships between closely related species and populations. The aim of the current study was to employ Ty1-copia group retrotransposons as molecular markers in cultivated Egyptian cottons, G. barbadense L. Restriction site ...

  2. Molecular characterization of Cymbidium kanran cultivars based on ...

    African Journals Online (AJOL)

    TUOYO

    2010-08-09

    Aug 9, 2010 ... Fifty-four Cymbidium kanran cultivars from China, Japan and Korea were examined and analyzed by using the successive screening of 3′-end extended random primer amplified polymorphic DNA (ERAPD) markers to determine their molecular diversity and relationships. In ERAPD analyses, the strand-.

  3. Engineering controllable bidirectional molecular motors based on myosin

    Science.gov (United States)

    Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

    2012-04-01

    Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

  4. Molecular filter-based diagnostics in high speed flows

    Science.gov (United States)

    Elliott, Gregory S.; Samimy, MO; Arnette, Stephen A.

    1993-01-01

    The use of iodine molecular filters in nonintrusive planar velocimetry methods is examined. Detailed absorption profiles are obtained to highlight the effects that determine the profile shape. It is shown that pressure broadening induced by the presence of a nonabsorbing vapor can be utilized to significantly change the slopes bounding the absorbing region while remaining in the optically-thick regime.

  5. Molecular phylogenetic implications in Brassica napus based on ...

    Indian Academy of Sciences (India)

    Brassica napus L. (canola, rapeseed) is one of the most important oil crops in many countries (Abdelmigid 2012;. Fayyaz et al. 2014), and thought to have originated from a cross where the maternal donor was closely related to two diploid species, B. oleracea (CC, 2n = 18) and B. rapa (AA, 2n = 20). Here, molecular ...

  6. Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

    NARCIS (Netherlands)

    Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

    2007-01-01

    This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

  7. Engineering controllable bidirectional molecular motors based on myosin

    Science.gov (United States)

    Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

    2012-01-01

    Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells1, and have potential applications in molecular detection and diagnostic devices2,3. Engineering molecular motors with dynamically controllable properties will allow selective perturbation of mechanical processes in living cells, and yield optimized device components for complex tasks such as molecular sorting and directed assembly3. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions4,5 and other signals6. Here we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies7–11 and guided by a structural model12 for the redirected power stroke of myosin VI, we constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our general strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should enable spatiotemporal control over a range of motor properties including processivity, stride size13, and branchpoint turning14. PMID:22343382

  8. LTR-retrotransposons-based molecular markers in cultivated ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... LTR-retrotransposons represent a standard component of the Gossypium Genome (Zaki and Abdel Ghany,. 2003). The analysis of the molecular existence and distribution of ancient and active LTR-retrotransposons, therefore, provides a comprehensive evaluation of the evolutionary history of Gossypium.

  9. Molecular characterization of Cymbidium kanran cultivars based on ...

    African Journals Online (AJOL)

    Fifty-four Cymbidium kanran cultivars from China, Japan and Korea were examined and analyzed by using the successive screening of 3'-end extended random primer amplified polymorphic DNA (ERAPD) markers to determine their molecular diversity and relationships. In ERAPD analyses, the strandspecific DNA ...

  10. Efeito de diferentes fontes de sílica nos parâmetros texturais da peneira molecular MCM-41

    Directory of Open Access Journals (Sweden)

    M. S. B. Fontes

    2016-03-01

    Full Text Available Resumo Nas últimas décadas, pesquisas estão sendo desenvolvidas para obtenção de materiais eficientes e economicamente viáveis para aplicação em diversos setores da indústria. Os materiais mesoporosos da família MCM-41 estão entre os candidatos eficazes pela facilidade de síntese e estrutura que favorece uma gama de aplicações. O objetivo desse trabalho foi apresentar uma abordagem rítica das características e propriedades dos materiais mesoporosos do tipo MCM-41, enfocando nos aspectos estruturais. Além isso, foram discutidas as vantagens e desvantagens do uso de sílica comerciais e alternativas. As fontes de sílica comerciais analisadas foram sílica gel e TEOS; já as fontes de sílica alternativas foram cinza da casca de arroz, quartzo e pó de vidro. Os materiais analisados foram sintetizados pelo método hidrotérmico e caracterizados por DRX, FTIR, BET e TG. Os resultados apresentados comprovam a eficiência das fontes de sílica alternativas na síntese do MCM-41, pois os materiais apresentaram propriedades texturais dentro dos padrões exigidos. Dessa forma, eles estão aptos a serem testados na indústria em substituição aos MCM-41 sintetizados com fonte de sílica comercial.

  11. Formas moleculares da gonadotrofina coriônica humana: características, ensaios e uso clínico Molecular forms of human chorionic gonadotropin: characteristics, assays and clinical use

    Directory of Open Access Journals (Sweden)

    Sebastião Freitas de Medeiros

    2006-04-01

    Full Text Available A gonadotrofina coriônica humana (hCG é estruturada pela combinação não covalente de duas subunidades, alfa (alfahCG e beta (betahCG, sintetizadas separadamente pelo tecido trofoblástico normal, mola hidatiforme, coriocarcinoma, células hipofisárias e tecidos tumorais de diversos tipos histológicos. A síntese da cadeia peptídica e sua glicosilação na célula secretora envolve complexa ação de várias enzimas. Esta complexidade resulta na secreção de moléculas heterogêneas. As diferentes formas moleculares secretadas podem ser encontradas no soro, urina e líquido amniótico de gestantes; soro, urina e vesículas em pacientes com mola hidatiforme ou coriocarcinoma e em fluidos biológicos de mulheres não grávidas e homens normais ou acometidos de tumores de diferente origem embrionária. Tanto a molécula hCG nativa, intacta,como suas subunidades nas formas livres e as variantes hCG hiperglicosilada (H-hCG, hCG clivada (N-hCG e fragmento-núcleo de betahCG (CF-betahCG têm aplicabilidade clínica relevante. Dependendo da forma molecular mais prevalente ou da proporção da molécula variante/molécula hCG intacta numa determinada condição clínica, há indicação para a dosagem específica de uma ou mais destas moléculas. Este texto revê o conhecimento básico e analisa o uso da hCG e suas variantes na detecção precoce da gravidez ectópica ou gestantes em risco de abortamento, na identificação precoce de anomalias cromossômicas êmbrio-fetais e estima o risco da gestação de evoluir com pré-eclâmpsia ou crescimento intra-uterino restrito. Examina, ainda, fora da gravidez, o emprego destas moléculas como marcadores laboratoriais de tumores com diferentes tipos histológicos e seguimento após a terapia inicial. Conclui-se ser útil o uso da dosagem de hCG e suas moléculas variantes na prática clínica, mas a dificuldade no desenvolvimento e obtenção de ensaios mais sensíveis e específicos restringe a

  12. Molecular confirmation of Maize rayado fino virus as the Brazilian corn streak virus Confirmação molecular do 'Maize rayado fino virus' como vírus da estria do milho

    Directory of Open Access Journals (Sweden)

    Rosemarie Wahnbaeck Hammond

    2005-12-01

    Full Text Available Maize rayado fino virus (MRFV, present in various countries in Latin America, has shown similarities to corn streak virus that occurs in Brazil, regarding pathogenic, serological and histological characteristics. In the current report both virus were molecularly compared to confirm the similarities between them. MRFV was identified by nucleic acid hybridization in samples of maize tissues exhibiting symptoms of "corn stunt" disease, collected from two Brazilian States - São Paulo and Minas Gerais. The coat protein gene and 3'non-translated region of MRFV were amplified from infected tissues by reverse transcription-polymerase chain reaction (RT-PCR using MRFV-specific primers, and were characterized by nucleotide sequence and phylogenetic analysis of the cloned PCR products. Phylogenetic analysis of the relationships between the Brazilian isolates and isolates obtained from Latin America and the United States reveals a close relationship to isolates from Brazil, Peru and Bolivia. Results support the proposal that the Brazilian corn streak virus be regarded as an isolate of MRFV and provide evidence for the presence of MRFV in "corn stunt' disease in Brazil.O vírus do rayado fino do milho (MRFV, presente em vários países da América Latina, tem mostrado semelhança ao vírus da risca do milho que ocorre no Brasil, em relação a características patogênicas, sorológicas e histológicas. No presente trabalho, ambos os vírus foram comparados molecularmente, visando confirmar a similaridade entre os mesmos. O MRFV foi identificado por hibridização de ácido nucléico em amostras de tecido que apresentavam sintomas de enfezamento, coletadas nos estados de São Paulo e Minas Gerais. O gene da capa protéica e a região 3' não traduzida do MRFV foram amplificados, a partir de tecidos infectados, através da transcrição reversa por reação em cadeia da polimerase (RT-PCR, usando-se os iniciadores específicos para o vírus, obtendo-se a seq

  13. Coordenadas cartesianas moleculares a partir da geometria dos modos normais de vibração Molecular cartesian coordinates from vibrational normal modes geometry

    Directory of Open Access Journals (Sweden)

    Emílio Borges

    2007-04-01

    Full Text Available A simple method to obtain molecular Cartesian coordinates as a function of vibrational normal modes is presented in this work. The method does not require the definition of special matrices, like the F and G of Wilson, neither of group theory. The Eckart's conditions together with the diagonalization of kinetic and potential energy are the only required expressions. This makes the present approach appropriate to be used as a preliminary study for more advanced concepts concerning vibrational analysis. Examples are given for diatomic and triatomic molecules.

  14. PUBLICAÇÕES RETROCEDIDAS DA BASE MEDLINE®: UMA ANÁLISE BIBLIOMÉTRICA

    Directory of Open Access Journals (Sweden)

    Henrique Rego Monteiro DA HORA

    2017-07-01

    Full Text Available A fraude científica deve ser combatida veementemente, pois sua prática não é saudável para a comunidade acadêmica. Este trabalho visa, por meio de técnicas de bibliometria, descrever a situação da base de conhecimento na National Library of Medicice (NLM, conhecida como MEDLINE®, em relação aos trabalhos retrocedidos. O estudo identificou 842 retrocessos presentes na base, e aponta que os casos aumentaram a partir de 2004 e entram em tendência de queda a partir de 2015, e que os casos de retrocessos são em majoritariamente de ocorrência única, tanto entre autores (92,40% quanto entre veículos (66,52%.

  15. Emoções e guerras: da Micronésia às bases militares americanas

    Directory of Open Access Journals (Sweden)

    Clara Saraiva

    2007-11-01

    Full Text Available Catherine Lutz tem um PhD em antropologia cultural da Universidade de Harvard, é professora do Departamento de Antropologia da Brown University, e investigadora do Watson Institute for International Studies da mesma universidade. Os seus temas de pesquisa debruçam-se sobre a antropologia das emoções, construção do género e da noção de raça, teoria crítica, mudanças na democracia e, mais recentemente, guerra, grupos militares e sociedade, nomeadamente através do estudo de bases militares americanas e do retorno de militares americanos dissidentes da guerra do Iraque. Lutz conduziu igualmente pesquisa para organizações activistas e todas estas temáticas se relacionam com a vontade de compreender as articulações socais e culturais das construções de poder e de desigualdade. Algumas das suas obras, influentes no campo da antropologia das emoções, da antropologia cognitiva e da história política são Unnatural Emotions: Everyday Sentiments on a Micronesian Atoll and their Challenge to Western Theory; Language and the Politics of Emotion(com Abu-Lughod; Reading National Geographic; Homefront: a Military City and the American 20th Century; Local Democracy under Siege: Activism, Public Interests, and Private Politics; The Bases of the Empire. The Struggle against US Military Posts, além de vários artigos como "Empire is in the details" e "Making war at home in the United States: militarization and the current crisis". Nesta entrevista Lutz fala sobre o que tem sido o seu trabalho e as suas preocupações académicas mas também sociais e interventivas.

  16. Adsorbate-driven cooling of carbene-based molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Foti, Giuseppe; Vázquez, Héctor

    2017-01-01

    Roč. 8, Oct (2017), s. 2060-2068 ISSN 2190-4286 R&D Projects: GA ČR GA15-19672S EU Projects: European Commission(XE) 702114 - HEATEXMOL Institutional support: RVO:68378271 Keywords : adsorbate * carbene * current-induced heating and cooling * molecular junction * vibrations Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 3.127, year: 2016

  17. Extending the molecular clutch beyond actin-based cell motility

    International Nuclear Information System (INIS)

    Havrylenko, Svitlana; Mezanges, Xavier; Batchelder, Ellen; Plastino, Julie

    2014-01-01

    Many cell movements occur via polymerization of the actin cytoskeleton beneath the plasma membrane at the front of the cell, forming a protrusion called a lamellipodium, while myosin contraction squeezes forward the back of the cell. In what is known as the ‘molecular clutch’ description of cell motility, forward movement results from the engagement of the acto-myosin motor with cell-matrix adhesions, thus transmitting force to the substrate and producing movement. However during cell translocation, clutch engagement is not perfect, and as a result, the cytoskeleton slips with respect to the substrate, undergoing backward (retrograde) flow in the direction of the cell body. Retrograde flow is therefore inversely proportional to cell speed and depends on adhesion and acto-myosin dynamics. Here we asked whether the molecular clutch was a general mechanism by measuring motility and retrograde flow for the Caenorhabditis elegans sperm cell in different adhesive conditions. These cells move by adhering to the substrate and emitting a dynamic lamellipodium, but the sperm cell does not contain an acto-myosin cytoskeleton. Instead the lamellipodium is formed by the assembly of major sperm protein, which has no biochemical or structural similarity to actin. We find that these cells display the same molecular clutch characteristics as acto-myosin containing cells. We further show that retrograde flow is produced both by cytoskeletal assembly and contractility in these cells. Overall this study shows that the molecular clutch hypothesis of how polymerization is transduced into motility via adhesions is a general description of cell movement regardless of the composition of the cytoskeleton. (paper)

  18. Electron dopable molecular wires based on the extended viologens

    Czech Academy of Sciences Publication Activity Database

    Kolivoška, Viliam; Gál, Miroslav; Pospíšil, Lubomír; Valášek, Michal; Hromadová, Magdaléna

    2011-01-01

    Roč. 13, č. 23 (2011), s. 11422-11429 ISSN 1463-9076 R&D Projects: GA ČR GA203/08/1157; GA ČR GA203/09/0705; GA AV ČR IAA400400802; GA MŠk(CZ) MEB041006 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z40550506 Keywords : electron transfer * spectroelectrochemistry * molecular wires Subject RIV: CG - Electrochemistry Impact factor: 3.573, year: 2011

  19. Epidemiological bases and molecular mechanisms linking obesity, diabetes, and cancer.

    Science.gov (United States)

    Gutiérrez-Salmerón, María; Chocarro-Calvo, Ana; García-Martínez, José Manuel; de la Vieja, Antonio; García-Jiménez, Custodia

    2017-02-01

    The association between diabetes and cancer was hypothesized almost one century ago. Today, a vast number of epidemiological studies support that obese and diabetic populations are more likely to experience tissue-specific cancers, but the underlying molecular mechanisms remain unknown. Obesity, diabetes, and cancer share many hormonal, immune, and metabolic changes that may account for the relationship between diabetes and cancer. In addition, antidiabetic treatments may have an impact on the occurrence and course of some cancers. Moreover, some anticancer treatments may induce diabetes. These observations aroused a great controversy because of the ethical implications and the associated commercial interests. We report an epidemiological update from a mechanistic perspective that suggests the existence of many common and differential individual mechanisms linking obesity and type 1 and 2 diabetes mellitus to certain cancers. The challenge today is to identify the molecular links responsible for this association. Classification of cancers by their molecular signatures may facilitate future mechanistic and epidemiological studies. Copyright © 2016 SEEN. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. Molecular markers derived from bombesin for tumor diagnosis by SPECT and PET; Marcadores moleculares derivados da bombesina para diagnostico de tumores por SPECT e PET

    Energy Technology Data Exchange (ETDEWEB)

    Pujatti, Priscilla Brunelli

    2012-07-01

    A high number of molecules have already been identified to have high affinity to some receptors overexpressed on tumour cells and the radiolabelling of those molecules offers the possibility of new compounds for tumour diagnosis and therapy by nuclear medicine. Among of those molecules, bombesin (BBN) has become focus of interest, as its BB{sub 2} receptors are known to be overexpressed in prostate, breast, colon, pancreatic and lung tumour, as long as glioblastomas and neuroblastomas. BBN agonists and antagonists have already been described for this purpose and promising results were obtained in preclinical studies. However, most of them exhibited high abdominal accumulation, especially in pancreas and intestines, which can compromise diagnosis accuracy and cause serious adverse effects in therapy. In this context, the goal of the present work to radiolabel new BBN derivatives with {sup 11}1In and {sup 68}Ga and to evaluate their potential for BB{sub 2} positive tumors diagnosis by single photon emission tomography (SPECT) and positron emission tomography (PET). The structure of studied peptides was Q-YG{sub n}-BBN(6-14), where Q is the chelator, n is the number of glycine aminoacids in the spacer YG{sub n} and BBN(6-14) is the original bombesin sequence from the aminoacid 6 to 14. The derivative in which the last aminoacid (methionine, Met) was replaced by norleucine (Nle) was also evaluated. The experimental evaluation of the bombesin derivatives was divided into four steps: computational studies, molecular markers for SPECT, molecular markers for PET and toxicological studies. The theoretical partition (log P) and distribution (log D) coefficients were calculated for all bombesin derivatives conjugated to DTPA (diethylenetriaminepentaacetic acid) and DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) chelators applying computational programmes. Bombesin derivatives for SPECT were developed by radiolabelling DTPA-conjugated bombesin derivatives with

  1. Avaliação eletroforética, cromatográfica e molecular da Hb D Los Angeles no Brasil Electrophoretical, chromatographic and molecular valuations of Hb D Los Angeles in Brazil

    Directory of Open Access Journals (Sweden)

    Ana R. Chinelato-Fernandes

    2003-01-01

    Full Text Available A variante de hemoglobina (Hb D mais comum, Hb D Los Angeles ou D Punjab, é originada de uma transversão GAA->CAA no códon 121 da globina beta; essa mutação resulta na substituição do ácido glutâmico por glutamina na proteína. É a terceira variante de hemoglobina mais freqüente da população brasileira. Como as hemoglobinas D apresentam migração similar à hemoglobina S em pH alcalino, e com a hemoglobina A em pH ácido, são necessários vários testes para o correto diagnóstico. No presente estudo objetivou-se relacionar os diferentes procedimentos laboratoriais de rotina diagnóstica, além da análise molecular, para estabelecer o perfil de Hb D Los Angeles no Brasil. Foram analisados 47 indivíduos da população brasileira com provável Hb D Los Angeles, por vários procedimentos eletroforéticos em diferentes condições de pH, além da cromatografia líquida de alta pressão, e testes moleculares para confirmação da mutação. Foram encontrados quatro tipos de combinações de hemoglobinas: 42 indivíduos portadores de hemoglobina AD Los Angeles, dois indivíduos com doença de Hb S/D Los Angeles, dois indivíduos com Hb D Los Angeles e talassemia beta e um indivíduo com Hb D Los Angeles e Hb Lepore. Os indivíduos heterozigotos para D Los Angeles são assintomáticos, entretanto, em associação com outras variantes e talassemias podem apresentar graus variáveis de manifestações clínicas. Os resultados apresentados enfatizaram a necessidade da associação de várias metodologias para a identificação da Hb D Los Angeles, além de auxiliar na elucidação de combinações raras.The most common Hb D variant, the Hb D-Los Angeles, also know as Hb D-Punjab, originates through a GAA->CAA change at the 121 codon of the beta globin gene; this mutation results in the replacement of glutamic acid for glutamine in the protein. It is the third most common hemoglobin variant in the Brazilian population. This variant has

  2. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    Science.gov (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  3. A WAO - ARIA - GA2LEN consensus document on molecular-based allergy diagnostics

    DEFF Research Database (Denmark)

    Canonica, Giorgio Walter; Ansotegui, Ignacio J; Pawankar, Ruby

    2013-01-01

    Molecular-based allergy (MA) diagnostics is an approach used to map the allergen sensitization of a patient at a molecular level, using purified natural or recombinant allergenic molecules (allergen components) instead of allergen extracts. Since its introduction, MA diagnostics has increasingly ...

  4. Molecular modeling of protonic acid doping of emeraldine base polyaniline for chemical sensors

    NARCIS (Netherlands)

    Chen, X.; Yuan, C.A.; Wong, C.K.Y.; Ye, H.; Leung, S.Y.Y.; Zhang, G.

    2012-01-01

    We proposed a molecular modeling methodology to study the protonic acid doping of emeraldine base polyaniline which can used in gas detection. The commercial forcefield COMPASS was used for the polymer and protonic acid molecules. The molecular model, which is capable of representing the polyaniline

  5. Molecular Imaging: A Useful Tool for the Development of Natural Killer Cell-Based Immunotherapies

    Directory of Open Access Journals (Sweden)

    Prakash Gangadaran

    2017-09-01

    Full Text Available Molecular imaging is a relatively new discipline that allows visualization, characterization, and measurement of the biological processes in living subjects, including humans, at a cellular and molecular level. The interaction between cancer cells and natural killer (NK cells is complex and incompletely understood. Despite our limited knowledge, progress in the search for immune cell therapies against cancer could be significantly improved by dynamic and non-invasive visualization and tracking of immune cells and by visualization of the response of cancer cells to therapies in preclinical and clinical studies. Molecular imaging is an essential tool for these studies, and a multimodal molecular imaging approach can be applied to monitor immune cells in vivo, for instance, to visualize therapeutic effects. In this review, we discuss the usefulness of NK cells in cancer therapies and the preclinical and clinical usefulness of molecular imaging in NK cell-based therapies. Furthermore, we discuss different molecular imaging modalities for use with NK cell-based therapies, and their preclinical and clinical applications in animal and human subjects. Molecular imaging has contributed to the development of NK cell-based therapies against cancers in animal models and to the refinement of current cell-based cancer immunotherapies. Developing sensitive and reproducible non-invasive molecular imaging technologies for in vivo NK cell monitoring and for real-time assessment of therapeutic effects will accelerate the development of NK cell therapies.

  6. Confirmação molecular do 'Maize rayado fino virus' como vírus da estria do milho

    OpenAIRE

    Hammond, Rosemarie Wahnbaeck; Bedendo, Ivan Paulo

    2005-01-01

    Maize rayado fino virus (MRFV), present in various countries in Latin America, has shown similarities to corn streak virus that occurs in Brazil, regarding pathogenic, serological and histological characteristics. In the current report both virus were molecularly compared to confirm the similarities between them. MRFV was identified by nucleic acid hybridization in samples of maize tissues exhibiting symptoms of "corn stunt" disease, collected from two Brazilian States - São Paulo and Minas G...

  7. Da-KGM based GO-reinforced FMBO-loaded aerogels for efficient arsenic removal in aqueous solution.

    Science.gov (United States)

    Ye, Shuxin; Jin, Weiping; Huang, Qing; Hu, Ying; Li, Yan; Li, Jing; Li, Bin

    2017-01-01

    Composites based on deacetylated konjac glucomannan (Da-KGM) and graphene oxide (GO) aerogels with iron and manganese oxides (FMBO) for effective removal of arsenic from contaminated water. Da-KGM, which was used as supporting composite matrix here, were firstly treated with GO and loaded FMBO. The obtained Da-KGM/GO/FMBO composite aerogels were characterized by compression test, thermo gravimetric analysis (TGA), X-ray diffraction (XRD), fourier transform infrared spectroscopy (FTIR) and scanning electron microscope (SEM). The characteristic results showed that addition of GO exhibited enhanced mechanical properties towards Da-KGM aerogels. What's more, results of FTIR indicated the strong intermolecular hydrogen bond interaction between KGM and GO. Batch adsorption tests were used to evaluate arsenic removal capacity. Da-KGM/GO loaded FMBO composite aerogels exhibited high adsorption ability for arsenite [As(III)] and arsenate [As(V)]. The adsorption results showed that the arsenic for both arsenite [As(III)] and arsenate [As(V)] removal process followed a pseudo-second-order rate equation and Langmuir monolayer adsorption. The maximum As(III) and As(V) uptake capacity of Da-KGM/GO(10%)/FMBO composite aerogels reached 30.21mgg -1 and 12.08mgg -1 respectively according to Langmuir isotherm at pH 7 and 323K. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Four new topological indices based on the molecular path code.

    Science.gov (United States)

    Balaban, Alexandru T; Beteringhe, Adrian; Constantinescu, Titus; Filip, Petru A; Ivanciuc, Ovidiu

    2007-01-01

    The sequence of all paths pi of lengths i = 1 to the maximum possible length in a hydrogen-depleted molecular graph (which sequence is also called the molecular path code) contains significant information on the molecular topology, and as such it is a reasonable choice to be selected as the basis of topological indices (TIs). Four new (or five partly new) TIs with progressively improved performance (judged by correctly reflecting branching, centricity, and cyclicity of graphs, ordering of alkanes, and low degeneracy) have been explored. (i) By summing the squares of all numbers in the sequence one obtains Sigmaipi(2), and by dividing this sum by one plus the cyclomatic number, a Quadratic TI is obtained: Q = Sigmaipi(2)/(mu+1). (ii) On summing the Square roots of all numbers in the sequence one obtains Sigmaipi(1/2), and by dividing this sum by one plus the cyclomatic number, the TI denoted by S is obtained: S = Sigmaipi(1/2)/(mu+1). (iii) On dividing terms in this sum by the corresponding topological distances, one obtains the Distance-reduced index D = Sigmai{pi(1/2)/[i(mu+1)]}. Two similar formulas define the next two indices, the first one with no square roots: (iv) distance-Attenuated index: A = Sigmai{pi/[i(mu + 1)]}; and (v) the last TI with two square roots: Path-count index: P = Sigmai{pi(1/2)/[i(1/2)(mu + 1)]}. These five TIs are compared for their degeneracy, ordering of alkanes, and performance in QSPR (for all alkanes with 3-12 carbon atoms and for all possible chemical cyclic or acyclic graphs with 4-6 carbon atoms) in correlations with six physical properties and one chemical property.

  9. Molecular dynamics computer simulations based on NMR data

    International Nuclear Information System (INIS)

    Vlieg, J. de.

    1989-01-01

    In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs

  10. Molecular interactions of nucleic acid bases. From ab initio calculations to molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří

    2002-01-01

    Roč. 223, - (2002), s. 212 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : quantum chemistry * base pairing * base stacking Subject RIV: BO - Biophysics

  11. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

    Science.gov (United States)

    Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

    2018-06-01

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

  12. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

    Science.gov (United States)

    Petrini, Paula Andreia; Lopes da Silva, Ricardo Magno; de Oliveira, Rafael Furlan; Merces, Leandro; Bufon, Carlos César Bof

    2018-04-06

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscope (STM). The incorporation of molecular materials in devices is not a trivial task since the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (kCuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensemble have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (< 30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (kCuPc = 4.5 ± 0.5). These values suggest a mild contribution of molecular orientation in the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology. © 2018 IOP Publishing Ltd.

  13. Detecção de potenciais marcadores moleculares séricos da doença de Hodgkin Detection of potential serum molecular markers for Hodgkin's disease

    Directory of Open Access Journals (Sweden)

    Paulo Costa Carvalho

    2005-06-01

    Full Text Available MOTIVAÇÃO: Neste trabalho foi analisado o perfil de proteínas séricas de pacientes com doença de Hodgkin (DH localizada e avançada em busca de novos e potenciais biomarcadores para o diagnóstico médico. MATERIAIS E MÉTODOS: O perfil de proteínas presentes no soro de 14 indivíduos saudáveis, 14 pacientes com DH avançada e 15 pacientes com DH localizada, assim como pools de soro dos respectivos grupos, foi analisado em gel desnaturante de poliacrilamida a 12% corado pela prata. A densitometria e a intensidade média das bandas de interesse foram estudadas utilizando-se o Kodak 1D Scientific Imaging System. RESULTADOS E CONCLUSÕES: O perfil protéico apresentou acentuada variação entre os pacientes examinados; entretanto foi observada a indução predominante de determinadas proteínas (aproximadamente 26kDa e 18kDa, cuja expressão foi substancialmente diferente quando em comparação com os controles (p AIM: In this work the serum protein profile of patients with localized and advanced Hodgkin's disease (HD was analyzed to search for new potential biomarkers of medical interest. MATERIALS AND METHODS: The serum protein profile of 14 healthy donors, 14 patients with advanced disease, 15 patients with localized disease and serum pools of the respective groups, were analyzed using silver stained 12% denaturating polyacrylamide gel. The densitometry and mean band intensity from the bands of interest were analyzed using the Kodak 1D Scientific Imaging System. RESULTS AND CONCLUSION: The patients' protein profiles presented heterogenous variations; however over-expressed proteins of approximately 26kDa and 18kDa were proven to be statistically different when compared to healthy donors. Such proteins could potentially constitute in molecular markers for diagnosis and patient treatment follow-up.

  14. Gliomatosis cerebri: Prognosis based on current molecular markers.

    Science.gov (United States)

    Maharaj, Monish M; Phan, Kevin; Xu, Joshua; Fairhall, Jacob; Reddy, Rajesh; Rao, Prashanth J V

    2017-09-01

    This study aims to review the literature and identify key molecular markers affecting the prognosis of Gliomatosis cerebri (2) to evaluate the level of evidence and identify outstanding markers requiring further study. A literature search was conducted across 5 major databases using the key terms: "Molecular markers" AND "Gliomatosis cerebri" OR "diffuse astrocytoma." Critical appraisal and data presentation was performed inline with the PRISMA guidelines. Following search strategy implementation, 11 studies were included in the final review process. Our data demonstrates significant prognostic value associated with IDH1 132H mutation and variable evidence surrounding the role of INA expression, MGMT promoter methylation and other factors. However, there are significant limitations in the level of evidence obtained. As the genetic basis for the pathogenesis of Gliomatosis cerebri continues to widen, there is little data on markers aside from IDH1 mutation available. IDH1 132H mutation has been demonstrated to have significant effect on survival, particularly in patients with Gliomatosis cerebri type 2. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Quantum-dots-encoded-microbeads based molecularly imprinted polymer.

    Science.gov (United States)

    Liu, Yixi; Liu, Le; He, Yonghong; He, Qinghua; Ma, Hui

    2016-03-15

    Quantum dots encoded microbeads have various advantages such as large surface area, superb optical properties and the ability of multiplexing. Molecularly imprinted polymer that can mimic the natural recognition entities has high affinity and selectivity for the specific analyte. Here, the concept of utilizing the quantum dots encoded microbeads as the supporting material and the polydopamine as the functional monomer to form the core-shell molecular imprinted polymer was proposed for the first time. The resulted imprinted polymer can provide various merits: polymerization can complete in aqueous environment; fabrication procedure is facile and universal; the obvious economic advantage; the thickness of the imprinting layer is highly controllable; polydopamine coating can improve the biocompatibility of the quantum dot encoded microbeads. The rabbit IgG binding and flow cytometer experiment result showed the distinct advantages of this strategy: cost-saving, facile and fast preparation procedure. Most importantly, the ability for the multichannel detection, which makes the imprinted polydopamine modified encoded-beads very attractive in protein pre-concentration, recognition, separation and biosensing. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. PET-based molecular nuclear neuro-imaging

    International Nuclear Information System (INIS)

    Kim, Jong Ho

    2004-01-01

    Molecular nuclear neuro-imaging in CNS drug discovery and development can be divided into four categories that are clearly inter-related. (1) Neuroreceptor mapping to examine the involvement of specific neurotransmitter system in CNS diseases, drug occupancy characteristics and perhaps examine mechanisms of action;(2) Structural and spectroscopic imaging to examine morphological changes and their consequences;(3) Metabolic mapping to provide evidence of central activity and CNS fingerprinting the neuroanatomy of drug effects;(4) Functional mapping to examine disease-drug interactions. In addition, targeted delivery of therapeutic agents could be achieved by modifying stem cells to release specific drugs at the site of transplantation('stem cell pharmacology'). Future exploitation of stem cell biology, including enhanced release of therapeutic factors through genetic stem cell engineering might thus constitute promising pharmaceutical approaches to treating diseases of the nervous system. With continued improvements in instrumentation, identification of better imaging probes by innovative chemistry, molecular nuclear neuro-imaging promise to play increasingly important roles in disease diagnosis and therapy

  17. PET-based molecular nuclear neuro-imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Ho [Gil Medical Center, Gachon (Korea, Republic of)

    2004-04-01

    Molecular nuclear neuro-imaging in CNS drug discovery and development can be divided into four categories that are clearly inter-related. (1) Neuroreceptor mapping to examine the involvement of specific neurotransmitter system in CNS diseases, drug occupancy characteristics and perhaps examine mechanisms of action;(2) Structural and spectroscopic imaging to examine morphological changes and their consequences;(3) Metabolic mapping to provide evidence of central activity and CNS fingerprinting the neuroanatomy of drug effects;(4) Functional mapping to examine disease-drug interactions. In addition, targeted delivery of therapeutic agents could be achieved by modifying stem cells to release specific drugs at the site of transplantation('stem cell pharmacology'). Future exploitation of stem cell biology, including enhanced release of therapeutic factors through genetic stem cell engineering might thus constitute promising pharmaceutical approaches to treating diseases of the nervous system. With continued improvements in instrumentation, identification of better imaging probes by innovative chemistry, molecular nuclear neuro-imaging promise to play increasingly important roles in disease diagnosis and therapy.

  18. [Establishing Individualized Medicine for Intractable Cancer Based on Clinical Molecular Pathogenesis].

    Science.gov (United States)

    Jono, Hirofumi

    2018-01-01

     Although cancer treatment has dramatically improved with the development of molecular-targeted agents over the past decade, identifying eligible patients and predicting the therapeutic effects remain a major challenge. Because intratumoral heterogeneity represents genetic and molecular differences affecting patients' responses to these therapeutic agents, establishing individualized medicine based on precise molecular pathological analysis of tumors is urgently required. This review focuses on the pathogenesis of oral squamous cell carcinoma (OSCC), a common head and neck neoplasm, and introduces our approaches toward developing novel anticancer therapies particularly based on clinical molecular pathogenesis. Deeper understanding of more precise molecular pathogenesis in clinical settings may open up novel strategies for establishing individualized medicine for OSCC.

  19. Análises da precipitação pluvial no Estado da Paraíba com base na teoria da entropia Use of entropy theory in analysis of rainfall and air temperature

    Directory of Open Access Journals (Sweden)

    Vicente de P. R. da Silva

    2003-08-01

    Full Text Available Os dados diários de precipitação pluvial de 58 postos pluviométricos do Estado da Paraíba e de temperatura média diária de Campina Grande, PB, foram utilizados para avaliar a variabilidade espacial e temporal da precipitação pluvial, com base na teoria da entropia. Analisou-se, também, a variabilidade temporal da temperatura do ar em Campina Grande, com base nessa mesma teoria. Os resultados evidenciaram que a entropia é alta em locais com intensa precipitação, e baixa quando ocorrem, nesses locais, baixos índices pluviométricos; conseqüentemente, nos períodos chuvosos a entropia é alta e, nos períodos de estiagem, é mínima. Este trabalho evidencia, ainda, que qualquer série temporal de entropia decresce exponencialmente com o aumento do seu desvio-padrão.The objective of this study was the evaluation of the rainfall variability in Paraíba state. Daily rainfall observed from a network of 58 rain gauges in Paraíba State and mean daily temperature observed at Campina Grande weather station were analyzed using entropy theory. The results showed that rainfall entropy is high in localities and periods with high rainfall values and is low in localities and periods with low rainfall values. Maximum values of rainfall entropy occurred in the rainy period and minimum values occurred in the dry period. However, the entropy of the temperature time serie was constant, with maximum value of 8.53 bits. This study shows that for any time series the entropy decreases exponentially with increase of standard deviation.

  20. Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

    DEFF Research Database (Denmark)

    Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu

    2014-01-01

    -based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search...... to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied...... but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts....

  1. Molecular bases of cellular senescence: Hayflick phenomenon 50 years later

    Directory of Open Access Journals (Sweden)

    Patrycja Sosińska

    2016-03-01

    Full Text Available Normal human somatic cells have strictly limited proliferative capacity and reach a state of senescence when it becomes exhausted. It is believed that senescence is a response to extensive and irreparable DNA injury, localized in telomeric and/or non-telomeric regions of the genome. Main cause of this damage is oxidative stress, increasing due to deteriorated function of mitochondria. Senescent cells accumulate in tissues during aging, which is causatively linked with the development of various pathologies in elderly individuals, including cancer. This paper, prepared exactly 50 years after Leonard Hayflick’s discovery of the relationship between cellular senescence and organismal aging is aimed at presenting the current knowledge about molecular determinants of senescence, with particular emphasis paid to the role of oxidative stress, effectors of senescence at the level of cell cycle, markers of this phenomenon, and the effect of senescent cells on the development of certain age-related diseases.

  2. ChemPreview: an augmented reality-based molecular interface.

    Science.gov (United States)

    Zheng, Min; Waller, Mark P

    2017-05-01

    Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www.metavision.com/. ChemPreview can be used to interact with a protein in an intuitive way using natural hand gestures, thereby making it appealing to computational chemists or structural biologists. The ability to manipulate atoms in real world could eventually provide new and more efficient ways of extracting structural knowledge, or designing new molecules in silico. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  4. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  5. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  6. Ansiedade na performance musical: estudo molecular de associação e validação da escala de \\"K-MPAI

    OpenAIRE

    Sergio de Figueiredo Rocha

    2012-01-01

    A performance musical requer um alto nível de habilidade em diversos parâmetros como coordenação motora, atenção e memória, o que a torna uma atividade particularmente susceptível aos estados de ansiedade. Pesquisas nessa área têm avançado com a introdução de instrumentos específicos para abordar a ansiedade na performance musical (MPA), como é o caso da the Kenny Music Performance Anxiety Inventory (K-MPAI). Estudos recentes apontam polimorfismos genéticos envolvidos na base do quadro de ans...

  7. Avaliação da simetria e descarga de peso entre os membros inferiores de atletas de futebol da categoria de base

    Directory of Open Access Journals (Sweden)

    Daniel Lucas Spagnuolo

    2013-12-01

    Full Text Available INTRODUÇÃO: A avaliação instrumentada dos saltos verticais informa sobre as capacidades funcionais e variáveis neuromusculares, auxiliando no atendimento dos atletas. Essencial dar atenção maior para as categorias de base, pois contém fases importantes do desenvolvimento dos atletas que serão o futuro do esporte. Objetivo: Avaliar as características funcionais e neuromusculares de atletas de futebol da categoria de base, no desempenho em saltos verticais. METODOLOGIA: Foram avaliados atletas de futebol com idade entre 15 e 17 anos. Foram realizados em duas plataformas de força os seguintes saltos verticais: salto em agachamento, salto em contramovimento, salto pliométrico de 40 cm de altura. Para análise das variáveis das forças concêntrica, excêntrica, impacto e altura dos saltos utilizou-se a prova estatística de Shapiro-Wilk, descrição das variáveis em média e desvio padrão, considerando quando p 0,05. Sem diferença na força concêntrica entre as categorias e os tipos de saltos. Maior força de impacto no contramovimento. Maior força em membro inferior direito em todos os saltos e variáveis de força. CONCLUSÕES: Encontramos assimetria entre os membros inferiores, podendo correlacionar com um déficit de potência muscular, má desaceleração do movimento e erros biomecânicos. Fatores predisponentes a lesões musculoesqueléticas, os quais podem ser prevenidos. A avaliação instrumentada da força através desses testes pode subsidiar os profissionais do clube como uma ferramenta de trabalho, capaz de aprimorar o treinamento, preparação e reabilitação. Entretanto, são necessárias mais pesquisas, de forma que momentos distintos da idade e da temporada do atleta sejam avaliados.

  8. Análise quantitativa e molecular de hemoglobina fetal em indivíduos da população brasileira

    Directory of Open Access Journals (Sweden)

    Zamaro Paula J. A.

    2003-01-01

    Full Text Available A hemoglobina fetal - Hb F, formada por duas cadeias gama e duas cadeias alfa, é característica do período fetal do desenvolvimento, tendo sua síntese diminuída no período pós-natal. Em algumas alterações hereditárias, a Hb F permanece aumentada, como nas delta-beta talassemia, beta talassemia e persistência hereditária de Hb F (PHHF. A síntese da globina gama também pode ser estimulada por fatores externos como leucemias, transplantes de medula óssea, induções químicas, dentre outros. Através da observação de Hb F aumentada em doadores de sangue por procedimentos eletroforéticos objetivou-se avaliar a quantidade de Hb F em amostras de sangue de candidatos à doação, visando estabelecer seus limites de normalidade na população de São José do Rio Preto e região, por meio de desnaturação alcalina e cromatografia líquida de alta pressão (HPLC, comparar as metodologias aplicadas e, nos indivíduos com Hb F aumentada, realizar estudos moleculares para identificar as mutações que alteram a expressão dos genes gama. Foram analisadas 208 amostras de sangue, sendo 119 de candidatos à doação e 89 de indivíduos sem sintomas de anemia ou achados hematológicos e com Hb F aumentada como grupo comparativo. Das 119 amostras de candidatos à doação, 110 foram utilizadas para traçar o perfil de normalidade de Hb F, comparando-se as metodologias de desnaturação alcalina e HPLC, onde se obteve a média de 1,48% e de 0,6%, respectivamente. A análise estatística por regressão linear mostrou diferença significativa na comparação entre as duas metodologias aplicadas, sendo a HPLC mais precisa para a quantificação de Hb F. Foram observados nos testes de rastreamento de hemoglobinas anormais nestas 110 amostras de sangue: 16,4% de alfa talassemia, 0,9% com Hb F aumentada, 0,9% com beta talassemia e 0,9% com hemoglobina variante de cadeia delta. Os outros nove doadores de sangue apresentaram Hb F acima de 10% em

  9. Sub-30 nm patterning of molecular resists based on crosslinking through tip based oxidation

    Science.gov (United States)

    Lorenzoni, Matteo; Wagner, Daniel; Neuber, Christian; Schmidt, Hans-Werner; Perez-Murano, Francesc

    2018-06-01

    Oxidation Scanning Probe Lithography (o-SPL) is an established method employed for device patterning at the nanometer scale. It represents a feasible and inexpensive alternative to standard lithographic techniques such as electron beam lithography (EBL) and nanoimprint lithography (NIL). In this work we applied non-contact o-SPL to an engineered class of molecular resists in order to obtain crosslinking by electrochemical driven oxidation. By patterning and developing various resist formulas we were able to obtain a reliable negative tone resist behavior based on local oxidation. Under optimal conditions, directly written patterns can routinely reach sub-30 nm lateral resolution, while the final developed features result wider, approaching 50 nm width.

  10. Clinicopathological and Molecular Histochemical Review of Skull Base Metastasis from Differentiated Thyroid Carcinoma

    International Nuclear Information System (INIS)

    Matsuno, Akira; Murakami, Mineko; Hoya, Katsumi; Yamada, Shoko M.; Miyamoto, Shinya; Yamada, So; Son, Jae-Hyun; Nishido, Hajime; Ide, Fuyuaki; Nagashima, Hiroshi; Sugaya, Mutsumi; Hirohata, Toshio; Mizutani, Akiko; Okinaga, Hiroko; Ishii, Yudo; Tahara, Shigeyuki; Teramoto, Akira; Osamura, R. Yoshiyuki; Yamazaki, Kazuto; Ishida, Yasuo

    2013-01-01

    Skull base metastasis from differentiated thyroid carcinoma including follicular thyroid carcinoma (FTC) and papillary thyroid carcinoma (PTC) is a rare clinical entity. Eighteen FTC cases and 10 PTC cases showing skull base metastasis have been reported. The most common symptom of skull base metastasis from FTC and PTC is cranial nerve dysfunction. Bone destruction and local invasion to the surrounding soft tissues are common on radiological imaging. Skull base metastases can be the initial clinical presentation of FTC and PTC in the presence of silent primary sites. The possibility of skull base metastasis from FTC and PTC should be considered in patients with the clinical symptoms of cranial nerve dysfunction and radiological findings of bone destruction. A variety of genetic alterations in thyroid tumors have been identified to have a fundamental role in their tumorigenesis. Molecular histochemical studies are useful for elucidating the histopathological features of thyroid carcinoma. Recent molecular findings may provide novel molecular-based treatment strategies for thyroid carcinoma

  11. Molecular-based recursive partitioning analysis model for glioblastoma in the temozolomide era a correlative analysis based on nrg oncology RTOG 0525

    NARCIS (Netherlands)

    Bell, Erica Hlavin; Pugh, Stephanie L.; McElroy, Joseph P.; Gilbert, Mark R.; Mehta, Minesh; Klimowicz, Alexander C.; Magliocco, Anthony; Bredel, Markus; Robe, Pierre; Grosu, Anca L.; Stupp, Roger; Curran, Walter; Becker, Aline P.; Salavaggione, Andrea L.; Barnholtz-Sloan, Jill S.; Aldape, Kenneth; Blumenthal, Deborah T.; Brown, Paul D.; Glass, Jon; Souhami, Luis; Lee, R. Jeffrey; Brachman, David; Flickinger, John; Won, Minhee; Chakravarti, Arnab

    2017-01-01

    IMPORTANCE: There is a need for a more refined, molecularly based classification model for glioblastoma (GBM) in the temozolomide era. OBJECTIVE: To refine the existing clinically based recursive partitioning analysis (RPA) model by incorporating molecular variables. DESIGN, SETTING, AND

  12. Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes.

    Science.gov (United States)

    Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

    2018-01-01

    Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes . A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes , providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes , providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen.

  13. Transforming bases to bytes: Molecular computing with DNA

    Indian Academy of Sciences (India)

    Despite the popular image of silicon-based computers for computation, an embryonic field of mole- cular computation is emerging, where molecules in solution perform computational ..... [4] Mao C, Sun W, Shen Z and Seeman N C 1999. A nanomechanical device based on the B-Z transition of DNA; Nature 397 144–146.

  14. The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein.

    Directory of Open Access Journals (Sweden)

    Kenrick A Vassall

    Full Text Available The classic isoforms of myelin basic protein (MBP are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99- containing a putative SH3-ligand, adjacent to a region that forms an amphipathic α-helix (P82-I90 upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP kinases. Here, we have investigated the structure of the α-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the α-helical region, by utilizing four 36-residue peptides (S72-S107 with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the α-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012. Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic α-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the α-helix upon temperature perturbation and affect the

  15. Griesinger e as bases da "Primeira psiquiatria biológica"

    Directory of Open Access Journals (Sweden)

    Mário Eduardo Costa Pereira

    2007-12-01

    Full Text Available Wilhelm Griesinger foi um personagem central na história da psiquiatria alemã. Considerado por muitos como um dos "pais da psiquiatria biológica", sua obra, na verdade, é extremamente complexa, apoiando-se em uma sofisticada teoria do eu e das desestruturação dos processos mentais na psicopatologia.

  16. Molecular Bases and Phenotypic Determinants of Aromatase Excess Syndrome

    Directory of Open Access Journals (Sweden)

    Maki Fukami

    2012-01-01

    Full Text Available Aromatase excess syndrome (AEXS is a rare autosomal dominant disorder characterized by gynecomastia. This condition is caused by overexpression of CYP19A1 encoding aromatase, and three types of cryptic genomic rearrangement around CYP19A1, that is, duplications, deletions, and inversions, have been identified in AEXS. Duplications appear to have caused CYP19A1 overexpression because of an increased number of physiological promoters, whereas deletions and inversions would have induced wide CYP19A1 expression due to the formation of chimeric genes consisting of a noncoding exon(s of a neighboring gene and CYP19A1 coding exons. Genotype-phenotype analysis implies that phenotypic severity of AEXS is primarily determined by the expression pattern of CYP19A1 and the chimeric genes and by the structural property of the fused exons with a promoter function (i.e., the presence or the absence of a natural translation start codon. These results provide novel information about molecular mechanisms of human genetic disorders and biological function of estrogens.

  17. Descifrando las bases moleculares de la resistencia cuantitativa

    Directory of Open Access Journals (Sweden)

    Camilo Lopez

    2011-05-01

    Full Text Available Uno de los factores mas importantes que afectan los cultivos son las enfermedades ocasionadas por los patógenos. La resistencia vegetal ha sido clásicamente dividida en dos tipos: i competa, vertical o cualitativa que es gobernada por un solo gen y ii incompleta, horizontal o cuantitativa la cual es gobernada por varios genes. Aunque la resistencia cuantitativa provee resistencia de amplio espectro y es durable, los mecanismo moleculares subyacentes no han sido estudiados en detalle. En esta revisión se propone un modelo basado en la co-localización de genes similares a los clásicos genes de resistencia cualitativa con QTLs (Quantitative Trait Loci para explicar el mecanismo involucrado en el reconocimiento del patógeno durante la resistencia cuantitativa. Además se presenta información acerca del progreso obtenido en los últimos tres años para entender este tipo de resistencia, que culminó con la clonación de varios genes asociados a la resistencia cuantitativa. En conjunto, estos datos proveen nuevas luces sobre la naturaleza genética de este tipo de resistencia y de cómo puede ser empleada en programas de mejoramiento genético.

  18. Structure-Function Based Molecular Relationships in Ewing's Sarcoma

    Science.gov (United States)

    2015-01-01

    Ewing's Sarcoma Oncogene (ews) on chromosome 22q12 is encoding a ubiquitously expressed RNA-binding protein (EWS) with unknown function that is target of tumor-specific chromosomal translocations in Ewing's sarcoma family of tumors. A model of transcription complex was proposed in which the heterodimer Rpb4/7 binds to EAD, connecting it to Core RNA Pol II. The DNA-binding domain, provided by EFP, is bound to the promoter. Rpb4/7 binds RNA, stabilizing the transcription complex. The complex Rpb4/7 can stabilize the preinitiation complexes by converting the conformation of RNA Pol II. EWS may change its conformation, so that NTD becomes accessible. Two different mechanisms of interaction between EWS and RNA Pol II are proposed: (I) an intermolecular EWS-EWS interaction between two molecules, pushing conformation from “closed” to “open” state, or (II) an intramolecular interaction inside the molecule of EWS, pushing conformation of the molecule from “closed” to “open” state. The modified forms of EWS may interact with Pol II subunits hsRpb5 and hsRpb7. The EWS and EFPs binding partners are described schematically in a model, an attempt to link the transcription with the splicing. The proposed model helps to understand the functional molecular interactions in cancer, to find new partners and ways to treat cancer. PMID:25688366

  19. QSAR models based on quantum topological molecular similarity.

    Science.gov (United States)

    Popelier, P L A; Smith, P J

    2006-07-01

    A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

  20. Transoral robotic surgery for the base of tongue squamous cell carcinoma: a preliminary comparison between da Vinci Xi and Si.

    Science.gov (United States)

    Alessandrini, Marco; Pavone, Isabella; Micarelli, Alessandro; Caporale, Claudio

    2017-09-13

    Considering the emerging advantages related to da Vinci Xi robotic platform, the aim of this study is to compare for the first time the operative outcomes of this tool to the previous da Vinci Si during transoral robotic surgery (TORS), both performed for squamous cell carcinomas (SCC) of the base of tongue (BOT). Intra- and peri-operative outcomes of eight patients with early stage (T1-T2) of the BOT carcinoma and undergoing TORS by means of the da Vinci Xi robotic platform (Xi-TORS) are compared with the da Vinci Si group ones (Si-TORS). With respect to Si-TORS group, Xi-TORS group demonstrated a significantly shorter overall operative time, console time, and intraoperative blood loss, as well as peri-operative pain intensity and length of mean hospital stays and nasogastric tube positioning. Considering recent advantages offered by surgical robotic techniques, the da Vinci Xi Surgical System preliminary outcomes could suggest its possible future routine implementation in BOT squamous cell carcinoma procedures.

  1. Determination of high molecular mass compounds from Amazonian plant's leaves; Determinacao de compostos de massa molecular alta em folhas de plantas da Amazonia

    Energy Technology Data Exchange (ETDEWEB)

    Siqueira, Denilson Soares de; Pereira, Alberto dos Santos; Aquino Neto, Francisco Radler de [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Quimica]. E-mail: ladetec@iq.gov.br; Cabral, Jose Augusto; Ferreira, Carlos Alberto Cid [Instituto Nacional de Pesquisas da Amazonia (INPA), Manaus, AM (Brazil); Simoneit, Bernd R.T. [Oregon State Univ., Corvallis, OR (United States). College of Oceanic and Atmospheric Sciences. Petroleum and Environmental Geochemistry Group; Elias, Vladimir O. [Analytical Solution, Rio de Janeiro, RJ (Brazil)

    2003-10-01

    The fractions of dichloromethane extracts of leaves from andiroba (Carapa guianensis - Meliaceae), caapi (Banisteriopsis caapi - Malpighiaceae), cocoa (Theobroma cacao - Sterculiaceae), Brazil nut (Bertholletia excelsa - Lecytidaceae), cupuacu (Theobroma grandiflorum - Sterculiaceae), marupa (Simaruba amara - Simaroubaceae) and rubber tree (Hevea brasiliensis - Euphorbiaceae), were analyzed by HT-HRGC and HT-HRGC-MS. Esters of homologous series of fatty acids and long chain alcohols, phytol, amyrines and tocopherols were characterized. The characterization of the compounds was based mainly in mass spectra data and in addition by usual spectrometric data ({sup 1}H and {sup 13}C NMR, IR). (author)

  2. Monitorização da força da ondulação na base da arriba (Pessegueiro, SW Portugal. Primeiros resultados

    Directory of Open Access Journals (Sweden)

    Mário Neves

    1997-11-01

    Full Text Available MEASUREMENT OF THE WAVE FORCE AT THE CLIFF BASE (PESSEGUEIRO, SW PORTUGAL. FIRST RESULTS. In this article the characteristicsof a new wave force sensor (EWIN are briefly described. This instrument was bolted to the shore platform of Pessegueiro on a first trial experience in Portugal. The maximum wave force records are also analysed in correlation with the wave climate accured in these occasions.

  3. Matrix and substrate effects on the sputtering of a 2 kDa molecule: Insights from molecular dynamics

    International Nuclear Information System (INIS)

    Delcorte, A.; Arezki, B.; Garrison, B.J.

    2003-01-01

    In an effort towards a more accurate theoretical description of matrix and substrate effects in organic sputtering, we report on molecular dynamics simulations of the desorption induced by 500 eV Ar projectiles bombarding samples composed of polystyrene (PS) oligomers embedded in a trimethylbenzene matrix or cast on a silver substrate. The ejection of intact PS molecules, sometimes accompanied by matrix molecules/silver atoms, is observed in the first 10 ps following the impact. For the 'matrix' sample, the results indicate that the emission of large amounts of organic material is mostly vibrationally induced. Extended calculations show that matrix:analyte clusters decay after emission, liberating the analyte in flight. In the case of the 'substrate' sample, the emission is oftentimes the result of the concerted upward motion of several metal atoms underneath the molecule. Finally, the comparison between a matrix:analyte sample confined in a nanostructured silver crystal and a purely organic sample under identical bombardment conditions shows that the presence of the silver medium significantly enhances the desorption yields

  4. A communication theoretical analysis of FRET-based mobile ad hoc molecular nanonetworks.

    Science.gov (United States)

    Kuscu, Murat; Akan, Ozgur B

    2014-09-01

    Nanonetworks refer to a group of nanosized machines with very basic operational capabilities communicating to each other in order to accomplish more complex tasks such as in-body drug delivery, or chemical defense. Realizing reliable and high-rate communication between these nanomachines is a fundamental problem for the practicality of these nanonetworks. Recently, we have proposed a molecular communication method based on Förster Resonance Energy Transfer (FRET) which is a nonradiative excited state energy transfer phenomenon observed among fluorescent molecules, i.e., fluorophores. We have modeled the FRET-based communication channel considering the fluorophores as single-molecular immobile nanomachines, and shown its reliability at high rates, and practicality at the current stage of nanotechnology. In this study, for the first time in the literature, we investigate the network of mobile nanomachines communicating through FRET. We introduce two novel mobile molecular nanonetworks: FRET-based mobile molecular sensor/actor nanonetwork (FRET-MSAN) which is a distributed system of mobile fluorophores acting as sensor or actor node; and FRET-based mobile ad hoc molecular nanonetwork (FRET-MAMNET) which consists of fluorophore-based nanotransmitter, nanoreceivers and nanorelays. We model the single message propagation based on birth-death processes with continuous time Markov chains. We evaluate the performance of FRET-MSAN and FRET-MAMNET in terms of successful transmission probability and mean extinction time of the messages, system throughput, channel capacity and achievable communication rates.

  5. PRATICANTES DA ESTRATÉGIA E AS BASES PRAXEOLÓGICAS DA INDÚSTRIA DO MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Cristiano Oliveira Maciel

    2015-10-01

    Full Text Available This paper goes beyond traditional explanations about the managerial fads that shape the management industry. Therefore, a praxeological perspective was adopted to examine the bases underlying this industry. Data were collected during a seven-month period through observation, documental research and interviews that were conducted within an organization in the emerging sector of online discount coupon selling. We analyzed the social construction process of strategy practitioners in different hierarchical domains and found that the ordinary dynamics within organizations – which are at the base of the management industry – occur through the articulation of central and peripheral strategy, discourse, and social trajectory praxes, and through the stratification of three organizational role categories.

  6. New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them.

    Science.gov (United States)

    Ehresmann, Bernd; de Groot, Marcel J; Alex, Alexander; Clark, Timothy

    2004-01-01

    New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.

  7. Integrative pathway knowledge bases as a tool for systems molecular medicine.

    Science.gov (United States)

    Liang, Mingyu

    2007-08-20

    There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

  8. Molecular MR Imaging of CD44 in Breast Cancer with Hyaluronan-Based Contrast Agents

    Science.gov (United States)

    2009-09-01

    linear polysaccharide composed of alternating (β-1,4)-linked d- glucuronic acid and (β-1,3) N-acetyl-d-glucosamine residues with molecular weights as...enzymatic reactions in-vivo that generate polysaccharides of decreasing sizes, which in principle may facilitate the timely excretion of HA based...14CO2) or in urine (as low molecular weight HA or monosaccharide fragments). The same authors also reported that the total amount of excretion into

  9. Influence of the host (Cho) and of the cultivation strategy on glycan structures and molecular properties of human thyrotrophin; Influencia do hospedeiro (Cho) e da estrategia de cultivo nas estruturas glicidicas e propriedades moleculares da tireotrofina humana

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Joao Ezequiel de

    2007-07-01

    .39 - 7.35 pl range. A considerably different distribution, with more forms in the acidic region, was observed, however, for two native pituitary preparations. When analyzed via a simple and precise single-dose bioassay, a slightly higher bioactivity (p<0.02) was found for r-hTSH-IPEN obtained in the presence of CO{sub 2}. This potency however, was not significantly different from that of Thyrogen, the two preparations being 1.6-1.8-fold more potent than the reference preparation of p-hTSH. We can conclude that, at least for the case of CHO-derived r-hTSH, different production processes do not greatly affect its N-glycan structures, charge isomer distribution or biological activity. Thyrogen and r-hTSH-IPEN, when compared to p-hTSH-NIDDK, presented about a 7% increased relative molecular mass (MR) determined by MALDI-TOF-MS analysis. This technique, allowing accurate heterodimer mass determinations, provided MR values of 29611, 29839 and 27829, respectively. Significant differences in hydrophobic properties, evaluated by RP-HPLC, were found for r-hTSH and p-hTSH. Also differences related to carbohydrate moiety, mainly in the amount of sialic acid and galactose, were found for these preparations, a much lower content of these sugar residues being observed in p-hTSH.(author)

  10. Discrete Biogeography Based Optimization for Feature Selection in Molecular Signatures.

    Science.gov (United States)

    Liu, Bo; Tian, Meihong; Zhang, Chunhua; Li, Xiangtao

    2015-04-01

    Biomarker discovery from high-dimensional data is a complex task in the development of efficient cancer diagnoses and classification. However, these data are usually redundant and noisy, and only a subset of them present distinct profiles for different classes of samples. Thus, selecting high discriminative genes from gene expression data has become increasingly interesting in the field of bioinformatics. In this paper, a discrete biogeography based optimization is proposed to select the good subset of informative gene relevant to the classification. In the proposed algorithm, firstly, the fisher-markov selector is used to choose fixed number of gene data. Secondly, to make biogeography based optimization suitable for the feature selection problem; discrete migration model and discrete mutation model are proposed to balance the exploration and exploitation ability. Then, discrete biogeography based optimization, as we called DBBO, is proposed by integrating discrete migration model and discrete mutation model. Finally, the DBBO method is used for feature selection, and three classifiers are used as the classifier with the 10 fold cross-validation method. In order to show the effective and efficiency of the algorithm, the proposed algorithm is tested on four breast cancer dataset benchmarks. Comparison with genetic algorithm, particle swarm optimization, differential evolution algorithm and hybrid biogeography based optimization, experimental results demonstrate that the proposed method is better or at least comparable with previous method from literature when considering the quality of the solutions obtained. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Three decades of structure- and property-based molecular design

    DEFF Research Database (Denmark)

    Müller, Klaus

    2014-01-01

    of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries...

  12. Projected [1H,15N]-HMQC-[1H,1H]-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex

    International Nuclear Information System (INIS)

    Galius, Veniamin; Leontiou, Chrysoula; Richmond, Timothy; Wider, Gerhard

    2008-01-01

    We present a projected [ 1 H, 15 N]-HMQC-[ 1 H, 1 H]-NOESY experiment for observation of NOE interactions between amide protons with degenerate 15 N chemical shifts in large molecular systems. The projection is achieved by simultaneous evolution of the multiple quantum coherence of the nitrogen spin and the attached proton spin. In this way NOE signals can be separated from direct-correlation peaks also in spectra with low resolution by fully exploiting both 1 H and 15 N frequency differences, such that sensitivity can be increased by using short maximum evolution times. The sensitivity of the experiment is not dependent on the projection angle for projections up to 45 deg. and no additional pulses or delays are required as compared to the conventional 2D [ 1 H, 15 N]-HMQC-NOESY. The experiment provides two distinct 2D spectra corresponding to the positive and negative angle projections, respectively. With a linear combination of 1D cross-sections from the two projections the unavoidable sensitivity loss in projection spectra can be compensated for each particular NOE interaction. We demonstrate the application of the novel projection experiment for the observation of an NOE interaction between two sequential glycines with degenerate 15 N chemical shifts in a 121.3 kDa complex of the linker H1 histone protein with a 152 bp linear DNA

  13. Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

    KAUST Repository

    Li, Haoyuan; Qiu, Yong; Duan, Lian

    2016-01-01

    A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using

  14. Molecular Engineering of Technetium and Rhenium Based Radiopharmaceuticals

    International Nuclear Information System (INIS)

    Zubieta, J.

    2003-01-01

    The research was based on the observation that despite the extraordinarily rich coordination chemistry of technetium and rhenium and several notable successes in reagent design, the extensive investigations by numerous research groups on a variety of N 2 S 2 and N 3 S donor type ligands and on HYNIC have revealed that the chemistries of these ligands with Tc and Re are rather complex, giving rise to considerable difficulties in the development of reliable procedures for the development of radiopharmaceutical reagents

  15. New polynomial-based molecular descriptors with low degeneracy.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available In this paper, we introduce a novel graph polynomial called the 'information polynomial' of a graph. This graph polynomial can be derived by using a probability distribution of the vertex set. By using the zeros of the obtained polynomial, we additionally define some novel spectral descriptors. Compared with those based on computing the ordinary characteristic polynomial of a graph, we perform a numerical study using real chemical databases. We obtain that the novel descriptors do have a high discrimination power.

  16. TARGET-ORIENTED GENERIC FINGERPRINT-BASED MOLECULAR REPRESENTATION

    OpenAIRE

    Petr Skoda; David Hoksza

    2014-01-01

    The screening of chemical libraries is an important step in the drug discovery process. The existing chemical libraries contain up to millions of compounds. As the screening at such scale is expensive, the virtual screening is often utilized. There exist several variants of virtual screening and ligand-based virtual screening is one of them. It utilizes the similarity of screened chemical compounds to known compounds. Besides the employed similarity measure, another aspect grea...

  17. O Core Curriculum da Unesco como Base para Formação em Bioética

    Directory of Open Access Journals (Sweden)

    Fabiano Maluf

    Full Text Available RESUMO A revolução biotecnológica das últimas décadas teve como resultado o desenvolvimento de um poder quase sem limites sobre a vida humana. Tal contexto exige do profissional uma visão globalizada dos problemas éticos e sociais da era contemporânea, alicerçada em sólidas bases filosóficas e legais. Este contexto torna necessária a promoção de novas competências e habilidades relacionadas à vida profissional. Neste sentido, o ensino da Bioética desponta como uma possibilidade de inovação curricular alternativa ao tradicional modelo prescritivo e normativo. Este artigo relata a experiência da Cátedra Unesco de Bioética da Universidade de Brasília com a utilização do Core Curriculum proposto pela Unesco como instrumento didático-pedagógico adequado ao ensino da Bioética. Entre os dilemas pedagógicos enfrentados pela Bioética como disciplina encontram-se: a construção de seus conteúdos, sua estruturação, as concepções teóricas a serem seguidas e seus objetivos. A contextualização e o aperfeiçoamento da estratégia proposta pelo Core Curriculum podem significar importantes instrumentos facilitadores para docentes que buscam organizar práticas didático-pedagógicas inovadoras em Bioética com o intuito de proporcionar resultados efetivos na formação de seus estudantes.

  18. Tunable separations based on a molecular size effect for biomolecules by poly(ethylene glycol) gel-based capillary electrophoresis.

    Science.gov (United States)

    Kubo, Takuya; Nishimura, Naoki; Furuta, Hayato; Kubota, Kei; Naito, Toyohiro; Otsuka, Koji

    2017-11-10

    We report novel capillary gel electrophoresis (CGE) with poly(ethylene glycol) (PEG)-based hydrogels for the effective separations of biomolecules containing sugars and DNAs based on a molecular size effect. The gel capillaries were prepared in a fused silica capillary modified with 3-(trimethoxysilyl)propylmethacrylate using a variety of the PEG-based hydrogels. After the fundamental evaluations in CGE regarding the separation based on the molecular size effect depending on the crosslinking density, the optimized capillary provided the efficient separation of glucose ladder (G1 to G20). In addition, another capillary showed the successful separation of DNA ladder in the range of 10-1100 base pair, which is superior to an authentic acrylamide-based gel capillary. For both glucose and DNA ladders, the separation ranges against the molecular size were simply controllable by alteration of the concentration and/or units of ethylene oxide in the PEG-based crosslinker. Finally, we demonstrated the separations of real samples, which included sugars carved out from monoclonal antibodies, mAbs, and then the efficient separations based on the molecular size effect were achieved. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Molecular monolayers for electrical passivation and functionalization of silicon-based solar energy devices

    NARCIS (Netherlands)

    Veerbeek, Janneke; Firet, Nienke J.; Vijselaar, Wouter; Elbersen, R.; Gardeniers, Han; Huskens, Jurriaan

    2017-01-01

    Silicon-based solar fuel devices require passivation for optimal performance yet at the same time need functionalization with (photo)catalysts for efficient solar fuel production. Here, we use molecular monolayers to enable electrical passivation and simultaneous functionalization of silicon-based

  20. Molecular typing of Staphylococcus aureus based on coagulase gene.

    Science.gov (United States)

    Javid, Faizan; Taku, Anil; Bhat, Mohd Altaf; Badroo, Gulzar Ahmad; Mudasir, Mir; Sofi, Tanveer Ahmad

    2018-04-01

    This study was conducted to study the coagulase gene-based genetic diversity of Staphylococcus aureus , isolated from different samples of cattle using restriction fragment length polymorphism (RFLP) and their sequence-based phylogenetic analysis. A total of 192 different samples from mastitic milk, nasal cavity, and pus from skin wounds of cattle from Military Dairy Farm, Jammu, India, were screened for the presence of S. aureus . The presumptive isolates were confirmed by nuc gene-based polymerase chain reaction (PCR). The confirmed S. aureus isolates were subjected to coagulase ( coa ) gene PCR. Different coa genotypes observed were subjected to RFLP using restriction enzymes Hae111 and Alu1 , to obtain the different restriction patterns. One isolate from each restriction pattern was sequenced. These sequences were aligned for maximum homology using the Bioedit softwareandsimilarity in the sequences was inferred with the help of sequence identity matrix. Of 192 different samples,39 (20.31%) isolates of S. aureus were confirmed by targeting nuc gene using PCR. Of 39 S. aureus isolates, 25 (64.10%) isolates carried coa gene. Four different genotypes of coa gene, i.e., 514 bp, 595 bp, 757 bp, and 802 bp were obtained. Two coa genotypes, 595 bp (15 isolates) and 802 bp (4 isolates), were observed in mastitic milk. 514 bp (2 isolates) and 757 bp (4 isolates) coa genotypes were observed from nasal cavity and pus from skin wounds, respectively. On RFLP using both restriction enzymes, four different restriction patterns P1, P2, P3, and P4 were observed. On sequencing, four different sequences having unique restriction patterns were obtained. The most identical sequences with the value of 0.810 were found between isolate S. aureus 514 (nasal cavity) and S. aureus 595 (mastitic milk), and thus, they are most closely related. While as the most distant sequences with the value of 0.483 were found between S. aureus 514 and S. aureus 802 isolates. The study, being localized

  1. Prospects of luminescence based molecular scale logic gates and logic circuits

    Energy Technology Data Exchange (ETDEWEB)

    Speiser, Shammai, E-mail: speiser@technion.ac.il

    2016-01-15

    In recent years molecular electronics has emerged as a rapidly growing research field. The aim of this review is to introduce this subject as a whole with special emphasis on molecular scale potential devices and applications. As a particular example we will discuss all optical molecular scale logic gates and logic circuits based on molecular fluorescence and electronic excitation transfer processes. Charge and electronic energy transfers (ET and EET) are well-studied examples whereby different molecules can signal their state from one (the donor, D) to the other (the acceptor, A). We show how a half-adder logic circuit can be implemented on one molecule that can communicate its logic output as input to another half-adder molecule. This is achieved as an electronic energy transfer from a donor to an acceptor, thus implementing a molecular full adder. We discuss a specific pair, the rhodamine–azulene, for which there is considerable spectroscopic data, but the scheme is general enough to allow a wide choice of D and A pairs. We present results based on this pair, in which, for the first time, an all optical half-adder and full-adder logic circuits are implemented. - Highlights: • Molecular scale logic • Photoquenching • Full adder.

  2. Prospects of luminescence based molecular scale logic gates and logic circuits

    International Nuclear Information System (INIS)

    Speiser, Shammai

    2016-01-01

    In recent years molecular electronics has emerged as a rapidly growing research field. The aim of this review is to introduce this subject as a whole with special emphasis on molecular scale potential devices and applications. As a particular example we will discuss all optical molecular scale logic gates and logic circuits based on molecular fluorescence and electronic excitation transfer processes. Charge and electronic energy transfers (ET and EET) are well-studied examples whereby different molecules can signal their state from one (the donor, D) to the other (the acceptor, A). We show how a half-adder logic circuit can be implemented on one molecule that can communicate its logic output as input to another half-adder molecule. This is achieved as an electronic energy transfer from a donor to an acceptor, thus implementing a molecular full adder. We discuss a specific pair, the rhodamine–azulene, for which there is considerable spectroscopic data, but the scheme is general enough to allow a wide choice of D and A pairs. We present results based on this pair, in which, for the first time, an all optical half-adder and full-adder logic circuits are implemented. - Highlights: • Molecular scale logic • Photoquenching • Full adder

  3. Electronic shift register memory based on molecular electron-transfer reactions

    Science.gov (United States)

    Hopfield, J. J.; Onuchic, Jose Nelson; Beratan, David N.

    1989-01-01

    The design of a shift register memory at the molecular level is described in detail. The memory elements are based on a chain of electron-transfer molecules incorporated on a very large scale integrated (VLSI) substrate, and the information is shifted by photoinduced electron-transfer reactions. The design requirements for such a system are discussed, and several realistic strategies for synthesizing these systems are presented. The immediate advantage of such a hybrid molecular/VLSI device would arise from the possible information storage density. The prospect of considerable savings of energy per bit processed also exists. This molecular shift register memory element design solves the conceptual problems associated with integrating molecular size components with larger (micron) size features on a chip.

  4. Surface based detection schemes for molecular interferometry experiments - implications and possible applications

    Science.gov (United States)

    Juffmann, Thomas; Milic, Adriana; Muellneritsch, Michael; Arndt, Markus

    2011-03-01

    Surface based detection schemes for molecular interferometry experiments might be crucial in the search for the quantum properties of larger and larger objects since they provide single particle sensitivity. Here we report on molecular interferograms of different biomolecules imaged using fluorescence microscopy. Being able to watch the build-up of an interferogram live and in situ reveals the matter-wave behavior of these complex molecules in an unprecedented way. We examine several problems encountered due to van-der-Waals forces between the molecules and the diffraction grating and discuss possible ways to circumvent these. Especially the advent of ultra-thin (1-100 atomic layers) diffraction masks might path the way towards molecular holography. We also discuss other possible applications such as coherent molecular microscopy.

  5. Large resistance change on magnetic tunnel junction based molecular spintronics devices

    Science.gov (United States)

    Tyagi, Pawan; Friebe, Edward

    2018-05-01

    Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.

  6. Analise da expressão de chaperonas moleculares em plantas e clonagem, purificação e caracterização inicial das proteinas Hsp100 e Hsp90 de cana-de-açucar

    OpenAIRE

    Thiago Carlos Cagliari

    2009-01-01

    Resumo: As proteinas sao macromoleculas que possuem importancia vital para o funcionamento celular, participando da maioria das reacoes biologicas e tambem como componentes estruturais. Para que uma proteina possa exercer sua funcao, precisa atingir sua estrutura nativa atraves de um processo denominado enovelamento proteico. Neste contexto, as chaperonas moleculares sao proteinas capazes de auxiliar no enovelamento de outras proteinas, atuando na prevencao de agregados, desagregacao, translo...

  7. Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.

    Science.gov (United States)

    Karthik, Govindasamy-Muralidharan; Rantalainen, Mattias; Stålhammar, Gustav; Lövrot, John; Ullah, Ikram; Alkodsi, Amjad; Ma, Ran; Wedlund, Lena; Lindberg, Johan; Frisell, Jan; Bergh, Jonas; Hartman, Johan

    2017-11-29

    Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics. In this study we applied RNA-sequencing to quantify gene expression in 43 pieces (2-5 pieces per tumor) from 12 breast tumors (Cohort 1). We determined molecular subtype and transcriptomic grade for all tumor pieces and analysed to what extent pieces originating from the same tumors are concordant or discordant with each other. Additionally, we validated our finding in an independent cohort consisting of 19 pieces (2-6 pieces per tumor) from 6 breast tumors (Cohort 2) profiled using microarray technique. Exome sequencing was also performed on this cohort, to investigate the extent of intra-tumor genomic heterogeneity versus the intra-tumor molecular subtype classifications. Molecular subtyping was consistent in 11 out of 12 tumors and transcriptomic grade assignments were consistent in 11 out of 12 tumors as well. Molecular subtype predictions revealed consistent subtypes in four out of six patients in this cohort 2. Interestingly, we observed extensive intra-tumor genomic heterogeneity in these tumor pieces but not in their molecular subtype classifications. Our results suggest that macroscopic intra-tumoral transcriptomic heterogeneity is limited and unlikely to have an impact on molecular diagnostics for most patients.

  8. Sequence analysis and molecular characterization of Clonorchis sinensis hexokinase, an unusual trimeric 50-kDa glucose-6-phosphate-sensitive allosteric enzyme.

    Directory of Open Access Journals (Sweden)

    Tingjin Chen

    Full Text Available Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis, is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK, the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small

  9. Sequence Analysis and Molecular Characterization of Clonorchis sinensis Hexokinase, an Unusual Trimeric 50-kDa Glucose-6-Phosphate-Sensitive Allosteric Enzyme

    Science.gov (United States)

    Chen, Tingjin; Ning, Dan; Sun, Hengchang; Li, Ran; Shang, Mei; Li, Xuerong; Wang, Xiaoyun; Chen, Wenjun; Liang, Chi; Li, Wenfang; Mao, Qiang; Li, Ye; Deng, Chuanhuan; Wang, Lexun; Wu, Zhongdao; Huang, Yan; Xu, Jin; Yu, Xinbing

    2014-01-01

    Clonorchiasis, which is induced by the infection of Clonorchis sinensis (C. sinensis), is highly associated with cholangiocarcinoma. Because the available examination, treatment and interrupting transmission provide limited opportunities to prevent infection, it is urgent to develop integrated strategies to prevent and control clonorchiasis. Glycolytic enzymes are crucial molecules for trematode survival and have been targeted for drug development. Hexokinase of C. sinensis (CsHK), the first key regulatory enzyme of the glycolytic pathway, was characterized in this study. The calculated molecular mass (Mr) of CsHK was 50.0 kDa. The obtained recombinant CsHK (rCsHK) was a homotrimer with an Mr of approximately 164 kDa, as determined using native PAGE and gel filtration. The highest activity was obtained with 50 mM glycine-NaOH at pH 10 and 100 mM Tris-HCl at pH 8.5 and 10. The kinetics of rCsHK has a moderate thermal stability. Compared to that of the corresponding negative control, the enzymatic activity was significantly inhibited by praziquantel (PZQ) and anti-rCsHK serum. rCsHK was homotropically and allosterically activated by its substrates, including glucose, mannose, fructose, and ATP. ADP exhibited mixed allosteric effect on rCsHK with respect to ATP, while inorganic pyrophosphate (PPi) displayed net allosteric activation with various allosteric systems. Fructose behaved as a dose-dependent V activator with the substrate glucose. Glucose-6-phosphate (G6P) displayed net allosteric inhibition on rCsHK with respect to ATP or glucose with various allosteric systems in a dose-independent manner. There were differences in both mRNA and protein levels of CsHK among the life stages of adult worm, metacercaria, excysted metacercaria and egg of C. sinensis, suggesting different energy requirements during different development stages. Our study furthers the understanding of the biological functions of CsHK and supports the need to screen for small molecule inhibitors

  10. Determinação de compostos de massa molecular alta em folhas de plantas da Amazônia

    Directory of Open Access Journals (Sweden)

    Siqueira Denilson Soares de

    2003-01-01

    Full Text Available The fractIons of dichloromethane extracts of leaves from andiroba (Carapa guianensis - Meliaceae, caapi (Banisteriopsis caapi - Malpighiaceae, cocoa (Theobroma cacao - Sterculiaceae, Brazil nut (Bertholletia excelsa - Lecytidaceae, cupuaçu (Theobroma grandiflorum - Sterculiaceae, marupá (Simaruba amara - Simaroubaceae and rubber tree (Hevea brasiliensis - Euphorbiaceae, were analyzed by HT-HRGC and HT-HRGC-MS. Esters of homologous series of fatty acids and long chain alcohols, phytol, amyrines and tocopherols were characterized. The characterization of the compounds was based mainly in mass spectra data and in addition by usual spectrometric data (¹H and 13C NMR, IR.

  11. Molecular MRI based on hyper-polarized xenon

    International Nuclear Information System (INIS)

    Tassali, Nawal

    2012-01-01

    Magnetic Resonance Imaging (MRI) has a high importance in medicine as it enables the observation of the organs inside the body without the use of radiative or invasive techniques. However it is known to suffer from poor sensitivity. To circumvent this limitation, a key solution resides in the use of hyper-polarized species. Among the entities with which we can drastically increase nuclear polarization, xenon has very specific properties through its interactions with its close environment that lead to a wide chemical shift bandwidth. The goal is thus to use it as a tracer. This PhD thesis focuses on the concept of 129 Xe MRI-based sensors for the detection of biological events. In this approach, hyper-polarized xenon is vectorized to biological targets via functionalized host systems, and then localized thanks to fast dedicated MRI sequences. The conception and set-up of a spin-exchange optical pumping device is first described. Then studies about the interaction of the hyper-polarized noble gas with new cryptophanes susceptible to constitute powerful host molecules are detailed. Also the implementation of recent MRI sequences optimized for the transient character of the hyper-polarization and taking profit of the xenon in-out exchange is described. Applications of this approach for the detection of metallic ions and cellular receptors are studied. Finally, our first in vivo results on a small animal model are presented. (author) [fr

  12. Recent advances in molecular electronics based on carbon nanotubes.

    Science.gov (United States)

    Bourgoin, Jean-Philippe; Campidelli, Stéphane; Chenevier, Pascale; Derycke, Vincent; Filoramo, Arianna; Goffman, Marcelo F

    2010-01-01

    Carbon nanotubes (CNTs) have exceptional physical properties that make them one of the most promising building blocks for future nanotechnologies. They may in particular play an important role in the development of innovative electronic devices in the fields of flexible electronics, ultra-high sensitivity sensors, high frequency electronics, opto-electronics, energy sources and nano-electromechanical systems (NEMS). Proofs of concept of several high performance devices already exist, usually at the single device level, but there remain many serious scientific issues to be solved before the viability of such routes can be evaluated. In particular, the main concern regards the controlled synthesis and positioning of nanotubes. In our opinion, truly innovative use of these nano-objects will come from: (i) the combination of some of their complementary physical properties, such as combining their electrical and mechanical properties, (ii) the combination of their properties with additional benefits coming from other molecules grafted on the nanotubes, and (iii) the use of chemically- or bio-directed self-assembly processes to allow the efficient combination of several devices into functional arrays or circuits. In this article, we outline the main issues concerning the development of carbon nanotubes based electronics applications and review our recent results in the field.

  13. Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

    Directory of Open Access Journals (Sweden)

    N.L.P Indi Dharmayanti

    2011-03-01

    Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

  14. Detecting Molecular Properties by Various Laser-Based Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hsin, Tse-Ming [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Four different laser-based techniques were applied to study physical and chemical characteristics of biomolecules and dye molecules. These techniques are liole burning spectroscopy, single molecule spectroscopy, time-resolved coherent anti-Stokes Raman spectroscopy and laser-induced fluorescence microscopy. Results from hole burning and single molecule spectroscopy suggested that two antenna states (C708 & C714) of photosystem I from cyanobacterium Synechocystis PCC 6803 are connected by effective energy transfer and the corresponding energy transfer time is ~6 ps. In addition, results from hole burning spectroscopy indicated that the chlorophyll dimer of the C714 state has a large distribution of the dimer geometry. Direct observation of vibrational peaks and evolution of coumarin 153 in the electronic excited state was demonstrated by using the fs/ps CARS, a variation of time-resolved coherent anti-Stokes Raman spectroscopy. In three different solvents, methanol, acetonitrile, and butanol, a vibration peak related to the stretch of the carbonyl group exhibits different relaxation dynamics. Laser-induced fluorescence microscopy, along with the biomimetic containers-liposomes, allows the measurement of the enzymatic activity of individual alkaline phosphatase from bovine intestinal mucosa without potential interferences from glass surfaces. The result showed a wide distribution of the enzyme reactivity. Protein structural variation is one of the major reasons that are responsible for this highly heterogeneous behavior.

  15. Biomedical wellness monitoring system based upon molecular markers

    Science.gov (United States)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  16. A inércia estrutural da base produtiva brasileira: o IDE e a transferência internacional de tecnologia

    Directory of Open Access Journals (Sweden)

    TULIO CHIARINI

    2016-06-01

    Full Text Available RESUMO O que pode explicar o fato de ter havido uma entrada maciça de IDE no Brasil e ter-se mantido uma inercial estrutural na base produtiva nacional? Existe uma série de fatos macroeconômicos que podem ajudar a explicar essa inércia, como a baixa taxa de investimento e a falta de ordenação dos preços-chave da economia (como taxas de juros e taxa de câmbio, mas a proposição aqui feita é que existe um problema microeconômico estrutural relevante: falta de aptidão tecnológica das empresas industriais brasileiras. Para analisar tal proposição parte-se da separação entre os tipos de IDE (greenfield, fusão e aquisição e 'em carteira' e os tipos de canais de transferência de tecnologia (horizontal e vertical. A partir de elementos empíricos e históricos constrói-se o argumento de que a falta de aptidão tecnológica é elemento-chave no entendimento da perda de dinamismo da indústria nacional.

  17. Spin-polarized transport properties of a pyridinium-based molecular spintronics device

    Science.gov (United States)

    Zhang, J.; Xu, B.; Qin, Z.

    2018-05-01

    By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

  18. Accuracy of a novel photoacoustic-based approach to surgical guidance performed with and without a da Vinci robot

    Science.gov (United States)

    Gandhi, Neeraj; Kim, Sungmin; Kazanzides, Peter; Lediju Bell, Muyinatu A.

    2017-03-01

    Minimally invasive surgery carries the deadly risk of rupturing major blood vessels, such as the internal carotid arteries hidden by bone in endonasal transsphenoidal surgery. We propose a novel approach to surgical guidance that relies on photoacoustic-based vessel separation measurements to assess the extent of safety zones during these type of surgical procedures. This approach can be implemented with or without a robot or navigation system. To determine the accuracy of this approach, a custom phantom was designed and manufactured for modular placement of two 3.18-mm diameter vessel-mimicking targets separated by 10-20 mm. Photoacoustic images were acquired as the optical fiber was swept across the vessels in the absence and presence of teleoperation with a research da Vinci Surgical System. When the da Vinci was used, vessel positions were recorded based on the fiber position (calculated from the robot kinematics) that corresponded to an observed photoacoustic signal. In all cases, compounded photoacoustic data from a single sweep displayed the four vessel boundaries in one image. Amplitude- and coherence-based photoacoustic images were used to estimate vessel separations, resulting in 0.52-0.56 mm mean absolute errors, 0.66-0.71 mm root mean square errors, and 65-68% more accuracy compared to fiber position measurements obtained through the da Vinci robot kinematics. Results indicate that with further development, photoacoustic image-based measurements of anatomical landmarks could be a viable method for real-time path planning in multiple interventional photoacoustic applications.

  19. EMERGÊNCIA DA TEMÁTICA IMPACTO SOCIAL: UMA ANÁLISE DA PRODUÇÃO CIENTÍFICA ATRAVÉS DA BASE WEB OF SCIENCE

    Directory of Open Access Journals (Sweden)

    vera Maria de Souza Mazza

    2016-12-01

    Full Text Available A fim de ampliar o conhecimento referente à produção científica relacionada a impactos sociais, este estudo teve como objetivo analisar as características das publicações sobre este tema na base de dados Web of Science, no período de 2005 a 2014, e identificar quais tópicos estudados junto a esta temática estão sendo mais pesquisados e quais os mais relevantes (hot topics. Esse estudo revelou, dentre outras questões, que cresce o volume de publicações nos anos mais recentes destacando-se como áreas que mais publicam: Engenharia (Engeneering e Ciências Ecológicas e Ambientais (Environmental Sciences Ecology, o que sugere que a temática relaciona-se com políticas, planos, projetos e programas de desenvolvimento, evidenciado na literatura referente a impactos sociais a qual tem origem nos estudos sobre impactos ambientais. A análise dos “tópicos quentes” (hot topics indicou que as áreas de Negócios e Economia (Business Economy e Administração Pública (Public Administration estão dentre as que mais publicam acerca da temática dos impactos sociais, representando um tema emergente junto a área da Administração.

  20. Molecular basis sets - a general similarity-based approach for representing chemical spaces.

    Science.gov (United States)

    Raghavendra, Akshay S; Maggiora, Gerald M

    2007-01-01

    A new method, based on generalized Fourier analysis, is described that utilizes the concept of "molecular basis sets" to represent chemical space within an abstract vector space. The basis vectors in this space are abstract molecular vectors. Inner products among the basis vectors are determined using an ansatz that associates molecular similarities between pairs of molecules with their corresponding inner products. Moreover, the fact that similarities between pairs of molecules are, in essentially all cases, nonzero implies that the abstract molecular basis vectors are nonorthogonal, but since the similarity of a molecule with itself is unity, the molecular vectors are normalized to unity. A symmetric orthogonalization procedure, which optimally preserves the character of the original set of molecular basis vectors, is used to construct appropriate orthonormal basis sets. Molecules can then be represented, in general, by sets of orthonormal "molecule-like" basis vectors within a proper Euclidean vector space. However, the dimension of the space can become quite large. Thus, the work presented here assesses the effect of basis set size on a number of properties including the average squared error and average norm of molecular vectors represented in the space-the results clearly show the expected reduction in average squared error and increase in average norm as the basis set size is increased. Several distance-based statistics are also considered. These include the distribution of distances and their differences with respect to basis sets of differing size and several comparative distance measures such as Spearman rank correlation and Kruscal stress. All of the measures show that, even though the dimension can be high, the chemical spaces they represent, nonetheless, behave in a well-controlled and reasonable manner. Other abstract vector spaces analogous to that described here can also be constructed providing that the appropriate inner products can be directly

  1. Fabrication of tunnel junction-based molecular electronics and spintronics devices

    International Nuclear Information System (INIS)

    Tyagi, Pawan

    2012-01-01

    Tunnel junction-based molecular devices (TJMDs) are highly promising for realizing futuristic electronics and spintronics devices for advanced logic and memory operations. Under this approach, ∼2.5 nm molecular device elements bridge across the ∼2-nm thick insulator of a tunnel junction along the exposed side edge(s). This paper details the efforts and insights for producing a variety of TJMDs by resolving multiple device fabrication and characterization issues. This study specifically discusses (i) compatibility between tunnel junction test bed and molecular solutions, (ii) optimization of the exposed side edge profile and insulator thickness for enhancing the probability of molecular bridging, (iii) effect of fabrication process-induced mechanical stresses, and (iv) minimizing electrical bias-induced instability after the device fabrication. This research will benefit other researchers interested in producing TJMDs efficiently. TJMD approach offers an open platform to test virtually any combination of magnetic and nonmagnetic electrodes, and promising molecules such as single molecular magnets, porphyrin, DNA, and molecular complexes.

  2. Fast parallel molecular algorithms for DNA-based computation: factoring integers.

    Science.gov (United States)

    Chang, Weng-Long; Guo, Minyi; Ho, Michael Shan-Hui

    2005-06-01

    The RSA public-key cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA public-key cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNA-based algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.

  3. Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

    Science.gov (United States)

    Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

    2018-08-01

    Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

  4. Design, synthesis, conformational and molecular docking study of some novel acyl hydrazone based molecular hybrids as antimalarial and antimicrobial agents.

    Science.gov (United States)

    Kumar, Parvin; Kadyan, Kulbir; Duhan, Meenakshi; Sindhu, Jayant; Singh, Vineeta; Saharan, Baljeet Singh

    2017-11-14

    Acyl hydrazones are an important class of heterocyclic compounds promising pharmacological characteristics. Malaria is a life-threatening mosquito-borne blood disease caused by a plasmodium parasite. In some places, malaria can be treated and controlled with early diagnosis. However, some countries lack the resources to do this effectively. The present work involves the design and synthesis of some novel acyl hydrazone based molecular hybrids of 1,4-dihydropyridine and pyrazole (5a-g). These molecular hybrids were synthesised by condensation of 1,4-dihydropyridin-4-yl-phenoxyacetohydrazides with differently substituted pyrazole carbaldehyde. The final compound (5) showed two conformations (the major, E, s-cis and the minor, E, s-trans) as revealed by NMR spectral data and further supported by the energy calculations (MOPAC2016 using PM7 method). All the synthesised compounds were screened for their in vitro antimalarial activities against chloroquine-sensitive malaria parasite Plasmodium falciparum (3D7) and antimicrobial activity against Gram positive bacteria i.e. Bacillus cereus, Gram negative bacteria i.e. Escherichia coli and antifungal activity against one yeast i.e. Aspergillus niger. All these compounds were found more potent than chloroquine and clotrimazole, the standard drugs. In vitro antiplasmodial IC 50 value of the most potent compound 5d was found to be 4.40 nM which is even less than all the three reference drugs chloroquine (18.7 nM), pyrimethamine (11 nM) and artimisinin (6 nM). In silico binding study of compound 5d with plasmodial cysteine protease falcipain-2 indicated the inhibition of falcipain-2 as the probable reason for the antimalarial potency of compound 5d. All the compounds had shown good to excellent antimicrobial and antifungal activities.

  5. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

    Science.gov (United States)

    Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

    2009-03-18

    It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

  6. Well-Defined Polyethylene-Based Random, Block, and Bilayered Molecular Cobrushes

    KAUST Repository

    Zhang, Hefeng

    2015-06-09

    Novel well-defined polyethylene-based random, block, and bilayered molecular cobrushes were synthesized through the macromonomer strategy. Two steps were involved in this approach: (i) synthesis of norbornyl-terminated macromonomers of polyethylene (PE), polycaprolactone (PCL), poly(ethylene oxide) (PEO), and polystyrene (PS), as well as polyethylene-b-polycaprolactone (PE-b-PCL), by esterification of the hydroxyl-terminated precursors (PE, PCL, PEO, PS, and PE-b-PCL) with 5-norbornene-2-carboxylic acid and (ii) ring-opening metathesis (co)polymerization of the resulting macromonomers to afford the PE-based molecular cobrushes. The PE-macromonomers were synthesized by polyhomologation of dimethylsulfoxonium methylide, while the others by anionic polymerization. Proton nuclear magnetic resonance spectroscopy (1H NMR) and high-temperature gel permeation chromatography (HT-GPC) were used to imprint the molecular characteristics of all macromonomers and molecular brushes and differential scanning calorimetry (DSC) for the thermal properties. The bilayered molecular cobrushes of P(PE-b-PCL) adopt a wormlike morphology on silica wafer as visualized by atomic force microscopy (AFM). © 2015 American Chemical Society.

  7. A facile molecularly imprinted polymer-based fluorometric assay for detection of histamine

    DEFF Research Database (Denmark)

    Feng, Xiaotong; Ashley, Jon; Zhou, Tongchang

    2018-01-01

    urgently needed. In this paper, we developed a facile and cost-effective molecularly imprinted polymer (MIP)-based fluorometric assay to directly quantify histamine. Histamine-specific MIP nanoparticles (nanoMIPs) were synthesized using a modified solid-phase synthesis method. They were then immobilized...

  8. Reversible, high molecular weight palladium and platinum coordination polymers based on phosphorus ligands

    NARCIS (Netherlands)

    Paulusse, J.M.J.; Huijbers, J.P.J.; Sijbesma, R.P.

    2005-01-01

    A general strategy for the preparation and characterization of high molecular weight coordination polymers based on bifunctional phosphorus ligands and palladium or platinum dichloride is described. Metal-to-ligand stoichiometry is of key importance for the formation of linear coordination polymers

  9. Reversible, High Molecular Weight Palladium and Platinum Coordination Polymers Based on Phosphorus Ligands

    NARCIS (Netherlands)

    Paulusse, Jos Marie Johannes; Huijbers, Jeroen P.J.; Sijbesma, Rint P.

    2005-01-01

    A general strategy for the preparation and characterization of high molecular weight coordination polymers based on bifunctional phosphorus ligands and palladium or platinum dichloride is described. Metal-to-ligand stoichiometry is of key importance for the formation of linear coordination polymers

  10. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  11. Molecularly imprinted fluorescent probe based on FRET for selective and sensitive detection of doxorubicin

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhifeng, E-mail: 897061147@qq.com [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China); Deng, Peihong; Li, Junhua [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China); Xu, Li [Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642 (China); Tang, Siping [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China)

    2017-04-15

    Highlights: • FRET-based molecularly imprinted probe for detection of doxorubicin was prepared. • The detection limit of the probe was 13.8 nM for doxorubicin. • The FRET-based probe had a higher selectivity for the template than ordinary MIMs. - Abstract: In this work, a new type of fluorescent probe for detection of doxorubicin has been constructed by the combined use of fluorescence resonance energy transfer (FRET) technology and molecular imprinting technique (MIT). Using doxorubicin as the template, the molecularly imprinted polymer thin layer was fabricated on the surfaces of carbon dot (CD) modified silica by sol-gel polymerization. The excitation energy of the fluorescent donor (CDs) could be transferred to the fluorescent acceptor (doxorubicin). The FRET based fluorescent probe demonstrated high sensitivity and selectivity for doxorubicin. The detection limit was 13.8 nM. The fluorescent probe was successfully applied for detecting doxorubicin in doxorubicin-spiked plasmas with a recovery of 96.8–103.8%, a relative standard deviation (RSD) of 1.3–2.8%. The strategy for construction of FRET-based molecularly imprinted materials developed in this work is very promising for analytical applications.

  12. Theoretical treatment of molecular photoionization based on the R-matrix method

    International Nuclear Information System (INIS)

    Tashiro, Motomichi

    2012-01-01

    The R-matrix method was implemented to treat molecular photoionization problem based on the UK R-matrix codes. This method was formulated to treat photoionization process long before, however, its application has been mostly limited to photoionization of atoms. Application of the method to valence photoionization as well as inner-shell photoionization process will be presented.

  13. Molecular modeling of the conductivity changes of the emeraldine base polyaniline due to protonic acid doping

    NARCIS (Netherlands)

    Chen, X.; Yuan, C.A.; Wong, C.K.Y.; Zhang, G.

    2012-01-01

    We propose a molecular modeling strategy, which is capable of predicting the conductivity change of emeraldine base polyaniline polymer due to different degree of protonic acid doping. The method is comprised of two key steps: (1) generating the amorphous unit cells with given number of polymer

  14. Encapsulation and solid state sequestration of gases by calix[6]arene-based molecular containers.

    Science.gov (United States)

    Lavendomme, Roy; Ajami, Daniela; Moerkerke, Steven; Wouters, Johan; Rissanen, Kari; Luhmer, Michel; Jabin, Ivan

    2017-06-13

    Two calix[6]arene-based molecular containers were synthesized in high yields. These containers can encapsulate small guests through a unique "rotating door" complexation process. The sequestration of greenhouse gases is clearly demonstrated. They can be stored in the solid state for long periods and released via dissolution of the inclusion complex.

  15. Fast parallel DNA-based algorithms for molecular computation: the set-partition problem.

    Science.gov (United States)

    Chang, Weng-Long

    2007-12-01

    This paper demonstrates that basic biological operations can be used to solve the set-partition problem. In order to achieve this, we propose three DNA-based algorithms, a signed parallel adder, a signed parallel subtractor and a signed parallel comparator, that formally verify our designed molecular solutions for solving the set-partition problem.

  16. Photo- and electro-chromism of diarylethene modified ITO electrodes - towards molecular based read-write-erase information storage

    NARCIS (Netherlands)

    Areephong, J.; Browne, W.R.; Katsonis, N.; Feringa, B.L.

    2006-01-01

    Molecular memory devices based on dithienylethene switch modified ITO electrodes undergo reversible ring opening/closing both photo- and electro-chemically with non-destructive electrochemical readout.

  17. Applications of nucleoside-based molecular probes for the in vivo assessment of tumour biochemistry using positron emission tomography (PET

    Directory of Open Access Journals (Sweden)

    Leonard I. Wiebe

    2007-05-01

    Full Text Available Positron emission tomography (PET is a non-invasive nuclear imaging technique. In PET, radiolabelled molecules decay by positron emission. The gamma rays resulting from positron annihilation are detected in coincidence and mapped to produce three dimensional images of radiotracer distribution in the body. Molecular imaging with PET refers to the use of positron-emitting biomolecules that are highly specific substrates for target enzymes, transport proteins or receptor proteins. Molecular imaging with PET produces spatial and temporal maps of the target-related processes. Molecular imaging is an important analytical tool in diagnostic medical imaging, therapy monitoring and the development of new drugs. Molecular imaging has its roots in molecular biology. Originally, molecular biology meant the biology of gene expression, but now molecular biology broadly encompasses the macromolecular biology and biochemistry of proteins, complex carbohydrates and nucleic acids. To date, molecular imaging has focused primarily on proteins, with emphasis on monoclonal antibodies and their derivative forms, small-molecule enzyme substrates and components of cell membranes, including transporters and transmembrane signalling elements. This overview provides an introduction to nucleosides, nucleotides and nucleic acids in the context of molecular imaging.A tomografia por emissão de pósitrons (TEP é uma técnica de imagem não invasiva da medicina nuclear. A TEP utiliza moléculas marcadas com emissores de radiação beta positiva (pósitrons. As radiações gama medidas que resultam do aniquilamento dos pósitrons são detectadas por um sistema de coincidência e mapeadas para produzir uma imagem tridimensional da distribuição do radiotraçador no corpo. A imagem molecular com TEP refere-se ao uso de biomoléculas marcadas com emissor de pósitron que são substratos altamente específicos para alvos como enzimas, proteínas transportadoras ou receptores prot

  18. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

    Science.gov (United States)

    Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

    2014-01-01

    DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

  19. Advances in understanding the genetic basis of inherited single gene skin barrier disorders: new clues to key genes that may be involved in the pathogenesis of atopic dermatitis Avanços no entendimento da base genética de doenças hereditárias monogênicas da barreira epidérmica: novas pistas para os principais genes que podem estar envolvidos na patogênese da dermatite atópica

    Directory of Open Access Journals (Sweden)

    Joey E Lai-Cheong

    2006-12-01

    Full Text Available Increasing knowledge of genomic DNA sequences and genetic databases has led to the characterization of the molecular basis of several inherited skin disorders. In this review we summarize some of the major recent discoveries that have been made in defining the pathogenic mutations that cause inherited disorders of the skin barrier leading to skin scaling or increased transepidermal water loss in either rare disorders (Netherton’s syndrome or harlequin ichthyosis or more common genodermatoses (ichthyosis vulgaris. These molecular breakthroughs have led to more accurate diagnoses, better genetic counselling and, where appropriate, the feasibility of DNA-based prenatal diagnosis, as well as the possibility of developing newer forms of treatment, including gene or protein therapy. Identifying the molecular basis of these conditions, especially ichthyosis vulgaris, has also provided dramatic new insight into the genetic abnormalities in the common disorder, atopic dermatitis. Thus research on the relatively rare single gene inherited skin disorders not only has benefits for patients and their families with these uncommon conditions but also has the potential to yield fresh and significant new information about very common skin diseases.O maior conhecimento sobre as de sequências genômicas de DNA e as bases de dados genéticas levou à caracterização da base molecular de várias doenças hereditárias de pele. Nesta revisão resumimos algumas das descobertas recentes mais importantes quanto à definição das mutações patogênicas que causam as doenças hereditárias da barreira cutânea, levando a descamação ou aumento da perda hídrica transepidérmica, seja em doenças raras, (síndrome de Netherton ou ictiose em Arlequim ou genodermatoses mais comuns (ictiose vulgar. Estas descobertas moleculares têm conduzido a diagnósticos mais acurados, melhor aconselhamento genético e, quando apropriado, à possibilidade de diagnóstico pr

  20. Estimativas da composição anatômica da carcaça de frangos de corte com base no nível de proteína da ração e peso da carcaça

    Directory of Open Access Journals (Sweden)

    Silva José Humberto Vilar da

    2003-01-01

    Full Text Available Um experimento foi desenvolvido com o objetivo de estimar as proporções dos cortes nobres da carcaça de frangos de corte pelo modelo linear. Foram utilizados 842 frangos machos da linhagem Avian Farms, de 22 a 42 dias de idade, distribuídos num delineamento inteiramente ao acaso em esquema fatorial 3x4. Foram fornecidas rações formuladas à base de milho e farelo de soja para conter 2.900 kcal de EM e 15,43; 17,26; 19,60; e 22,60% de PB; 3.100 kcal de EM e 16,49; 18,45; 20,95; e 24,22% de PB; e 3300 kcal de EM e 17,55; 19,64; 22,30; e 25,78% de PB, totalizando doze tratamentos. Cada tratamento foi constituído por quatro repetições de 18 aves. Fortes correlações foram observadas entre o peso vivo aos 42 dias e o peso da carcaça (r = 0,958, o peso da carcaça e o peso de pernas (r = 0,991, peso de peito+osso+pele (r = 0,965 e peso de peito desossado (r = 0,950. A porcentagem de lipídio foi negativamente correlacionada com a porcentagem de umidade da carcaça (r = -0,880. A equação linear é recomendada para a predição dos componentes anatômicos da carcaça de frangos de corte.

  1. Em busca das bases ontológicas da psicologia de Vygotsky

    Directory of Open Access Journals (Sweden)

    Francisca Maurilene do Carmo

    2013-12-01

    Full Text Available O estudo busca estabelecer os fundamentos ontológicos do pensamento de Vygotsky, indicando que a construção teórica erigida pelo e autor está centrada no trabalho, como o complexo que deu origem ao homem como ser social. Tal postulado seria consistente com os princípios do marxismo recuperado por Lukács como uma ontologia do ser social, superadora da tradição metafísica e idealista, firmando, nesse sentido, o caráter radicalmente histórico da essência humana. Apontam-se os equívocos fundamentais operado pelo neovygotskianismo, o qual, tratando as categorias vygotskianas da linguagem, cultura e interação apartadas do princípio marxiano do trabalho, acaba por isolar Vygotsky do campo ontológico e, por extensão, do projeto socialista. Reafirma-se, por fim, que, não obstante a explícita relevância atribuída à dimensão metodológica do marxismo, está pressuposto na obra de Vygotsky, o substrato ontológico sobre o qual se funda o método de Marx.

  2. Radiation-chemical yields of molecular hydrogen formation in cyclohexane based alcohols

    International Nuclear Information System (INIS)

    Val'ter, A.I.; Kovalev, G.V.

    1988-01-01

    Molecular hydrogen radiation-chemical yields in γ-irradiated cyclohexanol, 1.2-cis- and 1.2-trans-cyclohexandiols and inositol are determined within the general problem frameworks of radiolysis mechanism for cyclohexanering-base alcohols. Irradiation was conducted at 77 and 293 K, dose rate - 4 Gy/s. Hydrogen concentration in all irradiated alcohols depends linearly on the dose. Radiation-chemical yields of H 2 and of stabilized radicals, as well, in the irradiated crystalline alcohols are analyzed depending on the irradiation temperature, alcohol molecular structure

  3. pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

    Directory of Open Access Journals (Sweden)

    Ardita Shkurti

    2016-01-01

    Full Text Available The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced written in Python.

  4. First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, P., E-mail: ss_zhaop@ujn.edu.c [School of Science, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Qufu 273155 (China); Wang, P.J.; Zhang, Z. [School of Science, University of Jinan, Jinan 250022 (China); Fang, C.F.; Ji, G.M. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China)

    2011-02-15

    By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.

  5. First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

    International Nuclear Information System (INIS)

    Zhao, P.; Liu, D.S.; Wang, P.J.; Zhang, Z.; Fang, C.F.; Ji, G.M.

    2011-01-01

    By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.

  6. Bases para um referencial teorico sobre o fenômeno da cognição

    OpenAIRE

    Moreira, Adelson Fernandes; Borges, Oto

    2008-01-01

    Apresentamos um referencial teórico para investigar a sala de aula, que articulamos a partir das seguintes matrizes teórico-metodológicas: cognição situada, etnometodologia, fundamentos biológicos da cognição, cognição distribuída e fenomenologia. Discutimos as contribuições que extraímos dessas matrizes ao longo de uma investigação que comparouas práticas de interpretação de alunos em diferentes ambientes de aprendizagem. Com base nessa discussão propomos direções para olhar a sala de aula, ...

  7. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

    OpenAIRE

    Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

    2010-01-01

    Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactive...

  8. Formação do audiodescritor: a estética cinematográfica como base para o aprendizado da estética da audiodescrição - materiais, métodos e produtos

    Directory of Open Access Journals (Sweden)

    Soraya Ferreira Alves

    2016-09-01

    Full Text Available http://dx.doi.org/10.5007/2175-7968.2016v36n3p34 A Audiodescrição (AD, recurso utilizado para tornar o teatro, o cinema, a TV, bem como obras de arte visuais, acessíveis a pessoas com deficiência visual, vem aos poucos sendo implantada no Brasil e demandando profissionais capacitados. Com base nessa constatação, este artigo traz o relato de um projeto desenvolvido durante estágio pós-doutoral que se dedicou ao confronto da estética cinematográfica com as técnicas de audiodescrição a fim de verificar como o conhecimento da primeira pode contribuir para a formação do audiodescritor. Por meio da pesquisa-ação, foi produzido um curta-metragem adaptado de um conto de Mário de Andrade intitulado O Peru de Natal. O filme homônimo, assim como sua audiodescrição, foram realizados pelos alunos e professores da disciplina Tradução Intersemiótica do curso de Letras da Universidade Estadual do Ceará (UECE. Assim, pretendeu-se sugerir procedimentos didáticos que partiram da experiência dos alunos ao avaliarem suas escolhas e as implicações destas.

  9. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

    Directory of Open Access Journals (Sweden)

    Hsu Hui-Chi

    2011-04-01

    Full Text Available Abstract Background Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Methods Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. Results We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was

  10. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

    International Nuclear Information System (INIS)

    Kao, Kuo-Jang; Chang, Kai-Ming; Hsu, Hui-Chi; Huang, Andrew T

    2011-01-01

    Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was consistent with a unique subset of luminal A intrinsic

  11. Severe childhood asthma and allergy to furry animals: refined assessment using molecular-based allergy diagnostics.

    Science.gov (United States)

    Konradsen, Jon R; Nordlund, Björn; Onell, Annica; Borres, Magnus P; Grönlund, Hans; Hedlin, Gunilla

    2014-03-01

    Allergy to cats and dogs and polysensitization towards these animals are associated with severe childhood asthma. Molecular-based allergy diagnostics offers new opportunities for improved characterization and has been suggested to be particularly useful in patients with polysensitization and/or severe asthma. The aim was to use extract- and molecular-based allergy diagnostics to compare patterns of IgE sensitization towards aeroallergens in children with problematic severe and controlled asthma. Children with a positive ImmunoCAP towards any furry animal (cat, dog or horse) were recruited from a Nationwide Swedish study on severe childhood asthma. Severe (n = 37, age 13 years) and controlled (n = 28, age 14 years) asthmatics underwent assessment of allergic sensitization by ImmunoCap (kUA /l) and immunosolid-phase allergen chip (ISAC). In addition, Asthma Control Test, spirometry and a methacholine challenge were performed. Children with severe asthma had lower asthma control (p Molecular-based allergy diagnostics revealed a more complex molecular spreading of allergen components in children with the most severe disease. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Realizing tunable molecular thermal devices based on photoisomerism—Is it possible?

    Energy Technology Data Exchange (ETDEWEB)

    Ranganathan, Raghavan; Sasikumar, Kiran; Keblinski, Pawel, E-mail: keblip@rpi.edu [Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States)

    2015-01-14

    In this work, we address the question if it is possible to tune the thermal conductance through photoisomerism-capable molecular junctions. Using non-equilibrium molecular dynamics simulations, we study heat flow due to phonons between two silicon leads connected via two classes of photoisomeric molecules—(a) azobenzene and (b) Spiropyran (SP)–Merocyanine (MC) isomers. For the case of azobenzene, isomeric states with different conformations are realized via mechanical strain, while in the case of SP-MC, via a hybridization change. Based on the phononic contribution to thermal conductance, we observe that the thermal conductance of both junctions is rather insensitive to the isomeric state, thereby rendering the tunability of molecular thermal devices rather difficult. Consistent with these observations, the vibrational density of states for different configurations yields very similar spectra. We note that including the effect of electronic contribution to thermal conductance could enhance the tunability of thermal properties, albeit weakly.

  13. Possibility of gas sensor based on C{sub 20} molecular devices

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Wenkai [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Yang, Chuanlu, E-mail: yangchuanlu@126.com [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Zou, Dongqing [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Sun, Zhaopeng [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Ji, Guomin [Electrical and Computer Engineering, The University of Oklahoma, Norman, Tulsa, OK 74078 (United States)

    2017-06-09

    We theoretically investigate the possibility of diatomic gas detection (NO, CO, O{sub 2}) by making use of the transport properties of the C{sub 20} molecular junctions. The calculations are performed by using nonequilibrium Green's function (NEGF) formalism in combination with density functional theory (DFT). In this work, we systematically study the most stable adsorption structural configurations, adsorption energy, and the transport properties on C{sub 20} molecular junctions with these diatomic gas molecules. It is found that NO and O{sub 2} gas molecule can be detected selectively. We suggest its possibility of nanosensors for highly sensitive and selective based on C{sub 20} molecular junction systems. - Highlights: • The most favorable adsorption site is investigated. • The mechanism of gas sensors is revealed. • NO and O{sub 2} gas molecules can be detected by C{sub 20} selectively.

  14. Possibility of gas sensor based on C_2_0 molecular devices

    International Nuclear Information System (INIS)

    Zhao, Wenkai; Yang, Chuanlu; Zou, Dongqing; Sun, Zhaopeng; Ji, Guomin

    2017-01-01

    We theoretically investigate the possibility of diatomic gas detection (NO, CO, O_2) by making use of the transport properties of the C_2_0 molecular junctions. The calculations are performed by using nonequilibrium Green's function (NEGF) formalism in combination with density functional theory (DFT). In this work, we systematically study the most stable adsorption structural configurations, adsorption energy, and the transport properties on C_2_0 molecular junctions with these diatomic gas molecules. It is found that NO and O_2 gas molecule can be detected selectively. We suggest its possibility of nanosensors for highly sensitive and selective based on C_2_0 molecular junction systems. - Highlights: • The most favorable adsorption site is investigated. • The mechanism of gas sensors is revealed. • NO and O_2 gas molecules can be detected by C_2_0 selectively.

  15. [Molecular biology of renal cancer: bases for genetic directed therapy in advanced disease].

    Science.gov (United States)

    Maroto Rey, José Pablo; Cillán Narvaez, Elena

    2013-06-01

    There has been expansion of therapeutic options in the management of metastatic renal cell carcinoma due to a better knowledge of the molecular biology of kidney cancers. There are different tumors grouped under the term renal cell carcinoma, being clear cell cancer the most frequent and accounting for 80% of kidney tumors. Mutations in the Von Hippel-Lindau gene can be identified in up to 80% of sporadic clear cell cancer, linking a genetically inheritable disease where vascular tumors are frequent, with renal cell cancer. Other histologic types present specific alterations in molecular pathways, like c-MET in papillary type I tumors, and Fumarase Hydratase in papillary type II tumors. Identification of the molecular alteration for a specific tumor may offer an opportunity for treatment selection based on biomarkers, and, in the future, for developing an engineering designed genetic treatment.

  16. Current applications of molecular imaging and luminescence-based techniques in traditional Chinese medicine.

    Science.gov (United States)

    Li, Jinhui; Wan, Haitong; Zhang, Hong; Tian, Mei

    2011-09-01

    Traditional Chinese medicine (TCM), which is fundamentally different from Western medicine, has been widely investigated using various approaches. Cellular- or molecular-based imaging has been used to investigate and illuminate the various challenges identified and progress made using therapeutic methods in TCM. Insight into the processes of TCM at the cellular and molecular changes and the ability to image these processes will enhance our understanding of various diseases of TCM and will provide new tools to diagnose and treat patients. Various TCM therapies including herbs and formulations, acupuncture and moxibustion, massage, Gua Sha, and diet therapy have been analyzed using positron emission tomography, single photon emission computed tomography, functional magnetic resonance imaging and ultrasound and optical imaging. These imaging tools have kept pace with developments in molecular biology, nuclear medicine, and computer technology. We provide an overview of recent developments in demystifying ancient knowledge - like the power of energy flow and blood flow meridians, and serial naturopathies - which are essential to visually and vividly recognize the body using modern technology. In TCM, treatment can be individualized in a holistic or systematic view that is consistent with molecular imaging technologies. Future studies might include using molecular imaging in conjunction with TCM to easily diagnose or monitor patients naturally and noninvasively. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  17. Organic Photovoltaic Devices Based on Oriented n-Type Molecular Films Deposited on Oriented Polythiophene Films.

    Science.gov (United States)

    Mizokuro, Toshiko; Tanigaki, Nobutaka; Miyadera, Tetsuhiko; Shibata, Yousei; Koganezawa, Tomoyuki

    2018-04-01

    The molecular orientation of π-conjugated molecules has been reported to significantly affect the performance of organic photovoltaic devices (OPVs) based on molecular films. Hence, the control of molecular orientation is a key issue toward the improvement of OPV performance. In this research, oriented thin films of an n-type molecule, 3,4,9,10-Perylenetetracarboxylic Bisbenzimida-zole (PTCBI), were formed by deposition on in-plane oriented polythiophene (PT) films. Orientation of the PTCBI films was evaluated by polarized UV-vis spectroscopy and 2D-Grazing incidence X-ray diffraction. Results indicated that PTCBI molecules on PT film exhibit nearly edge-on and in-plane orientation (with molecular long axis along the substrate), whereas PTCBI molecules without PT film exhibit neither. OPVs composed of PTCBI molecular film with and without PT were fabricated and evaluated for correlation of orientation with performance. The OPVs composed of PTCBI film with PT showed higher power conversion efficiency (PCE) than that of film without PT. The experiment indicated that in-plane orientation of PTCBI molecules absorbs incident light more efficiently, leading to increase in PCE.

  18. In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors.

    Science.gov (United States)

    Mahapatra, Manoj Kumar; Bera, Krishnendu; Singh, Durg Vijay; Kumar, Rajnish; Kumar, Manoj

    2018-04-01

    Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.

  19. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  20. MOLECULAR COMPLEXES OF SULPHUR DIOXIDE WITH N,O-CONTAINING ORGANIC BASES (REVIEW

    Directory of Open Access Journals (Sweden)

    R. E. Khoma

    2016-10-01

    Full Text Available The literature data on the synthesis, stoichiometry, structure and relative stability of molecular  complexes of sulphur dioxide with N,O-containing organic bases have been systematized and  generalized. It was shown that the yield of the reaction product of sulfur dioxide with organic  bases (such as amines are strongly influenced by the conditions of synthesis: the nature of  the solvent (basicity, polarity, the temperature and SO2:L ratio in the reaction medium. The stoichiometry of SO2*nL molecular complexes depends on ligand denticity, as well as its  ability to H-bonding. The reaction of the sulfur oxide (IV with organic bases can give S←N and S←O complexes. With the increase of the value of base proton affinity the decrease ΔrSN values has been marked. Characteristic parameter Δr SN = r SN – a1(rS+ rN (where rSNis the S←N donor-acceptor bond length has been determined by microwave spectroscopy and X-ray analysis, rSand rNwere the tabulated values of the homopolar covalent radii of sulphur and nitrogen heteroatoms. The dependence of formation enthalpy of molecular complexes of basic amines and spectral characteristics has been noted; enthalpy-entropy compensation for S←N and S←O complex-es has been stated. Despite the limited experimental data on the thermodynamics of complex formation and the lengths of donor-acceptor bonds for the same compounds it has been found bond S←N strength in SO2 molecular complexes to depend on the intrinsic value of ΔrSN. The contribution of van der Waals forces and charge transfer forces to the formation of molecular complexes of sulphur dioxide has been stated.

  1. Molecular design toward highly efficient photovoltaic polymers based on two-dimensional conjugated benzodithiophene.

    Science.gov (United States)

    Ye, Long; Zhang, Shaoqing; Huo, Lijun; Zhang, Maojie; Hou, Jianhui

    2014-05-20

    As researchers continue to develop new organic materials for solar cells, benzo[1,2-b:4,5-b']dithiophene (BDT)-based polymers have come to the fore. To improve the photovoltaic properties of BDT-based polymers, researchers have developed and applied various strategies leading to the successful molecular design of highly efficient photovoltaic polymers. Novel polymer materials composed of two-dimensional conjugated BDT (2D-conjugated BDT) have boosted the power conversion efficiency of polymer solar cells (PSCs) to levels that exceed 9%. In this Account, we summarize recent progress related to the design and synthesis of 2D-conjugated BDT-based polymers and discuss their applications in highly efficient photovoltaic devices. We introduce the basic considerations for the construction of 2D-conjugated BDT-based polymers and systematic molecular design guidelines. For example, simply modifying an alkoxyl-substituted BDT to form an alkylthienyl-substituted BDT can improve the polymer hole mobilities substantially with little effect on their molecular energy level. Secondly, the addition of a variety of chemical moieties to the polymer can produce a 2D-conjugated BDT unit with more functions. For example, the introduction of a conjugated side chain with electron deficient groups (such as para-alkyl-phenyl, meta-alkoxyl-phenyl, and 2-alkyl-3-fluoro-thienyl) allowed us to modulate the molecular energy levels of 2D-conjugated BDT-based polymers. Through the rational design of BDT analogues such as dithienobenzodithiophene (DTBDT) or the insertion of larger π bridges, we can tune the backbone conformations of these polymers and modulate their photovoltaic properties. We also discuss the influence of 2D-conjugated BDT on polymer morphology and the blends of these polymers with phenyl-C61 (or C71)-butyric acid methyl ester (PCBM). Finally, we summarize the various applications of the 2D-conjugated BDT-based polymers in highly efficient PSC devices. Overall, this Account

  2. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Hanhui [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 (China); Liu, Ningning [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Fan, Jianren [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)

    2017-05-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  3. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren

    2017-01-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  4. Paradigma da disseminação local do carcinoma epidermóide da base de língua Paradigm of local spreading in squamous cell carcinoma of the base of the tongue

    Directory of Open Access Journals (Sweden)

    Francisco S. Amorim Filho

    2004-08-01

    Full Text Available OBJETIVO: Analisar o padrão de disseminação local através da delimitação clínica da extensão da lesão primária assim como os subsítios invadidos. FORMA DE ESTUDO: Clínico retrospectivo. MATERIAL E MÉTODO: Foram analisados os prontuários de 290 pacientes com carcinoma epidermóide de base de língua no Departamento de Cirurgia de Cabeça e Pescoço e Otorrinolaringologia do Hospital Heliópolis, Hosphel, São Paulo - Brasil, de 1977 a 2000, sendo estadiados pelo TNM da UICC, e os resultados analisados pelo teste do Quiquadrado para tabelas Z x N (Cochran para estudo da associação dos sítios e dimensão da neoplasia em relação à invasão da linha média. RESULTADOS: Com predomínio dos homens (8:1 e da 6ª década de vida (41,0%, 83,8% eram etilistas e tabagistas e em 4,7% os hábitos estavam ausentes. Quanto aos sintomas, odinofagia (37,6%, linfonodo (21,7% e a média de tempo entre o 1º sintoma e o diagnóstico de 6 meses (62,0%. Quanto ao estadiamento, tivemos T1-T2 (18,3%, T3 (32,4%, T4(50,7%. Quanto à disseminação local, em direção à valécula (25,3%, epiglote (18,7%, glote (2,7%, anteriormente para o v lingual em (22,4% e póstero lateralmente para a prega faringloepiglótica (6,6% e seio piriforme (2,2%. Quanto a ultrapassagem da linha média, isso ocorreu em 66,2% dos casos, sendo 42,2% (T2, 54,2% (T3 e 82,9% (T4. CONCLUSÃO: o carcinoma epidermóide no estádio T4 ultrapassa a linha média da base da língua em 82,9%.AIM: To analyse the local spreading pattern through clinical delimitation of primary lesion extension as well as subsites involvement. STUDY DESIGN: Chart review. MATERIAL AND METHOD: Files of 290 patients with squamous cell carcinoma (SCC of the base of the tongue from Department of Head Neck and Surgery and Otorhinolaryngology of Hospital Heliópolis, Hosphel, São Paulo, Brazil from 1977 to 2000, were analysed. They were staged through TNM from UICC, and then through thoygh K square text with Z x

  5. Grid-based Continual Analysis of Molecular Interior for Drug Discovery, QSAR and QSPR.

    Science.gov (United States)

    Potemkin, Andrey V; Grishina, Maria A; Potemkin, Vladimir A

    2017-01-01

    In 1979, R.D.Cramer and M.Milne made a first realization of 3D comparison of molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (Dynamic Lattice- Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities. Then, in 1988, the method which was called CoMFA (Comparative Molecular Field Analysis) was introduced and the appropriate software became commercially available. Since 1988, a lot of 3D QSAR methods, algorithms and their modifications are introduced for solving of virtual drug discovery problems (e.g., CoMSIA, CoMMA, HINT, HASL, GOLPE, GRID, PARM, Raptor, BiS, CiS, ConGO,). All the methods can be divided into two groups (classes):1. Methods studying the exterior of molecules; 2) Methods studying the interior of molecules. A series of grid-based computational technologies for Continual Molecular Interior analysis (CoMIn) are invented in the current paper. The grid-based analysis is fulfilled by means of a lattice construction analogously to many other grid-based methods. The further continual elucidation of molecular structure is performed in various ways. (i) In terms of intermolecular interactions potentials. This can be represented as a superposition of Coulomb, Van der Waals interactions and hydrogen bonds. All the potentials are well known continual functions and their values can be determined in all lattice points for a molecule. (ii) In the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum

  6. RAPD analysis of genetic variability in a multiprovenance base population of Eucalyptus grandis hill ex maiden Variabilidade genética através da técnica RAPD de uma população-base multiprocedências de Eucalyptus grandis hill ex maiden

    Directory of Open Access Journals (Sweden)

    Susi Meire Maximino Leite

    2008-12-01

    Full Text Available This study aimed to evaluate the genetic variability among individuals of a base population of Eucalyptus grandis and to build a molecular marker database for the analyzed populations. The Eucalyptus grandis base population comprised 327 individuals from Coff's Harbour, Atherton and Rio Claro. A few plants came from other sites (Belthorpe MT. Pandanus, Kenilworth, Yabbra, etc.. Since this base population had a heterogeneous composition, the groups were divided according to geographic localization (latitude and longitude, and genetic breeding level. Thus, the influence of those two factors (geographic localization and genetic breeding level on the genetic variability detected was discussed. The RAPD technique allowed the evaluation of 70 loci. The binary matrix was used to estimate the genetic similarity among individuals using Jaccard's Coefficient. Parametric statistical tests were used to compare within-group similarity of the means. The obtained results showed that the base population had wide genetic variability and a mean genetic similarity of 0.328. Sub-group 3 (wild materials from the Atherton region showed mean genetic similarity of 0.318. S.P.A. (from Coff's Harbour region had a mean genetic similarity of 0.322 and was found to be very important for maintenance of variation in the base population. This can be explained since the individuals from those groups accounted for most of the base population (48.3% for it. The base population plants with genetic similarity higher than 0.60 should be phenotypically analyzed again in order to clarify the tendency of genetic variability during breeding programs.Este estudo visou avaliar a variabilidade e distância genética dentro de uma população-base de melhoramento genético de Eucalyptus grandis. A avaliação da variabilidade genética tem como objetivos principais analisar a base genética da população-base e montar um banco de dados marcadores moleculares da população em an

  7. Pre-examination factors affecting molecular diagnostic test results and interpretation: A case-based approach.

    Science.gov (United States)

    Payne, Deborah A; Baluchova, Katarina; Peoc'h, Katell H; van Schaik, Ron H N; Chan, K C Allen; Maekawa, Masato; Mamotte, Cyril; Russomando, Graciela; Rousseau, François; Ahmad-Nejad, Parviz

    2017-04-01

    Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Genetic variability of hull-less barley accessions based on molecular and quantitative data

    Directory of Open Access Journals (Sweden)

    Ricardo Meneses Sayd

    2015-02-01

    Full Text Available The objective of this work was to characterize and quantify the genetic, molecular, and agronomic variability of hull-less barley genotypes, for the selection of parents and identification of genotypes adapted to the irrigated production system in the Brazilian Cerrado. Eighteen hull-less barley accessions were evaluated, and three covered barley accessions served as reference. The characterization was based on 157 RAPD molecular markers and ten agronomic traits. Genetic distance matrices were obtained based on molecular markers and quantitative traits. Graphic grouping and dispersion analyses were performed. Genetic, molecular, and agronomic variability was high among genotypes. Ethiopian accessions were genetically more similar, and the Brazilian ones were genetically more distant. For agronomic traits, two more consistent groupings were obtained, one with the most two-rowed materials, and the other with six-rowed materials. The more diverging materials were the two-rowed CI 13453, CN Cerrado 5, CN Cerrado 1, and CN Cerrado 2. The PI 356466, CN Cerrado 1, PI 370799, and CI 13453 genotypes show agronomic traits of interest and, as genetically different genotypes, they are indicated for crossing, in breeding programs.

  9. Personalized Medicine Based on Theranostic Radioiodine Molecular Imaging for Differentiated Thyroid Cancer.

    Science.gov (United States)

    Ahn, Byeong-Cheol

    2016-01-01

    Molecular imaging based personalized therapy has been a fascinating concept for individualized therapeutic strategy, which is able to attain the highest efficacy and reduce adverse effects in certain patients. Theranostics, which integrates diagnostic testing to detect molecular targets for particular therapeutic modalities, is one of the key technologies that contribute to the success of personalized medicine. Although the term "theranostics" was used after the second millennium, its basic principle was applied more than 70 years ago in the field of thyroidology with radioiodine molecular imaging. Differentiated thyroid cancer, which arises from follicular cells in the thyroid, is the most common endocrine malignancy, and theranostic radioiodine has been successfully applied to diagnose and treat differentiated thyroid cancer, the applications of which were included in the guidelines published by various thyroid or nuclear medicine societies. Through better pathophysiologic understanding of thyroid cancer and advancements in nuclear technologies, theranostic radioiodine contributes more to modern tailored personalized management by providing high therapeutic effect and by avoiding significant adverse effects in differentiated thyroid cancer. This review details the inception of theranostic radioiodine and recent radioiodine applications for differentiated thyroid cancer management as a prototype of personalized medicine based on molecular imaging.

  10. Molecular dynamics based enhanced sampling of collective variables with very large time steps

    Science.gov (United States)

    Chen, Pei-Yang; Tuckerman, Mark E.

    2018-01-01

    Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

  11. Estimativa da produtividade de café com base em um modelo agrometeorológico-espectral

    Directory of Open Access Journals (Sweden)

    Viviane Gomes Cardoso da Rosa

    2010-12-01

    Full Text Available O objetivo deste trabalho foi avaliar um modelo agrometeorológico-espectral, para estimar a produtividade de cafezais. Utilizaram-se imagens do sensor MODIS e dados agrometeorológicos do modelo regional de previsão do tempo (ETA, para fornecer as variáveis de entrada para o modelo agrometeorológico-espectral da mesorregião geográfica sul/sudoeste do estado de Minas Gerais nos anos-agrícolas de 2003/2004 a 2007/2008. A variável espectral de entrada do modelo agrometeorológico-espectral, índice de área foliar (IAF, usada no cálculo da produtividade máxima, foi estimada com o índice de vegetação por diferença normalizada (NDVI, obtido de imagens MODIS. Outras variáveis de entrada no modelo foram: dados meteorológicos gerados pelo modelo ETA e a capacidade de água disponível no solo. Ao comparar a produtividade média estimada pelo modelo com a fornecida oficialmente pelo IBGE, as diferenças relativas obtidas em escala regional foram de: 0,4, 3,0, 5,3, 1,5 e 8,5% para os anos agrícolas 2003/2004, 2004/2005, 2005/2006, 2006/2007 e 2007/2008, respectivamente. O modelo agrometeorólogico-espectral, que tem como base o modelo de Doorenbos & Kassan, foi tão eficaz para estimar a produtividade dos cafezais quanto o modelo oficial do IBGE. Além disso, foi possível espacializar a quebra de produtividade e prever 80% da produtividade final na primeira quinzena de fevereiro, antes do início da colheita

  12. 3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold.

    Science.gov (United States)

    Abbasi, Maryam; Sadeghi-Aliabadi, Hojjat; Amanlou, Massoud

    2018-05-01

    Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were also done. The steric and electrostatic contour map of CoMFA and CoMSIA were created. Hydrophobic, hydrogen bond donor and acceptor of CoMSIA model also were generated, and new compounds were predicted by CoMFA and CoMSIA contour maps. To investigate the binding modes of the predicted compounds in the active site of Hsp90, a molecular docking simulation was carried out. MD simulations were also conducted to evaluate the obtained results on the best predicted compound and the best reported Hsp90 inhibitors in the 3D-QSAR model. Findings indicate that the predicted ligands were stable in the active site of Hsp90.

  13. Caracterização molecular de populações do nematóide-de-cisto-da-soja com diferentes índices de parasitismo na cultivar Hartwig Molecular characterization of soybean cyst nematode populations with different parasitism index to the Hartwig cultivar

    Directory of Open Access Journals (Sweden)

    Ricardo Vilela Abdelnoor

    2001-02-01

    Full Text Available Recentemente, foi descoberta uma raça do nematóide-de-cisto-da-soja (NCS; Heterodera glycines que apresentou a capacidade de quebrar a resistência da cultivar Hartwig, até então considerada resistente a todas as raças conhecidas do nematóide. Essa população foi coletada no Município de Sorriso, Estado do Mato Grosso, e foi caracterizada como raça 4. Para verificar a diversidade genética entre esta e outras populações pertencentes às raças 4 e 9, foi feita uma caracterização molecular pela técnica de marcadores moleculares RAPD. Foram utilizadas nove populações do NCS, das quais quatro apresentavam a capacidade de parasitar 'Hartwig'. Foi verificado que as populações capazes de parasitar 'Hartwig' foram bastante diferentes das demais. Por meio de análise de agrupamento, com base nas distâncias genéticas encontradas, foram obtidos três grupos: o primeiro, constituído por indivíduos classificados como raça 4, mas que não parasitam 'Hartwig'; o segundo, constituído por quatro populações capazes de parasitar 'Hartwig', e o terceiro, por apenas uma população, classificado como raça 9, e que também não parasita 'Hartwig'. Este estudo confirmou que a população de NCS, encontrada em Sorriso, é geneticamente distinta das demais populações da raça 4 encontradas e constitui uma nova raça, denominada 4+.Recently, a new race of soybean cyst nematode (SCN (Heterodera glycines was discovered, which breaks the resistance of cultivar Hartwig, resistant to all known races of SCN. This population was obtained from soybean plants collected in the Sorriso county, state of Mato Grosso, Brazil, and is characterized as race 4. To verify if this isolate was different from others classified as races 4 and 9, their genetic diversity was analyzed by using the RAPD technique. Nine populations of SCN were analyzed, and only four populations were able to parasitize soybean plants cultivar Hartwig. Based on this study, it was

  14. Evaluation of the 18 kDa translocator protein (TSPO) as a target for molecular imaging and therapy of glioblastoma in an experimental rat model

    International Nuclear Information System (INIS)

    Awde, Ali Reda

    2012-01-01

    In France alone, there are 3000 new cases of glioblastoma multiform (GBM) per year and therefore GBM is the most common and aggressive form of the primary tumor in the central nervous system (CNS). The clinical prognosis for glioblastoma patients is extremely poor with a median survival period that rarely exceeds 15 months post-diagnosis. Since the study performed by Stupp and colleagues in 2005, the standard treatment for newly diagnosed glioblastoma consists of surgical removal of the tumor, followed by radiotherapy and concomitant chemotherapy with temozolomide. The 18 kDa Translocator Protein (TSPO), previously known as the peripheral benzodiazepine receptor (PBR) is a mitochondrial membrane protein known to be implicated in cholesterol transport, protein import, transport of porphyrin, cell proliferation and apoptosis through its interaction with VDAC (Voltage-Dependent Anion Channel) in the mitochondrial permeability transition pore (PTPM). Previous studies have reported overexpression of TSPO in brain tumors, suggesting that this protein may represent a molecular target for the therapy of GBM. In particular, Erucyl-phospho-homo-choline (ErPC3, erufosine), an alkyl-phosphocholine, seems to be a promising agent in the treatment of glioblastoma. Previous studies have reported its ability to induce apoptosis in otherwise highly apoptosis resistant glioma cell lines and ErPC3 induced apoptosis seems to require the presence TSPO. [ 18 F]DPA-714, a new TSPO radioligand for positron emission tomography (PET) imaging, was developed at the CEA and validated in different models of neuro-inflammation. The hypotheses underlying this thesis are: 1) that the overexpression of TSPO in GBM can be detected by PET imaging using [ 18 F]DPA-714 and 2) that the targeting of TSPO, via specific ligands or via ErPC3, can induce apoptosis in GBM. The objectives of the thesis were: 1) to evaluate the expression of TSPO in a panel of rodent and human glioma cell lines and 2) to

  15. Smartphone-Based Mobile Detection Platform for Molecular Diagnostics and Spatiotemporal Disease Mapping.

    Science.gov (United States)

    Song, Jinzhao; Pandian, Vikram; Mauk, Michael G; Bau, Haim H; Cherry, Sara; Tisi, Laurence C; Liu, Changchun

    2018-04-03

    Rapid and quantitative molecular diagnostics in the field, at home, and at remote clinics is essential for evidence-based disease management, control, and prevention. Conventional molecular diagnostics requires extensive sample preparation, relatively sophisticated instruments, and trained personnel, restricting its use to centralized laboratories. To overcome these limitations, we designed a simple, inexpensive, hand-held, smartphone-based mobile detection platform, dubbed "smart-connected cup" (SCC), for rapid, connected, and quantitative molecular diagnostics. Our platform combines bioluminescent assay in real-time and loop-mediated isothermal amplification (BART-LAMP) technology with smartphone-based detection, eliminating the need for an excitation source and optical filters that are essential in fluorescent-based detection. The incubation heating for the isothermal amplification is provided, electricity-free, with an exothermic chemical reaction, and incubation temperature is regulated with a phase change material. A custom Android App was developed for bioluminescent signal monitoring and analysis, target quantification, data sharing, and spatiotemporal mapping of disease. SCC's utility is demonstrated by quantitative detection of Zika virus (ZIKV) in urine and saliva and HIV in blood within 45 min. We demonstrate SCC's connectivity for disease spatiotemporal mapping with a custom-designed website. Such a smart- and connected-diagnostic system does not require any lab facilities and is suitable for use at home, in the field, in the clinic, and particularly in resource-limited settings in the context of Internet of Medical Things (IoMT).

  16. Molecular analysis of single oocyst of Eimeria by whole genome amplification (WGA) based nested PCR.

    Science.gov (United States)

    Wang, Yunzhou; Tao, Geru; Cui, Yujuan; Lv, Qiyao; Xie, Li; Li, Yuan; Suo, Xun; Qin, Yinghe; Xiao, Lihua; Liu, Xianyong

    2014-09-01

    PCR-based molecular tools are widely used for the identification and characterization of protozoa. Here we report the molecular analysis of Eimeria species using combined methods of whole genome amplification (WGA) and nested PCR. Single oocyst of Eimeria stiedai or Eimeriamedia was directly used for random amplification of the genomic DNA with either primer extension preamplification (PEP) or multiple displacement amplification (MDA), and then the WGA product was used as template in nested PCR with species-specific primers for ITS-1, 18S rDNA and 23S rDNA of E. stiedai and E. media. WGA-based PCR was successful for the amplification of these genes from single oocyst. For the species identification of single oocyst isolated from mixed E. stiedai or E. media, the results from WGA-based PCR were exactly in accordance with those from morphological identification, suggesting the availability of this method in molecular analysis of eimerian parasites at the single oocyst level. WGA-based PCR method can also be applied for the identification and genetic characterization of other protists. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Molecular-based tumour subtypes of canine mammary carcinomas assessed by immunohistochemistry

    Directory of Open Access Journals (Sweden)

    Sarli Giuseppe

    2010-01-01

    Full Text Available Abstract Background Human breast cancer is classified by gene expression profile into subtypes consisting of two hormone (oestrogen and/or progesterone receptor-positive types (luminal-like A and luminal-like B and three hormone receptor-negative types [human epidermal growth factor receptor 2-expressing, basal-like, and unclassified ("normal-like"]. Immunohistochemical surrogate panels are also proposed to potentially identify the molecular-based groups. The present study aimed to apply an immunohistochemical panel (anti-ER, -PR, -ERB-B2, -CK 5/6 and -CK14 in a series of canine malignant mammary tumours to verify the molecular-based classification, its correlation with invasion and grade, and its use as a prognostic aid in veterinary practice. Results Thirty-five tumours with luminal pattern (ER+ and PR+ were subgrouped into 13 A type and 22 B type, if ERB-B2 positive or negative. Most luminal-like A and basal-like tumours were grade 1 carcinomas, while the percentage of luminal B tumours was higher in grades 2 and 3 (Pearson Chi-square P = 0.009. No difference in the percentage of molecular subtypes was found between simple and complex/mixed carcinomas (Pearson Chi-square P = 0.47. No significant results were obtained by survival analysis, even if basal-like tumours had a more favourable prognosis than luminal-like lesions. Conclusion The panel of antibodies identified only three tumour groups (luminal-like A and B, and basal-like in the dog. Even though canine mammary tumours may be a model of human breast cancer, the existence of the same carcinoma molecular subtypes in women awaits confirmation. Canine mammary carcinomas show high molecular heterogeneity, which would benefit from a classification based on molecular differences. Stage and grade showed independent associations with survival in the multivariate regression, while molecular subtype grouping and histological type did not show associations. This suggests that caution should be

  18. Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

    Czech Academy of Sciences Publication Activity Database

    Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

    2012-01-01

    Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012

  19. Reactivity of etoricoxib based on computational study of molecular orbitals, molecular electrostatic potential surface and Mulliken charge analysis

    Science.gov (United States)

    Sachdeva, Ritika; Soni, Abhinav; Singh, V. P.; Saini, G. S. S.

    2018-05-01

    Etoricoxib is one of the selective cyclooxygenase inhibitor drug which plays a significant role in the pharmacological management of arthritis and pain. The theoretical investigation of its reactivity is done using Density Functional Theory calculations. Molecular Electrostatic Potential Surface of etoricoxib and its Mulliken atomic charge distribution are used for the prediction of its electrophilic and nucleophilic sites. The detailed analysis of its frontier molecular orbitals is also done.

  20. Estudos moleculares, estruturais e funcionais da Cel12A de Gloeophyllum trabeum, uma endo-1,4-β-glucanase da família 12 de hidrolases de glicosídeos

    OpenAIRE

    Lis Schwartz Miotto

    2014-01-01

    A produção de etanol de segunda geração, a partir da hidrólise enzimática da biomassa vegetal é considerada uma alternativa viável e promissora para enfrentarmos a crise energética mundial e diminuirmos a dependência das fontes fósseis de energia. Para isso, é necessário que ocorra a degradação das moléculas constituintes da parede celular como a lignina, a celulose e a hemicelulose a açúcares fermentescíveis. No entanto, a utilização de enzimas para esse fim ainda apresenta um custo elevado,...

  1. Sistema imunitário: Parte I. Fundamentos da imunidade inata com ênfase nos mecanismos moleculares e celulares da resposta inflamatória Immune system: Part I. Fundamentals of innate immunity with emphasis on molecular and cellular mechanisms of inflammatory response

    Directory of Open Access Journals (Sweden)

    Wilson de Melo Cruvinel

    2010-08-01

    Full Text Available O sistema imunológico é constituído por uma intrincada rede de órgãos, células e moléculas, e tem por finalidade manter a homeostase do organismo, combatendo as agressões em geral. A imunidade inata atua em conjunto com a imunidade adaptativa e caracteriza-se pela rápida resposta à agressão, independentemente de estímulo prévio, sendo a primeira linha de defesa do organismo. Seus mecanismos compreendem barreiras físicas, químicas e biológicas, componentes celulares e moléculas solúveis. A primeira defesa do organismo frente a um dano tecidual envolve diversas etapas intimamente integradas e constituídas pelos diferentes componentes desse sistema. A presente revisão tem como objetivo resgatar os fundamentos dessa resposta, que apresenta elevada complexidade e é constituída por diversos componentes articulados que convergem para a elaboração da resposta imune adaptativa. Destacamos algumas etapas: reconhecimento molecular dos agentes agressores; ativação de vias bioquímicas intracelulares que resultam em modificações vasculares e teciduais; produção de uma miríade de mediadores com efeitos locais e sistêmicos no âmbito da ativação e proliferação celulares, síntese de novos produtos envolvidos na quimioatração e migração de células especializadas na destruição e remoção do agente agressor, e finalmente a recuperação tecidual com o restabelecimento funcional do tecido ou órgão.The immune system consists of an intricate network of organs, cells, and molecules responsible for maintaining the body's homeostasis and responding to aggression in general. Innate immunity operates in conjunction with adaptive immunity and is characterized by rapid response to aggression, regardless of previous stimulus, being the organism first line of defense. Its mechanisms include physical, chemical and biological barriers, cellular components, as well as soluble molecules. The organism first line of defense against

  2. Sputum-Based Molecular Biomarkers for the Early Detection of Lung Cancer: Limitations and Promise

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Connie E. [Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016 (United States); Tchou-Wong, Kam-Meng; Rom, William N., E-mail: william.rom@nyumc.org [Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016 (United States); Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987 (United States)

    2011-07-19

    Lung cancer is the leading cause of cancer deaths, with an overall survival of 15% at five years. Biomarkers that can sensitively and specifically detect lung cancer at early stage are crucial for improving this poor survival rate. Sputum has been the target for the discovery of non-invasive biomarkers for lung cancer because it contains airway epithelial cells, and molecular alterations identified in sputum are most likely to reflect tumor-associated changes or field cancerization caused by smoking in the lung. Sputum-based molecular biomarkers include morphology, allelic imbalance, promoter hypermethylation, gene mutations and, recently, differential miRNA expression. To improve the sensitivity and reproducibility of sputum-based biomarkers, we recommend standardization of processing protocols, bronchial epithelial cell enrichment, and identification of field cancerization biomarkers.

  3. Capturing molecular multimode relaxation processes in excitable gases based on decomposition of acoustic relaxation spectra

    Science.gov (United States)

    Zhu, Ming; Liu, Tingting; Wang, Shu; Zhang, Kesheng

    2017-08-01

    Existing two-frequency reconstructive methods can only capture primary (single) molecular relaxation processes in excitable gases. In this paper, we present a reconstructive method based on the novel decomposition of frequency-dependent acoustic relaxation spectra to capture the entire molecular multimode relaxation process. This decomposition of acoustic relaxation spectra is developed from the frequency-dependent effective specific heat, indicating that a multi-relaxation process is the sum of the interior single-relaxation processes. Based on this decomposition, we can reconstruct the entire multi-relaxation process by capturing the relaxation times and relaxation strengths of N interior single-relaxation processes, using the measurements of acoustic absorption and sound speed at 2N frequencies. Experimental data for the gas mixtures CO2-N2 and CO2-O2 validate our decomposition and reconstruction approach.

  4. Baseline staging tests based on molecular subtype is necessary for newly diagnosed breast cancer.

    Science.gov (United States)

    Chen, Xuesong; Sun, Lichun; Cong, Yingying; Zhang, Tingting; Lin, Qiushi; Meng, Qingwei; Pang, Hui; Zhao, Yanbin; Li, Yu; Cai, Li; Dong, Xiaoqun

    2014-03-17

    Bone scanning (BS), liver ultrasonography (LUS), and chest radiography (CXR) are commonly recommended for baseline staging in patients with newly diagnosed breast cancer. The purpose of this study is to demonstrate whether these tests are indicated for specific patient subpopulation based on clinical staging and molecular subtype. A retrospective study on 5406 patients with newly diagnosed breast cancer was conducted to identify differences in occurrence of metastasis based on clinical staging and molecular subtypes. All patients had been evaluated by BS, LUS and CXR at diagnosis. Complete information on clinical staging was available in 5184 patients. For stage I, II, and III, bone metastasis rate was 0%, 0.6% and 2.7%, respectively (P diagnosed breast cancer.

  5. Potential of luminescence based molecular animal imaging in research areas pertaining to cancer biology and therapy

    International Nuclear Information System (INIS)

    Yadav, Hansa D.; Shetake, Neena G.; Balla Murali, M.S.; Kumar, Amit; Pandey, B.N.

    2017-01-01

    Animal imaging is getting tremendous importance in biomedical research areas including drug delivery, radiobiology and cancer research. Even though, imaging techniques like CT, PET, SPECT, MRI are available for experimental animals, luminescence-based molecular imaging is still considered as crucial and common tool for biomedical laboratories due to easy handling/maintenance, cost effectiveness and various strategies available to manipulate the molecules/cells employed for imaging purposes. The Molecular Animal Imaging System available in our laboratory is being utilized for various cancer research activities including measurement of tumor growth kinetics, angiogenesis, therapeutic efficacy evaluation and metastasis studies. Moreover, the imaging system is also been used for radio-luminescence imaging based on Cherenkov radiation of radio-pharmaceuticals. (author)

  6. Cellulose acetate-based molecularly imprinted polymeric membrane for separation of vanillin and o-vanillin

    OpenAIRE

    Zhang,Chunjing; Zhong,Shian; Yang,Zhengpeng

    2008-01-01

    Cellulose acetate-based molecularly imprinted polymeric membranes were prepared using vanillin as template molecule. The microscopic structure of the resultant polymeric membranes was characterized by SEM and FTIR spectroscopy, and the selective binding properties and separation capacity of the membranes for vanillin and o-vanillin were tested with binding experiments and separate experiments, respectively. The results showed that the vanillin-imprinted polymeric membranes displayed higher bi...

  7. Sensors based on carbon nanotube field-effect transistors and molecular recognition approaches

    OpenAIRE

    Cid Salavert, Cristina Carlota

    2009-01-01

    The general objective of this thesis is to develop chemical sensors whose sensing capacities are based on the principle of molecular recognition and where the transduction is carried out by single-walled carbon nanotubes (SWCNT).The sensing device used is the carbon nanotube field-effect transistor (CNTFET). The new structure of the CNTFET allows nanotubes to be integrated at the surface of the devices, thus exploiting SWCNTs' sensitivity to changes in their environment. The functionalization...

  8. Electrochemical control of quantum interference in anthraquinone-based molecular switches

    DEFF Research Database (Denmark)

    Markussen, Troels; Schiøtz, Jakob; Thygesen, Kristian Sommer

    2010-01-01

    Using first-principles calculations we analyze the electronic transport properties of a recently proposed anthraquinone-based electrochemical switch. Robust conductance on/off ratios of several orders of magnitude are observed due to destructive quantum interference present in the anthraquinone...... of hopping via the localized orbitals. The topology of the tight-binding model, which is dictated by the symmetries of the molecular orbitals, determines the amount of quantum interference....

  9. Desenvolvimento de um programa/base de dados para o controlo automático da engenharia/manutenção aeronáutica

    OpenAIRE

    Monteiro, Roberto Évora

    2012-01-01

    Este documento foi escrito para retratar o trabalho desenvolvido como tese de mestrado “Desenvolvimento de um Programa/Base de dados para o controlo automático da Engenharia/Manutenção Aeronáutica”. O programa criado tem como objectivo de gerir a aeronavegabilidade de uma frota de aeronaves, traduzindo todos os requisitos da autoridade que rege a aeronáutica na Europa. O mesmo fundamenta-se no desenvolvimento de um software aplicado a uma empresa que faz a gestão contínua da aeronavegabili...

  10. Proposição de um modelo de analise da competitividade organizacional com base no valor : aplicação no setor de ceramica para revestimento

    OpenAIRE

    Muller, Gisela Regina

    1996-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnologico A partir da revisão das principais abordagens existentes sobre o conceito de competitividade e de alguns dos principais modelos de análise da competitividade, é proposto um modelo de análise da competitividade organizacional com base no conceito de valor. Quando a questão central colocada é como analisar a competitividade empresarial, é necessário uma abordagem refinada, que permita captar as nuances dos fa...

  11. Feasibility study of molecular memory device based on DNA using methylation to store information

    International Nuclear Information System (INIS)

    Jiang, Liming; Al-Dirini, Feras; Qiu, Wanzhi; Skafidas, Efstratios; Hossain, Faruque M.; Evans, Robin

    2016-01-01

    DNA, because of its robustness and dense information storage capability, has been proposed as a potential candidate for next-generation storage media. However, encoding information into the DNA sequence requires molecular synthesis technology, which to date is costly and prone to synthesis errors. Reading the DNA strand information is also complex. Ideally, DNA storage will provide methods for modifying stored information. Here, we conduct a feasibility study investigating the use of the DNA 5-methylcytosine (5mC) methylation state as a molecular memory to store information. We propose a new 1-bit memory device and study, based on the density functional theory and non-equilibrium Green's function method, the feasibility of electrically reading the information. Our results show that changes to methylation states lead to changes in the peak of negative differential resistance which can be used to interrogate memory state. Our work demonstrates a new memory concept based on methylation state which can be beneficial in the design of next generation DNA based molecular electronic memory devices.

  12. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes

    2016-03-01

    Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

  13. Feasibility study of molecular memory device based on DNA using methylation to store information

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Liming; Al-Dirini, Feras [Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville 3010 (Australia); Center for Neural Engineering (CfNE), The University of Melbourne, Carlton 3053 (Australia); National ICT Australia, The University of Melbourne, Parkville 3010 (Australia); Qiu, Wanzhi; Skafidas, Efstratios, E-mail: sskaf@unimelb.edu.au [Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville 3010 (Australia); Center for Neural Engineering (CfNE), The University of Melbourne, Carlton 3053 (Australia); Hossain, Faruque M. [Center for Neural Engineering (CfNE), The University of Melbourne, Carlton 3053 (Australia); Evans, Robin [Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville 3010 (Australia)

    2016-07-14

    DNA, because of its robustness and dense information storage capability, has been proposed as a potential candidate for next-generation storage media. However, encoding information into the DNA sequence requires molecular synthesis technology, which to date is costly and prone to synthesis errors. Reading the DNA strand information is also complex. Ideally, DNA storage will provide methods for modifying stored information. Here, we conduct a feasibility study investigating the use of the DNA 5-methylcytosine (5mC) methylation state as a molecular memory to store information. We propose a new 1-bit memory device and study, based on the density functional theory and non-equilibrium Green's function method, the feasibility of electrically reading the information. Our results show that changes to methylation states lead to changes in the peak of negative differential resistance which can be used to interrogate memory state. Our work demonstrates a new memory concept based on methylation state which can be beneficial in the design of next generation DNA based molecular electronic memory devices.

  14. Thermophysical Properties of Homologous Tetracyanoborate-Based Ionic Liquids Using Experiments and Molecular Dynamics Simulations.

    Science.gov (United States)

    Koller, Thomas M; Ramos, Javier; Schulz, Peter S; Economou, Ioannis G; Rausch, Michael H; Fröba, Andreas P

    2017-04-27

    Thermophysical properties of low-viscosity ionic liquids (ILs) based on the tetracyanoborate ([B(CN) 4 ] - ) anion carrying a homologous series of 1-alkyl-3-methylimidazolium ([AMIM] + ) cations [EMIM] + (ethyl), [BMIM] + (butyl), [HMIM] + (hexyl), [OMIM] + (octyl), and [DMIM] + (decyl) were investigated by experimental methods and molecular dynamics (MD) simulations at atmospheric pressure and various temperatures. Spectroscopic methods based on nuclear magnetic resonance and surface light scattering were applied to measure the ion self-diffusion coefficients and dynamic viscosity, respectively. In terms of MD simulations, a nonpolarizable molecular model for [EMIM][B(CN) 4 ] developed by optimization to experimental data was transferred to the other homologous ILs. For the appropriate description of the inter- and intramolecular interactions, precise and approximate force fields (FFs) were tested regarding their transferability within the homologous IL series, aiming at reducing the computational effort in molecular simulations. It is shown that at comparable simulated and experimental densities, the calculated and measured data for viscosity and self-diffusion coefficients of the ILs agree well mostly within combined uncertainties, but deviate stronger for longer-chained ILs using an overly coarse FF model. For the [B(CN) 4 ] - -based ILs studied, a comparison with literature data, the influence of varying alkyl chain length in the cation on their structural and thermophysical properties, and a correlation between self-diffusivity and viscosity are discussed.

  15. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    International Nuclear Information System (INIS)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R.

    2014-01-01

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  16. The Influence of Single Nucleotide Polymorphism Microarray-Based Molecular Karyotype on Preimplantation Embryonic Development Potential.

    Directory of Open Access Journals (Sweden)

    Gang Li

    Full Text Available In order to investigate the influence of the molecular karyotype based on single nucleotide polymorphism (SNP microarray on embryonic development potential in preimplantation genetic diagnosis (PGD, we retrospectively analyzed the clinical data generated by PGD using embryos retrieved from parents with chromosome rearrangements in our center. In total, 929 embryos from 119 couples had exact diagnosis and development status. The blastocyst formation rate of balanced molecular karyotype embryos was 56.6% (276/488, which was significantly higher than that of genetic imbalanced embryos 24.5% (108/441 (P35 respectively. Blastocyst formation rates of male and female embryos were 44.5% (183/411 and 38.8% (201/518 respectively, with no significant difference between them (P>0.05. The rates of balanced molecular karyotype embryos vary from groups of embryos with different cell numbers at 68 hours after insemination. The blastocyst formation rate of embryos with 6-8 cells (48.1% was significantly higher than that of embryos with 8 cells (42.9% (P8 cells, embryos with 6-8 blastomeres have higher rate of balanced molecular karyotype and blastocyst formation.

  17. Synthesis and Guest Recognition of Switchable Pt-Salphen Based Molecular Tweezers

    Directory of Open Access Journals (Sweden)

    Lorien Benda

    2018-04-01

    Full Text Available Molecular tweezers are artificial receptors that have an open cavity generated by two recognition units pre-organized by a spacer. Switchable molecular tweezers, using a stimuli-responsive spacer, are particularly appealing as prototypes of the molecular machines that combine mechanical motion and allosteric recognition properties. In this present study, the synthesis of switchable molecular tweezers composed of a central terpyridine unit substituted in 4,4″ positions by two Pt(II-salphen complexes is reported. The terpyridine ligand can be reversibly converted upon Zn(II coordination from a free ‘U’-shaped closed form to a coordinated ‘W’ open form. This new substitution pattern enables a reverse control of the mechanical motion compared to the previously reported 6,6″ substituted terpyridine-based tweezers. Guest binding studies with aromatic guests showed an intercalation of coronene in the cavity created by the Pt-salphen moieties in the closed conformation. The formation of 1:1 host-guest complex was investigated by a combination of NMR studies and DFT calculations.

  18. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

    2014-06-10

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  19. Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

    Directory of Open Access Journals (Sweden)

    Subin eHada

    2014-06-01

    Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  20. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  1. Estômago em melancia, pericardite hemorrágica, tumor de pequenas células do pulmão e carcinoma pavimentocelular síncrono da base da língua

    Directory of Open Access Journals (Sweden)

    A. Murinello

    2010-07-01

    Full Text Available Resumo: Baseados num caso de gastropatia antral com ectasia vascular (estômago em melancia associado a pericardite hemorrágica e a um carcinoma de pequenas células do pulmão com metástases ganglionares ao longo do mediastino e a um carcinoma pavimentocelular síncrono da base da língua, os autores fazem uma revisão dos aspectos clínicos, endoscópicos e histopatológicos deste tipo de gastropatia, da sua associação a outras doenças e das possibilidades terapêuticas actuais por via endoscópica. Referem-se igualmente as causas mais frequentes de pericardite hemorrágica, salientando-se a necessidade de esclarecer se o derrame é ou não de origem neoplásica. Não está referida na literatura a associação deste tipo de gastropatia ao carcinoma de pequenas células do pulmão nem ao carcinoma pavimento-celular da base da língua. A invasão extensa dos gânglios mediastínicos pelo carcinoma de pequenas células do pulmão é ocorrência frequente.Rev Port Pneumol 2010; XVI (4: 659-670 Abstract: Based on a case of gastric antral vascular ectasia (watermelon stomach that was associated with hemorrhagic pericarditis, small cell lung carcinoma with mediastinal lymph node metastases and a synchronous squamous cell carcinoma of the base of the tongue, the authors made a review of the clinical, endoscopic and histopathological aspects of this type of gastropathy, and its association with other diseases, and of the results of its endoscopic therapy. The causes of hemorrhagic pericarditis are considered, emphasizing the necessity to know if the effusion has a malignant etiology. To the best of our knowledge the association of watermelon stomach to small cell lung carcinoma and squamous cell carcinoma of the base of the tongue has not yet been described. Extensive metastases to mediastal lymph nodes are common to small cell lung carcinoma.Rev Port Pneumol 2010; XVI (4: 659-670 Palavras-chave: Gastropatia antral com ectasia vascular, est

  2. DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.

    Science.gov (United States)

    Mazandu, Gaston K; Mulder, Nicola J

    2013-09-25

    The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis.

  3. The LEONARDO-DA-VINCI pilot project "e-learning-assistant" - Situation-based learning in nursing education.

    Science.gov (United States)

    Pfefferle, Petra Ina; Van den Stock, Etienne; Nauerth, Annette

    2010-07-01

    E-learning will play an important role in the training portfolio of students in higher and vocational education. Within the LEONARDO-DA-VINCI action programme transnational pilot projects were funded by the European Union, which aimed to improve the usage and quality of e-learning tools in education and professional training. The overall aim of the LEONARDO-DA-VINCI pilot project "e-learning-assistant" was to create new didactical and technical e-learning tools for Europe-wide use in nursing education. Based on a new situation-oriented learning approach, nursing teachers enrolled in the project were instructed to adapt, develop and implement e- and blended learning units. According to the training contents nursing modules were developed by teachers from partner institutions, implemented in the project centers and evaluated by students. The user-package "e-learning-assistant" as a product of the project includes two teacher training units, the authoring tool "synapse" to create situation-based e-learning units, a student's learning platform containing blended learning modules in nursing and an open sourced web-based communication centre. Copyright 2009 Elsevier Ltd. All rights reserved.

  4. Análise Bibliométrica da produção científica em gestão da informação na base de dados lisa / Bibliometrics analysis of scientific production in management information in the lisa database

    OpenAIRE

    Luiza da Silva Kleinubing

    2010-01-01

    Descreve e analisa as principais características bibliométricas das publicações relacionadas à área de gestão da informação da base de dados Lisa, uma das bases com maior visibilidade no campo da Biblioteconomia e Ciência da Informação. Foram analisados 138 artigos. A metodologia de pesquisa combina métodos bibliométricos e softwares, a característica da pesquisa é quantitativa, pois enumera e mede, e qualitativa, pois compreende e explica. Conclui-se sinalizando que os métodos bibliométricos...

  5. Gene expression-based molecular diagnostic system for malignant gliomas is superior to histological diagnosis.

    Science.gov (United States)

    Shirahata, Mitsuaki; Iwao-Koizumi, Kyoko; Saito, Sakae; Ueno, Noriko; Oda, Masashi; Hashimoto, Nobuo; Takahashi, Jun A; Kato, Kikuya

    2007-12-15

    Current morphology-based glioma classification methods do not adequately reflect the complex biology of gliomas, thus limiting their prognostic ability. In this study, we focused on anaplastic oligodendroglioma and glioblastoma, which typically follow distinct clinical courses. Our goal was to construct a clinically useful molecular diagnostic system based on gene expression profiling. The expression of 3,456 genes in 32 patients, 12 and 20 of whom had prognostically distinct anaplastic oligodendroglioma and glioblastoma, respectively, was measured by PCR array. Next to unsupervised methods, we did supervised analysis using a weighted voting algorithm to construct a diagnostic system discriminating anaplastic oligodendroglioma from glioblastoma. The diagnostic accuracy of this system was evaluated by leave-one-out cross-validation. The clinical utility was tested on a microarray-based data set of 50 malignant gliomas from a previous study. Unsupervised analysis showed divergent global gene expression patterns between the two tumor classes. A supervised binary classification model showed 100% (95% confidence interval, 89.4-100%) diagnostic accuracy by leave-one-out cross-validation using 168 diagnostic genes. Applied to a gene expression data set from a previous study, our model correlated better with outcome than histologic diagnosis, and also displayed 96.6% (28 of 29) consistency with the molecular classification scheme used for these histologically controversial gliomas in the original article. Furthermore, we observed that histologically diagnosed glioblastoma samples that shared anaplastic oligodendroglioma molecular characteristics tended to be associated with longer survival. Our molecular diagnostic system showed reproducible clinical utility and prognostic ability superior to traditional histopathologic diagnosis for malignant glioma.

  6. Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs.

    Science.gov (United States)

    Losilla, Sergio A; Watson, Mark A; Aspuru-Guzik, Alán; Sundholm, Dage

    2015-05-12

    We present a GPGPU implementation of the construction of the Fock matrix in the molecular orbital basis using the fully numerical, grid-based bubbles representation. For a test set of molecules containing up to 90 electrons, the total Hartree-Fock energies obtained from reference GTO-based calculations are reproduced within 10(-4) Eh to 10(-8) Eh for most of the molecules studied. Despite the very large number of arithmetic operations involved, the high performance obtained made the calculations possible on a single Nvidia Tesla K40 GPGPU card.

  7. Rectifying Properties of a Nitrogen/Boron-Doped Capped-Carbon-Nanotube-Based Molecular Junction

    International Nuclear Information System (INIS)

    Zhao Peng; Zhang Ying; Wang Pei-Ji; Zhang Zhong; Liu De-Sheng

    2011-01-01

    Based on the non-equilibrium Green's function method and first-principles density functional theory calculations, we investigate the electronic transport properties of a nitrogen/boron-doped capped-single-walled carbon-nanotube-based molecular junction. Obvious rectifying behavior is observed and it is strongly dependent on the doping site. The best rectifying performance can be carried out when the nitrogen/boron atom dopes at a carbon site in the second layer. Moreover, the rectifying performance can be further improved by adjusting the distance between the C 60 nanotube caps. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  8. Fast screening of ketamine in biological samples based on molecularly imprinted photonic hydrogels

    International Nuclear Information System (INIS)

    Meng, Liang; Meng, Pinjia; Zhang, Qingqing; Wang, Yanji

    2013-01-01

    Graphical abstract: A novel label-free colorimetric chemosensor: with the increase in the concentration of ketamine, the Bragg diffraction peak of MIPHs gradually shifted to the longer wavelength region. Accompanying the peak shift, the color change of MIPHs was also observed obviously: from green to red. Highlights: ► We developed the label-free colorimetric MIPHs for handy and fast screening of ketamine. ► The obvious color change of MIPHs was observed upon ketamine. ► The MIPHs exhibited good sensing abilities in an aqueous environment. ► The sensing mechanisms of the water-compatible MIPHs were investigated. ► The MIPHs were employed to screening ketamine in real biological samples. -- Abstract: A novel label-free colorimetric chemosensor was developed for handy and fast screening of ketamine with high sensitivity and specificity based on molecularly imprinted photonic hydrogels (MIPHs) that combined the colloidal-crystal with molecular imprinting technique. The unique inverse opal arrays with a thin polymer wall in which the imprinted nanocavities of ketamine moleculars distributed allowed high sensitive, quick responsive, specific detection of the target analyte, and good regenerating ability in an aqueous environment. Due to the hierarchical inverse opal structural characteristics, the specific ketamine molecular recognition process can induce obvious swelling of the MIPHs to be directly transferred into visually perceptible optical signal (change in color) which can be detected by the naked eye through Bragg diffractive shifts of ordered macroporous arrays. In order to enhance the recognition ability in aqueous environments, the MIPHs were designed as water-compatible and synthesized in a water–methanol system. The molecular recognition mechanisms were investigated. The proposed MIPHs were successfully employed to screen trace level ketamine in human urine and saliva samples, exhibiting high sensitivity, rapid response, and specificity in the

  9. Fast screening of ketamine in biological samples based on molecularly imprinted photonic hydrogels

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Liang [Department of Forensic Science, People' s Public Security University of China, Beijing (China); Meng, Pinjia, E-mail: mengpinjia@163.com [Department of Forensic Science, People' s Public Security University of China, Beijing (China); Zhang, Qingqing; Wang, Yanji [Department of Forensic Science, People' s Public Security University of China, Beijing (China)

    2013-04-10

    Graphical abstract: A novel label-free colorimetric chemosensor: with the increase in the concentration of ketamine, the Bragg diffraction peak of MIPHs gradually shifted to the longer wavelength region. Accompanying the peak shift, the color change of MIPHs was also observed obviously: from green to red. Highlights: ► We developed the label-free colorimetric MIPHs for handy and fast screening of ketamine. ► The obvious color change of MIPHs was observed upon ketamine. ► The MIPHs exhibited good sensing abilities in an aqueous environment. ► The sensing mechanisms of the water-compatible MIPHs were investigated. ► The MIPHs were employed to screening ketamine in real biological samples. -- Abstract: A novel label-free colorimetric chemosensor was developed for handy and fast screening of ketamine with high sensitivity and specificity based on molecularly imprinted photonic hydrogels (MIPHs) that combined the colloidal-crystal with molecular imprinting technique. The unique inverse opal arrays with a thin polymer wall in which the imprinted nanocavities of ketamine moleculars distributed allowed high sensitive, quick responsive, specific detection of the target analyte, and good regenerating ability in an aqueous environment. Due to the hierarchical inverse opal structural characteristics, the specific ketamine molecular recognition process can induce obvious swelling of the MIPHs to be directly transferred into visually perceptible optical signal (change in color) which can be detected by the naked eye through Bragg diffractive shifts of ordered macroporous arrays. In order to enhance the recognition ability in aqueous environments, the MIPHs were designed as water-compatible and synthesized in a water–methanol system. The molecular recognition mechanisms were investigated. The proposed MIPHs were successfully employed to screen trace level ketamine in human urine and saliva samples, exhibiting high sensitivity, rapid response, and specificity in the

  10. Water models based on a single potential energy surface and different molecular degrees of freedom

    Science.gov (United States)

    Saint-Martin, Humberto; Hernández-Cobos, Jorge; Ortega-Blake, Iván

    2005-06-01

    Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernández-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors—nonadditivity, polarizability, and intramolecular flexibility—are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force

  11. Electron induced conformational changes of an imine-based molecular switch on a Au(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Lotze, Christian; Henningsen, Nils; Franke, Katharina; Schulze, Gunnar; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    Azobenzene-based molecules exhibit a cis-trans configurational photoisomerisation in solution. Recently, the adsorption properties of azobenzene derivatives have been investigated on different metal surfaces in order to explore the possible changes in the film properties induced by external stimuli. In azobenzene, the diazo-bridge is a key group for the isomerization process. Its interaction with a metal surface is dominated through the N lone-pair electrons, which reduces the efficiency of the conformational change. In order to reduce the molecule-surface interaction, we explore an alternative molecular architecture by substituting the diazo-bridge (-N=N-) of azobenzene by an imine-group (-N=CH-). We have investigated the imine-based compound para-carboxyl-di-benzene-imine (PCI) adsorbed on a Au(111) surface. The carboxylic terminations mediates the formation of strongly bonded molecular dimers, which align in ordered rows preferentially following the fcc regions of the Au(111) herringbone reconstruction. Low temperature scanning tunneling microscopy was used to induce conformational changes between trans and cis state of individual molecules in a molecular monolayer.

  12. Characterization of nanoparticle-based contrast agents for molecular magnetic resonance imaging

    International Nuclear Information System (INIS)

    Shan, Liang; Chopra, Arvind; Leung, Kam; Eckelman, William C.; Menkens, Anne E.

    2012-01-01

    The development of molecular imaging agents is currently undergoing a dramatic expansion. As of October 2011, ∼4,800 newly developed agents have been synthesized and characterized in vitro and in animal models of human disease. Despite this rapid progress, the transfer of these agents to clinical practice is rather slow. To address this issue, the National Institutes of Health launched the Molecular Imaging and Contrast Agents Database (MICAD) in 2005 to provide freely accessible online information regarding molecular imaging probes and contrast agents for the imaging community. While compiling information regarding imaging agents published in peer-reviewed journals, the MICAD editors have observed that some important information regarding the characterization of a contrast agent is not consistently reported. This makes it difficult for investigators to evaluate and meta-analyze data generated from different studies of imaging agents, especially for the agents based on nanoparticles. This article is intended to serve as a guideline for new investigators for the characterization of preclinical studies performed with nanoparticle-based MRI contrast agents. The common characterization parameters are summarized into seven categories: contrast agent designation, physicochemical properties, magnetic properties, in vitro studies, animal studies, MRI studies, and toxicity. Although no single set of parameters is suitable to define the properties of the various types of contrast agents, it is essential to ensure that these agents meet certain quality control parameters at the preclinical stage, so that they can be used without delay for clinical studies.

  13. Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.

    Science.gov (United States)

    Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu; Karlsen, Jesper Lykkegaard; Nissen, Poul

    2016-03-01

    To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.

  14. Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers.

    Science.gov (United States)

    Blanco, Guillermo; Díaz de Tuesta, Juan A

    2018-04-13

    Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the

  15. Molecular Simulation Results on Charged Carbon Nanotube Forest-Based Supercapacitors.

    Science.gov (United States)

    Muralidharan, Ajay; Pratt, Lawrence R; Hoffman, Gary G; Chaudhari, Mangesh I; Rempe, Susan B

    2018-05-03

    Electrochemical double-layer capacitances of charged carbon nanotube (CNT) forests with tetraethyl ammonium tetrafluoro borate electrolyte in propylene carbonate are studied on the basis of molecular dynamics simulation. Direct molecular simulation of the filling of pore spaces of the forest is feasible even with realistic, small CNT spacings. The numerical solution of the Poisson equation based on the extracted average charge densities then yields a regular experimental dependence on the width of the pore spaces, in contrast to the anomalous pattern observed in experiments on other carbon materials and also in simulations on planar slot-like pores. The capacitances obtained have realistic magnitudes but are insensitive to electric potential differences between the electrodes in this model. This agrees with previous calculations on CNT forest supercapacitors, but not with experiments which have suggested electrochemical doping for these systems. Those phenomena remain for further theory/modeling work. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Successful Treatment of Advanced Metastatic Prostate Cancer following Chemotherapy Based on Molecular Profiling

    Directory of Open Access Journals (Sweden)

    Charles E. Myers

    2012-03-01

    Full Text Available After Taxotere fails, treatment options for metastatic prostate cancer are limited. The three drugs with FDA approval in this setting, Jevtana, Provenge and Zytiga, are associated with median survivals of less than 2 years. In part, the impact on survival is the result of low response rates, indicating a significant proportion of patients exhibiting de novo resistance to these agents. An alternate approach is to let treatment selection be governed by gene expression profiling so that the treatment is tailored to the specific patient. Here, we report a case of metastatic prostate cancer with a dramatic response to treatment selected based on molecular profiling. This patient had failed LHRH agonist, bicalutamide, Taxotere, and doxorubicin. Molecular profiling showed overexpression of the androgen receptor and he had a dramatic response of measurable disease to second-line hormonal therapy with ketoconazole, estrogen and Leukine.

  17. Single molecular switch based on thiol tethered iron(II)clathrochelate on gold

    Energy Technology Data Exchange (ETDEWEB)

    Viswanathan, Subramanian [Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-747 Olsztyn (Poland); Voloshin, Yan Z. [Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 119991 Moscow (Russian Federation); Radecka, Hanna [Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-747 Olsztyn (Poland); Radecki, Jerzy [Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-747 Olsztyn (Poland)], E-mail: radecki@pan.olsztyn.pl

    2009-09-30

    Molecular electronics has been associated with high density nano-electronic devices. Developments of molecular electronic devices were based on reversible switching of molecules between the two conductive states. In this paper, self-assembled monolayers of dodecanethiol (DDT) and thiol tethered iron(II)clathrochelate (IC) have been prepared on gold film. The electrochemical and electronic properties of IC molecules inserted into the dodecanethiol monolayer (IC-DDT SAM) were investigated using voltammetric, electrochemical impedance spectroscopy (EIS), scanning tunneling microscopy (STM) and cross-wire tunneling measurements. The voltage triggered switching behaviour of IC molecules on mixed SAM was demonstrated. Deposition of polyaniline on the redox sites of IC-DDT SAM using electrochemical polymerization of aniline was performed in order to confirm that this monolayer acts as nano-patterned semiconducting electrode surface.

  18. Surface plasmon resonance based optical fiber riboflavin sensor by using molecularly imprinted gel

    Science.gov (United States)

    Verma, Roli; Gupta, Banshi D.

    2013-05-01

    We report the fabrication and characterization of surface plasmon resonance (SPR) based optical fiber riboflavin/vitamin B2 sensor using combination of colloidal crystal templating and molecularly imprinted gel. The sensor works on spectral interrogation method. The operating range of the sensor lies from 0 μg/ml to 320 μg/ml, the suitable amount of intakes of riboflavin recommended for different age group. The SPR spectra show blue shift with increasing concentration of riboflavin, which is due to the interaction of riboflavin molecule over specific binding sites caused by molecular imprinting. The present sensor has many advantageous features such as fast response, small probe size, low cost and can be used for remote/online monitoring.

  19. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  20. Molecular characterisation of lumpy skin disease virus and sheeppox virus based on P32 gene

    Directory of Open Access Journals (Sweden)

    P.M.A.Rashid

    2017-06-01

    Full Text Available Lumpy skin disease virus (LSDV and sheeppox virus (SPV have a considerable economic impact on the cattle and small ruminant industry. They are listed in group A of contagious disease by the World Organization for Animal Health (OIE. This study addressed molecular characterisation of first LSDV outbreak and an endemic SPV in Kurdistan region of Iraq based on P32 gene. The results indicated that P32 gene can be successfully used for diagnosis of LSDV. The phylogenic and molecular analysis showed that there may be a new LSDV isolate circulating in Kurdistan which uniquely shared the same characteristic amino acid sequence with SPV and GPV, leucine at amino acid position 51 in P32 gene as well as few genetically distinct SPV causing pox disease in Kurdistan sheep. This study provided sequence information of P32 gene for several LSDV isolates, which positively affects the epidemiological study of Capripoxvirus

  1. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Energy Technology Data Exchange (ETDEWEB)

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  2. A room-temperature non-volatile CNT-based molecular memory cell

    Science.gov (United States)

    Ye, Senbin; Jing, Qingshen; Han, Ray P. S.

    2013-04-01

    Recent experiments with a carbon nanotube (CNT) system confirmed that the innertube can oscillate back-and-forth even under a room-temperature excitation. This demonstration of relative motion suggests that it is now feasible to build a CNT-based molecular memory cell (MC), and the key to bring the concept to reality is the precision control of the moving tube for sustained and reliable read/write (RW) operations. Here, we show that by using a 2-section outertube design, we are able to suitably recalibrate the system energetics and obtain the designed performance characteristics of a MC. Further, the resulting energy modification enables the MC to operate as a non-volatile memory element at room temperatures. Our paper explores a fundamental understanding of a MC and its response at the molecular level to roadmap a novel approach in memory technologies that can be harnessed to overcome the miniaturization limit and memory volatility in memory technologies.

  3. Atitude empreendedora: validação de um instrumento de medida com base no modelo de resposta gradual da teoria da resposta ao item.

    Directory of Open Access Journals (Sweden)

    Antônio Cezar Bornia

    2013-10-01

    Full Text Available A escala instrumento de medida de atitude empreendedora (Imae, desenvolvida por Souza e Lopes Jr. (2005, contém duas dimensões: prospecção e inovação, e gestão e persistência. Com a finalidade de verificar a validade e o intervalo em que propicia a medida de atitude empreendedora, além de investigar sua capacidade de discriminar a resposta que o indivíduo está apto a dar, o objetivo deste artigo é validar a escala Imae por meio do modelo de resposta gradual da teoria da resposta ao item (TRI, que revolucionou a teoria de medidas. A TRI, construtos da psicologia utilizados em estudos de discriminação de respostas, em especial em grandes amostras de respondentes a um determinado fenômeno, é constituída de modelos matemáticos que relacionam um ou mais traços latentes (não observados de um indivíduo com a probabilidade de este dar uma determinada resposta a um item. O ponto crucial da TRI é que ela leva em consideração o item particularmente, sem relevar os escores totais, portanto as conclusões não dependem apenas do teste ou questionário, mas de cada elemento que o compõe. Os principais resultados encontrados foram a identificação de dois níveis da escala, denominados âncoras, que permitem interpretar tendências de pessoas com atitude empreendedora e a constatação de que os itens da escala Imae apresentam boa capacidade de discriminar a resposta que o indivíduo está apto a dar, o que confere qualidade aos itens e, portanto, à escala. A importância deste estudo reside no papel fundamental que a atitude desempenha nas escolhas que as pessoas fazem em relação à própria vida, de modo a ajudá-las a determinar seus próprios atos.

  4. Modelagem molecular da interação entre a proteína de fusão do vírus sincicial respiratório humano e inibidores da ação viral. -

    OpenAIRE

    Cravo, Haroldo de Lima Pimentel [UNESP

    2012-01-01

    O Vírus Sincicial Respiratório Humano (hRSV) foi identificado em 1957 e mesmo após vários anos de investigação, nenhuma vacina foi desenvolvida. Acredita-se que a chave de inibição da ação viral são suas glicoproteínas de membrana, em especial a proteína de fusão (F), que com auxílio da proteína de ligação (G), é responsável pela instalação do hRSV na célula hospedeira. Há evidências experimentais de que compostos como flavonóides e glicosaminoglicanos podem diminuir a infecção viral, sendo e...

  5. Molecular dynamics simulation based on the multi-component molecular orbital method: Application to H5O2+,D5O2+,andT5O2+

    International Nuclear Information System (INIS)

    Ishimoto, Takayoshi; Koyama, Michihisa

    2012-01-01

    Graphical abstract: Molecular dynamics method based on multi-component molecular orbital method was applied to basic hydrogen bonding systems, H 5 O 2 + , and its isotopomers (D 5 O 2 + andT 5 O 2 + ). Highlights: ► Molecular dynamics method with nuclear quantum effect was developed. ► Multi-component molecular orbital method was used as ab initio MO calculation. ► Developed method applied to basic hydrogen bonding system, H 5 O 2 + , and isotopomers. ► O ⋯ O vibrational stretching reflected to the distribution of protonic wavefunctions. ► H/D/T isotope effect was also analyzed. - Abstract: We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC M O) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC M O based MD (MC M O-MD) method is applied to the basic structures, H 5 O 2 + (called “Zundel ion”), and its isotopomers (D 5 O 2 + andT 5 O 2 + ). We clearly demonstrate the geometrical difference of hydrogen bonded O ⋯ O distance induced by H/D/T isotope effect because the O ⋯ O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O ⋯ O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O ⋯ O distance becomes short during the dynamics. Our proposed MC M O-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.

  6. Nanomedicine-based combination anticancer therapy between nucleic acids and small-molecular drugs.

    Science.gov (United States)

    Huang, Wei; Chen, Liqing; Kang, Lin; Jin, Mingji; Sun, Ping; Xin, Xin; Gao, Zhonggao; Bae, You Han

    2017-06-01

    Anticancer therapy has always been a vital challenge for the development of nanomedicine. Repeated single therapeutic agent may lead to undesirable and severe side effects, unbearable toxicity and multidrug resistance due to complex nature of tumor. Nanomedicine-based combination anticancer therapy can synergistically improve antitumor outcomes through multiple-target therapy, decreasing the dose of each therapeutic agent and reducing side effects. There are versatile combinational anticancer strategies such as chemotherapeutic combination, nucleic acid-based co-delivery, intrinsic sensitive and extrinsic stimulus combinational patterns. Based on these combination strategies, various nanocarriers and drug delivery systems were engineered to carry out the efficient co-delivery of combined therapeutic agents for combination anticancer therapy. This review focused on illustrating nanomedicine-based combination anticancer therapy between nucleic acids and small-molecular drugs for synergistically improving anticancer efficacy. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Molecular diversification of Trichuris spp. from Sigmodontinae (Cricetidae) rodents from Argentina based on mitochondrial DNA sequences.

    Science.gov (United States)

    Callejón, Rocío; Robles, María Del Rosario; Panei, Carlos Javier; Cutillas, Cristina

    2016-08-01

    A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob). The taxa consisted of nine populations of whipworm from five species of Sigmodontinae rodents from Argentina. Bayesian Inference, Maximum Parsimony, and Maximum Likelihood methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data and the combined mitochondrial and nuclear dataset. Phylogenetic results based on cox1 and cob mitochondrial DNA (mtDNA) revealed three clades strongly resolved corresponding to three different species (Trichuris navonae, Trichuris bainae, and Trichuris pardinasi) showing phylogeographic variation, but relationships among Trichuris species were poorly resolved. Phylogenetic reconstruction based on concatenated sequences had greater phylogenetic resolution for delimiting species and populations intra-specific of Trichuris than those based on partitioned genes. Thus, populations of T. bainae and T. pardinasi could be affected by geographical factors and co-divergence parasite-host.

  8. A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: advantages of pathway-based discovery.

    Science.gov (United States)

    Hellerstein, Marc K

    2008-01-01

    Contemporary drug discovery and development (DDD) is dominated by a molecular target-based paradigm. Molecular targets that are potentially important in disease are physically characterized; chemical entities that interact with these targets are identified by ex vivo high-throughput screening assays, and optimized lead compounds enter testing as drugs. Contrary to highly publicized claims, the ascendance of this approach has in fact resulted in the lowest rate of new drug approvals in a generation. The primary explanation for low rates of new drugs is attrition, or the failure of candidates identified by molecular target-based methods to advance successfully through the DDD process. In this essay, I advance the thesis that this failure was predictable, based on modern principles of metabolic control that have emerged and been applied most forcefully in the field of metabolic engineering. These principles, such as the robustness of flux distributions, address connectivity relationships in complex metabolic networks and make it unlikely a priori that modulating most molecular targets will have predictable, beneficial functional outcomes. These same principles also suggest, however, that unexpected therapeutic actions will be common for agents that have any effect (i.e., that complexity can be exploited therapeutically). A potential operational solution (pathway-based DDD), based on observability rather than predictability, is described, focusing on emergent properties of key metabolic pathways in vivo. Recent examples of pathway-based DDD are described. In summary, the molecular target-based DDD paradigm is built on a naïve and misleading model of biologic control and is not heuristically adequate for advancing the mission of modern therapeutics. New approaches that take account of and are built on principles described by metabolic engineers are needed for the next generation of DDD.

  9. NONLINEAR OPTICAL MOLECULAR CRYSTAL BASED ON 2,6-DIAMINOPYRIDINE: SYNTHESIS AND CHARACTERIZATION

    Directory of Open Access Journals (Sweden)

    I. M. Pavlovetc

    2014-05-01

    Full Text Available The paper deals with investigation of a new nonlinear optical material based on nonlinear optical chromophore (4-Nitrophenol and aminopyridine (2,6-Diaminopyridine. Calculation results are presented for molecular packing in the crystalline compound, based on the given components. According to these results the finite material must have a noncentrosymmetric lattice, which determines the presence of the second order nonlinear optical response. Investigations carried out in this work confirm these calculations. Results of experiments are given describing the co-crystallization of these components and the following re-crystallization of the obtained material. In order to get a monocrystal form, the optimal conditions for the synthesis of molecular crystals based on these components are determined. Sufficiently large homogeneous crystals are obtained, that gave the possibility to record their spectra in the visible and near infrared parts of the spectrum, to determine their nonlinear optical properties and the level of homogeneity. Their optical (optical transmission and optical laser damage threshold and nonlinear optical properties are presented. For observation and measurement of the nonlinear optical properties an installation was built which implements the comparative method for measurements of nonlinear optical properties. A potassium titanyl oxide phosphate crystal was used as a sample for comparison. Results are given for the conversion efficiency of the primary laser radiation in the second optical harmonic relative to the signal obtained on the potassium titanyl oxide phosphate crystal. Obtained results show that the molecular co-crystal based on 2,6-Diaminopyridine is a promising nonlinear optical material for generating the second optical harmonic on the Nd: YAG laser (532 nm.

  10. A novel approach for differentiating pathogenic and non-pathogenic Leptospira based on molecular fingerprinting.

    Science.gov (United States)

    Xiao, Di; Zhang, Cuicai; Zhang, Huifang; Li, Xiuwen; Jiang, Xiugao; Zhang, Jianzhong

    2015-04-24

    Leptospirosis is a worldwide, deadly zoonotic disease. Pathogenic Leptospira causes leptospirosis. The rapid and accurate identification of pathogenic and non-pathogenic Leptospira strains is essential for appropriate therapeutic management and timely intervention for infection control. The molecular fingerprint is a simple and rapid alternative tool for microorganisms identification, which is based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this study, molecular fingerprint was performed to identify pathogenic strains of Leptospira. Phylogenetic analysis based on 16S rRNA gene sequences was used as the reference method. In addition, a label-free technique was used to reveal the different proteins of pathogenic or non-pathogenic Leptospira. A reference database was constructed using 30 Leptospira strains, including 16 pathogenic strains and 14 non-pathogenic strains. Two super reference spectra that were associated with pathogenicity were established. Overall, 33 Leptospira strains were used for validation, and 32 of 33 Leptospira strains could be identified on the species level and all the 33 could be classified as pathogenic or non-pathogenic. The super reference spectra and the major spectra projection (MSP) dendrogram correctly categorized the Leptospira strains into pathogenic and non-pathogenic groups, which was consistent with the 16S rRNA reference methods. Between the pathogenic and non-pathogenic strains, 108 proteins were differentially expressed. molecular fingerprint is an alternative to conventional molecular identification and can rapidly distinguish between pathogenic and non-pathogenic Leptospira strains. Therefore, molecular fingerprint may play an important role in the clinical diagnosis, treatment, surveillance, and tracking of epidemic outbreaks of leptospirosis. Leptospirosis is a worldwide zoonosis that is caused by spirochetes of the genus Leptospira. Leptospirosis is a serious zoonotic

  11. Iterative random vs. Kennard-Stone sampling for IR spectrum-based classification task using PLS2-DA

    Science.gov (United States)

    Lee, Loong Chuen; Liong, Choong-Yeun; Jemain, Abdul Aziz

    2018-04-01

    External testing (ET) is preferred over auto-prediction (AP) or k-fold-cross-validation in estimating more realistic predictive ability of a statistical model. With IR spectra, Kennard-stone (KS) sampling algorithm is often used to split the data into training and test sets, i.e. respectively for model construction and for model testing. On the other hand, iterative random sampling (IRS) has not been the favored choice though it is theoretically more likely to produce reliable estimation. The aim of this preliminary work is to compare performances of KS and IRS in sampling a representative training set from an attenuated total reflectance - Fourier transform infrared spectral dataset (of four varieties of blue gel pen inks) for PLS2-DA modeling. The `best' performance achievable from the dataset is estimated with AP on the full dataset (APF, error). Both IRS (n = 200) and KS were used to split the dataset in the ratio of 7:3. The classic decision rule (i.e. maximum value-based) is employed for new sample prediction via partial least squares - discriminant analysis (PLS2-DA). Error rate of each model was estimated repeatedly via: (a) AP on full data (APF, error); (b) AP on training set (APS, error); and (c) ET on the respective test set (ETS, error). A good PLS2-DA model is expected to produce APS, error and EVS, error that is similar to the APF, error. Bearing that in mind, the similarities between (a) APS, error vs. APF, error; (b) ETS, error vs. APF, error and; (c) APS, error vs. ETS, error were evaluated using correlation tests (i.e. Pearson and Spearman's rank test), using series of PLS2-DA models computed from KS-set and IRS-set, respectively. Overall, models constructed from IRS-set exhibits more similarities between the internal and external error rates than the respective KS-set, i.e. less risk of overfitting. In conclusion, IRS is more reliable than KS in sampling representative training set.

  12. Indicadores da sustentabilidade de uma propriedade rural de base familiar no estado de Mato Grosso do Sul

    Directory of Open Access Journals (Sweden)

    Anderson de Souza Gallo

    2016-08-01

    Full Text Available O presente trabalho avalia a sustentabilidade de uma propriedade rural de base familiar, no estado de Mato Grosso do Sul, com o objetivo de apresentar linhas de trabalho para os aspectos menos sustentáveis e, dessa forma, alcançar maior sustentabilidade do sistema. O estudo foi realizado através de diagnóstico visual, baseando-se nos indicadores de sustentabilidade do método MESMIS “Marco para Evaluación de Sistemas de Manejo de Recursos Naturales Incorporando Indicadores de Sustentabilidad”. Para avaliação foram utilizados 36 indicadores e três parâmetros, abordando aspectos ambientais, sociais e econômicos. O resultado obtido com a avaliação da unidade de produção rural evidencia que a propriedade se encontrada alterada, demonstrando a necessidade de intervenções para se alcançar maior sustentabilidade ambiental, social e econômica. A propriedade apresenta alguns pontos críticos relacionados à ausência de área de preservação permanente e/ou reserva legal, baixa adoção da prática de rotação de culturas, aplicação de defensivos agrícolas, não aproveitamento dos resíduos orgânicos da cozinha, descarte inadequado do óleo de cozinha residual, assistência técnica ineficiente e /ou ausente e a não utilização de equipamentos de proteção individual (EPI nas atividades laborais. O estudo possibilitou traçar planos e metas para que o produtor possa alcançar maior êxito na busca da sustentabilidade de sua propriedade e, dessa forma, inserir-se no mercado agrícola comprometido com um desenvolvimento ambientalmente amigável, socialmente justo e economicamente viável.

  13. Variabilidade genética de acessos de maracujá-suspiro com base em marcadores moleculares Genetic variability of wild passion fruit determined by molecular markers

    Directory of Open Access Journals (Sweden)

    Keize Pereira Junqueira

    2007-01-01

    Full Text Available Passiflora nitida é uma espécie silvestre amplamente distribuída pelo território brasileiro, constituindo-se em fonte de resistência a doenças foliares e de raízes. O objetivo deste trabalho foi avaliar a variabilidade genética entre acessos de P. nitida procedentes de diferentes tipos fitofisionômicos de Cerrado e estados brasileiros (Goiás, Distrito Federal, Tocantins, Mato Grosso e Amazonas, usando marcadores moleculares RAPD. O DNA genômico de cada acesso foi extraído, e doze iniciadores decâmeros foram utilizados para a obtenção de marcadores moleculares RAPD, que foram convertidos em matriz de dados binários, a partir da qual foram estimadas as distâncias genéticas entre os acessos e realizadas análises de agrupamento e de dispersão gráfica. Foram obtidos 196 marcadores para P. nitida, dos quais 63,81% foram polimórficos. As distâncias genéticas entre os acessos de maracujá variaram de 0,031 a 0,614 e, considerando apenas P. nitida, de 0,031 a 0,417. Os marcadores moleculares demonstraram alta variabilidade genética dos acessos de P. nitida. Menores distâncias genéticas foram verificadas entre os acessos originados do mesmo estado. Considerando-se os acessos de um mesmo estado, menores distâncias genéticas foram verificadas entre os acessos provenientes de tipos fitofisionômicos próximos. O acesso "Manaus 2" apresentou o maior distanciamento genético em relação aos demais acessos.Passiflora nitida is a wild species widely distributed in Brazilian territory. It is a source of resistance to foliar and soil borne diseases. The objective of this work was to evaluate the genetic variability among accessions of P. nitida proceeding from different types of Cerrado (Brazilian savannah vegetation and brazilian states (Goiás, Distrito Federal, Tocantins, Mato Grosso and Amazonas using RAPD molecular markers. The genomic DNA of each origin was extracted and amplified using 12 decamer primers to obtain RAPD

  14. Systematic studies of Australian stipoid grasses (Austrostipa based on micro-morphological and molecular characteristics

    Directory of Open Access Journals (Sweden)

    BETTY MAULIYA BUSTAM

    2010-01-01

    Full Text Available Bustam BM (2010 Systematic studies of Australian stipoid grasses (Austrostipa based on micro-morphological and molecular characteristics. Biodiversitas 11: 9-14. This research is one of many studies on stipoid grasses organized by the International Stipeae Working Group (ISWG. This research tested the subgeneric classification of Austrostipa proposed by Jacobs and Everett (1996 and tested how informative the micro morphological characters used. Data were collected from herbarium specimens of 36 species (33 species of Austrostipa, two species of Hesperostipa and one species of Anemanthele at Royal Botanic Gardens, Sydney. Twenty eight micro morphological characters were used. The data were collected from both adaxial and abaxial surfaces of leaves, and from the lemma epidermis using a scanning electron microscope (SEM. ISWG provided the molecular data. Parsimony analysis and a distance method (Unweighteic Pair Group with Arithmatic Mean: UPGMA were used to analyze mico morphological and molecular data separately. Only UPGMA analysis was used to analyze the combined data. The results support the monophyly of Austrostipa. However, there is a little support for the subgeneric classification of Austrostipa proposed by Jacobs and Everett (1996, other than for the consistent recognition of Falcatae. The characters for comparisons between genera are too homoplasious at this level and do not contain enough information for analyses at subgeneric level, a problem apparently shared with the DNA sequences.

  15. Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences.

    Science.gov (United States)

    Kochzius, Marc; Söller, Rainer; Khalaf, Maroof A; Blohm, Dietmar

    2003-09-01

    This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) "Pterois" clade (Pterois miles and Pterois volitans), and (2) "Pteropterus-Dendrochirus" clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the "Pteropterus-Dendrochirus" clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.

  16. Test-beds for molecular electronics: metal-molecules-metal junctions based on Hg electrodes.

    Science.gov (United States)

    Simeone, Felice Carlo; Rampi, Maria Anita

    2010-01-01

    Junctions based on mesoscopic Hg electrodes are used to characterize the electrical properties of the organic molecules organized in self-assembled monolayers (SAMs). The junctions M-SAM//SAM-Hg are formed by one electrode based on metals (M) such as Hg, Ag, Au, covered by a SAM, and by a second electrode always formed by a Hg drop carrying also a SAM. The electrodes, brought together by using a micromanipulator, sandwich SAMs of different nature at the contact area (approximately = 0.7 microm2). The high versatility of the system allows a series of both electrical and electrochemical junctions to be assembled and characterized: (i) The compliant nature of the Hg electrodes allows incorporation into the junction and measurement of the electrical behavior of a large number of molecular systems and correlation of their electronic structure to the electrical behavior; (ii) by functionalizing both electrodes with SAMs exposing different functional groups, X and Y, it is possible to compare the rate of electron transfer through different X...Y molecular interactions; (iii) when the junction incorporates one of the electrode formed by a semitransparent film of Au, it allows electrical measurements under irradiation of the sandwiched SAMs. In this case the junction behaves as a photoswitch; iv) incorporation of redox centres with low lying, easily reachable energy levels, provides electron stations as indicated by the hopping mechanism dominating the current flow; (v) electrochemical junctions incorporating redox centres by both covalent and electrostatic interactions permit control of the potential of the electrodes with respect to that of the redox state by means of an external reference electrode. Both these junctions show an electrical behavior similar to that of conventional diodes, even though the mechanism generating the current flow is different. These systems, demonstrating high mechanical stability and reproducibility, easy assembly, and a wide variety of

  17. Quantum dot-based molecular imaging of cancer cell growth using a clone formation assay.

    Science.gov (United States)

    Geng, Xia-Fei; Fang, Min; Liu, Shao-Ping; Li, Yan

    2016-10-01

    This aim of the present study was to investigate clonal growth behavior and analyze the proliferation characteristics of cancer cells. The MCF‑7 human breast cancer cell line, SW480 human colon cancer cell line and SGC7901 human gastric cancer cell line were selected to investigate the morphology of cell clones. Quantum dot‑based molecular targeted imaging techniques (which stained pan‑cytokeratin in the cytoplasm green and Ki67 in the cell nucleus yellow or red) were used to investigate the clone formation rate, cell morphology, discrete tendency, and Ki67 expression and distribution in clones. From the cell clone formation assay, the MCF‑7, SW480 and SGC7901 cells were observed to form clones on days 6, 8 and 12 of cell culture, respectively. These three types of cells had heterogeneous morphology, large nuclear:cytoplasmic ratios, and conspicuous pathological mitotic features. The cells at the clone periphery formed multiple pseudopodium. In certain clones, cancer cells at the borderline were separated from the central cell clusters or presented a discrete tendency. With quantum dot‑based molecular targeted imaging techniques, cells with strong Ki67 expression were predominantly shown to be distributed at the clone periphery, or concentrated on one side of the clones. In conclusion, cancer cell clones showed asymmetric growth behavior, and Ki67 was widely expressed in clones of these three cell lines, with strong expression around the clones, or aggregated at one side. Cell clone formation assay based on quantum dots molecular imaging offered a novel method to study the proliferative features of cancer cells, thus providing a further insight into tumor biology.

  18. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    Science.gov (United States)

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

  19. ANÁLISE DE RELATÓRIOS AMBIENTAIS PRÉVIOS DE CURITIBA/PR COM BASE NOS PRINCÍPIOS DO PLANEJAMENTO DA PAISAGEM

    Directory of Open Access Journals (Sweden)

    Laura Freire Estêvez

    2015-09-01

    Full Text Available O Planejamento da Paisagem aplicado ao meio urbanizado tem como um dos princípios a manutenção ou melhoria da qualidade ambiental urbana, que pode ser diminuída com a crescente instalação de empreendimentos na cidade. Para avaliar os impactos ambientais desses empreendimentos antes da sua instalação, o Estatuto da Cidade (BRASIL, 2001 instituiu o Estudo Prévio de Impacto de Vizinhança - EIV. O Município de Curitiba realiza estudos de impactos ambientais de empreendimentos e suas atividades desde 1997 com o estabelecimento do Relatório Ambiental Prévio – RAP (CURITIBA, 1997. O objetivo do trabalho foi analisar RAPs elaborados em Curitiba, PR, com base nos princípios do Planejamento da Paisagem e com isso fornecer subsídios para a reflexão sobre a possibilidade de um planejamento urbano que considere a qualidade ambiental. Para a avaliação dos RAPs foram definidos critérios e parâmetros, com base nos estudos de qualidade ambiental urbana, nos estudos sobre cidades saudáveis da Organização Mundial da Saúde e em princípios da Flor da Permacultura. Os critérios definidos foram: Espaços Livres, Cobertura Vegetal, Verticalidade das Edificações, Usos Potencialmente Poluidores, Estilos de Vida Saudável e Pegada Ecológica. Apesar de tratar sobre alguns impactos ambientais negativos de forma superficial, os RAPs não contemplam a grande maioria dos impactos ambientais negativos relacionados à qualidade ambiental urbana e, mesmo assim, forneceram diagnósticos favoráveis à instalação dos empreendimentos. Esse diagnóstico foi aceito pelo poder público que permitiu a instalação dos empreendimentos, que resultaram em diminuição da qualidade ambiental urbana.

  20. Determination of liquid's molecular interference function based on X-ray diffraction and dual-energy CT in security screening

    International Nuclear Information System (INIS)

    Zhang, Li; YangDai, Tianyi

    2016-01-01

    A method for deriving the molecular interference function (MIF) of an unknown liquid for security screening is presented. Based on the effective atomic number reconstructed from dual-energy computed tomography (CT), equivalent molecular formula of the liquid is estimated. After a series of optimizations, the MIF and a new effective atomic number are finally obtained from the X-ray diffraction (XRD) profile. The proposed method generates more accurate results with less sensitivity to the noise and data deficiency of the XRD profile. - Highlights: • EDXRD combined with dual-energy CT has been utilized for deriving the molecular interference function of an unknown liquid. • The liquid's equivalent molecular formula is estimated based on the effective atomic number reconstructed from dual-energy CT. • The proposed method provides two ways to estimate the molecular interference function: the simplified way and accurate way. • A new effective atomic number of the liquid could be obtained.

  1. Radiation chemical yields for formation of molecular hydrogen in alcohols based on the cyclohexane ring

    International Nuclear Information System (INIS)

    Val'ter, A.I.; Kovalev, G.V.

    1989-01-01

    Within the framework of the general problem of studying the radiolysis mechanism for alcohols based on the cyclohexane ring, we have determined the yields of molecular hydrogen in γ-irradiated cyclohexanol, 1,2-cis- and 1,2-trans-cyclohexanediols, and inositol (cyclohexanehexol). The cyclohexanol and also powders of the polyols were placed into ampuls, deaerated in a vacuum apparatus and irradiated with 60 Co γ-rays at 77 K and 293 K. After irradiation, the samples were heated up to 373 K (the polyol crystals were heated until melting) and the hydrogen evolved from the liquid phase was determined by gas chromatography

  2. The rational development of molecularly imprinted polymer-based sensors for protein detection.

    Science.gov (United States)

    Whitcombe, Michael J; Chianella, Iva; Larcombe, Lee; Piletsky, Sergey A; Noble, James; Porter, Robert; Horgan, Adrian

    2011-03-01

    The detection of specific proteins as biomarkers of disease, health status, environmental monitoring, food quality, control of fermenters and civil defence purposes means that biosensors for these targets will become increasingly more important. Among the technologies used for building specific recognition properties, molecularly imprinted polymers (MIPs) are attracting much attention. In this critical review we describe many methods used for imprinting recognition for protein targets in polymers and their incorporation with a number of transducer platforms with the aim of identifying the most promising approaches for the preparation of MIP-based protein sensors (277 references).

  3. The Design of a Molecular Assembly Line Based on Biological Molecules

    Science.gov (United States)

    2003-06-01

    parenthesis in figure 1.8 is a bi-stable toggle switch. Introduction: Molecular assembly lines O=P-O- O O HOH H0P-0- O -O- 4 Polymerase HO H--- O HHO ...sample. Therefore, the samples are self-consistent. From here on, the calculated temperature based on FAM emission MNSowmm" RF Biology: Results and...irradiation for one hour. Figure 2.11 shows the fluorescence spectra of FAM emission (4 scans averaged over 200 seconds) in a 300MHz field. The increased

  4. Reconstruction for limited-projection fluorescence molecular tomography based on projected restarted conjugate gradient normal residual.

    Science.gov (United States)

    Cao, Xu; Zhang, Bin; Liu, Fei; Wang, Xin; Bai, Jing

    2011-12-01

    Limited-projection fluorescence molecular tomography (FMT) can greatly reduce the acquisition time, which is suitable for resolving fast biology processes in vivo but suffers from severe ill-posedness because of the reconstruction using only limited projections. To overcome the severe ill-posedness, we report a reconstruction method based on the projected restarted conjugate gradient normal residual. The reconstruction results of two phantom experiments demonstrate that the proposed method is feasible for limited-projection FMT. © 2011 Optical Society of America

  5. Molecular Solid EOS based on Quasi-Harmonic Oscillator approximation for phonons

    Energy Technology Data Exchange (ETDEWEB)

    Menikoff, Ralph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-09-02

    A complete equation of state (EOS) for a molecular solid is derived utilizing a Helmholtz free energy. Assuming that the solid is nonconducting, phonon excitations dominate the specific heat. Phonons are approximated as independent quasi-harmonic oscillators with vibrational frequencies depending on the specific volume. The model is suitable for calibrating an EOS based on isothermal compression data and infrared/Raman spectroscopy data from high pressure measurements utilizing a diamond anvil cell. In contrast to a Mie-Gruneisen EOS developed for an atomic solid, the specific heat and Gruneisen coefficient depend on both density and temperature.

  6. Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support.

    Science.gov (United States)

    Wang, Jack T H

    2017-08-15

    Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Mass Spectrometry-based Approaches to Understand the Molecular Basis of Memory

    Directory of Open Access Journals (Sweden)

    Arthur Henriques Pontes

    2016-10-01

    Full Text Available The central nervous system is responsible for an array of cognitive functions such as memory, learning, language and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS have enable the identification and quantification of thousand of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.

  8. Molecular Monolayers for Electrical Passivation and Functionalization of Silicon-Based Solar Energy Devices.

    Science.gov (United States)

    Veerbeek, Janneke; Firet, Nienke J; Vijselaar, Wouter; Elbersen, Rick; Gardeniers, Han; Huskens, Jurriaan

    2017-01-11

    Silicon-based solar fuel devices require passivation for optimal performance yet at the same time need functionalization with (photo)catalysts for efficient solar fuel production. Here, we use molecular monolayers to enable electrical passivation and simultaneous functionalization of silicon-based solar cells. Organic monolayers were coupled to silicon surfaces by hydrosilylation in order to avoid an insulating silicon oxide layer at the surface. Monolayers of 1-tetradecyne were shown to passivate silicon micropillar-based solar cells with radial junctions, by which the efficiency increased from 8.7% to 9.9% for n + /p junctions and from 7.8% to 8.8% for p + /n junctions. This electrical passivation of the surface, most likely by removal of dangling bonds, is reflected in a higher shunt resistance in the J-V measurements. Monolayers of 1,8-nonadiyne were still reactive for click chemistry with a model catalyst, thus enabling simultaneous passivation and future catalyst coupling.

  9. Cell adhesion monitoring of human induced pluripotent stem cell based on intrinsic molecular charges

    Science.gov (United States)

    Sugimoto, Haruyo; Sakata, Toshiya

    2014-01-01

    We have shown a simple way for real-time, quantitative, non-invasive, and non-label monitoring of human induced pluripotent stem (iPS) cell adhesion by use of a biologically coupled-gate field effect transistor (bio-FET), which is based on detection of molecular charges at cell membrane. The electrical behavior revealed quantitatively the electrical contacts of integrin-receptor at the cell membrane with RGDS peptide immobilized at the gate sensing surface, because that binding site was based on cationic α chain of integrin. The platform based on the bio-FET would provide substantial information to evaluate cell/material bio-interface and elucidate biding mechanism of adhesion molecules, which could not be interpreted by microscopic observation.

  10. Matched molecular pair-based data sets for computer-aided medicinal chemistry

    Science.gov (United States)

    Bajorath, Jürgen

    2014-01-01

    Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the ChEMBL database (release 17) for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community. PMID:24627802

  11. Synthesis and molecular characterization of chitosan based polyurethane elastomers using aromatic diisocyanate.

    Science.gov (United States)

    Zia, Khalid Mahmood; Anjum, Sohail; Zuber, Mohammad; Mujahid, Muhammad; Jamil, Tahir

    2014-05-01

    The present research work was performed to synthesize a new series of chitosan based polyurethane elastomers (PUEs) using poly(ɛ-caprolactone) (PCL). The chitosan based PUEs were prepared by step-growth polymerization technique using poly(ɛ-caprolactone) (PCL) and 2,4-toluene diisocyanate (TDI). In the second step the PU prepolymer was extended with different mole ratios of chitosan and 1,4-butane diol (BDO). Molecular engineering was carried out during the synthesis. The conventional spectroscopic characterization of the synthesized samples using FT-IR confirms the existence of the proposed chitosan based PUEs structure. Internal morphology of the prepared PUEs was studied using SEM analysis. The SEM images confirmed the incorporation of chitosan molecules into the PU backbone. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient.

    Science.gov (United States)

    Shi, Junwei; Zhang, Bin; Liu, Fei; Luo, Jianwen; Bai, Jing

    2013-09-15

    For the ill-posed fluorescent molecular tomography (FMT) inverse problem, the L1 regularization can protect the high-frequency information like edges while effectively reduce the image noise. However, the state-of-the-art L1 regularization-based algorithms for FMT reconstruction are expensive in memory, especially for large-scale problems. An efficient L1 regularization-based reconstruction algorithm based on nonlinear conjugate gradient with restarted strategy is proposed to increase the computational speed with low memory consumption. The reconstruction results from phantom experiments demonstrate that the proposed algorithm can obtain high spatial resolution and high signal-to-noise ratio, as well as high localization accuracy for fluorescence targets.

  13. Film-based Sensors with Piezoresistive Molecular Conductors as Active Components Strain Damage and Thermal Regeneration

    Directory of Open Access Journals (Sweden)

    Elena Laukhina

    2011-02-01

    Full Text Available The article is addressed to the development of flexible all-organic bi layer (BL film-based sensors being capable of measuring strain as a well-defined electrical signal in a wide range of elongations and temperature. The purpose was achieved by covering polycarbonate films with the polycrystalline layer of a high piezoresistive organic molecular conductor. To determine restrictions for sensor applications, the effect of monoaxial strain on the resistance and texture of the sensing layers of BL films was studied. The experiments have shown that the maximum strain before fracture is about 1 %. A thermal regeneration of the sensing layer of the BL film-based sensors that were damaged by cyclic load is also described. These sensors are able to take the place of conventional metal-based strain and pressure gages in low cost innovative controlling and monitoring technologies.

  14. A symmetry-controlled and face-driven approach for the assembly of cerium-based molecular polyhedra.

    Science.gov (United States)

    Liu, Yang; Lin, Zhihua; He, Cheng; Zhao, Liang; Duan, Chunying

    2010-12-14

    A well-defined Ce-based molecular tetrahedron and a cube-like architecture were achieved via self-assembly by incorporating NOO tridentate chelators into the rationally designed ligands with C(3) or C(2v) symmetries, respectively.

  15. Recent research in flaxseed (oil seed) on molecular structure and metabolic characteristics of protein, heat processing-induced effect and nutrition with advanced synchrotron-based molecular techniques.

    Science.gov (United States)

    Doiron, Kevin J; Yu, Peiqiang

    2017-01-02

    Advanced synchrotron radiation-based infrared microspectroscopy is able to reveal feed and food structure feature at cellular and molecular levels and simultaneously provides composition, structure, environment, and chemistry within intact tissue. However, to date, this advanced synchrotron-based technique is still seldom known to food and feed scientists. This article aims to provide detailed background for flaxseed (oil seed) protein research and then review recent progress and development in flaxseed research in ruminant nutrition in the areas of (1) dietary inclusion of flaxseed in rations; (2) heat processing effect; (3) assessing dietary protein; (4) synchrotron-based Fourier transform infrared microspectroscopy as a tool of nutritive evaluation within cellular and subcellular dimensions; (5) recent synchrotron applications in flaxseed research on a molecular basis. The information described in this paper gives better insight in flaxseed research progress and update.

  16. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2011-01-01

    Full Text Available Abstract Background Lung cancer is the leading cause of cancer deaths worldwide. Many studies have investigated the carcinogenic process and identified the biomarkers for signature classification. However, based on the research dedicated to this field, there is no highly sensitive network-based method for carcinogenesis characterization and diagnosis from the systems perspective. Methods In this study, a systems biology approach integrating microarray gene expression profiles and protein-protein interaction information was proposed to develop a network-based biomarker for molecular investigation into the network mechanism of lung carcinogenesis and diagnosis of lung cancer. The network-based biomarker consists of two protein association networks constructed for cancer samples and non-cancer samples. Results Based on the network-based biomarker, a total of 40 significant proteins in lung carcinogenesis were identified with carcinogenesis relevance values (CRVs. In addition, the network-based biomarker, acting as the screening test, proved to be effective in diagnosing smokers with signs of lung cancer. Conclusions A network-based biomarker using constructed protein association networks is a useful tool to highlight the pathways and mechanisms of the lung carcinogenic process and, more importantly, provides potential therapeutic targets to combat cancer.

  17. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

    Science.gov (United States)

    Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

    2013-10-07

    Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

  18. Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation Análise molecular da diversidade bacteriana de um consórcio degradador de óleo diesel

    Directory of Open Access Journals (Sweden)

    Douglas Antonio Alvaredo Paixão

    2010-06-01

    desse produto contribuem significativamente para derrames acidentais, ocasionando sérios problemas ecológicos no solo e água, alterando assim toda a diversidade microbiológica do ambiente. A estratégia de clonagem e sequenciamento do gene 16S rRNA é uma das técnicas moleculares que permitem estimar e comparar a diversidade microbiana de diferentes amostras ambientais, sejam elas impactadas ou não. O objetivo deste trabalho foi estimar a diversidade de microrganismos pertencentes ao domínio Bacteria em um consórcio degradador de óleo diesel por meio de sequenciamento parcial do gene 16S rRNA. Após extração do DNA metagenômico, o material foi amplificado por reação de PCR com oligonucleotídeos iniciadores específicos para o gene 16S rRNA. Os produtos da reação de PCR foram clonados em vetor pGEM T Easy (Promega e transformados em células competentes de Escherichia coli. O sequenciamento parcial dos clones foi feito com oligonucleotídeos universais do vetor. A biblioteca obtida gerou 431 clones. Todos os clones mostraram similaridade com o filo Proteobacteria, onde as Gammaproteobacteria compreenderam o grupo de maior representatividade, com 49,8 % dos clones, seguida das Alphaproteobacteira, com 44,8 %, e das Betaproteobacteria, com 5,4 %. O gênero Pseudomonas destacou-se como representante com maior frequência de clones na biblioteca, seguido pelos gêneros Parvibaculum e Sphingobium. Após o sequenciamento parcial do gene 16S rRNA, a diversidade bacteriana do consórcio foi estimada utilizando-se o software DOTUR. Essas sequências, quando comparadas com as do banco do National Center for Biotechnology Information (NCBI, mostraram grande correlação entre os dados gerados pelo software utilizado e aqueles depositados no NCBI.

  19. Bases celulares e bioquímicas da doença pulmonar obstrutiva crônica Cellular and biochemical bases of chronic obstructive pulmonary disease

    Directory of Open Access Journals (Sweden)

    Rogério Rufino

    2006-06-01

    Full Text Available A doença pulmonar obstrutiva crônica é uma doença inflamatória com participação ativa de macrófagos, neutrófilos e linfócitos CD8+ em sua patogênese, associada a estímulos oxidantes diretos das estruturas pulmonares, que desencadeiam reações bioquímicas, levando a progressiva desorganização das pequenas vias aéreas e ao remodelamento estrutural não reversível. A liberação de substâncias provenientes das células recrutadas e do estresse oxidativo leva ao desequilíbrio inicialmente temporário dos mecanismos de defesa pulmonar. A permanência desse desequilíbrio é uma das chaves da fisiopatogenia atual. Os autores descrevem as alterações celulares e bioquímicas da doença pulmonar obstrutiva crônica.Chronic obstructive pulmonary disease is an inflammatory disease. Together with oxidant stimuli, which directly affect lung structures, macrophages, neutrophils and CD8+ lymphocytes actively participate in the pathogenesis of the disease and promote biochemical reactions that result in progressive alteration of the upper airways and irreversible lung remodeling. The release of substances promoted by inflammatory cell recruitment and by oxidative stress lead to a temporary imbalance in the pulmonary defense mechanisms. Understanding the long-term maintenance of this imbalance is key to understanding the current physiopathology of the disease. The present study explores the cellular and molecular alterations seen in chronic obstructive pulmonary disease.

  20. A bibliometria na exploração de bases de dados: a importância da Lingüística

    Directory of Open Access Journals (Sweden)

    Rogério Mugnaini

    Full Text Available A utilização das bases de dados para levantamento do estado da arte, procedimento necessário a qualquer pesquisador, exige dos mesmos a definição de estratégias para a recuperação eficaz da informação. A Bibliometria pode ser uma ferramenta útil neste processo, permitindo a filtragem de grandes quantidades de informação. Por se tratar de uma análise estatística de dados, a qualidade destes dados é de vital importância e o procedimento de indexação para representação da informação se torna essencial. Pretende-se aclarar a importância da Estatística, Lingüística e Indexação para a Ciência da Informação, focalizando alguns aspectos de suas relações e destacando a necessidade da utilização conjunta dessas disciplinas.

  1. Hybrid Materials Based on Magnetic Layered Double Hydroxides: A Molecular Perspective.

    Science.gov (United States)

    Abellán, Gonzalo; Martí-Gastaldo, Carlos; Ribera, Antonio; Coronado, Eugenio

    2015-06-16

    Design of functional hybrids lies at the very core of synthetic chemistry as it has enabled the development of an unlimited number of solids displaying unprecedented or even improved properties built upon the association at the molecular level of quite disparate components by chemical design. Multifunctional hybrids are a particularly appealing case among hybrid organic/inorganic materials. Here, chemical knowledge is used to deploy molecular components bearing different functionalities within a single solid so that these properties can coexist or event interact leading to unprecedented phenomena. From a molecular perspective, this can be done either by controlled assembly of organic/inorganic molecular tectons into an extended architecture of hybrid nature or by intercalation of organic moieties within the empty channels or interlamellar space offered by inorganic solids with three-dimensional (MOFs, zeolites, and mesoporous hosts) or layered structures (phosphates, silicates, metal dichalcogenides, or anionic clays). This Account specifically illustrates the use of layered double hydroxides (LDHs) in the preparation of magnetic hybrids, in line with the development of soft inorganic chemistry processes (also called "Chimie Douce"), which has significantly contributed to boost the preparation hybrid materials based on solid-state hosts and subsequent development of applications. Several features sustain the importance of LDHs in this context. Their magnetism can be manipulated at a molecular level by adequate choice of constituting metals and interlayer separation for tuning the nature and extent of magnetic interactions across and between planes. They display unparalleled versatility in accommodating a broad range of anionic species in their interlamellar space that encompasses not only simple anions but chemical systems of increasing dimensionality and functionalities. Their swelling characteristics allow for their exfoliation in organic solvents with high

  2. Detecção molecular de vírus da bronquite infecciosa em plantéis de avós, matrizes e frangos de corte no Rio Grande do Sul e Mato Grosso Molecular detection of infectious bronchitis virus in flocks of grandmothers, mothers and broiler chicken in Rio Grande do Sul and Mato Grosso

    Directory of Open Access Journals (Sweden)

    Bárbara Nascimento

    2013-03-01

    Full Text Available O vírus da Bronquite Infecciosa das galinhas (VBI pertence ao grupo 3 da família Coronaviridae e é o causador de desordens respiratórias e renais em frangos de corte. A vacinação com vacinas vivas é praticada em matrizes e avós e muitas vezes também nos plantéis destinados ao abate. As vacinas utilizadas no Brasil são usualmente do sorogrupo Massachusetts e baseadas nas amostras H120 e H52. É comum que após a vacinação o vírus vacinal seja detectado por isolamento em ovos embrionados ou por métodos moleculares por até 4 semanas. Após essa data, normalmente, não há detecção de vírus e o VBI, quando encontrado, pode representar recirculação do vírus vacinal no plantel ou a introdução de uma nova cepa do vírus. No presente estudo, para avaliar a circulação do vírus em plantéis de frangos e reprodutoras nos estados do Rio Grande do Sul e Mato Grosso do Sul, foram coletadas 240 traqueias e rins de aves de 48 plantéis, sendo (20 exemplares/4 plantéis de avós, (80 exemplares/16 plantéis de matrizes e (140 exemplares/28 plantéis de frangos de corte, as quais foram analisadas em misturas de cinco amostras. Todos os animais eram vacinados e as amostras foram coletadas ao redor de 2 a 48 semanas após a vacinação. A presença de VBI foi determinada com auxílio de uma reação em cadeia da polimerase tipo nested, direcionada ao gene da proteína S1, padronizada neste estudo. Das 48 amostras testadas, 14 resultaram positivas: cinco foram oriundas de aves vacinadas há menos de quatro semanas na data da coleta e nove eram de amostras de aves vacinadas há mais de quatro semanas, o que pode ser devido à recirculação do vírus vacinal ou mesmo introdução de vírus selvagem nos plantéis.Infectious bronchitis virus (IBV, Avian Coronavirus from chickens belongs to group 3 of the family Coronaviridae and causes respiratory and renal disorders in broilers. Vaccination using live vaccines is generally performed in

  3. Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.

    Science.gov (United States)

    Babbitt, Gregory A; Coppola, Erin E; Mortensen, Jamie S; Ekeren, Patrick X; Viola, Cosmo; Goldblatt, Dallan; Hudson, André O

    2018-02-01

    Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.

  4. Avaliação eletroforética, cromatográfica e molecular da Hb D Los Angeles no Brasil

    OpenAIRE

    Chinelato-Fernandes Ana R.; Leoneli Guilherme G.; Calderan Patrícia O.; Oliveira Rute Blasi de; Silva Jr. Wilson Araújo da; Hidalgo Claudia Augusta; Bonini- Domingos Claudia Regina

    2003-01-01

    A variante de hemoglobina (Hb) D mais comum, Hb D Los Angeles ou D Punjab, é originada de uma transversão GAA->CAA no códon 121 da globina beta; essa mutação resulta na substituição do ácido glutâmico por glutamina na proteína. É a terceira variante de hemoglobina mais freqüente da população brasileira. Como as hemoglobinas D apresentam migração similar à hemoglobina S em pH alcalino, e com a hemoglobina A em pH ácido, são necessários vários testes para o correto diagnóstico. No presente estu...

  5. Realization and optimization of AES algorithm on the TMS320DM6446 based on DaVinci technology

    Science.gov (United States)

    Jia, Wen-bin; Xiao, Fu-hai

    2013-03-01

    The application of AES algorithm in the digital cinema system avoids video data to be illegal theft or malicious tampering, and solves its security problems. At the same time, in order to meet the requirements of the real-time, scene and transparent encryption of high-speed data streams of audio and video in the information security field, through the in-depth analysis of AES algorithm principle, based on the hardware platform of TMS320DM6446, with the software framework structure of DaVinci, this paper proposes the specific realization methods of AES algorithm in digital video system and its optimization solutions. The test results show digital movies encrypted by AES128 can not play normally, which ensures the security of digital movies. Through the comparison of the performance of AES128 algorithm before optimization and after, the correctness and validity of improved algorithm is verified.

  6. Strategies of molecular imprinting-based fluorescence sensors for chemical and biological analysis.

    Science.gov (United States)

    Yang, Qian; Li, Jinhua; Wang, Xiaoyan; Peng, Hailong; Xiong, Hua; Chen, Lingxin

    2018-07-30

    One pressing concern today is to construct sensors that can withstand various disturbances for highly selective and sensitive detecting trace analytes in complicated samples. Molecularly imprinted polymers (MIPs) with tailor-made binding sites are preferred to be recognition elements in sensors for effective targets detection, and fluorescence measurement assists in highly sensitive detection and user-friendly control. Accordingly, molecular imprinting-based fluorescence sensors (MI-FL sensors) have attracted great research interest in many fields such as chemical and biological analysis. Herein, we comprehensively review the recent advances in MI-FL sensors construction and applications, giving insights on sensing principles and signal transduction mechanisms, focusing on general construction strategies for intrinsically fluorescent or nonfluorescent analytes and improvement strategies in sensing performance, particularly in sensitivity. Construction strategies are well overviewed, mainly including the traditional indirect methods of competitive binding against pre-bound fluorescent indicators, employment of fluorescent functional monomers and embedding of fluorescence substances, and novel rational designs of hierarchical architecture (core-shell/hollow and mesoporous structures), post-imprinting modification, and ratiometric fluorescence detection. Furthermore, MI-FL sensor based microdevices are discussed, involving micromotors, test strips and microfluidics, which are more portable for rapid point-of-care detection and in-field diagnosing. Finally, the current challenges and future perspectives of MI-FL sensors are proposed. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. A sol-gel based molecular imprint incorporating carbon dots for fluorometric determination of nicotinic acid

    International Nuclear Information System (INIS)

    Zuo, Pengli; Gao, Junfa; Liu, Jianha; Zhao, Mingming; Zhao, Jiahong; Peng, Jun; Zuo, Pengjian; He, Hua

    2016-01-01

    We are introducing functionalized carbon dots (C-dots) coated with a shell of molecularly imprinted sol-gel as a new tool in molecular imprint-based detection. Specifically, an imprint recognizing nicotinic acid (NA) was prepared in two steps. The first involves pyrolytic decomposition of citric acid in the presence of aminopropyltriethoxysilane to yield triethoxysilyl-modified C-dots with a typical size of 2.8 ± 1.1 nm. These are then polycondensed in the presence of tetraethoxysilane and NA at room temperature to give spherical silica nanoparticles (SiNPs) with a typical size of ∼300 nm and containing C-dots and NA in the silica matrix. NA was then removed by extraction. The resulting SiNPs are well permeable to NA, photostable, display strong blue luminescence and can bind NA fairly selectively. The fluorometric detection scheme is based on the finding that increasing concentrations of NA quench the fluorescence of the C-dots in the SiNPs. NA can be determined by this method in the 0.5 to 10.5 μM concentration range, with a 12.6 nM detection limit. The composite was successfully utilized as a fluorescent probe for the determination of NA in spiked human urine samples. The method is believed to have a wider scope in being applicable to other analytes that are capable of quenching the fluorescence of C-dots. (author)

  8. Hydrazone based molecular glasses for solid-state dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Aich, R.; Tran-Van, F.; Goubard, F.; Beouch, L.; Michaleviciute, A.; Grazulevicius, J.V.; Ratier, B.; Chevrot, C.

    2008-01-01

    Biscarbazole and terthiophene based molecular glasses with hydrazone functional goups (named respectively 2CzMPH and 3TDPH) have been synthesized and the thermal, optical and electrochemical properties have been studied. Differential scanning calorimetry characterizations confirm the metastable amorphous properties of these molecules with glass transition temperatures at 80 deg. C for the 3TDPH and 93 deg. C for the 2CzMPH. Their electrochemical properties have been studied and showed the effect of the conjugated hydrazone groups on the electronic delocalization of the structures. The concept of solid state dye-sensitized solar cells using hydrazone based molecular glasses has been verified with the elaboration of a SnO 2 : F/nc-TiO 2 /Ru-dye/2CzMPH /Au devices. Under full sunlight (98 mW/cm 2 , air mass 1.5) the I-V characterization of the device give a short circuit photocurrents I sc = 0.42 mA/cm 2 , open circuit voltage V oc = 500 mV with a fill factor of 0.35

  9. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

  10. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Directory of Open Access Journals (Sweden)

    Kuan Peng

    2010-01-01

    Full Text Available As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SPn, and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  11. Study on photon transport problem based on the platform of molecular optical simulation environment.

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  12. Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

    Science.gov (United States)

    Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

    2018-05-15

    Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

  13. Hydrazone based molecular glasses for solid-state dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Aich, R. [Laboratoire de Physicochimie des Polymeres et des Interfaces (EA 2528), Universite de Cergy-Pontoise, 5 mail Gay Lussac, 95031 Cergy Pontoise (France); Ecole Electricite de Production et Methodes Industrielles, Cergy Pontoise (France); Tran-Van, F. [Laboratoire de Physicochimie des Polymeres et des Interfaces (EA 2528), Universite de Cergy-Pontoise, 5 mail Gay Lussac, 95031 Cergy Pontoise (France)], E-mail: francois.tran-van@u-cergy.fr; Goubard, F.; Beouch, L. [Laboratoire de Physicochimie des Polymeres et des Interfaces (EA 2528), Universite de Cergy-Pontoise, 5 mail Gay Lussac, 95031 Cergy Pontoise (France); Michaleviciute, A.; Grazulevicius, J.V. [Department of Organic Technology, Kaunas University of Technology, Radvilenu Plentas 19, Kaunas LT-50254 (Lithuania); Ratier, B. [X-LIM., departement MINACOM, UMR 6172, Faculte des Sciences, 123 av. Albert Thomas 87060 Limoges cedex France (France); Chevrot, C. [Laboratoire de Physicochimie des Polymeres et des Interfaces (EA 2528), Universite de Cergy-Pontoise, 5 mail Gay Lussac, 95031 Cergy Pontoise (France)

    2008-08-30

    Biscarbazole and terthiophene based molecular glasses with hydrazone functional goups (named respectively 2CzMPH and 3TDPH) have been synthesized and the thermal, optical and electrochemical properties have been studied. Differential scanning calorimetry characterizations confirm the metastable amorphous properties of these molecules with glass transition temperatures at 80 deg. C for the 3TDPH and 93 deg. C for the 2CzMPH. Their electrochemical properties have been studied and showed the effect of the conjugated hydrazone groups on the electronic delocalization of the structures. The concept of solid state dye-sensitized solar cells using hydrazone based molecular glasses has been verified with the elaboration of a SnO{sub 2}: F/nc-TiO{sub 2}/Ru-dye/2CzMPH /Au devices. Under full sunlight (98 mW/cm{sup 2}, air mass 1.5) the I-V characterization of the device give a short circuit photocurrents I{sub sc} = 0.42 mA/cm{sup 2}, open circuit voltage V{sub oc} = 500 mV with a fill factor of 0.35.

  14. Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences.

    Science.gov (United States)

    Xiang, Xiao-Guo; Schuiteman, André; Li, De-Zhu; Huang, Wei-Chang; Chung, Shih-Wen; Li, Jian-Wu; Zhou, Hai-Lang; Jin, Wei-Tao; Lai, Yang-Jun; Li, Zhen-Yu; Jin, Xiao-Hua

    2013-12-01

    Dendrobium is one of the three largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae. Based on five DNA markers and a broad sampling of Dendrobium and its relatives from mainland Asia (109 species), our results indicate that mainland Asia Dendrobium is divided into eight clades (with two unplaced species) that form polytomies along the spine of the cladogram. Both Dendrobium and Epigeneium are well supported as monophyletic, whereas sect. Dendrobium, sect. Densiflora, sect. Breviflores, sect. Holochrysa, are paraphyletic/polyphyletic. Many ignored phylogenetic relationships, such as the one of major clades formed by D. jenkinsii and D. lindleyi (two members of sect. Densiflora), the Aphyllum group, the Devonianum group, the Catenatum group, the Crepidatum group, and the Dendrobium moniliforme complex are well supported by both molecular and morphological evidence. Based on our data, we propose to broaden sect. Dendrobium to include sect. Stuposa, sect. Breviflores, and sect. Holochrysa and to establish a new section to accommodate D. jenkinsii and D. lindleyi. Our results indicated that it is preferable to use a broad generic concept of Dendrobium and to pursue an improved infrageneric classification at sectional level, taking into account both morphology and current molecular findings. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Carbon Molecular Sieve Membranes Derived from Tröger's Base-Based Microporous Polyimide for Gas Separation.

    Science.gov (United States)

    Wang, Zhenggong; Ren, Huiting; Zhang, Shenxiang; Zhang, Feng; Jin, Jian

    2018-03-09

    Carbon molecular sieve (CMS)-based membranes have attracted great attention because of their outstanding gas-separation performance. The polymer precursor is a key point for the preparation of high-performance CMS membranes. In this work, a microporous polyimide precursor containing a Tröger's base unit was used for the first time to prepare CMS membranes. By optimizing the pyrolysis procedure and the soaking temperature, three TB-CMS membranes were obtained. Gas-permeation tests revealed that the comprehensive gas-separation performance of the TB-CMS membranes was greatly enhanced relative to that of most state-of-the-art CMS membranes derived from polyimides reported so far. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Incremento na dissolução da caffeine em base de ammonium acryloyldimethyltaurate/vp copolymer: desenvolvimento farmacotécnico de géis anti-celulite

    OpenAIRE

    Éder Menezes Fernandes; Gabriel Azevedo de Brito Damasceno; Márcio Ferrari; Eduardo Pereira Azevedo

    2015-01-01

    A hidrolipodistrofia ginóide (HLDG), popularmente conhecida como “celulite”, consiste em uma alteração patológica do tecido adiposo e da função veno-linfática. Géis contendo caffeine tem sido empregados no tratamento não-invasivo da HLDG, oferecendo resultados satisfatórios a baixos custos. Devido a baixa hidrossolubilidade da caffeine, este gel apresenta como principal inconveniente a formação de precipitados/grumos, oriundos da precipitação da caffeine na base hidrofílica (gel). Este trabal...

  17. Remote stabilization of copper paddlewheel based molecular building blocks in metal-organic frameworks

    KAUST Repository

    Gao, Wenyang

    2015-03-24

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal-organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu2(O2C-)4], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu3O(N4-x(CH)xC-)3] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1. © 2015 American Chemical Society.

  18. Fuzzy method of recognition of high molecular substances in evidence-based biology

    Science.gov (United States)

    Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

    2017-10-01

    Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

  19. The importance of the rotor in hydrazone-based molecular switches

    Directory of Open Access Journals (Sweden)

    Xin Su

    2012-06-01

    Full Text Available The pH-activated E/Z isomerization of a series of hydrazone-based systems having different functional groups as part of the rotor (R = COMe, CN, Me, H, was studied. The switching efficiency of these systems was compared to that of a hydrazone-based molecular switch (R = COOEt whose E/Z isomerization is fully reversible. It was found that the nature of the R group is critical for efficient switching to occur; the R group should be a moderate H-bond acceptor in order to (i provide enough driving force for the rotor to move upon protonation, and (ii stabilize the obtained Z configuration, to achieve full conversion.

  20. Selective detection of heavy metal ions by calixarene-based fluorescent molecular sensors

    Science.gov (United States)

    Zhang, Haitao; Faye, Djibril; Zhang, Han; Lefevre, Jean-Pierre; Delaire, J. A.; Leray, Isabelle

    2012-06-01

    The synthesis, spectroscopic characterization and complexing properties of calixarene-based fluorescent sensors are reported. The calixarene bearing four dansyl fluorophores (Calix-DANS4) exhibits a very high affinity for the detection of lead. A fluorimetric micro-device based on the use of a Y-shape microchannel was developed and allows lead detection with a 5 ppb detection limit. For mercury detection, a fluorescent molecular sensor containing a calixarene anchored with four 8-quinolinoloxy groups (Calix-Q) has been synthesized. The absorption and fluorescence spectra of this sensor are sensitive to the presence of metal cations. An efficient fluorescence quenching is observed upon mercury complexation because of a photoinduced electron transfer from the fluorophore to the bound mercury. Calix-Q shows a high selectivity towards Hg2+ over interfering cations (Na+, K+, Ca2+, Cu2+, Zn2+, Cd2+ and Pb2+) and a 70 ppb sensitivity.

  1. Remote stabilization of copper paddlewheel based molecular building blocks in metal-organic frameworks

    KAUST Repository

    Gao, Wenyang; Cai, Rong; Pham, Tony T.; Forrest, Katherine A.; Hogan, Adam; Nugent, Patrick S.; Williams, Kia R.; Wojtas, Łukasz; Luebke, Ryan; Weselinski, Lukasz Jan; Zaworotko, Michael J.; Space, Brian; Chen, Yusheng; Eddaoudi, Mohamed; Shi, Xiaodong; Ma, Shengqian

    2015-01-01

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal-organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu2(O2C-)4], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu3O(N4-x(CH)xC-)3] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1. © 2015 American Chemical Society.

  2. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

    2012-05-01

    MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

  3. Innovative molecular-based fluorescent nanoparticles for multicolor single particle tracking in cells

    International Nuclear Information System (INIS)

    Daniel, Jonathan; Blanchard-Desce, Mireille; Godin, Antoine G; Palayret, Matthieu; Lounis, Brahim; Cognet, Laurent

    2016-01-01

    Based on an original molecular-based design, we present bright and photostable fluorescent organic nanoparticles (FONs) showing excellent colloidal stability in various aqueous environments. Complementary near-infrared emitting and green emitting FONs were prepared using a simple, fast and robust protocol. Both types of FONs could be simultaneously imaged at the single-particle level in solution as well as in biological environments using a monochromatic excitation and a dual-color fluorescence microscope. No evidence of acute cytotoxicity was found upon incubation of live cells with mixed solutions of FONs, and both types of nanoparticles were found internalized in the cells where their motion could be simultaneously tracked at video-rate up to minutes. These fluorescent organic nanoparticles open a novel non-toxic alternative to existing nanoparticles for imaging biological structures, compatible with live-cell experiments and specially fitted for multicolor single particle tracking. (paper)

  4. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    Science.gov (United States)

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  5. Molecular bases of the ABO blood groups of Indians from the Brazilian Amazon region.

    Science.gov (United States)

    Franco, R F; Simões, B P; Guerreiro, J F; Santos, S E; Zago, M A

    1994-01-01

    Phenotype studies of ABO blood groups in most Amerindian populations revealed the exclusive presence of group O. Since group O is the result of the absence of glycosyltransferase activity, its molecular bases may be heterogeneous. We carried out ABO blood group genotyping by analysis of DNA of 30 Indians from 2 Amazonian tribes (Yanomami and Arara), and compared the findings with other populations (Caucasians and Blacks). Two segments of the glycosyltransferase gene were amplified by PCR and digested with KpnI or AluI to detect deletion or base change at positions 258 and 700, respectively. For all subjects, the gene basis of blood group O is the deletion of a single nucleotide at position 258 of the glycosyltransferase A gene, similar to that observed in Caucasoids and Negroids. DNA sequencing of limited regions of the gene supports this conclusion. This finding does not exclude, however, that a heterogeneity of the O allele may be revealed by a more extensive analysis.

  6. Cucurbiturils: molecular nanocapsules for time-resolved fluorescence-based assays.

    Science.gov (United States)

    Marquez, Cesar; Huang, Fang; Nau, Werner M

    2004-03-01

    A new fluorescent host-guest system based on the inclusion of the fluorophore 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) into the cavity of the molecular container compound cucurbit[7]uril (CB7) has been designed which possesses an exceedingly long-lived emission (690 ns in aerated water). The large binding constant of (4 +/- 1) x 10(5) M(-1) along with the resistance of the CB7.DBO complex toward external fluorescence quenchers allow the use of CB7 as an enhancer in time-resolved fluorescence-based assays, e.g., to screen enzyme activity or inhibition by using DBO-labeled peptides as substrates. The response of CB7.DBO to different environmental conditions and possible quenchers are described.

  7. Adsorption of molecular additive onto lead halide perovskite surfaces: A computational study on Lewis base thiophene additive passivation

    Science.gov (United States)

    Zhang, Lei; Yu, Fengxi; Chen, Lihong; Li, Jingfa

    2018-06-01

    Organic additives, such as the Lewis base thiophene, have been successfully applied to passivate halide perovskite surfaces, improving the stability and properties of perovskite devices based on CH3NH3PbI3. Yet, the detailed nanostructure of the perovskite surface passivated by additives and the mechanisms of such passivation are not well understood. This study presents a nanoscopic view on the interfacial structure of an additive/perovskite interface, consisting of a Lewis base thiophene molecular additive and a lead halide perovskite surface substrate, providing insights on the mechanisms that molecular additives can passivate the halide perovskite surfaces and enhance the perovskite-based device performance. Molecular dynamics study on the interactions between water molecules and the perovskite surfaces passivated by the investigated additive reveal the effectiveness of employing the molecular additives to improve the stability of the halide perovskite materials. The additive/perovskite surface system is further probed via molecular engineering the perovskite surfaces. This study reveals the nanoscopic structure-property relationships of the halide perovskite surface passivated by molecular additives, which helps the fundamental understanding of the surface/interface engineering strategies for the development of halide perovskite based devices.

  8. Molecular and cell-based therapies for muscle degenerations: a road under construction.

    Science.gov (United States)

    Berardi, Emanuele; Annibali, Daniela; Cassano, Marco; Crippa, Stefania; Sampaolesi, Maurilio

    2014-01-01

    Despite the advances achieved in understanding the molecular biology of muscle cells in the past decades, there is still need for effective treatments of muscular degeneration caused by muscular dystrophies and for counteracting the muscle wasting caused by cachexia or sarcopenia. The corticosteroid medications currently in use for dystrophic patients merely help to control the inflammatory state and only slightly delay the progression of the disease. Unfortunately, walkers and wheel chairs are the only options for such patients to maintain independence and walking capabilities until the respiratory muscles become weak and the mechanical ventilation is needed. On the other hand, myostatin inhibition, IL-6 antagonism and synthetic ghrelin administration are examples of promising treatments in cachexia animal models. In both dystrophies and cachectic syndrome the muscular degeneration is extremely relevant and the translational therapeutic attempts to find a possible cure are well defined. In particular, molecular-based therapies are common options to be explored in order to exploit beneficial treatments for cachexia, while gene/cell therapies are mostly used in the attempt to induce a substantial improvement of the dystrophic muscular phenotype. This review focuses on the description of the use of molecular administrations and gene/stem cell therapy to treat muscular degenerations. It reviews previous trials using cell delivery protocols in mice and patients starting with the use of donor myoblasts, outlining the likely causes for their poor results and briefly focusing on satellite cell studies that raise new hope. Then it proceeds to describe recently identified stem/progenitor cells, including pluripotent stem cells and in relationship to their ability to home within a dystrophic muscle and to differentiate into skeletal muscle cells. Different known features of various stem cells are compared in this perspective, and the few available examples of their use in

  9. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

    Science.gov (United States)

    Dissanayake, Thakshila; Swails, Jason M; Harris, Michael E; Roitberg, Adrian E; York, Darrin M

    2015-02-17

    The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.

  10. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase; Determinacao da estrutura molecular do ciclooctano por metodos Ab Initio e difracao de eletrons na fase gasosa

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Wagner B. de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica

    2000-10-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  11. A distance-dependent metal-enhanced fluorescence sensing platform based on molecular beacon design.

    Science.gov (United States)

    Zhou, Zhenpeng; Huang, Hongduan; Chen, Yang; Liu, Feng; Huang, Cheng Zhi; Li, Na

    2014-02-15

    A new metal-enhanced fluorescence (MEF) based platform was developed on the basis of distance-dependent fluorescence quenching-enhancement effect, which combined the easiness of Ag-thiol chemistry with the MEF property of noble-metal structures as well as the molecular beacon design. For the given sized AgNPs, the fluorescence enhancement factor was found to increase with a d(6) dependency in agreement with fluorescence resonance energy transfer mechanism at shorter distance and decrease with a d(-3) dependency in agreement with plasmonic enhancement mechanism at longer distance between the fluorophore and the AgNP surface. As a proof of concept, the platform was demonstrated by a sensitive detection of mercuric ions, using thymine-containing molecular beacon to tune silver nanoparticle (AgNP)-enhanced fluorescence. Mercuric ions were detected via formation of a thymine-mercuric-thymine structure to open the hairpin, facilitating fluorescence recovery and AgNP enhancement to yield a limit of detection of 1 nM, which is well below the U.S. Environmental Protection Agency regulation of the Maximum Contaminant Level Goal (10nM) in drinking water. Since the AgNP functioned as not only a quencher to reduce the reagent blank signal but also an enhancement substrate to increase fluorescence of the open hairpin when target mercuric ions were present, the quenching-enhancement strategy can greatly improve the detection sensitivity and can in principle be a universal approach for various targets when combined with molecular beacon design. © 2013 Elsevier B.V. All rights reserved.

  12. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

    Science.gov (United States)

    Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang

    2009-03-31

    Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of

  13. Molecular phylogeny of Anopheles hyrcanus group (Diptera: Culicidae) based on mtDNA COI.

    Science.gov (United States)

    Fang, Yuan; Shi, Wen-Qi; Zhang, Yi

    2017-05-08

    The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy. Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range. The results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions. In summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay

  14. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

    Directory of Open Access Journals (Sweden)

    Li Honglin

    2009-03-01

    Full Text Available Abstract Background Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. Results The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112. Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. Conclusion On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms

  15. Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

    International Nuclear Information System (INIS)

    Yu, P.

    2008-01-01

    More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

  16. Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

    Science.gov (United States)

    Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

    2018-05-01

    In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

  17. A WAO - ARIA - GA²LEN consensus document on molecular-based allergy diagnostics.

    Science.gov (United States)

    Canonica, Giorgio Walter; Ansotegui, Ignacio J; Pawankar, Ruby; Schmid-Grendelmeier, Peter; van Hage, Marianne; Baena-Cagnani, Carlos E; Melioli, Giovanni; Nunes, Carlos; Passalacqua, Giovanni; Rosenwasser, Lanny; Sampson, Hugh; Sastre, Joaquin; Bousquet, Jean; Zuberbier, Torsten

    2013-10-03

    Molecular-based allergy (MA) diagnostics is an approach used to map the allergen sensitization of a patient at a molecular level, using purified natural or recombinant allergenic molecules (allergen components) instead of allergen extracts. Since its introduction, MA diagnostics has increasingly entered routine care, with currently more than 130 allergenic molecules commercially available for in vitro specific IgE (sIgE) testing.MA diagnostics allows for an increased accuracy in allergy diagnosis and prognosis and plays an important role in three key aspects of allergy diagnosis: (1) resolving genuine versus cross-reactive sensitization in poly-sensitized patients, thereby improving the understanding of triggering allergens; (2) assessing, in selected cases, the risk of severe, systemic versus mild, local reactions in food allergy, thereby reducing unnecessary anxiety for the patient and the need for food challenge testing; and (3) identifying patients and triggering allergens for specific immunotherapy (SIT).Singleplex and multiplex measurement platforms are available for MA diagnostics. The Immuno-Solid phase Allergen Chip (ISAC) is the most comprehensive platform currently available, which involves a biochip technology to measure sIgE antibodies against more than one hundred allergenic molecules in a single assay. As the field of MA diagnostics advances, future work needs to focus on large-scale, population-based studies involving practical applications, elucidation and expansion of additional allergenic molecules, and support for appropriate test interpretation. With the rapidly expanding evidence-base for MA diagnosis, there is a need for allergists to keep abreast of the latest information. The aim of this consensus document is to provide a practical guide for the indications, determination, and interpretation of MA diagnostics for clinicians trained in allergology.

  18. PROOF-based analysis on the ATLAS grid facilities: first experience with the PoD/PanDa plugin

    International Nuclear Information System (INIS)

    Vilucchi, E; Nardo, R Di; Mancini, G; Pineda, A R Sanchez; Salvo, A De; Donato, C Di; Doria, A; Ganis, G; Manafov, A; Mazza, S; Preltz, F; Rebatto, D; Salvucci, A

    2014-01-01

    In the ATLAS computing model Grid resources are managed by PanDA, the system designed for production and distributed analysis, and data are stored under various formats in ROOT files. End-user physicists have the choice to use either the ATHENA framework or directly ROOT, that provides users the possibility to use PROOF to exploit the computing power of multi-core machines or to dynamically manage analysis facilities. Since analysis facilities are, in general, not dedicated to PROOF only, PROOF-on-Demand (PoD) is used to enable PROOF on top of an existing resource management system. In a previous work we investigated the usage of PoD to enable PROOF-based analysis on Tier-2 facilities using the PoD/gLite plug-in interface. In this paper we present the status of our investigations using the recently developed PoD/PanDA plug-in to enable PROOF and a real end-user ATLAS physics analysis as payload. For this work, data were accessed using two different protocols: XRootD and file protocol. The former in the site where the SRM interface is Disk Pool Manager (DPM) and the latter where the SRM interface is StoRM with GPFS file system. We will first describe the results of some benchmark tests we run on the ATLAS Italian Tier-1 and Tier-2s sites and at CERN. Then, we will compare the results of different types of analysis, comparing performances accessing data in relation to different types of SRM interfaces and accessing data with XRootD in the LAN and in the WAN using the ATLAS XROOTD storage federation infrastructure.

  19. Problemas na padronização da reação em cadeia da polimerase para diagnóstico da tuberculose pulmonar

    Directory of Open Access Journals (Sweden)

    Bollela Valdes R.

    1999-01-01

    Full Text Available OBJETIVO: Padronizar reação em cadeia da polimerase para diagnóstico de tuberculose pulmonar, comparando os resultados obtidos com as técnicas microbiológicas clássicas, e analisar seu uso numa região de alta prevalência da tuberculose. MÉTODOS: Foram descontaminadas, após a baciloscopia, 42 amostras de escarro de pacientes. Em seguida, procedeu-se ao cultivo em Lowenstein-Jensen e à reação em cadeia da polimerase com "primers" que amplificam um fragmento de 123 pares de base do genoma do Mycobacterium tuberculosis. RESULTADOS: Das 42 amostras de escarro, 10 apresentaram cultura positiva para M. tuberculosis. Dez foram positivas à baciloscopia e 16 mostraram-se positivas na reação em cadeia da polimerase. A sensibilidade e especificidade do teste em relação à cultura foi de 90% e 81%, respectivamente. CONCLUSÕES: A reação em cadeia da polimerase tem sensibilidade comparável à da cultura e pode ser realizada em apenas um dia, resultando em tratamento precoce e melhor controle da doença. A padronização e avaliação de técnicas de biologia molecular no diagnóstico da tuberculose no Brasil é imprescindível na discussão da implantação deste exame na rotina diagnóstica em centros de referência.

  20. Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications.

    Science.gov (United States)

    Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman; Ramamurthy, Praveen C

    2017-01-01

    A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1 , exhibited a highest occupied molecular orbital (HOMO) energy level at -5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2 , were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3 .

  1. Method for assessing the reliability of molecular diagnostics based on multiplexed SERS-coded nanoparticles.

    Directory of Open Access Journals (Sweden)

    Steven Y Leigh

    Full Text Available Surface-enhanced Raman scattering (SERS nanoparticles have been engineered to generate unique fingerprint spectra and are potentially useful as bright contrast agents for molecular diagnostics. One promising strategy for biomedical diagnostics and imaging is to functionalize various particle types ("flavors", each emitting a unique spectral signature, to target a large multiplexed panel of molecular biomarkers. While SERS particles emit narrow spectral features that allow them to be easily separable under ideal conditions, the presence of competing noise sources and background signals such as detector noise, laser background, and autofluorescence confounds the reliability of demultiplexing algorithms. Results obtained during time-constrained in vivo imaging experiments may not be reproducible or accurate. Therefore, our goal is to provide experimentalists with a metric that may be monitored to enforce a desired bound on accuracy within a user-defined confidence level. We have defined a spectral reliability index (SRI, based on the output of a direct classical least-squares (DCLS demultiplexing routine, which provides a measure of the reliability of the computed nanoparticle concentrations and ratios. We present simulations and experiments to demonstrate the feasibility of this strategy, which can potentially be utilized for a range of instruments and biomedical applications involving multiplexed SERS nanoparticles.

  2. Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

    Science.gov (United States)

    Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

    2009-10-01

    Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.

  3. Magnetic-graphene based molecularly imprinted polymer nanocomposite for the recognition of bovine hemoglobin.

    Science.gov (United States)

    Guo, Junxia; Wang, Yuzhi; Liu, Yanjin; Zhang, Cenjin; Zhou, Yigang

    2015-11-01

    The protein imprinted technique combining surface imprinting and nanomaterials has been an attractive strategy for recognition and rapid separation of proteins. In this work, magnetic-graphene (MG) was chosen as the supporting substrate for the magnetic nanomaterials, which served to absorb the targeting imprinting molecules, bovine hemoglobin (BHb). Acryl amide (AAm) with a high affinity to BHb and N,N'- methylenebisacrylamide (MBA) were selected as the functional monomer and cross-linking agent, respectively. After in-situ polymerization, the proposed magnetic-graphene based molecularly imprinted polymer (MG-MIP) was obtained with a further extraction step of imprinted BHb. Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), raman spectroscopy(RS), X-ray diffraction (XRD) and vibrating sample magnetometer (VSM) were employed to characterize the resulted MG-MIP. The maximum adsorption capability (Qmax) was determined by Langmuir Isotherm Plots and was 186.73 mg/g for imprinted nanomaterials (MIP) with an imprinting factor of 1.96. The selectivity of MG-MIP was investigated by using several proteins that are different in molecular mass and isoelectric points as the reference. The results showed that the shape memory effect of imprinted cavities, the size of proteins and the charge effect of proteins were the major factors for the selective recognition. The proposed method was also employed to specifically capture BHb from a binary protein mixture. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Creatinine sensor based on a molecularly imprinted polymer-modified hanging mercury drop electrode.

    Science.gov (United States)

    Lakshmi, Dhana; Prasad, Bhim Bali; Sharma, Piyush Sindhu

    2006-09-15

    Molecularly imprinted polymers (MIP) have been elucidated to work as artificial receptors. In our present study, a MIP was applied as a molecular recognition element to a chemical sensor. We have constructed a creatinine sensor based on a MIP layer selective for creatinine and its differential pulse, cathodic stripping voltammetric detection (DPCSV) on a hanging mercury drop electrode (HMDE). The creatinine sensor was fabricated by the drop coating of dimethylformamide (DMF) solution of a creatinine-imprinted polymer onto the surface of HMDE. The modified-HMDE, preanodised in neutral medium at +0.4V versus Ag/AgCl for 120s, exhibited a marked enhancement in DPCSV current in comparison to the less anodised (

  5. Facilitating in vivo tumor localization by principal component analysis based on dynamic fluorescence molecular imaging

    Science.gov (United States)

    Gao, Yang; Chen, Maomao; Wu, Junyu; Zhou, Yuan; Cai, Chuangjian; Wang, Daliang; Luo, Jianwen

    2017-09-01

    Fluorescence molecular imaging has been used to target tumors in mice with xenograft tumors. However, tumor imaging is largely distorted by the aggregation of fluorescent probes in the liver. A principal component analysis (PCA)-based strategy was applied on the in vivo dynamic fluorescence imaging results of three mice with xenograft tumors to facilitate tumor imaging, with the help of a tumor-specific fluorescent probe. Tumor-relevant features were extracted from the original images by PCA and represented by the principal component (PC) maps. The second principal component (PC2) map represented the tumor-related features, and the first principal component (PC1) map retained the original pharmacokinetic profiles, especially of the liver. The distribution patterns of the PC2 map of the tumor-bearing mice were in good agreement with the actual tumor location. The tumor-to-liver ratio and contrast-to-noise ratio were significantly higher on the PC2 map than on the original images, thus distinguishing the tumor from its nearby fluorescence noise of liver. The results suggest that the PC2 map could serve as a bioimaging marker to facilitate in vivo tumor localization, and dynamic fluorescence molecular imaging with PCA could be a valuable tool for future studies of in vivo tumor metabolism and progression.

  6. Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines.

    Science.gov (United States)

    Romano, Paolo; Manniello, Assunta; Aresu, Ottavia; Armento, Massimiliano; Cesaro, Michela; Parodi, Barbara

    2009-01-01

    The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.

  7. Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds.

    Science.gov (United States)

    Prosdocimi, Tommaso; Mollica, Luca; Donini, Stefano; Semrau, Marta S; Lucarelli, Anna Paola; Aiolfi, Egidio; Cavalli, Andrea; Storici, Paola; Alfei, Silvana; Brullo, Chiara; Bruno, Olga; Parisini, Emilio

    2018-05-01

    Selected members of the large rolipram-related GEBR family of type 4 phosphodiesterase (PDE4) inhibitors have been shown to facilitate long-term potentiation and to improve memory functions without causing emetic-like behavior in rodents. Despite their micromolar-range binding affinities and their promising pharmacological and toxicological profiles, few if any structure-activity relationship studies have been performed to elucidate the molecular bases of their action. Here, we report the crystal structure of a number of GEBR library compounds in complex with the catalytic domain of PDE4D as well as their inhibitory profiles for both the long PDE4D3 isoform and the catalytic domain alone. Furthermore, we assessed the stability of the observed ligand conformations in the context of the intact enzyme using molecular dynamics simulations. The longer and more flexible ligands appear to be capable of forming contacts with the regulatory portion of the enzyme, thus possibly allowing some degree of selectivity between the different PDE4 isoforms.

  8. Fluorescent molecularly imprinted polymer based on Navicula sp. frustules for optical detection of lysozyme.

    Science.gov (United States)

    Lim, Guat Wei; Lim, Jit Kang; Ahmad, Abdul Latif; Chan, Derek Juinn Chieh

    2016-03-01

    The direct correlation between disease and lysozyme (LYZ) levels in human body fluids makes the sensitive and convenient detection of LYZ the focus of scientific research. Fluorescent molecularly imprinted polymer has emerged as a new alternative for LYZ detection in order to resolve the limitation of immunoassays, which are expensive, unstable, require complex preparation, and are time consuming. In this study, a novel fluorescence molecularly imprinted polymer based on Navicula sp. frustules (FITC-MIP) has been synthesized via post-imprinting treatment for LYZ detection. Navicula sp. frustules were used as supported material because of their unique properties of moderate surface area, reproducibility, and biocompatibility, to address the drawbacks of nanoparticle core material with low adsorption capacity. The FITC acts as recognition signal and optical readout, whereas MIP provides LYZ selectivity. The synthesized FITC-MIP showed a response time as short as 5 min depending on the concentration of LYZ. It is found that the LYZ template can significantly quench the fluorescence intensity of FITC-MIP linearly within a concentration range of 0 to 0.025 mg mL(-1), which is well described by Stern-Volmer equation. The FITC-MIP can selectively and sensitively detect down to 0.0015 mg mL(-1) of LYZ concentration. The excellent sensing performance of FITC-MIP suggests that FITC-MIP is a potential biosensor in clinical diagnosis applications.

  9. Development and characterization of an electrochemical sensor for furosemide detection based on electropolymerized molecularly imprinted polymer.

    Science.gov (United States)

    Kor, Kamalodin; Zarei, Kobra

    2016-01-01

    A novel electrochemical sensor based on a molecularly imprinted polymer, poly(o-phenylenediamine) (PoPD), has been developed for selective and sensitive detection of furosemide. The sensor was prepared by incorporating of furosemide as template molecules during the electropolymerization of o-phenylenediamine on a gold electrode. To develop the molecularly imprinted polymer (MIP), the template molecules were removed from the modified electrode's surface by washing it with 0.25 mol L(-1) NaOH solution. The imprinted layer was characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM). The sensor's preparation conditions including furosemide concentration, the number of CV cycles in the electropolymerization process, extraction solution of the template from the imprinted film, the incubation time and the pH level were optimized. The incubation of the MIP-modified electrode, with respect to furosemide concentration, resulted in a suppression of the K4[Fe(CN)6] oxidation process. Under the optimal experimental conditions, the response of the imprinted sensor was linear in the range of 1.0×10(-7)-7.0×10(-6) mol L(-1) of furosemide. The detection limit was obtained as 7.0×10(-8) mol L(-1) for furosemide by using this sensor. The sensor was successfully used to determine the furosemide amount in the tablet and in human urine samples with satisfactory results. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. A Vertical Channel Model of Molecular Communication based on Alcohol Molecules

    Directory of Open Access Journals (Sweden)

    Pengfei Lu

    2016-05-01

    Full Text Available The study of Molecular Communication(MC is more and more prevalence, and channel model of MC plays an important role in the MC System. Since different propagation environment and modulation techniques produce different channel model, most of the research about MC are in horizontal direction,but in nature the communications between nano machines are in short range and some of the information transportation are in the vertical direction, such as transpiration of plants, biological pump in ocean, and blood transportation from heart to brain. Therefore, this paper we propose a vertical channel model which nano-machines communicate with each other in the vertical direction based on pure diffusion. We rst propose a vertical molecular communication model, we mainly considered the gravity as the factor, though the channel model is also affected by other main factors, such as the ow of the medium, the distance between the transmitter and the receiver, the delay or sensitivity of the transmitter and the receiver. Secondly, we set up a test-bed for this vertical channel model, in order to verify the difference between the theory result and the experiment data. At last, we use the data we get from the experiment and the non-linear least squares method to get the parameters to make our channel model more accurate.

  11. Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

    Science.gov (United States)

    Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman

    2017-01-01

    A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at −5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2, were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3. PMID:28546844

  12. Phylogenetic reconstruction of Syntermitinae (Isoptera, Termitidae based on morphological and molecular data.

    Directory of Open Access Journals (Sweden)

    Mauricio M Rocha

    Full Text Available The subfamily Syntermitinae comprises a group of Neotropical termites with 18 genera and 101 species described. It has been considered a natural group, but relationships among the genera within the subfamily remain uncertain, and some genera appear to be non-monophyletic. Here, we provide a comprehensive phylogeny including six Neotropical species of Termitinae as outgroup, 42 Syntermitinae species as ingroup, 92 morphological characters (from external and internal anatomy of soldier and worker castes and 117 molecular sequences (109 obtained for this study and 8 from GenBank of 4 gene regions (41 and 22 from Cytochrome Oxidase I and II respectively, 19 from Cytochrome b, and 35 from 16S rDNA. Morphological and molecular data were analyzed in combination, with the Bayesian inference method, and the important aspects of termite biology, defense and feeding habits are discussed based on the resulting tree. Although useful for providing diagnostic characters, the morphology of the soldier caste reveals several cases of convergence; whereas the feeding habit shows indications of evolutionary significance.

  13. New potentiometric sensor based on molecularly imprinted nanoparticles for cocaine detection.

    Science.gov (United States)

    Smolinska-Kempisty, K; Ahmad, O Sheej; Guerreiro, A; Karim, K; Piletska, E; Piletsky, S

    2017-10-15

    Here we present a potentiometric sensor for cocaine detection based on molecularly imprinted polymer nanoparticles (nanoMIPs) produced by the solid-phase imprinting method. The composition of polymers with high affinity for cocaine was optimised using molecular modelling. Four compositions were selected and polymers prepared using two protocols: chemical polymerisation in water and UV-initiated polymerisation in organic solvent. All synthesised nanoparticles had very good affinity to cocaine with dissociation constants between 0.6nM and 5.3nM. Imprinted polymers produced in organic solvent using acrylamide as a functional monomer demonstrated the highest yield and affinity, and so were selected for further sensor development. For this, nanoparticles were incorporated within a PVC matrix which was then used to prepare an ion-selective membrane integrated with a potentiometric transducer. It was demonstrated that the sensor was able to quantify cocaine in blood serum samples in the range of concentrations between 1nM and 1mM. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Chemodosimeter-based fluorescent detection of L-cysteine after extracted by molecularly imprinted polymers.

    Science.gov (United States)

    Cai, Xiaoqiang; Li, Jinhua; Zhang, Zhong; Wang, Gang; Song, Xingliang; You, Jinmao; Chen, Lingxin

    2014-03-01

    A chemodosimeter-based fluorescent detection method coupled with molecularly imprinted polymers (MIPs) extraction was developed for determination of L-cysteine (L-Cys) by combining molecular imprinting technique with fluorescent chemodosimeter. The MIPs prepared by precipitation polymerization with L-Cys as template, possessed high specific surface area of 145 m(2)/g and good thermal stability without decomposition lower than 300 °C, and were successfully applied as an adsorbent with excellent selectivity for L-Cys over other amino acids, and enantioselectivity was also demonstrated. A novel chemodosimeter, rhodamine B1, was synthesized for discriminating L-Cys from its structurally similar homocysteine and glutathione as well as various possibly co-existing biospecies in aqueous solutions with notable fluorescence enhancement when adding L-Cys. As L-Cys was added with increasing concentrations, an emission band peaked at 580 nm occurred and significantly increased in fluorescence intensity, by which the L-Cys could be sensed optically. High detectability up to 12.5 nM was obtained. An excellent linearity was found within the wide range of 0.05-50 μM (r=0.9996), and reasonable relative standard deviations ranging from 0.3% to 3.5% were attained. Such typical features as high selectivity, high sensitivity, easy operation and low cost enabled this MIPs-fluorometry to be potentially applicable for routine detection of trace L-Cys. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Nonequilibrium molecular dynamics simulation of coupling between nanoparticles and base-fluid in a nanofluid

    International Nuclear Information System (INIS)

    Kang, Hongbo; Zhang, Yuwen; Yang, Mo; Li, Ling

    2012-01-01

    The intent of this study is to examine nonequilibrium heat transfer in a copper–argon nanofluid by molecular dynamics simulation. Two different methods, the physical definition method and the curve fitting method, are introduced to calculate the coupling factor between nanoparticles and base fluid. The results show that the coupling factors obtained by these two methods are consistent. The coupling factor is proportional to the volume fraction of the nanoparticle and inversely proportional to nanoparticle diameter. In the temperature range of 90–200 K, the coupling factor is not affected by temperature. The nanoparticle aggregation results in a decrease of the coupling factor. -- Highlights: ► Nonequilibrium heat transfer in a copper–argon nanofluid is investigated by molecular dynamics simulation. ► The coupling factor is proportion to the volume fraction of the nanoparticle and inverse proportion to nanoparticle diameter. ► In the temperature range of 90–200 K, there is no temperature effect on the coupling factor. ► The nanoparticle aggregation results in a decrease of the coupling factor.

  16. Phylogenetic Study of Haemonchus Species from Iran Based On Morpho-Molecular Characterization.

    Directory of Open Access Journals (Sweden)

    Behnam Meshgi

    2015-06-01

    Full Text Available Haemonchosis has a negative effect on the farming industry throughout the world, especially in the tropic and sub-tropic countries. The present study was carried out to differentiate Haemonchus species from its main hosts in Iran, including sheep, goat and camel.The identification took place based on the morphometrics of the spicules and molecular characters. Two hundred seventy adult male nematodes were collected from the abomasums of different ruminants (90 samples from each animal at the slaughterhouses from different localities in Iran. Samples were morphologically identified according to the spicules' morphometric measurements. In the section on molecular study, 10 samples of each Haemonchus isolates were genetically examined. A simple PCR-restriction fragment length polymorphism (PCR-RFLP assay of the second internal transcribed spacer of ribosomal DNA (ITS2-rDNA were described to confirm the PCR results.PCR-RFLP profile obtained from the restriction enzyme HPa1 in H. contortus and H. longistipes indicated 1 (278 bp and 2 (113 and 135 bp different fragments, respectively. The morphological parameters clearly distinguish H. contortus from H. longistipes. Moreover, regarding the ITS2-rDNA, sequences of 295 bp and 314 bp were obtained from H. contortus and H. longistipes, respectively.The genotypic results are in agreement with the phenotypic findings of both species.

  17. An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Matthew W. Thompson

    2017-10-01

    Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

  18. Fletcher-Reeves based Particle Swarm Optimization for prediction of molecular structure.

    Science.gov (United States)

    Agrawal, Shikha; Silakari, Sanjay

    2014-04-01

    The determination of the most stable conformers of a molecule can be formulated as a global optimization problem. Knowing the stable conformers of a molecule is important because it allows us to understand its properties and behavior based on its structure. The most stable conformation is that involving the global minimum of potential energy. The problem of finding this global minimum is highly complex, and is computationally difficult because of the number of local minima, which grows exponentially with molecular size. In this paper, we propose a hybrid approach combining Particle Swarm Optimization (PSO) and the Fletcher-Reeves algorithm to minimize the potential energy function. The proposed hybrid algorithm is applied to a simplified molecular potential energy function in problems with up to 100 degrees of freedom and also to a realistic potential energy function modeling a pseudoethane molecule. The computational results for both the cases show that the proposed method performs significantly better than the other algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Phylogenetic reconstruction of Syntermitinae (Isoptera, Termitidae) based on morphological and molecular data.

    Science.gov (United States)

    Rocha, Mauricio M; Morales-Corrêa E Castro, Adriana C; Cuezzo, Carolina; Cancello, Eliana M

    2017-01-01

    The subfamily Syntermitinae comprises a group of Neotropical termites with 18 genera and 101 species described. It has been considered a natural group, but relationships among the genera within the subfamily remain uncertain, and some genera appear to be non-monophyletic. Here, we provide a comprehensive phylogeny including six Neotropical species of Termitinae as outgroup, 42 Syntermitinae species as ingroup, 92 morphological characters (from external and internal anatomy of soldier and worker castes) and 117 molecular sequences (109 obtained for this study and 8 from GenBank) of 4 gene regions (41 and 22 from Cytochrome Oxidase I and II respectively, 19 from Cytochrome b, and 35 from 16S rDNA). Morphological and molecular data were analyzed in combination, with the Bayesian inference method, and the important aspects of termite biology, defense and feeding habits are discussed based on the resulting tree. Although useful for providing diagnostic characters, the morphology of the soldier caste reveals several cases of convergence; whereas the feeding habit shows indications of evolutionary significance.

  20. A molecular-mechanics based finite element model for strength prediction of single wall carbon nanotubes

    International Nuclear Information System (INIS)

    Meo, M.; Rossi, M.

    2007-01-01

    The aim of this work was to develop a finite element model based on molecular mechanics to predict the ultimate strength and strain of single wallet carbon nanotubes (SWCNT). The interactions between atoms was modelled by combining the use of non-linear elastic and torsional elastic spring. In particular, with this approach, it was tried to combine the molecular mechanics approach with finite element method without providing any not-physical data on the interactions between the carbon atoms, i.e. the CC-bond inertia moment or Young's modulus definition. Mechanical properties as Young's modulus, ultimate strength and strain for several CNTs were calculated. Further, a stress-strain curve for large deformation (up to 70%) is reported for a nanotube Zig-Zag (9,0). The results showed that good agreement with the experimental and numerical results of several authors was obtained. A comparison of the mechanical properties of nanotubes with same diameter and different chirality was carried out. Finally, the influence of the presence of defects on the strength and strain of a SWNT was also evaluated. In particular, the stress-strain curve a nanotube with one-vacancy defect was evaluated and compared with the curve of a pristine one, showing a reduction of the ultimate strength and strain for the defected nanotube. The FE model proposed demonstrate to be a reliable tool to simulate mechanical behaviour of carbon nanotubes both in the linear elastic field and the non-linear elastic field

  1. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  2. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

  3. Electrochemical sensor based on magnetic molecularly imprinted nanoparticles modified magnetic electrode for determination of Hb.

    Science.gov (United States)

    Sun, Binghua; Ni, Xinjiong; Cao, Yuhua; Cao, Guangqun

    2017-05-15

    A fast and selective electrochemical sensor for determination of hemoglobin (Hb) was developed based on magnetic molecularly imprinted nanoparticles modified on the magnetic glassy carbon electrode. The nanoparticles Fe 3 O 4 @SiO 2 with a magnetic core and a molecularly imprinted shell had regular structures and good monodispersity. Hb could be determined directly by electrochemical oxidization with the modified electrode. A magnetic field increased electrochemical response to Hb by two times. Imprinting Hb on the surface of Fe 3 O 4 @SiO 2 shortened the response time within 7min. Under optimum conditions, the imprinting factor toward the non-imprinted sensor was 2.8, and the separation factor of Hb to horseradish peroxidase was 2.6. The oxidation peak current had a linear relationship with Hb concentration ranged from 0.005mg/ml to 0.1mg/ml with a detection limit (S/N =3) of 0.0010mg/ml. The sensors were successfully applied to analysis of Hb in whole blood samples with recoveries between 95.7% and 105%. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. An Adhesive Patch-Based Skin Biopsy Device for Molecular Diagnostics and Skin Microbiome Studies.

    Science.gov (United States)

    Yao, Zuxu; Moy, Ronald; Allen, Talisha; Jansen, Burkhard

    2017-10-01

    A number of diagnoses in clinical dermatology are currently histopathologically confirmed and this image recognition-based confirmation generally requires surgical biopsies. The increasing ability of molecular pathology to corroborate or correct a clinical diagnosis based on objective gene expression, mutation analysis, or molecular microbiome data is on the horizon and would be further supported by a tool or procedure to collect samples non-invasively. This study characterizes such a tool in form of a 'bladeless' adhesive patch-based skin biopsy device. The performance of this device was evaluated through a variety of complementary technologies including assessment of sample biomass, electron microscopy demonstrating the harvesting of layers of epidermal tissue, and isolation of RNA and DNA from epidermal skin samples. Samples were obtained by application of adhesive patches to the anatomical area of interest. Biomass assessment demonstrated collection of approximately 0.3mg of skin tissue per adhesive patch and electron microscopy confirmed the nature of the harvested epidermal skin tissue. The obtained tissue samples are stored in a stable fashion on adhesive patches over a wide range of temperatures (-80oC to +60oC) and for extended periods of time (7 days or more). Total human RNA, human genomic DNA and microbiome DNA yields were 23.35 + 15.75ng, 27.72 + 20.71ng and 576.2 + 376.8pg, respectively, in skin samples obtained from combining 4 full patches collected non-invasively from the forehead of healthy volunteers. The adhesive patch skin sampling procedure is well tolerated and provides robust means to obtain skin tissue, RNA, DNA, and microbiome samples without involving surgical biopsies. The non-invasively obtained skin samples can be shipped cost effectively at ambient temperature by mail or standard courier service, and are suitable for a variety of molecular analyses of the skin microbiome as well as of keratinocytes, T cells, dendritic cells

  5. DNA-based molecular markers as tools for the discovery of γ-induced mutants in cereals and soybean

    International Nuclear Information System (INIS)

    Bondarenco, E.; Bondarenco, V.; Barbacar, N.; Coretchi, L.

    2009-01-01

    γ-induced mutagenesis is one of the present techniques effective in producing crops with enhanced quality and novel properties. The fast detection of mutants can be nowadays assured by the employment of DNA-based molecular markers. Different kinds of molecular markers are being widely used all over the world to monitor DNA sequence variation and identification of desired traits. In the given paper we present a short overview of the types of molecular markers and the first steps of the attempt of their use for mutants' characterization in the Republic of Moldova (authors)

  6. Well-Defined Polyethylene-Based Random, Block, and Bilayered Molecular Cobrushes

    KAUST Repository

    Zhang, Hefeng; Zhang, Zhen; Gnanou, Yves; Hadjichristidis, Nikolaos

    2015-01-01

    by anionic polymerization. Proton nuclear magnetic resonance spectroscopy (1H NMR) and high-temperature gel permeation chromatography (HT-GPC) were used to imprint the molecular characteristics of all macromonomers and molecular brushes and differential

  7. Lipoatrofia marrón, obesidad y daño vascular: mecanismos moleculares de resistencia a la insulina en células cardiovasculares

    OpenAIRE

    Fernández Otero, Yolanda

    2010-01-01

    En las sociedades occidentales se ha producido un aumento de la prevalencia de la obesidad y de las enfermedades metabólicas relacionadas con ella, tales como el síndrome metabólico y la diabetes tipo 2 [Haffner, S. y Taegtmeyer 2003]. Los individuos aquejados de las dolencias citadas, sufren los efectos de la resistencia a la acción de la insulina [Saltiel y Kahn 2001] y del daño cardiovascular, y éste es una de las principales causas de muerte en la población con enfermedad cardiovascular. ...

  8. Triple-helix molecular switch-based aptasensors and DNA sensors.

    Science.gov (United States)

    Bagheri, Elnaz; Abnous, Khalil; Alibolandi, Mona; Ramezani, Mohammad; Taghdisi, Seyed Mohammad

    2018-07-15

    Utilization of traditional analytical techniques is limited because they are generally time-consuming and require high consumption of reagents, complicated sample preparation and expensive equipment. Therefore, it is of great interest to achieve sensitive, rapid and simple detection methods. It is believed that nucleic acids assays, especially aptamers, are very important in modern life sciences for target detection and biological analysis. Aptamers and DNA-based sensors have been widely used for the design of various sensors owing to their unique features. In recent years, triple-helix molecular switch (THMS)-based aptasensors and DNA sensors have been broadly utilized for the detection and analysis of different targets. The THMS relies on the formation of DNA triplex via Watson-Crick and Hoogsteen base pairings under optimal conditions. This review focuses on recent progresses in the development and applications of electrochemical, colorimetric, fluorescence and SERS aptasensors and DNA sensors, which are based on THMS. Also, the advantages and drawbacks of these methods are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. XML-based approaches for the integration of heterogeneous bio-molecular data.

    Science.gov (United States)

    Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

    2009-10-15

    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

  10. Optimization and performance evaluation of a conical mirror based fluorescence molecular tomography imaging system

    Science.gov (United States)

    Zhao, Yue; Zhang, Wei; Zhu, Dianwen; Li, Changqing

    2016-03-01

    We performed numerical simulations and phantom experiments with a conical mirror based fluorescence molecular tomography (FMT) imaging system to optimize its performance. With phantom experiments, we have compared three measurement modes in FMT: the whole surface measurement mode, the transmission mode, and the reflection mode. Our results indicated that the whole surface measurement mode performed the best. Then, we applied two different neutral density (ND) filters to improve the measurement's dynamic range. The benefits from ND filters are not as much as predicted. Finally, with numerical simulations, we have compared two laser excitation patterns: line and point. With the same excitation position number, we found that the line laser excitation had slightly better FMT reconstruction results than the point laser excitation. In the future, we will implement Monte Carlo ray tracing simulations to calculate multiple reflection photons, and create a look-up table accordingly for calibration.

  11. Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

  12. A micro seismometer based on molecular electronic transducer technology for planetary exploration

    International Nuclear Information System (INIS)

    Huang, Hai; Tang, Rui; Carande, Bryce; Oiler, Jonathan; Zaitsev, Dmitri; Agafonov, Vadim; Yu, Hongyu

    2013-01-01

    This letter describes an implementation of micromachined seismometer based on molecular electronic transducer (MET) technology. As opposed to a solid inertial mass, MET seismometer senses the movement of liquid electrolyte relative to fixed electrodes. The employment of micro-electro-mechanical systems techniques reduces the internal size of the sensing cell to 1μm and improves the reproducibility of the device. For operating bias of 600 mV, a sensitivity of 809 V/(m/s 2 ) was measured under acceleration of 400μg(g≡9.81m/s 2 ) at 0.32 Hz. A −115 dB (relative to (m/s 2 )/√(Hz)) noise level at 1 Hz was achieved. This work develops an alternative paradigm of seismic sensing device with small size, high sensitivity, low noise floor, high shock tolerance, and independence of installation angle, which is promising for next generation seismometers for planetary exploration.

  13. Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles.

    Science.gov (United States)

    Campbell, Eleanor A; Peterson, Evan; Kolpashchikov, Dmitry M

    2017-07-05

    DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Molecular Simulations of Graphene-Based Electric Double-Layer Capacitors

    Science.gov (United States)

    Kalluri, Raja K.; Konatham, Deepthi; Striolo, Alberto

    2011-03-01

    Towards deploying renewable energy sources it is crucial to develop efficient and cost-effective technologies to store electricity. Traditional batteries are plagued by a number of practical problems that at present limit their widespread applicability. One possible solution is represented by electric double-layer capacitors (EDLCs). To deploy EDLCs at the large scale it is necessary to better understand how electrolytes pack and diffuse within narrow charged pores. We present here simulation results for the concentrated aqueous solutions of NaCl, CsCl, and NaI confined within charged graphene-based porous materials. We discuss how the structure of confined water, the salt concentration, the ions size, and the surface charge density determine the accumulation of electrolytes within the porous network. Our results, compared to data available for bulk systems, are critical for relating macroscopic observations to molecular-level properties of the confined working fluids. Research supported by the Department of Energy.

  15. Molecular performance of commercial MTG variety oil palm based on RAPD markers

    Science.gov (United States)

    Putri, L. A. P.; Setyo, I. E.; Basyuni, M.; Bayu, E. S.; Setiado, H.; Reynaldi, N. F.; Laia, H.; Puteri, S. A. K.; Arifiyanto, D.; Syahputra, I.

    2018-02-01

    The oil palm, an economically important tree in Indonesia, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. This research is conducted by taking individual tree sample of commercial MTG variety germplasm oil palm one years old. The purpose of this research is to analyse molecular performance of some oil palm MTG variety based on RAPD markers. In this experiment, the DNA profile diversity was assessed using markers of oil palm’s random RAPD markers (OPD-20, SB-19, OPM-01 and OPO-11). A total of 15 trees commercial MTG oil palm variety were used for analysis. The results of the experiment indicated out of 4 RAPD markers (OPD-20, SB-19, OPM-01 and OPO-11) showed polymorphic of PCR product. These preliminary results demonstrated RAPD marker can be used to evaluate genetic relatedness among trees of commercial MTG variety oil palm and detecting either genetic variants or mislabelled.

  16. A three-step reconstruction method for fluorescence molecular tomography based on compressive sensing

    DEFF Research Database (Denmark)

    Zhu, Yansong; Jha, Abhinav K.; Dreyer, Jakob K.

    2017-01-01

    Fluorescence molecular tomography (FMT) is a promising tool for real time in vivo quantification of neurotransmission (NT) as we pursue in our BRAIN initiative effort. However, the acquired image data are noisy and the reconstruction problem is ill-posed. Further, while spatial sparsity of the NT...... matrix coherence. The resultant image data are input to a homotopy-based reconstruction strategy that exploits sparsity via ℓ1 regularization. The reconstructed image is then input to a maximum-likelihood expectation maximization (MLEM) algorithm that retains the sparseness of the input estimate...... and improves upon the quantitation by accurate Poisson noise modeling. The proposed reconstruction method was evaluated in a three-dimensional simulated setup with fluorescent sources in a cuboidal scattering medium with optical properties simulating human brain cortex (reduced scattering coefficient: 9.2 cm-1...

  17. Fragment-based drug discovery and molecular docking in drug design.

    Science.gov (United States)

    Wang, Tao; Wu, Mian-Bin; Chen, Zheng-Jie; Chen, Hua; Lin, Jian-Ping; Yang, Li-Rong

    2015-01-01

    Fragment-based drug discovery (FBDD) has caused a revolution in the process of drug discovery and design, with many FBDD leads being developed into clinical trials or approved in the past few years. Compared with traditional high-throughput screening, it displays obvious advantages such as efficiently covering chemical space, achieving higher hit rates, and so forth. In this review, we focus on the most recent developments of FBDD for improving drug discovery, illustrating the process and the importance of FBDD. In particular, the computational strategies applied in the process of FBDD and molecular-docking programs are highlighted elaborately. In most cases, docking is used for predicting the ligand-receptor interaction modes and hit identification by structurebased virtual screening. The successful cases of typical significance and the hits identified most recently are discussed.

  18. Wilsonosiphonia gen. nov. (Rhodomelaceae, Rhodophyta) based on molecular and morpho-anatomical characters.

    Science.gov (United States)

    Bustamante, Danilo E; Won, Boo Yeon; Miller, Kathy Ann; Cho, Tae Oh

    2017-04-01

    Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot-shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts. © 2017 Phycological Society of America.

  19. A multifunctional molecularly imprinted polymer-based biosensor for direct detection of doxycycline in food samples

    DEFF Research Database (Denmark)

    Ashley, Jon; Feng, Xiaotong; Sun, Yi

    2018-01-01

    In this study, we developed a new type of multifunctional molecularly imprinted polymer (MIP) composite as an all-in-one biosensor for the low-cost, rapid and sensitive detection of doxycycline in pig plasma. The MIP composite consisted of a magnetic core for ease of manipulation, and a shell...... of fluorescent MIPs for selective recognition of doxycycline. By simply incorporating a small amount of fluorescent monomer (fluorescein-Oacrylate), the fluorescent MIP layer was successfully grafted onto the magnetic core via a surface imprinting technique. The resultant MIP composites showed significant....... The multifunctional MIP composites were used to directly extract doxycycline from spiked pig plasma samples and quantify the antibiotics based on the quenched fluorescence signals. Recoveries of doxycycline were found in the range of 88–107%....

  20. Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

    Science.gov (United States)

    Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

    2014-07-21

    In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

  1. Molecular design and theoretical characterization of benzodithiophene based organic photovoltaic materials

    Science.gov (United States)

    Bhattacharya, Labanya; Sahu, Sridhar

    2018-05-01

    Two different oligomers, containing methyl substituted Benzodithiophene (BDT) as donor unit, fluorinated thiophene as the π-bridge unit and two different kinds of acceptors based on fluorinated benzothiadiazole, fluorinated benzoselenadiazole units are designed for bulk heterojunction (BHJ) organic solar cell (OSC). The ground and excited state properties of those donor-π-acceptor-π-donor (D-π-A-π-D) oligomeric configurations are characterized via density functional (DFT) and time dependent density functional theory (TD-DFT). The parameters such as dipole moment (ρ), chemical potential (µ), electronegativity (χ), frontier molecular orbital (FMO) analysis, HOMO-LUMO gap, open circuit voltage (Voc) and driving force (ΔE) are calculated to analyze geometrical, electronic structural, quantum chemical and photovoltaic properties of the compounds. In addition, optical absorption spectra are also presented for the optical characterization of the compounds.

  2. Molecular detection with terahertz waves based on absorption-induced transparency metamaterials

    Science.gov (United States)

    G. Rodrigo, Sergio; Martín-Moreno, L.

    2016-10-01

    A system for the detection of spectral signatures of chemical compounds at the Terahertz regime is presented. The system consists on a holey metal film whereby the presence of a given substance provokes the appearance of spectral features in transmission and reflection induced by the molecular specimen. These induced effects can be regarded as an extraordinary optical transmission phenomenon called absorption-induced transparency (AIT). The phenomenon consist precisely in the appearance of peaks in transmission and dips in reflection after sputtering of a chemical compound onto an initially opaque holey metal film. The spectral signatures due to AIT occur unexpectedly close to the absorption energies of the molecules. The presence of a target, a chemical compound, would be thus revealed as a strong drop in reflectivity measurements. We theoretically predict the AIT based system would serve to detect amounts of hydrocyanic acid (HCN) at low rate concentrations.

  3. As bases históricas da gestão da qualidade: a abordagem clássica da administração e seu impacto na moderna gestão da qualidade The historical principles of quality management: the classical management approach and its impact on modern quality management

    OpenAIRE

    Edson Pacheco Paladini

    1998-01-01

    Este artigo mostra como a Gestão da Qualidade, tal qual conhecemos hoje, embasou seu desenvolvimento em escolas fundamentais da Administração. Em particular, enfoca-se aqui a Escola Clássica, suas identidades e confrontos com a Gestão da Qualidade e seus reflexos nas suas principais ferramentas. Esta análise permite entender o verdadeiro alcance de conceitos e estratégias da Gestão da Qualidade, garantindo assim sua correta aplicação.This paper shows how Quality Management, as we understand i...

  4. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    Science.gov (United States)

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic

  5. A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study.

    Science.gov (United States)

    Klähn, Marco; Seduraman, Abirami; Wu, Ping

    2008-11-06

    We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes

  6. Molecular Allergen-Specific IgE Assays as a Complement to Allergen Extract-Based Sensitization Assessment

    NARCIS (Netherlands)

    Aalberse, Rob C.; Aalberse, Joost A.

    2015-01-01

    Molecular allergen-based component-resolved diagnostic IgE antibody tests have emerged in the form of singleplex assays and multiplex arrays. They use both native and recombinant allergen molecules, sometimes in combination with each other, to supplement allergen extract-based IgE antibody analyses.

  7. High-Performance Near-Infrared Phototransistor Based on n-Type Small-Molecular Organic Semiconductor

    KAUST Repository

    Li, Feng

    2016-12-13

    A solution-processed near-infrared (NIR) organic phototransistor (OPT) based on n-type organic small molecular material BODIPY-BF2 has been successfully fabricated. Its unprecedented performance, as well as its easy fabrication and good stability, mark this BODIPY-BF2 based OPT device as a very promising candidate for optoelectronic applications in the NIR regime.

  8. High-Performance Near-Infrared Phototransistor Based on n-Type Small-Molecular Organic Semiconductor

    KAUST Repository

    Li, Feng; Chen, Yin; Ma, Chun; Buttner, Ulrich; Leo, Karl; Wu, Tao

    2016-01-01

    A solution-processed near-infrared (NIR) organic phototransistor (OPT) based on n-type organic small molecular material BODIPY-BF2 has been successfully fabricated. Its unprecedented performance, as well as its easy fabrication and good stability, mark this BODIPY-BF2 based OPT device as a very promising candidate for optoelectronic applications in the NIR regime.

  9. Latest research results on the effects of nanomaterials on humans and the environment: DaNa – Knowledge Base Nanomaterials

    International Nuclear Information System (INIS)

    Marquardt, C; Nau, K; Kühnel, D; Richter, V; Krug, H F; Mathes, B; Steinbach, C

    2013-01-01

    Nanotechnology is considered one of the key technologies of the 21st century. The success of this fascinating technology is based on its versatility. It will bring about fundamental changes of basic research as well as of many sectors of industry and also of daily life from electronics to the health care system. However, consumers often miss reliable and understandable information on nanomaterials and all aspects of this versatile technology. A huge body of data on the potential hazards of nanoobjects towards human and environmental health already exists, but is either not easily accessible for a broad audience or presented unprocessable for nonexperts. But risk communication is an essential and thus integral component of risk management. For that purpose, the DaNa-Project aims at filling this gap by collecting and evaluating scientific results in an interdisciplinary approach with scientists from different research areas, such as human and environmental toxicology, biology, physics, chemistry, and sociology. Research findings from the field of human and environmental nanotoxicology are being prepared and presented together with material properties and possible applications for interested laymen and stakeholders. For the evaluation of literature a 'Literature Criteria Checklist' has been developed as well as a Standard Operation Procedure template (SOP) based on careful scientific practice.

  10. ETBP (Extended True Boiling Point) curve extension of extra heavy crudes; Extensao da curva PEV (Ponto de Ebulicao Verdadeiro) de petroleos extrapesados por destilacao molecular e ampliacao da caracterizacao

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Rodrigo S.; Batistella, Cesar B.; Maciel, Maria Regina W.; Maciel Filho, Rubens [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Faculdade de Engenharia Quimica; Medina, Lilian C. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES)

    2008-07-01

    For the determination of the TBP (True Boiling Point) Curve, which defines the yield of petroleum products, the ASTM D2892 method for petroleum distillation and ASTM D5236 method for vacuum distillation of heavy hydrocarbons were applied. Furthermore, from these distillations, cuts that are submitted to several analyses to determine its physical-chemical properties are obtained, and all this information generates the evaluation of petroleum. For heavy petroleum, these conventional methods have been limited, since the total distilled percentage determined for temperatures up to 565 deg C (maximum reached with ASTM D5236 method) is lower for these oils, reducing the points of the curve, limiting its information. To improve this data set for heavy oils, a methodology for the extension of TBP curve through molecular distillation was established. It was possible to reach values up to 700 deg C, representing a considerable progress for the extension of TBP curve. The objective of this work is to present the results of Extended TBP curve for a heavy petroleum and characterization carried out through the cuts and residues obtained in molecular distillation of the residue 'Zeta' 400 deg C+ (fancy name), made by ASTM D2892 method. (author)

  11. Does size matter? Study of performance of pseudo-ELISAs based on molecularly imprinted polymer nanoparticles prepared for analytes of different sizes.

    Science.gov (United States)

    Cáceres, C; Canfarotta, F; Chianella, I; Pereira, E; Moczko, E; Esen, C; Guerreiro, A; Piletska, E; Whitcombe, M J; Piletsky, S A

    2016-02-21

    The aim of this work is to evaluate whether the size of the analyte used as template for the synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) can affect their performance in pseudo-enzyme linked immunosorbent assays (pseudo-ELISAs). Successful demonstration of a nanoMIPs-based pseudo-ELISA for vancomycin (1449.3 g mol(-1)) was demonstrated earlier. In the present investigation, the following analytes were selected: horseradish peroxidase (HRP, 44 kDa), cytochrome C (Cyt C, 12 kDa) biotin (244.31 g mol(-1)) and melamine (126.12 g mol(-1)). NanoMIPs with a similar composition for all analytes were synthesised by persulfate-initiated polymerisation in water. In addition, core-shell nanoMIPs coated with polyethylene glycol (PEG) and imprinted for melamine were produced in organics and tested. The polymerisation of the nanoparticles was done using a solid-phase approach with the correspondent template immobilised on glass beads. The performance of the nanoMIPs used as replacement for antibodies in direct pseudo-ELISA (for the enzymes) and competitive pseudo-ELISA for the smaller analytes was investigated. For the competitive mode we rely on competition for the binding to the nanoparticles between free analyte and corresponding analyte-HRP conjugate. The results revealed that the best performances were obtained for nanoMIPs synthesised in aqueous media for the larger analytes. In addition, this approach was successful for biotin but completely failed for the smallest template melamine. This problem was solved using nanoMIP prepared by UV polymerisation in an organic media with a PEG shell. This study demonstrates that the preparation of nanoMIP by solid-phase approach can produce material with high affinity and potential to replace antibodies in ELISA tests for both large and small analytes. This makes this technology versatile and applicable to practically any target analyte and diagnostic field.

  12. Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

    Science.gov (United States)

    Fernandes, E.K.K.; Keyser, C.A.; Chong, J.P.; Rangel, D.E.N.; Miller, M.P.; Roberts, D.W.

    2010-01-01

    Aims: The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties. Methods and Results: Molecular-based techniques [AFLP and rDNA (ITS1, ITS2 and 5??8S) gene sequencing] were used to characterize morphologically identified Metarhizium spp. isolates from a wide range of sources. Conidial suspensions of isolates were exposed to wet heat (45 ?? 0??2??C) and plated on potato dextrose agar plus yeast extract (PDAY) medium. After 8-h exposure, the isolates divided clearly into two groups: (i) all isolates of Metarhizium anisopliae var. anisopliae (Ma-an) and Metarhizium from the flavoviride complex (Mf) had virtually zero conidial relative germination (RG), (ii) Metarhizium anisopliae var. acridum (Ma-ac) isolates demonstrated high heat tolerance (c. 70-100% RG). Conidial suspensions also were plated on PDAY and incubated at 5??C for 15 days, during which time RGs for Ma-an and Ma-ac isolates were virtually zero, whereas the two Mf were highly cold active (100% RG). Conclusions: Heat and cold exposures can be used as rapid tools to tentatively identify some important Metarhizium species and varieties. Significance and Impact of the Study: Identification of Metarhizium spp. currently relies primarily on DNA-based methods; we suggest a simple temperature-based screen to quickly obtain tentative identification of isolates as to species or species complexes. ?? 2009 The Society for Applied Microbiology.

  13. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

    Science.gov (United States)

    Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J

    2010-03-01

    PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. PyRosetta is a stand-alone package available at http://www.pyrosetta.org under the Rosetta license which is free for academic and non-profit users. A tutorial, user's manual and sample scripts demonstrating usage are also available on the web site.

  14. Colorimetric test-systems for creatinine detection based on composite molecularly imprinted polymer membranes.

    Science.gov (United States)

    Sergeyeva, T A; Gorbach, L A; Piletska, E V; Piletsky, S A; Brovko, O O; Honcharova, L A; Lutsyk, O D; Sergeeva, L M; Zinchenko, O A; El'skaya, A V

    2013-04-03

    An easy-to-use colorimetric test-system for the efficient detection of creatinine in aqueous samples was developed. The test-system is based on composite molecularly imprinted polymer (MIP) membranes with artificial receptor sites capable of creatinine recognition. A thin MIP layer was created on the surface of microfiltration polyvinylidene fluoride (PVDF) membranes using method of photo-initiated grafting polymerization. The MIP layer was obtained by co-polymerization of a functional monomer (e.g. 2-acrylamido-2-methyl-1-propanesulfonic acid, itaconic acid or methacrylic acid) with N, N'-methylenebisacrylamide as a cross-linker. The choice of the functional monomer was based on the results of computational modeling. The creatinine-selective composite MIP membranes were used for measuring creatinine in aqueous samples. Creatinine molecules were selectively adsorbed by the MIP membranes and quantified using color reaction with picrates. The intensity of MIP membranes staining was proportional to creatinine concentration in an analyzed sample. The colorimetric test-system based on the composite MIP membranes was characterized with 0.25 mM detection limit and 0.25-2.5mM linear dynamic range. Storage stability of the MIP membranes was estimated as at least 1 year at room temperature. As compared to the traditional methods of creatinine detection the developed test-system is characterized by simplicity of operation, small size and low cost. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus.

    Science.gov (United States)

    Lee, Chun-Ching; Liao, Yu-Chieh; Lai, Yu-Hsuan; Lee, Chang-Chun David; Chuang, Min-Chieh

    2015-01-01

    A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.

  16. Molecular characterization of a peanut variety and its derivatives based on SSR and COP analysis

    Institute of Scientific and Technical Information of China (English)

    Xiaoping REN; Boshou LIAO; Huifang JIANG; Zhongyuan YUAN; Yuning CHEN; Xiaojing ZHOU; Li HUANG; Jiaquan HUANG; Yong LEI; Liying YAN

    2016-01-01

    Despite the economic importance of the peanut,no studies have been carried out to determine the correlation between genetic distances based on molecular markers and on coefficient of parentage (COP) data.In this study,simple sequence repeat (SSR) and pedigree data were used to assess the genetic distance between the Fuhuasheng variety and its derivative cultivars.A total of 39 SSR polymorphism primers were used,and 151 bands were obtained,with an average of 2.04 bands in each primer.The genetic SSR-based distance (GD) values ranged from 0.02 to 0.81,while the COP-based GD ranged from 0.25 to 0.98.Certain Fuhuasheng loci displayed higher transmission rates.These loci or nearby chromosomal regions might be associated with desirable traits in Fuhuasheng variety,thus being frequently selected in breeding programs.Therefore,it can be suggested that COP analysis should be the preferred method for estimating genetic diversity invarieties with available complete pedigree information and parents.In this case,marker analysis would provide the best estimations.

  17. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

    Science.gov (United States)

    Chaudhury, Sidhartha; Lyskov, Sergey; Gray, Jeffrey J.

    2010-01-01

    Summary: PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has