Science.gov

Sample records for ao dna em

  1. Telescópio de pequeno porte como suporte ao ensino em cidades com intensa poluição luminosa II

    NASA Astrophysics Data System (ADS)

    Pereira, P. C. R.; Santos-Júnior, J. M.; Cruz, W. S.

    2003-08-01

    Para a maioria dos estudantes, sua passagem pelo ensino formal fundamental envolve a transmissão de fatos que devem ser guardados para um exame, a habilidade para lembrar fórmulas e, eventualmente, a repetição de experimentos que devem produzir resultados exigidos pelo professor. O resultado deste modelo de ensino, ao longo dos anos, é conhecido por todos: desconhecimento e descontentamento, por parte dos estudantes, de temas relativos ao papel e aos processos da ciência. Acreditamos que a Astronomia, pelo seu caráter observacional, é uma das áreas do conhecimento que pode contribuir neste cenário. A Fundação Planetário da Cidade do Rio de Janeiro possui um telescópio Meade LX-200 (25cm) que, juntamente com as câmeras CCD ST-7E e ST8E, tem sido utilizado em projetos voltados aos estudantes do ensino médio desde o ano 2000. Tais projetos envolvem a condução de um projeto de pesquisa observacional num nível apropriado, e possibilitam o contato com técnicas e novas tecnologias: computador, software para manipulação de dados e gráficos, programas de tratamento e redução de dados, uso de equipamentos óptico-eletrônicos (telescópio e CCD), bem como o processo de aquisição de conhecimento. Dentro da proposta dos anos anteriores, priorizamos projetos de uma noite, ou seja, procuramos trabalhar com fenômenos que apresentem variabilidade com intervalo de recorrência relativamente curto. Em todos os casos, optamos pela fotometria diferencial, que tem se mostrado bastante eficiente para o céu luminoso como o da cidade do Rio de Janeiro. Neste painel, apresentamos alguns dos projetos desenvolvidos no último ano, com 25 estudantes. Apresentamos os resultados da observação da variável pulsante AI Vel (V = 6,6) e da variável cataclísmica FO Aqr (V = 13,5), e do monitoramento do trânsito da lua de Júpiter, Europa, ocorrido em 30 de abril de 2003. As curvas de luz produzidas para as primeiras estão concordantes com as da literatura, assim

  2. Aquecimento alfvênico viscoso-resistivo em discos de acresção ao redor de estrelas T Tauri clássicas

    NASA Astrophysics Data System (ADS)

    Santana, W. M.; Vasconcelos, M. J.

    2003-08-01

    Com a crescente disponibilidade de dados observacionais sobre estrelas T Tauri, a busca por modelos mais precisos vem se tornando cada vez maior. Estes modelos devem explicar, entre outras coisas, o mecanismo dissipativo responsável pelo transporte de momento angular no disco de acresção que acredita-se, circunda estas estrelas. O mecanismo mais viável, do ponto de vista teórico, é uma instabilidade MHD conhecida como "instabilidade magnetorotacional ou Balbus-Hawley" (IBH). Esta instabilidade veio mostrar que o campo magnético desempenha um papel importante na evolução destes objetos mas requer, no entanto, um acoplamento mínimo entre o gás e o campo magnético no disco que não é atingido para os valores de temperatura obtidos do modelo padrão. Contudo, alguns mecanismos de aquecimento para o disco precisam ser examinados. Neste trabalho, propomos a dissipação de ondas Alfvén como uma fonte de aquecimento para o disco. Se o gás apresentar uma condutividade elétrica finita e viscosidade, teremos um tipo de amortecimento para as ondas denominado amortecimento viscoso-resistivo que será aqui considerado. Este mecanismo é aplicado ao modelo de disco em camadas. Calculam-se as taxas de aquecimento Alfvênico, a temperatura efetiva do disco bem como as taxas de ionização decorrentes deste aquecimento e do aquecimento gerado pela absorção de raios cósmicos. Comparações com os dados observacionais de Kitamura et. al. (2001) são efetuadas, ressaltando-se os pontos comuns entre suas observações e nossos dados teóricos.

  3. AO Camelopardalis

    NASA Astrophysics Data System (ADS)

    Milone, E. F.; Piggott, D. H.; Morris, S. L.

    1982-04-01

    The first UBV light curves of the system AO Cam are presented, and reveal a W UMa light curve with a period of 0.329917 days. Fourier coefficients for the full B and V light curves were used to place approximate empirical limits on the 75-80 deg inclination, fill-out parameter of approximately 0.8, and mass-ratio in the 0.7-0.8 range, following the methods of Rucinski (1973, 1974). The spectral type of the system is about G5.

  4. Uranyl acetate induces hprt mutations and uranium-DNA adducts in Chinese hamster ovary EM9 cells.

    PubMed

    Stearns, Diane M; Yazzie, Monica; Bradley, Andrew S; Coryell, Virginia H; Shelley, Jake T; Ashby, Adam; Asplund, Craig S; Lantz, R Clark

    2005-11-01

    Questions about possible adverse health effects from exposures to uranium have arisen as a result of uranium mining, residual mine tailings and use of depleted uranium in the military. The purpose of the current study was to measure the toxicity of depleted uranium as uranyl acetate (UA) in mammalian cells. The activity of UA in the parental CHO AA8 line was compared with that in the XRCC1-deficient CHO EM9 line. Cytotoxicity was measured by clonogenic survival. A dose of 200 microM UA over 24 h produced 3.1-fold greater cell death in the CHO EM9 than the CHO AA8 line, and a dose of 300 microM was 1.7-fold more cytotoxic. Mutagenicity at the hypoxanthine (guanine) phosphoribosyltransferase (hprt) locus was measured by selection with 6-thioguanine. A dose of 200 microM UA produced approximately 5-fold higher averaged induced mutant frequency in the CHO EM9 line relative to the CHO AA8 line. The generation of DNA strand breaks was measured by the alkaline comet assay at 40 min and 24 h exposures. DNA strand breaks were detected in both lines; however a dose response may have been masked by U-DNA adducts or crosslinks. Uranium-DNA adducts were measured by inductively coupled plasma optical emission spectroscopy (ICP-OES) at 24 and 48 h exposures. A maximum adduct level of 8 U atoms/10(3) DNA-P for the 300 microM dose was found in the EM9 line after 48 h. This is the first report of the formation of uranium-DNA adducts and mutations in mammalian cells after direct exposure to a depleted uranium compound. Data suggest that uranium could be chemically genotoxic and mutagenic through the formation of strand breaks and covalent U-DNA adducts. Thus the health risks for uranium exposure could go beyond those for radiation exposure. PMID:16195314

  5. Compilação de dados atômicos e moleculares do UV ao IV próximo para uso em síntese espectral

    NASA Astrophysics Data System (ADS)

    Coelho, P.; Barbuy, B.; Melendez, J.; Allen, D. M.; Castilho, B.

    2003-08-01

    Espectros sintéticos são utéis em uma grande variedade de aplicações, desde análise de abundâncias em espectros estelares de alta resolução ao estudo de populações estelares em espectros integrados. A confiabilidade de um espectro sintético depende do modelo de atmosfera adotado, do código de formação de linhas e da qualidade dos dados atômicos e moleculares que são determinantes no cálculo das opacidades da fotosfera. O nosso grupo no departamento de Astronomia no IAG tem utilizado espectros sintéticos há mais de 15 anos, em aplicações voltadas principalmente para a análise de abundâncias de estrelas G, K e M e populações estelares velhas. Ao longo desse tempo, as listas de linhas vieram sendo construídas e atualizadas continuamente, e alguns acréscimos recentes podem ser citados: Castilho (1999, átomos e moléculas no UV), Schiavon (1998, bandas moleculares de TiO) e Melendez (2001, átomos e moléculas no IV próximo). Com o intuito de calcular uma grade de espectros do UV ao IV próximo para uso no estudo de populações estelares velhas, se fazia necessário compilar e homogeneizar as diversas listas em apenas uma lista atômica e uma molecular. Nesse processo, a nova lista compilada foi correlacionada com outras bases de dados (NIST, Kurucz Database, O' Brian et al. 1991) para atualização dos parâmetros que caracterizam a transição atômica (comprimento de onda, log gf e potencial de excitação). Adicionalmente as constantes de interação C6 foram calculadas segundo a teoria de Anstee & O'Mara (1995) e artigos posteriores. As bandas moleculares de CH e CN foram recalculadas com o programa LIFBASE (Luque & Crosley 1999). Nesse poster estão detalhados os procedimentos citados acima, as comparações entre espectros calculados com as novas listas e espectros observados em alta resolução do Sol e de Arcturus, e uma análise do impacto decorrente da utilização de diferentes modelos de atmosfera no espectro sintético. Ao

  6. Cometas: Das Lendas aos Fatos

    NASA Astrophysics Data System (ADS)

    Voelzke, M. R.

    O descobrimento de cometas, devido ao seu aparecimento espetacular, tem registro nas mais antigas culturas humanas. A primeira referência situa-se no ano de 1095 antes de Cristo [a.C.; HO; HO, 1962]. A quantidade de registros de descobrimentos cometários, principalmente provenientes do território chinês em particular e do oriente em geral, aumentou gradualmente a partir do quarto século depois de Cristo (d.C.). É de origem chinesa a primeira referência ao cometa P/Halley no ano de 240 a.C. [VOELZKE, 1993]. Com o desenvolvimento da astronomia relativamente às técnicas observacionais os descobrimentos bem como as observações cometárias aumentaram sensivelmente a partir do século XVII, sendo que a partir do século XIX um novo incremento ocorreu devido ao emprego da fotografia e a resultante melhora de sensibilidade na observação.

  7. Connectivity across the Caribbean Sea: DNA barcoding and morphology unite an enigmatic fish larva from the Florida straits with a new species of sea bass from deep reefs off Curaçao.

    PubMed

    Baldwin, Carole C; Johnson, G David

    2014-01-01

    Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern-most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon. PMID:24825118

  8. Connectivity across the Caribbean Sea: DNA Barcoding and Morphology Unite an Enigmatic Fish Larva from the Florida Straits with a New Species of Sea Bass from Deep Reefs off Curaçao

    PubMed Central

    Baldwin, Carole C.; Johnson, G. David

    2014-01-01

    Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern–most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon. PMID:24825118

  9. Numerical Methods in Electromagnetics: Evanescent Nanometry for DNA Sequencing, and EM Induction for UXO Detection and Discrimination

    NASA Astrophysics Data System (ADS)

    Bijamov, Alex

    The main goals of this work are to extend forward and apply inverse EM numerical methods to enhance the fundamental understanding of ultra-wideband frequency range EM fields in complex geometries. The particular emphases are made on medical device development for whole human genome sequencing using force spectroscopy; and underwater target detection, and live sites UXO discrimination. Force spectroscopy is a powerful technique used to manipulate single biomolecules and study their interactions. In these experiments one end of a macromolecule is immobilized on a substrate, while its free end is attached to an externally-manipulated microscopic bead. Crucial to the application of force spectroscopy to DNA sequencing is the ability to apply pulling forces reaching hundreds of pico-Newtons and image molecular extensions with sub-nanometer resolution. To achieve both goals the behavior of EM fields in the vicinity of the beads and the associated far fields need to be investigated using numerical simulations. In recent years our group has developed a numerical technique---the Method of Auxiliary Sources---which was modified here for these problems. In this work the physics of bead scattering and fluorescent responses is studied for a variety of bead and substrate compositions and geometries, including layered structures, to understand their potential in increasing imaging sensitivity. This thesis also studies the inversion problems related to the underwater UXO detection and live-site UXO discrimination. Rigorous analysis of underlying physics of low-frequency EM field scattering from conducting objects in underwater environments is performed. The effects of seawater surface roughness on transmitted EM signals and the associated noise levels are analyzed. A new, magnetic field-based geolocation system is studied numerically for GPS-denied underwater environments. Finally, the performances of statistical and machine learning methods are analyzed for automatic

  10. Retinal AO OCT

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Miller, Donald T.

    The last two decades have witnessed extraordinary advances in optical technology to image noninvasively and at high resolution the posterior segment of the eye. Two of the most impactful technological advancements over this period have arguably been optical coherence tomography (OCT) and adaptive optics (AO). The strengths of these technologies complement each other and when combined have been shown to provide unprecedented, micron-scale resolution (<3 μm) in all three dimensions and sensitivity to image the cellular retina in the living eye. This powerful extension of OCT, that is AO-OCT, is the focus of this chapter. It presents key aspects of designing and implementing AO-OCT systems. Particular attention is devoted to the relevant optical properties of the eye that ultimately define these systems, AO componentry and operation tailored for ophthalmic use, and of course use of the latest technologies and methods in OCT for ocular imaging. It surveys the wide range of AO-OCT designs that have been developed for retinal imaging, with AO integrated into every major OCT design configuration. Finally, it reviews the scientific and clinical studies reported to date that show the exciting potential of AO-OCT to image the microscopic retina and fundus in ways not previously possible with other noninvasive methods and a look to future developments in this rapidly growing field.

  11. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  12. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  13. AO Group Annual Report

    SciTech Connect

    Olivier, S

    2005-10-04

    The Adaptive Optics (AO) Group in I Division develops and tests a broad range of advanced wavefront control technologies. Current applications focus on: Remote sensing, High power lasers, Astronomy, and Human vision. In the area of remote sensing, the AO Group leads a collaborative effort with LLNL's Nonproliferation, Arms Control & International Security (NAI) Directorate on Enhanced Surveillance Imaging. The ability to detect and identify individual people or vehicles from long-range is an important requirement for proliferation detection and homeland security. High-resolution imaging along horizontal paths through the atmosphere is limited by turbulence, which blurs and distorts the image. For ranges over {approx}one km, visible image resolution can be reduced by over an order of magnitude. We have developed an approach based on speckle imaging that can correct the turbulence-induced blurring and provide high resolution imagery. The system records a series of short exposure images which freeze the atmospheric effects. We can then estimate the image magnitude and phase using a bispectral estimation algorithm which cancels the atmospheric effects while maintaining object information at the diffraction limit of the imaging system.

  14. cryo-EM structures of the E. coli replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and τ

    PubMed Central

    Fernandez-Leiro, Rafael; Conrad, Julian; Scheres, Sjors HW; Lamers, Meindert H

    2015-01-01

    The replicative DNA polymerase PolIIIα from Escherichia coli is a uniquely fast and processive enzyme. For its activity it relies on the DNA sliding clamp β, the proofreading exonuclease ε and the C-terminal domain of the clamp loader subunit τ. Due to the dynamic nature of the four-protein complex it has long been refractory to structural characterization. Here we present the 8 Å resolution cryo-electron microscopy structures of DNA-bound and DNA-free states of the PolIII-clamp-exonuclease-τc complex. The structures show how the polymerase is tethered to the DNA through multiple contacts with the clamp and exonuclease. A novel contact between the polymerase and clamp is made in the DNA bound state, facilitated by a large movement of the polymerase tail domain and τc. These structures provide crucial insights into the organization of the catalytic core of the replisome and form an important step towards determining the structure of the complete holoenzyme. DOI: http://dx.doi.org/10.7554/eLife.11134.001 PMID:26499492

  15. The effect of hyperthermia on DNA in mouse HepA cells--an analysis with computer and observation with EM.

    PubMed

    Yu, D; Liu, R; Zhou, J; Liu, Y

    2000-01-01

    A computer analysis system, automated imaging cytometry (AIC), flow cytometry (FCM) and EM, were used to study the relationship of apoptosis and the change of DNA in mouse HepA cells subjected to hyperthermia. Our results showed that pyknotic rate in the 44 degrees C group was significantly increased (P < 0.01) when compared with that in the 37 degrees C group, both the diploid rate and aneuploid rate in the 44 degrees C group were significantly decreased (P < 0.01) when compared with that in the 37 degrees C group. The pyknotic rate determined by ALC was in conformity with the apoptotic index (AI) determined by FCM. Under EM, ultrastructures of HapA cells appeared typical apoptosis changes in the 44 degrees C group. We are led to conclude that (1) when the temperature is 42 degrees C or 44 degrees C for 2 h, it did not promote the necrosis of HepA cells; (2) when the temperature is 42 degrees C for 2 h, it did not obviously induce the apoptosis of HepA cells, and the 44 degrees C for 2 h obviously induced the apoptosis of HepA cells; (3) AIC method can be used as an aid for the measurement of apoptotic index. Further study is needed to established it as a novel, simple and convenient method for determining the apoptosis. PMID:12840908

  16. MEMS AO for Planet Finding

    NASA Technical Reports Server (NTRS)

    Rao, Shanti; Wallace, J. Kent; Shao, Mike; Schmidtlin, Edouard; Levine, B. Martin; Samuele, Rocco; Lane, Benjamin; Chakrabarti, Supriya; Cook, Timothy; Hicks, Brian; Jung, Paul

    2008-01-01

    This slide presentation reviews a method for planet finding using microelectromechanical systems (MEMS) Adaptive Optics (AO). The use of a deformable mirror (DM) is described as a part of the instrument that was designed with a nulling interferometer. The strategy that is used is described in detail.

  17. Aperture masking behind AO systems

    NASA Astrophysics Data System (ADS)

    Ireland, Michael J.

    2012-07-01

    Sparse Aperture-Mask Interferometry (SAM or NRM) behind Adaptive Optics (AO) has now come of age, with more than a dozen astronomy papers published from several 5-10m class telescopes around the world. I will describe the reasons behind its success in achieving relatively high contrasts ( 1000:1 at lambda/ D) and repeatable binary astronomy at the diffraction limit, even when used behind laser-guide star adaptive optics. Placed within the context of AO calibration, the information in an image can be split into pupil-plane phase, Fourier amplitude and closure-phase. It is the closure-phase observable, or its generalisation to Kernel phase, that is immune to pupil-plane phase errors at first and second-order and has been the reason for the technique's success. I will outline the limitations of the technique and the prospects for aperture-masking and related techniques in the future.

  18. Difficulties of First Years Elementary School Teachers with the Teaching of Astronomy. (Breton Title: Dificuldades de Professores dos Anos Iniciais do Ensino Fundamental em Relação ao Ensino da Astronomia. ) Dificultades de LOS Profesores de los Primeros Años de la Escuela Primaria en Relación a la Enseñanza de la Astronomía

    NASA Astrophysics Data System (ADS)

    Langhi, Rodolfo; Nardi, Roberto

    2005-12-01

    This paper reports Primary School teachers' discourses analysis about their difficulties related to the teaching of Astronomy. It reports partial data of a master's level research carried out in the last two years, named "An exploratory study for inserting Astronomy in primary school teachers' education" (LANGHI, 2004). The study took into consideration students' and teachers' common sense conceptions about astronomical phenomena, conceptual mistakes in textbooks, and Astronomy's suggestions given by the PCN (Parâmetros Curriculares Nacionais - The Brazilian National Curriculum Standards). The paper aims to characterize teachers' difficulties, in order to provide subsides to the implementation of an initial or continuing education program. This study is justified by the fact that courses plans like these only will be adapted to the teacher's (and students') reality, if there is a primary investigation about what the teachers really need to know about Astronomy. This fact was possible here by the enunciations interpretation of a teachers' sample using semi-structured interviews, according to discourse analysis procedures. The research outcomes show difficulties related to factors like: those of personal order, methodological, on teacher's formation, educational infrastructure and other related to information sources for educators. Este artigo, que relata as dificuldades de professores em relação ao ensino da Astronomia, faz parte de um estudo exploratório para a inserção da Astronomia na formação de professores dos anos iniciais do Ensino Fundamental. Esse estudo leva em consideração as concepções alternativas de alunos e professores sobre fenômenos astronômicos, os erros conceituais em livros didáticos e as sugestões de conteúdos de Astronomia constantes nos PCN (Parâmetros Curriculares Nacionais). Caracterizar as dificuldades dos professores é a questão central deste texto, apontando para o objetivo de contribuir com subsídios para um futuro

  19. Difficulties of First Years Elementary School Teachers with the Teaching of Astronomy. (Breton Title: Dificuldades de Professores dos Anos Iniciais do Ensino Fundamental em Relação ao Ensino da Astronomia. ) Dificultades de LOS Profesores de los Primeros Años de la Escuela Primaria en Relación a la Enseñanza de la Astronomía

    NASA Astrophysics Data System (ADS)

    Langhi, Rodolfo; Nardi, Roberto

    2005-12-01

    This paper reports Primary School teachers' discourses analysis about their difficulties related to the teaching of Astronomy. It reports partial data of a master's level research carried out in the last two years, named "An exploratory study for inserting Astronomy in primary school teachers' education" (LANGHI, 2004). The study took into consideration students' and teachers' common sense conceptions about astronomical phenomena, conceptual mistakes in textbooks, and Astronomy's suggestions given by the PCN (Parâmetros Curriculares Nacionais - The Brazilian National Curriculum Standards). The paper aims to characterize teachers' difficulties, in order to provide subsides to the implementation of an initial or continuing education program. This study is justified by the fact that courses plans like these only will be adapted to the teacher's (and students') reality, if there is a primary investigation about what the teachers really need to know about Astronomy. This fact was possible here by the enunciations interpretation of a teachers' sample using semi-structured interviews, according to discourse analysis procedures. The research outcomes show difficulties related to factors like: those of personal order, methodological, on teacher's formation, educational infrastructure and other related to information sources for educators. Este artigo, que relata as dificuldades de professores em relação ao ensino da Astronomia, faz parte de um estudo exploratório para a inserção da Astronomia na formação de professores dos anos iniciais do Ensino Fundamental. Esse estudo leva em consideração as concepções alternativas de alunos e professores sobre fenômenos astronômicos, os erros conceituais em livros didáticos e as sugestões de conteúdos de Astronomia constantes nos PCN (Parâmetros Curriculares Nacionais). Caracterizar as dificuldades dos professores é a questão central deste texto, apontando para o objetivo de contribuir com subsídios para um futuro

  20. Isolation and characterization of a novel bacterium, Sphingomonas bisphenolicum strain AO1, that degrades bisphenol A.

    PubMed

    Oshiman, Ko-ichi; Tsutsumi, Yuji; Nishida, Tomoaki; Matsumura, Yoshinobu

    2007-04-01

    Bisphenol A (2,2-bis(4-hydroxyphenyl) propane, BPA), which is used as a synthetic resin material or a plasticizer, is a pollutant that possesses endocrine-disrupting activity. Bioremediation of BPA is used to decrease its polluting effects, and here we report a novel bacterial strain AO1, which is able to degrade BPA. This strain was isolated using enrichment cultivation from a soil sample from a vegetable-growing field; the sample was one of 500 soil samples collected across Japan. Strain AO1 degraded 100 mg/l BPA to an undetectable level within 6 h in MYPG medium (containing malt extract, yeast extract, peptone, and glucose) and within 48 h in minimum medium containing 1% glucose at 30 degrees C. Strain AO1 can utilize BPA as a sole source of carbon and as an energy source under aerobic conditions. The estrogenic activity of BPA in MYPG medium was ultimately reduced by strain AO1, although the activity initially increased. Taxonomical analysis showed that strain AO1 is closely related to Sphingomonas chlorophenolicum and S. herbicidovorans, neither of which have a capacity for BPA degradation. DNA-DNA hybridization showed that strain AO1 is a novel species of the Sphingomonas genus, and we designated AO1 as S. bisphenolicum. PMID:16821103

  1. The Universe in a Box: Introduction to the Study of Astronomy in the Initial Formation of Physics Teachers. (Spanish Title: El Universo Representado en Una Caja: Introducción al Estudio de la Astronomía en la Formación Inicial de Profesores de Física.) O Universo Representado em Uma Caixa: Introdução ao Estudo da Astronomia NA Formação Inicial de Professores de Física

    NASA Astrophysics Data System (ADS)

    Longhini, Marcos Daniel

    2009-07-01

    This is a report of an activity of introduction to the study of Astronomy developed with a group of future Physics teachers at a Brazilian public university. Such activity had the goal of giving privileged emphasis to notions of spatiality, alternative conceptions of the participants and the process of interaction among peers, and consisted of the representation, in a three dimensional space, of the models of the universe that the participants had. The results, which were categorized as miscellaneous, geocentric, heliocentric and acentric models of the universe, were qualitatively analyzed. Analyses of the activity in the perspective of the participants are indicated and additional considerations are made regarding its use as a resource for teaching Astronomy and for teacher training. Este es el informe de una actividad para presentar un estudio introductorio de la Astronomía, desarrollado con una clase de futuros profesores de física en una universidad pública brasileña. Esta actividad tuvo como objetivo centrar las nociones de espacialidad, las concepciones alternativas de los participantes y el proceso de interacción entre pares, y consistió en la representación en un espacio tridimensional, de los modelos del universo que los participantes habían. Los resultados, que se clasificaron en universo miscelania, geocéntrico, heliocéntrico y acentrico, se analizaron cualitativamente. Son identificadas análisis de la actividad por los participantes, e hizo observaciones sobre su uso como recurso para la enseñanza de la astronomía y la formación de docentes. Trata-se do relato de uma atividade de introdução ao estudo da Astronomia, desenvolvida com uma turma de futuros professores de Física, em uma universidade pública brasileira. Tal atividade teve como meta privilegiar noções de espacialidade, as concepções alternativas dos participantes e o processo de interação entre pares e constou da representação, em um espaço tridimensional, dos

  2. Aerosol Observing System (AOS) Handbook

    SciTech Connect

    Jefferson, A

    2011-01-17

    The Aerosol Observing System (AOS) is a suite of in situ surface measurements of aerosol optical and cloud-forming properties. The instruments measure aerosol properties that influence the earth’s radiative balance. The primary optical measurements are those of the aerosol scattering and absorption coefficients as a function of particle size and radiation wavelength and cloud condensation nuclei (CCN) measurements as a function of percent supersaturation. Additional measurements include those of the particle number concentration and scattering hygroscopic growth. Aerosol optical measurements are useful for calculating parameters used in radiative forcing calculations such as the aerosol single-scattering albedo, asymmetry parameter, mass scattering efficiency, and hygroscopic growth. CCN measurements are important in cloud microphysical models to predict droplet formation.

  3. The triple system AO Monocerotis

    NASA Astrophysics Data System (ADS)

    Wolf, M.; Kučáková, H.; Hynek, T.; Melcer, L. Å.

    2010-05-01

    The variable star AO Mon is a relatively bright but seldom investigated early-type eccentric eclipsing binary. Thirty new eclipses were measured as a part of our long-term observational project or derived from previous measurements. Based on a new solution of the current O-C diagram, we found for the first time a rapid apsidal advance superimposed with a light-time effect caused by a third unseen body in the system. Their short periods are 33.8 years and 3.6 years for the apsidal motion and the third-body circular orbit, respectively. The observed internal structure constant was derived to be log k2, obs = -2.23, which is close to the theoretically expected value. The relativistic as well as the third-body effects on the apsidal advance are negligible, as they are only about 3% of the total apsidal motion rate. Partly based on observations secured at the South African Astronomical Observatory, Sutherland, South Africa, in April 2004.

  4. The Magellan Telescope adaptive secondary AO system

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Gasho, Victor; Kopon, Derek; Hinz, Phil M.; Hoffmann, William F.; Uomoto, Alan; Hare, Tyson

    2008-07-01

    The Magellan Clay telescope is a 6.5m Gregorian telescope located in southern Chile at Las Campanas Observatory. The Gregorian design allows for an adaptive secondary mirror that can be tested off-sky in a straight-forward manner. We have fabricated a 85 cm diameter aspheric adaptive secondary with our subcontractors and partners. This secondary has 585 actuators with <1 msec response times. The chopping adaptive secondary will allow low emissivity AO science. We will achieve very high Strehls (~98%) in the Mid-IR AO (8-26 microns) with the BLINC/MIRAC4 Mid-IR science camera. This will allow the first "super-resolution" and nulling Mid-IR studies of dusty southern objects. We will employ a high order (585 mode) pyramid wavefront sensor similar to that used in the Large Binocular Telescope AO systems. The relatively high actuator count will allow modest Strehls to be obtained in the visible (~0.8μm). Our visible light AO (Vis AO) science camera is fed by an advanced ADC and beamsplitter piggy-backed on the WFS optical table. The system science and performance requirements, and an overview the design, interface and schedule for the Magellan AO system are presented here.

  5. Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008

    SciTech Connect

    Morgan, William F; Kovalchuk, Olga; Dolinoy, Dana C; Dubrova, Yuri E; Coleman, Matthew A; Schär, Primo; Pogribny, Igor; Hendzel, Michael

    2010-02-19

    The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.

  6. Into the blue: AO science with MagAO in the visible

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Males, Jared R.; Follette, Katherine B.; Hinz, Phil; Morzinski, Katie; Wu, Ya-Lin; Kopon, Derek; Riccardi, Armando; Esposito, Simone; Puglisi, Alfio; Pinna, Enrico; Xompero, Marco; Briguglio, Runa; Quiros-Pacheco, Fernando

    2014-08-01

    We review astronomical results in the visible (λ<1μm) with adaptive optics. Other than a brief period in the early 1990s, there has been little astronomical science done in the visible with AO until recently. The most productive visible AO system to date is our 6.5m Magellan telescope AO system (MagAO). MagAO is an advanced Adaptive Secondary system at the Magellan 6.5m in Chile. This secondary has 585 actuators with < 1 msec response times (0.7 ms typically). We use a pyramid wavefront sensor. The relatively small actuator pitch (~23 cm/subap) allows moderate Strehls to be obtained in the visible (0.63-1.05 microns). We use a CCD AO science camera called "VisAO". On-sky long exposures (60s) achieve <30mas resolutions, 30% Strehls at 0.62 microns (r') with the VisAO camera in 0.5" seeing with bright R < 8 mag stars. These relatively high visible wavelength Strehls are made possible by our powerful combination of a next generation ASM and a Pyramid WFS with 378 controlled modes and 1000 Hz loop frequency. We'll review the key steps to having good performance in the visible and review the exciting new AO visible science opportunities and refereed publications in both broad-band (r,i,z,Y) and at Halpha for exoplanets, protoplanetary disks, young stars, and emission line jets. These examples highlight the power of visible AO to probe circumstellar regions/spatial resolutions that would otherwise require much larger diameter telescopes with classical infrared AO cameras.

  7. Characterization of an AO-OCT system

    SciTech Connect

    Evans, J W; Zawadzki, R J; Jones, S; Olivier, S; Werner, J S

    2007-07-26

    Adaptive optics (AO) and optical coherence tomography (OCT) are powerful imaging modalities that, when combined, can provide high-volumetric-resolution, images of the retina. The AO-OCT system at UC Davis has been under development for 2 years and has demonstrated the utility of this technology for microscopic, volumetric, in vivo retinal imaging [1]. The current system uses an AOptix bimorph deformable mirror (DM) for low-order, high-stroke correction [2] and a 140-actuator Boston Micromachines DM for high-order correction [3]. We are beginning to investigate the potential for increasing the image contrast in this system using higher-order wavefront correction. The first step in this analysis is to quantify the residual wavefront error (WFE) in the current system. Developing an error budget is a common tool for improved performance and system design in astronomical AO systems [4, 5]. The process for vision science systems is also discussed in several texts e.g. [6], but results from this type of analysis have rarely been included in journal articles on AO for vision science. Careful characterization of the AO system will lead to improved performance and inform the design of a future high-contrast system. In general, an AO system error budget must include an analysis of three categories of residual WFE: errors in measuring the phase, errors caused by limitations of the DM(s), and errors introduced by temporal variation. Understanding the mechanisms and relative size of these errors is critical to improving system performance. In this paper we discuss the techniques for characterizing these error sources in the AO-OCT system. It is useful to first calculate an error budget for the simpler case using a model eye, and then add the additional errors introduced for the case of a human subject. Measurement error includes calibration error, wavefront sensor (WFS) CCD noise, and sampling errors. Calibration errors must be measured by an external system. Typically this

  8. The Subaru Coronagraphic Extreme AO Project

    NASA Astrophysics Data System (ADS)

    Martinache, Frantz; Guyon, O.; Lozi, J.; Tamura, M.; Hodapp, K.; Suzuki, R.; Hayano, Y.; McElwain, M. W.

    2009-01-01

    While the existence of large numbers of extrasolar planets around solar type stars has been unambiguously demonstrated by radial velocity, transit and microlensing surveys, attempts at direct imaging with AO-equipped large telescopes remain unsuccessful. Because they supposedly offer more favorable contrast ratios, young systems consitute prime targets for imaging. Such observations will provide key insights on the formation and early evolution of planets and disks. Current surveys are limited by modest AO performance which limits inner working angle to 0.2", and only reach maximum sensitivity outside 1". This translates into orbital distances greater than 10 AU even on most nearby systems, while only 5 % of the known exoplanets have a semimajor axis greater than 10 AU. This calls for a major change of approach in the techniques used for direct imaging of the direct vicinity of stars. A sensible way to do the job is to combine coronagraphy and Extreme AO. Only accurate and fast control of the wavefront will permit the detection of high contrast planetary companions within 10 AU. The SCExAO system, currently under assembly, is an upgrade of the HiCIAO coronagraphic differential imaging camera, mounted behind the 188-actuator curvature AO system on Subaru Telescope. This platform includes a 1000-actuator MEMS deformable mirror for high accuracy wavefront correction and a PIAA coronagraph which delivers high contrast at 0.05" from the star (5 AU at 100 pc). Key technologies have been validated in the laboratory: high performance wavefront sensing schemes, spider vanes and central obstruction removal, and lossless beam apodization. The project is designed to be highly flexible to continuously integrate new technologies with high scientific payoff. Planned upgrades include an integral field unit for spectral characterization of planets/disks and a non-redundant aperture mask to push the performance of the system toward separations less than lambda/D.

  9. Experimental comparison of Wide Field AO control schemes using the Homer AO bench.

    NASA Astrophysics Data System (ADS)

    Parisot, Amélie; Petit, Cyril; Fusco, Thierry

    2011-09-01

    Wide Field Adaptive Optics (WFAO) concepts, such as Laser Tomography AO (LTAO) or Multi-Conjugate AO (MCAO) have been developed in order to overcome the anisoplanatism limit of classical AO. Most of the future AO-assisted instruments of ELTs rely on such concepts which have raised critical challenges such as tomographic estimation and from laser and natural guide star combined with efficient DM(s) control. In that context, the experimental validation of the various clever control solutions proposed by several teams in the past years is now essential to reach a level of maturity compatible with their implementation in future WFAO developments for ELT. The ONERA wide field AO facility (HOMER bench) has been developed for these very issues. Gathering a 3D turbulence generator, laser and natural guide stars, two deformable mirrors with variable altitude positions and a PC-based flexible and user-friendly RTC , HOMER allows the implementation and comparison of control schemes from the simplest least-square to the optimal Linear Quadratic Gaussian solutions including Virtual DM and Pseudo-closed loop approaches. After a description of the bench internal calibrations and ultimate performance, all the control schemes are compared experimentally. Their evolutions as a function of wavefront sensors SNR as well as their robustness to calibration / model errors are particularly emphasised. Finally, we derive from the previous works some specific calibrations and identifications procedures ensuring both robustness and efficiency of WFAO systems and we extrapolate their applications to the future ELT AO systems.

  10. MEMS DM development at Iris AO, Inc.

    NASA Astrophysics Data System (ADS)

    Helmbrecht, Michael A.; He, Min; Kempf, Carl J.; Besse, Marc

    2011-03-01

    Iris AO is actively developing piston-tip-tilt (PTT) segmented MEMS deformable mirrors (DM) and adaptive optics (AO) controllers for these DMs. This paper discusses ongoing research at Iris AO that has advanced the state-of-the-art of these devices and systems over the past year. Improvements made to open-loop operation and mirror fabrication enables mirrors to open-loop flatten to 4 nm rms. Additional testing of an anti snap-in technology was conducted and demonstrates that the technology can withstand 100 million snap-in events without failure. Deformable mirrors with dielectric coatings are shown that are capable of handling 630 W/cm2 of incident laser power. Over a localized region on the segment, the dielectric coatings can withstand 100kW/cm2 incident laser power for 30 minutes. Results from the first-ever batch of PTT489 DMs that were shipped to pilot customers are reported. Optimizations made to the open-loop PTT controller are shown to have latencies of 157.5 μs and synchronous array update rates of nearly 6.5 kHz. Finally, plans for the design and fabrication of the next-generation PTT939 DM are presented.

  11. Into the Blue: AO Science in the Visible with MagAO

    NASA Astrophysics Data System (ADS)

    Close, Laird; Males, Jared; Morzinski, Katie; Kopon, Derek; Follette, Kate; Rodigas, Timothy; Hinz, Philip; Wu, Ya-Lin; Puglisi, Alfio; Esposito, Simone; Riccardi, Armando; Pinna, Enrico; Xompero, Marco; Briguglio, Runa; Uomoto, Alan; Hare, Tison

    2013-12-01

    The Magellan Clay telescope is a 6.5m Gregorian telescope located in Chile at Las Campanas Observatory. We have fabricated an 85 cm diameter aspheric adaptive secondary with our subcontractors and partners, MagAO passed acceptance tests in spring 2012, and the entire System was commissioned from Nov 17 to Dec 7, 2012. This secondary has 585 actuators with < 1 msec response times (0.7 ms typically). We fabricated a high order (585 mode) pyramid wavefront sensor (similar to that of LBT's FLAO). The relatively high actuator count allows moderate Strehls to be obtained in the visible (0.63-1.05 microns). We have built an CCD science camera called "jVisAO". On-sky long exposures (60s) achieve 30% Strehls at 0.62 microns (r') with the VisAO camera in 0.5" seeing with bright R < 8 mag stars. These relatively high optical wavelength Strehls are made possible by our powerful combination of a next generation ASM and a Pyramid WFS with 200-400 controlled modes and 1000 Hz loop frequencies. To minimize non-common path errors and enable visible AO the VisAO science camera is fed by an advanced triplet ADC and is piggy-backed on the WFS optical board itself. Despite the ability to make 25 mas images we still have ~4 mas of resolution loss to residual vibrations. We will discuss what the most difficult aspects are for visible AO on ELTs scaling from our experience with MagAO.

  12. The first VisAO-fed integral field spectrograph: VisAO IFS

    NASA Astrophysics Data System (ADS)

    Follette, Katherine B.; Close, Laird M.; Kopon, Derek; Males, Jared R.; Gasho, Victor; Brutlag, Kevin M.; Uomoto, Alan

    2010-07-01

    We present the optomechanical design of the Magellan VisAO Integral Field Spectrograph (VisAO IFS), designed to take advantage of Magellan's AO system and its 85.1cm concave ellipsoidal Adaptive Secondary Mirror (ASM). With 585 actuators and an equal number of actively-controlled modes, this revolutionary second generation ASM will be the first to achieve moderate Strehl ratios into the visible wavelength regime. We have designed the VisAO IFS to be coupled to either Magellan's LDSS-3 spectrograph or to the planned facility M2FS fiber spectrograph and to optimize VisAO science. Designed for narrow field-of-view, high spatial resolution science, this lenslet-coupled fiberfed IFS will offer exciting opportunities for scientific advancement in a variety of fields, including protoplanetary disk morphology and chemistry, resolution and spectral classification of tight astrometric binaries, seasonal changes in the upper atmosphere of Titan, and a better understanding of the black hole M-sigma relation.

  13. Testing the VLT AO facility with ASSIST

    NASA Astrophysics Data System (ADS)

    Stuik, Remko; Arsenault, Robin; Boland, Wilfried; Deep, Atul; Delabre, Bernard; Hubin, Norbert; Kolb, Johann; La Penna, Paolo; Molster, Frank; Wiegers, Emiel

    2010-07-01

    The testing and verification of ESO Very Large Telescope Adaptive Optics Facility (VLT-AOF) requires new and innovative techniques to deal with the absence of an intermediate focus on the telescope. ASSIST, The Adaptive Secondary Setup and Instrument STimulator, was developed to provide a testing facility for the ESO AOF and will allow off-telescope testing of three elements of the VLT Adaptive Optics Facility; the Deformable Secondary Mirror (DSM) and the AO systems for MUSE and HAWK-I (GALACSI and GRAAL). ASSIST will provide a full testing environment which includes an interferometric testing mode for the DSM, an on-axis testing mode with a single wavefront sensor and full operation testing modes for both the AO systems. Both natural as well as laser guide stars will be simulated under various asterisms and a realistic turbulent atmosphere will be provided for varying atmospheric conditions. ASSIST passed its final design review and is now being manufactured, integrated and tested and will be operational in mid 2011, in time for first testing with the DSM.

  14. AO Observations of Three Powerful Radio Galaxies

    SciTech Connect

    de Vries, W; van Bruegel, W; Quirrenbach, A

    2002-08-01

    The host galaxies of powerful radio sources are ideal laboratories to study active galactic nuclei (AGN). The galaxies themselves are among the most massive systems in the universe, and are believed to harbor supermassive black holes (SMBH). If large galaxies are formed in a hierarchical way by multiple merger events, radio galaxies at low redshift represent the end-products of this process. However, it is not clear why some of these massive ellipticals have associated radio emission, while others do not. Both are thought to contain SMBHs, with masses proportional to the total luminous mass in the bulge. It either implies every SMBH has recurrent radio-loud phases, and the radio-quiet galaxies happen to be in the ''low'' state, or that the radio galaxy nuclei are physically different from radio-quiet ones, i.e. by having a more massive SMBH for a given bulge mass. Here we present the first results from our adaptive optics imaging and spectroscopy pilot program on three nearby powerful radio galaxies. Initiating a larger, more systematic AO survey of radio galaxies (preferentially with Laser Guide Star equipped AO systems) has the potential of furthering our understanding of the physical properties of radio sources, their triggering, and their subsequent evolution.

  15. Cleaving DNA with DNA

    NASA Astrophysics Data System (ADS)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  16. Measuring Atmospheric Dynamics on Titan with AO

    NASA Astrophysics Data System (ADS)

    Adamkovics, Mate; de Pater, I.; Hartung, M.

    2009-05-01

    The cycling of fluid methane between Titan's atmosphere and surface, via seemingly familiar meteorological phenomena, is often compared to Earth's hydrology. Near-IR observations with AO resolve the moon's 1" disk, measure spatial variation in both the surface reflectivity and scattering in the atmosphere, and constrain the methane cycle. Forward models of the atmosphere are compared to observations and used to identify and quantify sources and altitudes of atmospheric opacity; including aerosols, clouds, and precipitation. The ubiquitous submicron aerosol hazes are tracers of global stratospheric dynamics over yearly timescales. Cloud properties may constrain the tropospheric circulation and are observed to change on hourly, daily, and seasonal timescales. Here we present observations of the daily life-cycle of a cloud system, a signature of tropospheric precipitation, seasonal changes in aerosol, and discuss the models that are used to quantify the observed meteorology.

  17. DNA repair

    SciTech Connect

    Friedberg, E.C.; Hanawalt, P.C. )

    1988-01-01

    Topics covered in this book included: Eukaryote model systems for DNA repair study; Sensitive detection of DNA lesions and their repair; and Defined DNA sequence probes for analysis of mutagenesis and repair.

  18. The Magellan Telescope Adaptive Secondary AO System: a visible and mid-IR AO facility

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Gasho, Victor; Kopon, Derek; Males, Jared; Follette, Katherine B.; Brutlag, Kevin; Uomoto, Alan; Hare, Tyson

    2010-07-01

    The Magellan Clay telescope is a 6.5m Gregorian telescope located in Chile at Las Campanas Observatory. The Gregorian design allows for an adaptive secondary mirror that can be tested off-sky in a straightforward manner. We have fabricated a 85 cm diameter aspheric adaptive secondary with our subcontractors and partners, the ASM passed acceptance tests in July 2010. This secondary has 585 actuators with <1 msec response times (0.7 ms typically). This adaptive secondary will allow low emissivity AO science. We will achieve very high Strehls (~98%) in the Mid-IR (3-26 microns) with the BLINC/MIRAC4 Mid-IR science camera. This will allow the first "super-resolution" and nulling Mid-IR studies of dusty southern objects. We will employ a high order (585 mode) pyramid wavefront sensor similar to that now successfully used at the Large Binocular Telescope. The relatively high actuator count will allow modest Strehls to be obtained in the visible (0.63-1.05 μm). Moderate (~20%) Strehls have already been obtained at 0.8 μm at the LBT with the same powerful combination of a next generation ASM and Pyramid WFS as we are providing for Magellan. Our visible light AO (VisAO) science camera is fed by an advanced triplet ADC and is piggy-backed on the WFS optical board. We have designed an additional "clean-up" very fast (2 kHz) tilt stabilization system for VisAO. Also a high-speed shutter will be used to block periods of poor correction. The VisAO facility can be reconfigured to feed an optical IFU spectrograph with 20 mas spaxels. The entire system passed CDR in June 2009, and is now finished the fabrication phase and is entering the integration phase. The system science and performance requirements, and an overview the design, interface and schedule for the Magellan AO system are presented here.

  19. LGS-AO Imaging of Every Kepler Planet Candidate: the Robo-AO KOI Survey

    NASA Astrophysics Data System (ADS)

    Baranec, Christoph; Law, Nicholas; Morton, Timothy; Ziegler, Carl; Nofi, Larissa; Atkinson, Dani; Riddle, Reed

    2015-12-01

    The Robo-AO Kepler Planetary Candidate Survey is observing every Kepler planet candidate host star with laser adaptive optics imaging, to search for blended nearby stars which may be physically associated companions and/or responsible for transit false positives. We will present the results from searching for companions around over 3,000 Kepler planet hosts in 2012-2015. We will describe our first data release covering 715 planet candidate hosts, and give a preview of ongoing results including improved statistics on the likelihood of false positive planet detections in the Kepler dataset, many new planets in multiple star systems, and new exotic multiple star systems containing Kepler planets. We will also describe the automated Robo-AO survey data reduction methods, including a method of using the large ensemble of target observations as mutual point-spread-function references, along with a new automated companion-detection algorithm designed for extremely large adaptive optics surveys. Our first data release covered 715 objects, searching for companions from 0.15” to 2.5” separation with contrast up to 6 magnitudes. We measured the overall nearby-star-probability for Kepler planet candidates to be 7.4+/-1.0%, and we will detail the variations in this number with stellar host parameters. We will also discuss plans to extend the survey to other transiting planet missions such as K2 and TESS as Robo-AO is in the process of being re-deployed to the 2.1-m telescope at Kitt Peak for 3 years and a higher-contrast Robo-AO system is being developed for the 2.2-m UH telescope on Maunakea.

  20. Electromagnetic DM technology meets future AO demands

    NASA Astrophysics Data System (ADS)

    Hamelinck, Roger; Rosielle, Nick; Steinbuch, Maarten; Doelman, Niek

    New deformable mirror technology is developed by the Technische Universiteit Eindhoven, Delft University of Technology and TNO Science and Industry. Several prototype adaptive deformable mirrors are realized mirrors, up to 427 actuators and ∅150mm diameter, with characteristics suitable for future AO systems. The prototypes consist of a 100µm thick, continuous facesheet on which low voltage, electromagnetic, push-pull actuators impose out-of-plane displacements. The variable reluctance actuators with ±10µm stroke and nanometer resolution are located in a standard actuator module. Each module with 61 actuators connects to a single PCB with dedicated, 16 bit, PWM based, drivers. A LVDS multi-drop cable connects up to 32 actuator modules. With the actuator module, accompanying PCB and multi-drop system the deformable mirror technology is made modular in its mechanics and electronics. An Ethernet-LVDS bridge enables any commercial PC to control the mirror using the UDP standard. Latest results of the deformable mirror technology development are presented.

  1. Low-order AO system in LAMOST

    NASA Astrophysics Data System (ADS)

    Yuan, Xiangyan; Cui, Xiangqun; Liu, Genrong; Zhang, Yong; Qi, Yongjun

    2006-06-01

    The large sky area multi-object fiber spectroscopic telescope (LAMOST) is a special reflecting Schmidt telescope with its main optical axis on the meridian plane tilted by an angle of 25° to the horizontal. The clear aperture is 4m, working in optical band. The light path is 60m long when working in observing mode and it will be doubled if work in auto-collimation mode. So the image quality is affected clearly by the ground seeing and the dome seeing. In order to improve the seeing condition of the long light path, we enclosed the spherical primary and the focus unit in a tunnel enclosure and cooled the tunnel. This is an effective but passive method. Corresponding experiments and simulations show the main part of the aberrations caused by the ground seeing and dome seeing is slowly changed low order items such as tip-tilt, defocus, astigmatism, coma and spherical aberration. Thus we plan to develop the low-order AO system based on the low-cost 37-channel OKO deformable mirror for the telescope to better the ground seeing and the dome seeing, not aimed to reach diffraction limited image. This work is being carried on now.

  2. First closed-loop visible AO test results for the advanced adaptive secondary AO system for the Magellan Telescope: MagAO's performance and status

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Males, Jared R.; Kopon, Derek A.; Gasho, Victor; Follette, Katherine B.; Hinz, Phil; Morzinski, Katie; Uomoto, Alan; Hare, Tyson; Riccardi, Armando; Esposito, Simone; Puglisi, Alfio; Pinna, Enrico; Busoni, Lorenzo; Arcidiacono, Carmelo; Xompero, Marco; Briguglio, Runa; Quiros-Pacheco, Fernando; Argomedo, Javier

    2012-07-01

    The heart of the 6.5 Magellan AO system (MagAO) is a 585 actuator adaptive secondary mirror (ASM) with <1 msec response times (0.7 ms typically). This adaptive secondary will allow low emissivity and high-contrast AO science. We fabricated a high order (561 mode) pyramid wavefront sensor (similar to that now successfully used at the Large Binocular Telescope). The relatively high actuator count (and small projected ~23 cm pitch) allows moderate Strehls to be obtained by MagAO in the “visible” (0.63-1.05 μm). To take advantage of this we have fabricated an AO CCD science camera called "VisAO". Complete “end-to-end” closed-loop lab tests of MagAO achieve a solid, broad-band, 37% Strehl (122 nm rms) at 0.76 μm (i’) with the VisAO camera in 0.8” simulated seeing (13 cm ro at V) with fast 33 mph winds and a 40 m Lo locked on R=8 mag artificial star. These relatively high visible wavelength Strehls are enabled by our powerful combination of a next generation ASM and a Pyramid WFS with 400 controlled modes and 1000 Hz sample speeds (similar to that used successfully on-sky at the LBT). Currently only the VisAO science camera is used for lab testing of MagAO, but this high level of measured performance (122 nm rms) promises even higher Strehls with our IR science cameras. On bright (R=8 mag) stars we should achieve very high Strehls (>70% at H) in the IR with the existing MagAO Clio2 (λ=1-5.3 μm) science camera/coronagraph or even higher (~98% Strehl) the Mid-IR (8-26 microns) with the existing BLINC/MIRAC4 science camera in the future. To eliminate non-common path vibrations, dispersions, and optical errors the VisAO science camera is fed by a common path advanced triplet ADC and is piggy-backed on the Pyramid WFS optical board itself. Also a high-speed shutter can be used to block periods of poor correction. The entire system passed CDR in June 2009, and we finished the closed-loop system level testing phase in December 2011. Final system acceptance (

  3. AO 0235+164 and Surrounding Field: Surprising HST Results

    NASA Technical Reports Server (NTRS)

    Burbidge, E. M.; Beaver, E. A.; Cohen, Ross D.; Junkkarinen, V. T.; Lyons, R. W.

    1996-01-01

    Results obtained with the Hubble Space Telescope on the highly variable radio, x-ray, and gamma-ray emitting QSO (or BL Lac object) AO 0235 + 164 are presented and analyzed. WFPC2 images were obtained in 1994 June, when AO 0235 + 164 was bright (m approx. 17), and the results are described in Sec. 3. After subtraction of the PSF of the QSO, hereafter called AO following the nomenclature of Yanny et al. (1989), the companion object named A, 2 sec south of AO, is discovered not to be an elliptical galaxy as hypothesized earlier, but to be an AGN object, with a central UV-bright point-source nucleus and faint surrounding nebulosity extending to AO. The second companion object 1.3 sec east of AO discovered by Yanny et al. (1989) and named object Al, appears more like a normal spiral galaxy. We have measured the positions, luminosities, and colors of some 30 faint objects in the field around AO 0235 + 16; most are extended and may be star-forming galaxies in a loose group or cluster. Our most surprising result of the HST observations comes from FOS spectra obtained in 1995 July, discussed in Sec. 4. Because of a positioning error of the telescope and AO's faintness at that time (m approx. 20), object A was observed instead of the intended target AO. Serendipitously, we discovered A to have broad deep BALQSO-type absorptions of C IV, Si IV, N V shortward of broad emissions. A is thus ejecting high velocity, highly ionized gas into the surrounding IGM. We discuss in Sec. 5 the relationship of the objects in the central 10 sec X 1O sec region around AO, where redshifts z(sub e) = 0.94, z(sub a) = 0.524, 0.851 in AO, (sub e) = 0.524 and Z(sub BAL)=0.511 in A, are found. We hypothesize that some of the 30 faint objects in the 77 sec. x 77 sec. field may be part of a large star-forming region at z approx. 0.5, as suggested for a few objects by Yanny et al. (1989). The proximity of two highly active extragalactic objects, AO 0235+164 and its AGN companion A, is remarkable and

  4. The Subaru Coronagraphic Extreme AO Project: Progress and Upgrades

    NASA Astrophysics Data System (ADS)

    Jovanovic, Nemanja; Martinache, F.; Guyon, O.; Clergeon, C.; Garrel, V.

    2013-01-01

    The Subaru Coronagraphic Extreme AO (SCExAO) instrument consists of a high performance Phase Induced Amplitude Apodisation (PIAA) coronagraph combined with an extreme Adaptive Optics (AO) system operating in the near-infrared (H band). The extreme AO system driven by the 2000 element deformable mirror will allow for Strehl ratios>90% to be achieved in the H-band when it goes closed loop. This makes the SCExAO instrument a powerful platform for high contrast imaging down to angular separations of the order of 1 λ/D. In this paper we report on the recent progress in regards to the development of the instrument, which includes the addition of a visible bench that makes use of the light at shorter wavelengths not currently utilized by SCExAO and closing the loop on the tip/tilt wavefront sensor. We will also discuss two exciting guest instruments which will expand the capabilities of SCExAO over the next few years; namely CHARIS which is a integral field spectrograph as well as VAMPIRES, a visible aperture masking experiment based on polarimetric analysis of circumstellar disks.

  5. Mitochondrial DNA.

    ERIC Educational Resources Information Center

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  6. DNA Banking

    SciTech Connect

    Reilly, P.R. )

    1992-11-01

    The author is involved in the ethical, legal, and social issues of banking of DNA and data from DNA analysis. In his attempt to determine the extent of DNA banking in the U.S., the author surveyed some commercial companies performing DNA banking services. This article summarizes the results of that survey, with special emphasis on the procedures the companies use to protect the privacy of individuals. 4 refs.

  7. SCExAO: First Results and On-Sky Performance

    NASA Technical Reports Server (NTRS)

    Currie, Thayne; Guyon, Olivier; Martinache, Frantz; Clergeon, Christophe; McElwain, Michael; Thalmann, Christian; Jovanovic, Nemanja; Singh, Garima; Kudo, Tomoyuki

    2013-01-01

    We present new on-sky results for the Subaru Coronagraphic Extreme Adaptive Optics imager (SCExAO) verifying and quantifying the contrast gain enabled by key components: the closed-loop coronagraphic low-order wavefront sensor (CLOWFS) and focal plane wavefront control ("speckle nulling"). SCExAO will soon be coupled with a high-order, Pyramid wavefront sensor which will yield greater than 90% Strehl ratio and enable 10(exp 6) -10(exp 7) contrast at small angular separations allowing us to image gas giant planets at solar system scales. Upcoming instruments like VAMPIRES, FIRST, and CHARIS will expand SCExAO's science capabilities.

  8. SCExAO: First Results and On-Sky Performance

    NASA Astrophysics Data System (ADS)

    Currie, Thayne; Guyon, Olivier; Martinache, Frantz; Clergeon, Christophe; McElwain, Michael; Thalmann, Christian; Jovanovic, Nemanja; Singh, Garima; Kudo, Tomoyuki

    2014-01-01

    We present new on-sky results for the Subaru Coronagraphic Extreme Adaptive Optics imager (SCExAO) verifying and quantifying the contrast gain enabled by key components: the closed-loop coronagraphic low-order wavefront sensor (CLOWFS) and focal plane wavefront control (``speckle nulling''). SCExAO will soon be coupled with a high-order, Pyramid wavefront sensor which will yield > 90% Strehl ratio and enable 106-107 contrast at small angular separations allowing us to image gas giant planets at solar system scales. Upcoming instruments like VAMPIRES, FIRST, and CHARIS will expand SCExAO's science capabilities.

  9. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  10. Reproducibility of the Tronzo and AO classifications for transtrochanteric fractures☆

    PubMed Central

    Mattos, Carlos Augusto; Jesus, Alexandre Atsushi Koza; Floter, Michelle dos Santos; Nunes, Luccas Franco Bettencourt; Sanches, Bárbara de Baptista; Zabeu, José Luís Amim

    2015-01-01

    Objective To analyze the reproducibility of the Tronzo and AO classifications for transtrochanteric fractures. Method This was a cross-sectional study in which the intraobserver and interobserver concordance between two readings made by 11 observers was analyzed. The analysis of the variations used the kappa statistical method. Results Moderate concordance was found in relation to the AO classification, while slight concordance was found for the Tronzo classification. Conclusion This study found that the AO/Asif classification for transtrochanteric presented greater intra and interobserver reproducibility and that greater concordance was correlated with greater experience of the observers. Without division into subgroups, the AO/Asif classification was shown, as described in the literature, to be acceptable for clinical use in relation to transtrochanteric fractures of the femur, although it did not show absolute concordance, given that its concordance level was only moderate. Nonetheless, its concordance was better than that of the Tronzo classification. PMID:26535193

  11. LGS-AO Imaging of Every Kepler Planet Candidate: the Robo-AO KOI Survey

    NASA Astrophysics Data System (ADS)

    Law, Nicholas Michael; Baranec, Christoph; Morton, Timothy; Ziegler, Carl; Atkinson, Dani; Riddle, Reed

    2015-08-01

    The Robo-AO Kepler Planetary Candidate Survey is observing every Kepler planet candidate host star with laser adaptive optics imaging, to search for blended nearby stars which may be physically associated companions and/or responsible for transit false positives. We will present the results from searching for companions around over 3,000 Kepler planet hosts in 2012-2015. We will describe our first data release covering 715 planet candidate hosts, and give a preview of ongoing results including improved statistics on the likelihood of false positive planet detections in the Kepler dataset, many new planets in multiple star systems, and new exotic multiple star systems containing Kepler planets.We will also describe the automated Robo-AO survey data reduction methods, including a method of using the large ensemble of target observations as mutual point-spread-function references, along with a new automated companion-detection algorithm designed for extremely large adaptive optics surveys.Our first data release covered 715 objects, searching for companions from 0.15” to 2.5” separation with contrast up to 6 magnitudes. We measured the overall nearby-star-probability for Kepler planet candidates to be 7.4+/-1.0%, and we will detail the variations in this number with stellar host parameters. We will also discuss several KOIs of particular interest, including KOI-191 and KOI-1151, which are both multi-planet systems with detected stellar companions whose unusual planetary system architecture might be best explained if they are ``coincident multiple'' systems, with several transiting planets shared between the two stars. Finally, we will discuss and update the 98%-confidence evidence from our survey that third bodies in star/planet systems produce an excess of close-in giant planets.

  12. A Large-Telescope Natural Guide Star AO System

    NASA Technical Reports Server (NTRS)

    Redding, David; Milman, Mark; Needels, Laura

    1994-01-01

    None given. From overview and conclusion:Keck Telescope case study. Objectives-low cost, good sky coverage. Approach--natural guide star at 0.8um, correcting at 2.2um.Concl- Good performance is possible for Keck with natural guide star AO system (SR>0.2 to mag 17+).AO-optimized CCD should b every effective. Optimizing td is very effective.Spatial Coadding is not effective except perhaps at extreme low light levels.

  13. Experimental and theoretical investigation effect of flavonols antioxidants on DNA damage.

    PubMed

    Ensafi, Ali A; Heydari-Soureshjani, E; Jafari-Asl, M; Rezaei, B; Ghasemi, Jahan B; Aghaee, Elham

    2015-08-01

    A new electrochemical biosensor was developed to demonstrate the effect of Acridine Orange (AO) on DNA damage. Then, the biosensor was used to check the inhibitors effect of three flavonols antioxidants (myricetin, fisetin and kaempferol) on DNA damage. Acridine Orange (AO) was used as a damaging agent because it shows a high affinity to nucleic acid and stretch of the double helical structure of DNA. Decreasing on the oxidation signals of adenine and guanine (in the DNA) in the presence of AO were used as probes to study the antioxidants power, using DNA-modified screen printed graphene electrode (DNA/SPGE). The results of our study showed that the DNA-biosensor could be suitable biosensor to investigate the inhibitors ability of the flavonols antioxidants on the DNA damage. The linear dependency was detected in the two regions in the ranges of 1.0-15.0 and 15.0-500.0 pmol L(-1). The detection limit was found 0.5 pmol L(-1) and 0.6 pmol L(-1) for guanine and adenine, respectively. To confirm the electrochemical results, Uv-Vis and fluorescence spectroscopic methods were used too. Finally molecular dynamic (MD) simulation was performed on the structure of DNA in a water box to study any interaction between the antioxidant, AO and DNA. PMID:26320789

  14. DNA Immunization

    PubMed Central

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed. PMID:24510291

  15. Beyond the Blur: Construction and Characterization of the First Autonomous AO System, and, An AO Survey of Magnetar Proper Motions

    NASA Astrophysics Data System (ADS)

    Tendulkar, Shriharsh Prakash

    Adaptive optics (AO) corrects distortions created by atmospheric turbulence and delivers diffraction-limited images on ground-based telescopes. The vastly improved spatial resolution and sensitivity has been utilized for studying everything from the magnetic fields of sunspots upto the internal dynamics of high-redshift galaxies. This thesis about AO science from small and large telescopes is divided into two parts: Robo-AO and magnetar kinematics. In the first part, I discuss the construction and performance of the world's first fully autonomous visible light AO system, Robo-AO, at the Palomar 60-inch telescope. Robo-AO operates extremely efficiently with an overhead < 50s, typically observing about 22 targets every hour. We have performed large AO programs observing a total of over 7,500 targets since May 2012. In the visible band, the images have a Strehl ratio of about 10% and achieve a contrast of upto 6 magnitudes at a separation of 1‧‧. The full-width at half maximum achieved is 110-130 milli-arcsecond. I describe how Robo-AO is used to constrain the evolutionary models of low-mass pre-main-sequence stars by measuring resolved spectral energy distributions of stellar multiples in the visible band, more than doubling the current sample. I conclude this part with a discussion of possible future improvements to the Robo-AO system. In the second part, I describe a study of magnetar kinematics using high-resolution near-infrared (NIR) AO imaging from the 10-meter Keck II telescope. Measuring the proper motions of five magnetars with a precision of upto 0.7 milli-arcsecond/yr -1, we have more than tripled the previously known sample of magnetar proper motions and proved that magnetar kinematics are equivalent to those of radio pulsars. We conclusively showed that SGR 1900+14 and SGR 1806-20 were ejected from the stellar clusters with which they were traditionally associated. The inferred kinematic ages of these two magnetars are 6 +/- 1.8 kyr and 650 +/-3 00

  16. DNA ALTERATIONS

    EPA Science Inventory

    The exposure of an organism to genotoxic chemicals may induce a cascade of genetic events. nitially, structural alterations to DNA are formed. ext, the DNA damage is processed and subsequently expressed in mutant gene products. inally, diseases result from the genetic damage. he ...

  17. Molecular cloning of the cDNA coding for mouse aldehyde oxidase: tissue distribution and regulation in vivo by testosterone.

    PubMed Central

    Kurosaki, M; Demontis, S; Barzago, M M; Garattini, E; Terao, M

    1999-01-01

    The cDNA coding for mouse aldehyde oxidase (AO), a molybdoflavoprotein, has been isolated and characterized. The cDNA is 4347 nt long and consists of an open reading frame predicting a polypeptide of 1333 amino acid residues, with 5' and 3' untranslated regions of 13 and 335 nt respectively. The apparent molecular mass of the translation product in vitro derived from the corresponding cRNA is consistent with that of the monomeric subunit of the AO holoenzyme. The cDNA codes for a catalytically active form of AO, as demonstrated by transient transfection experiments conducted in the HC11 mouse mammary epithelial cell line. The deduced primary structure of the AO protein contains consensus sequences for two distinct 2Fe-2S redox centres and a molybdopterin-binding site. The amino acid sequence of the mouse AO has a high degree of similarity with the human and bovine counterparts, and a significant degree of relatedness to AO proteins of plant origin. Northern blot and in situ hybridization analyses demonstrate that hepatocytes, cardiocytes, lung endothelial or epithelial cells and oesophagus epithelial cells express high levels of AO mRNA. In the various tissues and organs considered, the level of AO mRNA expression is not strictly correlated with the amount of the corresponding protein, suggesting that the synthesis of the AO enzyme is under translational or post-translational control. In addition, we observed sex-related regulation of AO protein synthesis. In the liver of male animals, despite similar amounts of AO mRNA, the levels of the AO enzyme and corresponding polypeptide are significantly higher than those in female animals. Treatment of female mice with testosterone increases the amounts of AO mRNA and of the relative translation product to levels similar to those in male animals. PMID:10377246

  18. High-Performance CCSDS AOS Protocol Implementation in FPGA

    NASA Technical Reports Server (NTRS)

    Clare, Loren P.; Torgerson, Jordan L.; Pang, Jackson

    2010-01-01

    The Consultative Committee for Space Data Systems (CCSDS) Advanced Orbiting Systems (AOS) space data link protocol provides a framing layer between channel coding such as LDPC (low-density parity-check) and higher-layer link multiplexing protocols such as CCSDS Encapsulation Service, which is described in the following article. Recent advancement in RF modem technology has allowed multi-megabit transmission over space links. With this increase in data rate, the CCSDS AOS protocol implementation needs to be optimized to both reduce energy consumption and operate at a high rate.

  19. Initial Performance of the Keck AO Wavefront Controller System

    SciTech Connect

    Johansson, E M; Acton, D S; An, J R; Avicola, K; Beeman, B V; Brase, J M; Carrano, C J; Gathright, J; Gavel, D T; Hurd, R L; Lai, O; Lupton, W; Macintosh, B A; Max, C E; Olivier, S S; Shelton, J C; Stomski, P J; Tsubota, K; Waltjen, K E; Watson, J A; Wizinowich, P L

    2001-03-01

    The wavefront controller for the Keck Observatory AO system consists of two separate real-time control loops: a tip-tilt control loop to remove tilt from the incoming wavefront, and a deformable mirror control loop to remove higher-order aberrations. In this paper, we describe these control loops and analyze their performance using diagnostic data acquired during the integration and testing of the AO system on the telescope. Disturbance rejection curves for the controllers are calculated from the experimental data and compared to theory. The residual wavefront errors due to control loop bandwidth are also calculated from the data, and possible improvements to the controller performance are discussed.

  20. Structure of DNA-liposome complexes

    SciTech Connect

    Lasic, D.D.; Strey, H.; Podgornik, R.; Stuart, M.C.A.; Frederik, P.M.

    1997-01-29

    Despite numerous studies and commericially available liposome kits, however, the structure of DNA-cationic liposome complexes is still not yet well understood. We have investigated the structure of these complexes using high-resolution cryo electron microscopy (EM) and small angle X-ray scattering (SAXS). 14 refs., 3 figs.

  1. [DNA computing].

    PubMed

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  2. Apple fruit copper amine oxidase isoforms: peroxisomal MdAO1 prefers diamines as substrates, whereas extracellular MdAO2 exclusively utilizes monoamines.

    PubMed

    Zarei, Adel; Trobacher, Christopher P; Cooke, Alison R; Meyers, Ashley J; Hall, J Christopher; Shelp, Barry J

    2015-01-01

    4-Aminobutyrate (GABA) accumulates in apple fruit during controlled atmosphere storage. A potential source of GABA is the polyamine putrescine, which can be oxidized via copper-containing amine oxidase (CuAO), resulting in the production 4-aminobutanal/Δ(1)-pyrroline, with the consumption of O2 and release of H2O2 and ammonia. Five putative CuAO genes (MdAO genes) were cloned from apple (Malus domestica Borkh. cv. Empire) fruit, and the deduced amino acid sequences found to contain the active sites typically conserved in CuAOs. Genes encoding two of these enzymes, MdAO1 and MdAO2, were highly expressed in apple fruit and selected for further analysis. Amino acid sequence analysis predicted the presence of a C-terminal peroxisomal targeting signal 1 tripeptide in MdAO1 and an N-terminal signal peptide and N-glycosylation site in MdAO2. Transient expression of green fluorescent fusion proteins in Arabidopsis protoplasts or onion epidermal cells revealed a peroxisomal localization for MdAO1 and an extracellular localization for MdAO2. The enzymatic activities of purified recombinant MdAO1 and MdAO2 were measured continuously as H2O2 production using a coupled reaction. MdAO1 did not use monoamines or polyamines and displayed high catalytic efficiency for 1,3-diaminopropane, putrescine and cadaverine, whereas MdAO2 exclusively utilized aliphatic and aromatic monoamines, including 2-phenylethylamine and tyramine. Together, these results indicate that MdAO1 may contribute to GABA production via putrescine oxidation in the peroxisome of apple fruit under controlled atmosphere conditions. MdAO2 seems to be involved in deamination of 2-phenylethylamine, which is a step in the biosynthesis of 2-phenylethanol, a contributor to fruit flavor and flower fragrance. PMID:25378687

  3. PREVALÊNCIA DE ENDOSSIMBIONTES Cardinium EM POPULAÇÕES DE ÁCAROS Brevipalpus phoenicis DE DIFERENTES REGIÕES BRASILEIRAS.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Em B. phoenicis (Geijskes) (Acari: Tenuipalpidae), ácaro vetor de importantes fitovírus, a presença de endossimbiontes do gênero Cardinium relaciona-se ao processo de feminilização dos machos, acarretando em elevada proporção de fêmeas em populações naturais. Até o momento, não é conhecido se este e...

  4. Dancing DNA.

    ERIC Educational Resources Information Center

    Pennisi, Elizabeth

    1991-01-01

    An imaging technique that uses fluorescent dyes and allows scientists to track DNA as it moves through gels or in solution is described. The importance, opportunities, and implications of this technique are discussed. (KR)

  5. Unravelling DNA

    NASA Astrophysics Data System (ADS)

    Conroy, Rs; Danilowicz, C.

    2004-04-01

    The forces involved in the biology of life are carefully balanced between stopping thermal fluctuations ripping our DNA apart and having bonds weak enough to allow enzymes to function. The application of recently developed techniques for measuring piconewton forces and imaging at the nanometre scale on a molecule-by-molecule basis has dramatically increased the impact of single-molecule biophysics. This article describes the most commonly used techniques for imaging and manipulating single biomolecules. Using these techniques, the mechanical properties of DNA can be investigated, for example through measurements of the forces required to stretch and unzip the DNA double helix. These properties determine the ease with which DNA can be folded into the cell nucleus and the size and complexity of the accompanying cellular machinery. Part of this cellular machinery is enzymes, which manipulate, repair and transcribe the DNA helix. Enzymatic function is increasingly being investigated at the single molecule level to give better understanding of the forces and processes involved in the genetic cycle. One of the challenges is to transfer this understanding of single molecules into living systems. Already there have been some notable successes, such as the development of techniques for gene expression through the application of mechanical forces to cells, and the imaging and control of viral infection of a cell. This understanding and control of DNA has also been used to design molecules, which can self-assemble into a range of structures.

  6. What Is Mitochondrial DNA?

    MedlinePlus

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  7. Holocene Evolution of Qing'ao Embayment, Southern China

    NASA Astrophysics Data System (ADS)

    Switzer, A. D.; Yu, F.; Chen, B.; Zheng, Z.; Wang, D.

    2012-12-01

    The Holocene evolution of the Qing'ao embayment, Nan'ao Island, southern China, is primarily the result of the interaction of tectonic activity, climate variation and changes in relative sea level. Characterizing the evolutionary history of the relatively small Qing'ao embayment during the Holocene will help improve our understanding of the driving mechanisms of coastal evolution in the area. To reconstruct the Holocene evolution history we analyzed the grain size, loss on ignition (LOI) and carbonate content of modern and core samples. Modern environmental analogs were examined in surface samples ranging from the coastal sand dunes through to offshore. The results of these modern samples suggest that dune sand (mean size of ~2.33Phi) are slightly finer than beach sand (mean size of 2.13Phi), and nearshore sediment is much coarser than offshore sediment (mean size of 5.90Phi). This modern analogs were then applied to 8 percussion cores from the Qing'ao embayment. A chronological framework obtained from 11 radiocarbon samples suggests that the embayment started to accept deposition since early Holocene, ~8500 cal. yr. BP. Three main phases of Holocene evolution were identified. A basin wide shell-rich sand sheet forms the basal Holocene facies and overlies clay rich presumably Pleistocene sediments or bedrock. This facies records an initial sedimentation phase associated with the early Holocene transgression into the embayment (~8500-6000 cal. yr. BP). The basal facies grades upward to a mixed sandy-mud facies which includes lagoonal clayey-silts, flood tide delta sands and records an estuarine phase lasting from ~6000-1000 cal. yr. BP that appears coincident with falling regional sea levels. Coincident with the estuarine phase is a period of coastal dune building recorded as yet undated massive sands that are found in the upper fill. Toward the end of the estuarine phase it is apparent that dune migration has restricted the lagoon entrance and that this was

  8. Ancient DNA

    PubMed Central

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

  9. DNA vaccines

    NASA Astrophysics Data System (ADS)

    Gregersen, Jens-Peter

    2001-12-01

    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  10. Click-EM for imaging metabolically tagged nonprotein biomolecules.

    PubMed

    Ngo, John T; Adams, Stephen R; Deerinck, Thomas J; Boassa, Daniela; Rodriguez-Rivera, Frances; Palida, Sakina F; Bertozzi, Carolyn R; Ellisman, Mark H; Tsien, Roger Y

    2016-06-01

    EM has long been the main technique for imaging cell structures with nanometer resolution but has lagged behind light microscopy in the crucial ability to make specific molecules stand out. Here we introduce click-EM, a labeling technique for correlative light microscopy and EM imaging of nonprotein biomolecules. In this approach, metabolic labeling substrates containing bioorthogonal functional groups are provided to cells for incorporation into biopolymers by endogenous biosynthetic machinery. The unique chemical functionality of these analogs is exploited for selective attachment of singlet oxygen-generating fluorescent dyes via bioorthogonal 'click chemistry' ligations. Illumination of dye-labeled structures generates singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product that is readily imaged by EM. We describe the application of click-EM in imaging metabolically tagged DNA, RNA and lipids in cultured cells and neurons and highlight its use in tracking peptidoglycan synthesis in the Gram-positive bacterium Listeria monocytogenes. PMID:27110681

  11. Mutagenesis in Oocytes of DROSOPHILA MELANOGASTER. I. Scheduled Synthesis of Nuclear and Mitochondrial DNA and Unscheduled DNA Synthesis

    PubMed Central

    Kelley, Mark R.; Lee, William R.

    1983-01-01

    As a model system for studying mutagenesis, the oocyte of Drosophila melanogaster has exhibited considerable complexity. Very few experiments have been conducted on the effect of exposing oocytes to chemical mutagens, presumably due to their lower mutational response relative to sperm and spermatids. This lower response may be due either to a change in probability of mutation induction per adduct due to a change in the type of DNA repair or to a lower dose of the mutagen to the female germ line. To study molecular dosimetry and DNA repair in the oocyte, the large number of intracellular constituents (mtDNA, RNA, nucleic acid precursors and large quantities of proteins and lipids) must be separated from nuclear DNA. In this paper we present results showing reliable separation of such molecules enabling us to detect scheduled nuclear and mitochondrial DNA synthesis. We also, by understanding the precise timing of such events, can detect unscheduled DNA synthesis (UDS) as a measure of DNA repair. Furthermore, by comparing the UDS results in a repair competent (Ore-R) vs. a repair deficient (mei-9L1 ) strain, we have shown the oocyte capable of DNA repair after treatment with ethyl methanesulfonate (EMS). We conclude that the important determinant of mutation induction in oocytes after treatment with EMS is the time interval between DNA alkylation and DNA synthesis after fertilization, i.e., the interruption of continuous DNA repair. PMID:17246137

  12. Diffraction limited operation with ARGOS: a hybrid AO system

    NASA Astrophysics Data System (ADS)

    Bonaglia, M.; Busoni, L.; Quirós-Pacheco, F.; Esposito, S.

    2010-07-01

    ARGOS, the Laser Guide Star (LGS) facility of the Large Binocular Telescope (LBT), implements a Ground Layer Adaptive Optics (GLAO) system, using 3 low-altitude beacons, to improve the resolution over the 4'×4' FoV of the imager and Multi Object Spectrograph (MOS) LUCIFER. In this paper we discuss the performance and the reconstruction scheme of an hybrid AO system using the ARGOS Rayleigh beacons complemented with a single faint high-altitude star (NGS or sodium beacon) to sense the turbulence of the upper atmosphere allowing an high degree of on-axis correction. With the ARGOS system, the NGS-upgrade can be immediately implemented at LBT using the already existing Pyramid WFS offering performance similar to the NGS AO system with the advantage of a larger sky coverage.

  13. High-Resolution Imaging of Asteroids/Satellites with AO

    NASA Astrophysics Data System (ADS)

    Merline, William

    2012-02-01

    We propose to make high-resolution observations of asteroids using AO, to measure size, shape, and pole position (spin vectors), and/or to search for satellites. We have demonstrated that AO imaging allows determination of the pole/dimensions in 1 or 2 nights on a single target, rather than the years of observations with lightcurve inversion techniques that only yield poles and axial ratios, not true dimensions. Our new technique (KOALA) combines AO imaging with lightcurve and occultation data for optimum size/shape determinations. We request that LGS be available for faint targets, but using NGS AO, we will measure several large and intermediate asteroids that are favorably placed in spring/summer of 2012 for size/shape/pole. Accurately determining the volume from the often-irregular shape allows us to derive densities to much greater precision in cases where the mass is known, e.g., from the presence of a satellite. We will search several d! ozen asteroids for the presence of satellites, particularly in under-studied populations, particularly NEOs (we have recently achieved the first-ever optical image of an NEO binary [Merline et al. 2008b, IAUC 8977]). Satellites provide a real-life lab for testing collisional models. We will search for satellites around special objects at the request of lightcurve observers, and we will make a search for debris in the vicinity of Pluto, in support of the New Horizons mission. Our shape/size work requires observations over most of a full rotation period (typically several hours).

  14. LDEF results for polymer matrix composite experiment AO 180

    NASA Technical Reports Server (NTRS)

    Tennyson, R. C.

    1992-01-01

    This report represents a summary of the results obtained to-date on a polymer matrix composite experiment (AO 180) located at station D-12, about 82 deg off the 'ram' direction. Different material systems comprised of graphite, boron, and aramid (Kevlar) fiber reinforcements were studied. Although previous results were presented on in-situ thermal-vacuum cycling effects, particularly dimensional changes associated with outgassing, additional comparative data will be shown from ground-based tests on control and flight samples. The system employed was fully automated for thermal-vacuum cycling using a laser interferometer for monitoring displacements. Erosion of all three classes of materials due to atomic oxygen (AO) will also be discussed, including angle of incidence effects. Data from this experiment will be compared to published results for similar materials in other LDEF experiments. Composite materials' erosion yields will be presented on an AO design nomogram useful for estimating total material loss for given exposure conditions in low Earth orbit (LEO). Optical properties of these materials will also be compared with control samples. A survey of the damage caused by micrometeoroids/debris impacts will be addressed as they relate to polymer matrix composites. Correlations between hole size and damage pattern will be given. Reference to a new nomogram for estimating the number distribution of micrometeoroid/debris impacts for a given space structure as a function of time in LEO will be addressed based on LDEF data.

  15. DNA codes

    SciTech Connect

    Torney, D. C.

    2001-01-01

    We have begun to characterize a variety of codes, motivated by potential implementation as (quaternary) DNA n-sequences, with letters denoted A, C The first codes we studied are the most reminiscent of conventional group codes. For these codes, Hamming similarity was generalized so that the score for matched letters takes more than one value, depending upon which letters are matched [2]. These codes consist of n-sequences satisfying an upper bound on the similarities, summed over the letter positions, of distinct codewords. We chose similarity 2 for matches of letters A and T and 3 for matches of the letters C and G, providing a rough approximation to double-strand bond energies in DNA. An inherent novelty of DNA codes is 'reverse complementation'. The latter may be defined, as follows, not only for alphabets of size four, but, more generally, for any even-size alphabet. All that is required is a matching of the letters of the alphabet: a partition into pairs. Then, the reverse complement of a codeword is obtained by reversing the order of its letters and replacing each letter by its match. For DNA, the matching is AT/CG because these are the Watson-Crick bonding pairs. Reversal arises because two DNA sequences form a double strand with opposite relative orientations. Thus, as will be described in detail, because in vitro decoding involves the formation of double-stranded DNA from two codewords, it is reasonable to assume - for universal applicability - that the reverse complement of any codeword is also a codeword. In particular, self-reverse complementary codewords are expressly forbidden in reverse-complement codes. Thus, an appropriate distance between all pairs of codewords must, when large, effectively prohibit binding between the respective codewords: to form a double strand. Only reverse-complement pairs of codewords should be able to bind. For most applications, a DNA code is to be bi-partitioned, such that the reverse-complementary pairs are separated

  16. EM International. Volume 1

    SciTech Connect

    Not Available

    1993-07-01

    It is the intent of EM International to describe the Office of Environmental Restoration and Waste Management`s (EM`s) various roles and responsibilities within the international community. Cooperative agreements and programs, descriptions of projects and technologies, and synopses of visits to international sites are all highlighted in this semiannual journal. Focus on EM programs in this issue is on international collaboration in vitrification projects. Technology highlights covers: in situ sealing for contaminated sites; and remote sensors for toxic pollutants. Section on profiles of countries includes: Arctic contamination by the former Soviet Union, and EM activities with Germany--cooperative arrangements.

  17. DNA computing.

    PubMed

    Gibbons, A; Amos, M; Hodgson, D

    1997-02-01

    DNA computation is a novel and exciting recent development at the interface of computer science and molecular biology. We describe the current activity in this field following the seminal work of Adleman, who recently showed how techniques of molecular biology may be applied to the solution of a computationally intractable problem. PMID:9013647

  18. DNA Music.

    ERIC Educational Resources Information Center

    Miner, Carol; della Villa, Paula

    1997-01-01

    Describes an activity in which students reverse-translate proteins from their amino acid sequences back to their DNA sequences then assign musical notes to represent the adenine, guanine, cytosine, and thymine bases. Data is obtained from the National Institutes of Health (NIH) on the Internet. (DDR)

  19. DNA Investigations.

    ERIC Educational Resources Information Center

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  20. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:26442938

  1. SIMS chemical and isotopic analysis of impact features from LDEF experiments AO187-1 and AO187-2

    NASA Technical Reports Server (NTRS)

    Stadermann, Frank J.; Amari, Sachiko; Foote, John; Swan, Pat; Walker, Robert M.; Zinner, Ernst

    1995-01-01

    Previous secondary ion mass spectrometry (SIMS) studies of extended impact features from LDEF capture cell experiment AO187-2 showed that it is possible to distinguish natural and man-made particle impacts based on the chemical composition of projectile residues. The same measurement technique has now been applied to specially prepared gold target impacts from experiment AO187-1 in order to identify the origins of projectiles that left deposits too thin to be analyzed by conventional energy-dispersive x-ray (EDX) spectroscopy. The results indicate that SIMS may be the method of choice for the analysis of impact deposits on a variety of sample surfaces. SIMS was also used to determine the isotopic compositions of impact residues from several natural projectiles. Within the precision of the measurements all analyzed residues show isotopically normal compositions.

  2. [Investigation on circulation of Ao shi shang han jin jing lu (Ao's Golden mirror of cold pathogenic diseases) in Japan].

    PubMed

    Liang, Rong

    2003-01-01

    Being the earliest extant work on tongue diagnostics, Ao shi jin jing lu was block-printed and published in 1654 after it was spread into Japan, on the basis of which many kinds of manuscripts were made. This book not only exerted profound influence on the Kampo diagnostics in Edo age, but also laid down a foundation for the formation of pulse diagnostic school of tongue diagnostics in Kampo medicine. PMID:12921588

  3. Identification of system misregistrations during AO-corrected observations

    NASA Astrophysics Data System (ADS)

    Béchet, C.; Thiébaut, É.; .; Tallon, M.; Kolb, J.; Madec, P.-Y.

    2011-09-01

    The E-ELT will be equipped with a deformable mirror inside the telescope. The performance of reconstruction and control depends on the calibration of the interaction matrix- or a model of the interaction matrix- , which characterizes the system and the relationship between the commands sent to the deformable mirrors (DM) and the wavefront sensors (WFS) slopes. Such a calibration will be more complex than for the current systems at the VLT since it will have to be at least partly measured on sky and for a much larger number of degrees of freedom (more than 5000). In addition, gravity or temperature variations for instance are likely to introduce slow evolution of the matching between the M4 Deformable mirror and the WFS geometry. This can occur during observations and therefore degrade the adaptive optics (AO) correction. To relax the need of frequent painful calibrations and to prevent a loss of performance due to misregistrations, we investigate how to track the evolution of the interaction matrix errors in closed-loop without introducing any degradation in the observations. This is done thanks to identification methods and optimization theory. First, we formally describe the problem and the difficulties of such an identification in closed-loop configuration. Then, we present 2 solutions, based on the optimization of the error of estimates of the WFS slopes, at the output of the closed-loop AO. The performance of the methods and their limitations are discussed formally and thanks to numerical simulations of a high order AO system. We finally explore to which extent these methods currently studied for the Adaptive Optics Facility (AOF) at the VLT can be applied to the E-ELT.

  4. Intramedullary locking femoral nails. Experience with the AO nail.

    PubMed Central

    Fogarty, A. B.; Yeates, H. A.

    1991-01-01

    The AO interlocking nail was introduced to the Ulster Hospital, Dundonald in 1988 and since then has been used in over 50 patients with femoral shaft fractures. We have reviewed 45 patients with 46 femoral shaft fractures treated between June 1988 and April 1990. These included four compound fractures and 13 comminuted fractures. The results compare favourably with other series. The union rate was 98% and there were no instances of deep infection. The alternative treatment methods available are discussed along with a review of the relevant literature. Images Fig 3 Fig 5 PMID:1785145

  5. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C03

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C03 The IDE mounting plate and the detector frames are coated with a brown stain similiar to that seen on the other experiments in this and other trays located nearby. The stain seems to be slightly darker along the lower edge of the solar sensor mounting plate. The colors and designs seen on the detectors are reflections of the surrounding area. The thin brown film on the detectors metallic surface has resulted in a duller reflection of a technician, in the upper left, and other items.

  6. Stream-Field Interactions in the Magnetic Accretor AO Piscium

    NASA Astrophysics Data System (ADS)

    Hellier, Coel; van Zyl, Liza

    2005-06-01

    UV spectra of the magnetic accretor AO Psc show absorption features for half the binary orbit. The absorption is unlike the wind-formed features often seen in similar stars. Instead, we attribute it to a fraction of the stream that overflows the impact with the accretion disk. Rapid velocity variations can be explained by changes in the trajectory of the stream depending on the orientation of the white dwarf's magnetic field. Hence, we are directly observing the interaction of an accretion stream with a rotating field. We compare this behavior to that seen in other intermediate polars and in SW Sex stars.

  7. Titanium alloys (AoN) and their involvement in osseointegration

    PubMed Central

    Danza, Matteo; Zollino, Ilaria; Candotto, Valentina; Cura, Francesca; Carinci, Francesco

    2012-01-01

    Background: Osseointegration is essential for a long-term successful and inflammation-free dental implant. Such a result depends on osteoblastic cells growth and differentiation at the tissue-implant interface. The aim of this study was to compare two different AoN titanium layers (GR4 and GR5) to investigate which one had a greater osteoconductive power using human osteoblasts (HOb) culture at two different time-points. Materials and Methods: The expression levels of some bone-related (ALPL, COL1A1, COL3A1, SPP1, RUNX2, and SPARC) were analyzed using real time reverse transcription-polymerase chain reaction (real time RT-PCR). Results: Real-time RT-PCR data showed that after 3 days of treatment with TiA4GR, the genes up-regulated were COL3A1, ALPL, SPP1, and RUNX2. Moreover, no difference in gene expression was noticed 4 days later. On the other hand, the genes that overexpressed after 3 days of treatment with AoN5GR were ALPL, SPP1, and RUNX2. In both cases, the expression of COL1A1 and SPARC was negatively regulated. Conclusion: Our data showed that both titanium surfaces led to osteoblasts recruitment, maturation, and differentiation, thus promoting osseointegration at the tissue-implant interface. PMID:23814585

  8. Robo-AO: autonomous and replicable laser-adaptive-optics and science system

    NASA Astrophysics Data System (ADS)

    Baranec, C.; Riddle, R.; Ramaprakash, A. N.; Law, N.; Tendulkar, S.; Kulkarni, S.; Dekany, R.; Bui, K.; Davis, J.; Burse, M.; Das, H.; Hildebrandt, S.; Punnadi, S.; Smith, R.

    2012-07-01

    We have created a new autonomous laser-guide-star adaptive-optics (AO) instrument on the 60-inch (1.5-m) telescope at Palomar Observatory called Robo-AO. The instrument enables diffraction-limited resolution observing in the visible and near-infrared with the ability to observe well over one-hundred targets per night due to its fully robotic operation. Robo-AO is being used for AO surveys of targets numbering in the thousands, rapid AO imaging of transient events and long-term AO monitoring not feasible on large diameter telescope systems. We have taken advantage of cost-effective advances in deformable mirror and laser technology while engineering Robo-AO with the intention of cloning the system for other few-meter class telescopes around the world.

  9. DNA Microarrays

    NASA Astrophysics Data System (ADS)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  10. Transcription initiation complex structures elucidate DNA opening.

    PubMed

    Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

    2016-05-19

    Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. PMID:27193681

  11. Wrinkled DNA.

    PubMed Central

    Arnott, S; Chandrasekaran, R; Puigjaner, L C; Walker, J K; Hall, I H; Birdsall, D L; Ratliff, R L

    1983-01-01

    The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detected in other poly d(PuPy):poly d(PuPy) DNAs such as poly d(IC):poly d(IC) and poly d(AT):poly d(AT) in their D forms which have tetragonal crystal environments. This suggests that such perturbations are intrinsic to all stretches of duplex DNA where purines and pyrimidines alternate and may play a role in the detection and exploitation of such sequences by regulatory proteins. Images PMID:6572358

  12. Optical DNA

    NASA Astrophysics Data System (ADS)

    Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko

    A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object’s physical “fingerprint,” a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a “fingerprint” for each optical disc: its optical DNA. The “fingerprint” is signed using publisher’s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher’s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.

  13. Searching and Studying Binary Asteroids with AO Systems

    NASA Astrophysics Data System (ADS)

    Marchis, F.; Descamps, P.; Berthier, J.; Hestroffer, D.; de Pater, I.; Conrad, A.; Le Mignant, D.; Chaffee, F.; Gavel, D.

    2003-05-01

    Our group has conducted adaptive optics observations of asteroids since 2001. Our main goal is the search and study of binary asteroids using several AO systems (Lick, Keck, VLT) and related technique such as Appulse (Berthier and Marchis, 2002) and Laser Guide Star observations (Marchis et al., AGU-EGS, 2003) to broaden the sample of asteroids observed from the main-belt out to the Kuiper Belt. We focussed our program last year on Trojan Asteroids. Six of them were observed using Appulses with Keck AO ( ˜0.05-0.10", mv=15.4-18.5), 6 with the LGS at Lick ( ˜0.25-0.35", mv<16) and 12 with the VLT/NACO system ( ˜0.10-0.14"; mv<16.7). None of these observations reveals the presence of a companion. Based on this sample, and including 617 Patroclus binary asteroid discovered by Merline et al. (IAU, 7741, 2001), we deduce that the proportion of binary Trojan asteroids larger than 40 km is less than 4%. We will promote and discuss a technique of the analysis of negative discovery in large samples. In January 2003, we conducted an observing campaign spanning 5 days of 121 Hermione with NACO, the new AO system offered at VLT. This C-type asteroid was discovered by Merline et al. (IAU, 7980, 2002). The companion, 6.1 mag fainter than the primary, is easily detected despite the faintness of the asteroid (mv ˜13). We use the method described in Marchis et al. (Icarus, 2003) to determine the orbit of the companion. Its orbital elements are a=794.7+/-2.1 km, and P=1.643+/-0.005 days. We derived a mass =1.47E19 kg, and a density of 3.1+/-0.8 g cm-3 (using IRAS diameter of 209+/-4.7 km). Considering typical densities of meteorite analogues (CI or CM carboneceous chondrite) would led to an extremely low macro-porosity of p<3%. This suggests that the volume of Hermione is ˜30% larger, which is also supported by our resolved images of this body. This work supported by the National Science Foundation Science and Technology Center for Adaptive Optics, based partly on observations

  14. Nao/ao Variability In The Coupled Bergen Climate Model

    NASA Astrophysics Data System (ADS)

    Sorteberg, A.; Furevik, T.; Bentsen, M.; Drange, H.; Kvamsto, N. G.; Thorstensen-Kindem, I.

    A new fully coupled atmosphere-ocean-sea ice model, known as the Bergen Climate Model (BCM), has been developed. The coupled model can be run with stretched co- ordinates both in the atmosphere and ocean and consists of the atmospheric model ARPEGE/IFS, and a global version of the isopycnal ocean model MICOM, including a sea ice model. The atmospheric model ARPEGE/IFS (c22) is a spectral model devel- oped jointly by Meteo-France and the European Centre for Medium-Range Weather Forecasts (ECMWF). The ocean circulation model is the Miami Isopycnic Coordinate Ocean Model (MI- COM). Several modifications have been done to the MICOM model including the incorporation of a thermodynamic and dynamic sea ice model, the use of tempera- ture as a prognostic variable instead of salinity, and the use of a metric scale factor in both lateral, so the model can easily be configured on a general orthogonal grid. Also,the thickness diffusion has been modified to better handle diffusion near bottom topography and the base of the mixed layer. Coupling has been done with the library OASIS where 14 different fields are ex- changed using Montecarlo mapping and subgrid interpolation. Continental runoff into the correct rivers and discharge into the correct ocean grid cells are performed using the Total Runoff Integrating Pathways (TRIP) data set. Results will be present from a 300 years flux adjusted control integration of BCM with todays climate, using a unstretched T63 truncation in the atmosphere and a 0.8 by 2.4 degree resolution (near the equator gradually transforming to approximate square grid cells towards the poles) in the ocean. The model output has been analysed for large scale variability in both the ocean and atmosphere, with emphasise on the North Atlantic and Arctic climate. Statistical properties of the NAO/AO signal, and its im- pacts on the climate components, are identified and compared with observations. The NAO/AO mode of variability show up in the model with

  15. Diferentes metodologias aplicadas ao ensino de astronomia no Ensino Médio

    NASA Astrophysics Data System (ADS)

    Albrecht, E.; Voelzke, M. R.

    2009-03-01

    O presente trabalho de intervenção foi realizado junto à Escola Estadual Colònia dos Pescadores na cidade de Caraguatatuba, com très turmas do terceiro ano do Ensino Médio, envolvendo 119 alunos com idades entre 16 e 19 anos. A fase inicial foi composta de um questionário de vinte questíes dissertativas e objetivas, aplicado pelo professor titular da sala, que era o mesmo nas très turmas, para diagnosticar nos educandos os conceitos prévios sobre Astronomia e, partindo destes realizar um trabalho de intervenção nas classes envolvidas utilizando, em cada uma, metodologias diferentes: (A) sob forma de seminários, elaborados e apresentados pelos educandos, no qual o educador faz apenas as intervençíes necessárias; (B) de forma tradicional, com auxílio de multimídias para desenvolvimento das aulas e a terceira (C) tradicional, fazendo uso exclusivo de lousa e giz. Ao final do trabalho os alunos responderam novamente o questionário inicial para diagnosticar dentre as très metodologias utilizadas qual apresentou melhores aplicaçíes, os resultados iniciais foram comparados com os finais. Quando questionados a respeito do significado de Astronomia observou-se inicialmente que os acertos na turma A foram de 100%, turma B: 64%, turma C: 84%, após a intervenção os acertos foram: 100%, 97% e 85% respectivamente, demonstrando que houve um avanço significativo na turma B, a turma A manteve seu índice e a turma C evoluiu, porém não tanto quanto a B. Quando interrogados sobre quantos planetas vocè acha que existem em nosso Sistema Solar? os acertos foram: turma A: 39%, turma B: 48% e turma C: 46%, após o desenvolvimento do trabalho os acertos foram 94%, 97% e 90% respectivamente. Dentro das respostas obtidas observa-se que a metodologia tradicional com o auxílio de multimeios, aplicada na turma B, demonstrou melhores resultados, sendo a mais significativa. Outra conclusão muito importante é que apesar de o tema Astronomia ser amplamente

  16. LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray C09

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray C09 The flight photograph was taken during the LDEF retrieval and provides an on-orbit view of the C09 integrated tray. When comparing this photograph with the prelaunch photograph, very little difference can be seen. A brown stain is visible around some of the fasteners and on mounting plates. The stain has been attributed to outgassing and contamination from the LDEF and experiment related materials being flown. When compared to the prelaunch photograph, the C09 integrated tray seems to be in excellent condition. The Interplanetary Dust Experiment appears to have a thin brown stain around some of the fasteners and also a small rectangular stain, in the center, along the bottom edge of the detector mounting plate. The IDE seems to be in excellent condition with all hardware intact. The colors seen in the detectors is a reflection of the Orbiter's white cargo bay liner.

  17. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C09

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C09 The postflight photograph was taken prior to the experiment tray being removed from the LDEF. The tray corner clamp blocks are un-anodized aluminum and that alone accounts for the major difference in color between the corner clamp blocks and the center clamp blocks. The IDE mounting plate and the detector frames and detectors seem to be in excellent condition. Close inspection of the photograph reveals several locations where impacts on detector surfaces are visible. A faint gold or tan stain can be seen around several of the fasteners and in a rectangular configuration, near the center, along the bottom edge of the detector mounting plate. Stains can also be seen near the top right edge of the solar sensor, on the mounting plate, and around the extreme edges of the solar sensor baseplate. The colors and designs seen on the detectors are reflections of the surrounding area.

  18. The 1987 outburst of the BL Lacertid AO 0235 + 164

    NASA Astrophysics Data System (ADS)

    Webb, J. R.; Smith, A. G.

    1989-08-01

    The violently variable BL Lacertid AO 0235 + 164 displayed a 3.24 magnitude outburst in early 1987. This outburst was observed intensively from Rosemary Hill Observatory in three colors. Long term monitoring observations made at Rosemary Hill are examined in an effort to find any recurring timescales associated with this outburst and previous large amplitude outbursts. The energetics of the 1987 outburst are analyzed in terms of the Shields and Wheeler model of a magnetized accretion disk. The timescales identified in the power spectrum (2.8 and 1.6 yr) are input into the model as the storage timescales. Since the emitted energy calculated from the optical burst cannot be stored in a magnetized disk at an allowable radius, it is concluded that either the storage timescales are longer than those identified in the power spectrum, or relativistic beaming effects must be considered, with a Doppler factor of 1.3 to 1.6.

  19. NFIRAOS: first facility AO system for the Thirty Meter Telescope

    NASA Astrophysics Data System (ADS)

    Herriot, Glen; Andersen, David; Atwood, Jenny; Boyer, Corinne; Byrnes, Peter; Caputa, Kris; Ellerbroek, Brent; Gilles, Luc; Hill, Alexis; Ljusic, Zoran; Pazder, John; Rosensteiner, Matthias; Smith, Malcolm; Spano, Paolo; Szeto, Kei; Véran, Jean-Pierre; Wevers, Ivan; Wang, Lianqi; Wooff, Robert

    2014-07-01

    NFIRAOS, the Thirty Meter Telescope's first adaptive optics system is an order 60x60 Multi-Conjugate AO system with two deformable mirrors. Although most observing will use 6 laser guide stars, it also has an NGS-only mode. Uniquely, NFIRAOS is cooled to -30 °C to reduce thermal background. NFIRAOS delivers a 2-arcminute beam to three client instruments, and relies on up to three IR WFSs in each instrument. We present recent work including: robust automated acquisition on these IR WFSs; trade-off studies for a common-size of deformable mirror; real-time computing architectures; simplified designs for high-order NGS-mode wavefront sensing; modest upgrade concepts for high-contrast imaging.

  20. DNA mimicry by proteins.

    PubMed

    Dryden, D T F; Tock, M R

    2006-04-01

    It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins. PMID:16545103

  1. Mitochondrial DNA replacement versus nuclear DNA persistence

    NASA Astrophysics Data System (ADS)

    Serva, Maurizio

    2006-10-01

    In this paper we consider two populations whose generations are not overlapping and whose size is large. The number of males and females in both populations is constant. Any generation is replaced by a new one and any individual has two parents concerning nuclear DNA and a single one (the mother) concerning mtDNA. Moreover, at any generation some individuals migrate from the first population to the second. In a finite random time T, the mtDNA of the second population is completely replaced by the mtDNA of the first. In the same time, the nuclear DNA is not completely replaced and a fraction F of the ancient nuclear DNA persists. We compute both T and F. Since this study shows that complete replacement of mtDNA in a population is compatible with the persistence of a large fraction of nuclear DNA, it may have some relevance for the 'out of Africa'/multiregional debate in palaeoanthropology.

  2. DNA modifications: Another stable base in DNA

    NASA Astrophysics Data System (ADS)

    Brazauskas, Pijus; Kriaucionis, Skirmantas

    2014-12-01

    Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.

  3. Synthesis of DNA

    DOEpatents

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  4. Sperm DNA oxidative damage and DNA adducts.

    PubMed

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  5. Robo-AO KP: A new era in robotic adaptive optics

    NASA Astrophysics Data System (ADS)

    Riddle, Reed L.; Baranec, Christoph; Law, Nicholas M.; Kulkarni, Shrinivas R.; Duev, Dmitry; Ziegler, Carl; Jensen-Clem, Rebecca M.; Atkinson, Dani Eleanor; Tanner, Angelle M.; Zhang, Celia; Ray, Amy

    2016-01-01

    Robo-AO is the first and only fully automated adaptive optics laser guide star AO instrument. It was developed as an instrument for 1-3m robotic telescopes, in order to take advantage of their availability to pursue large survey programs and target of opportunity observations that aren't possible with other AO systems. Robo-AO is currently the most efficient AO system in existence, and it can achieve an observation rate of 20+ science targets per hour. In more than three years of operations at Palomar Observatory, it has been quite successful, producing technology that is being adapted by other AO systems and robotic telescope projects, as well as several high impact scientific publications. Now, Robo-AO has been selected to take over operation of the Kitt Peak National Observatory 2.1m telescope. This will give Robo-AO KP the opportunity to pursue multiple science programs consisting of several thousand targets each during the three years it will be on the telescope. One-sixth of the observing time will be allocated to the US community through the NOAO TAC process. This presentation will discuss the process adapting Robo-AO to the KPNO 2.1m telescope, the plans for integration and initial operations, and the science operations and programs to be pursued.

  6. DNA encoding a DNA repair protein

    DOEpatents

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  7. DNA polymerases and cancer

    PubMed Central

    Lange, Sabine S.; Takata, Kei-ichi; Wood, Richard D.

    2013-01-01

    There are fifteen different DNA polymerases encoded in mammalian genomes, which are specialized for replication, repair or the tolerance of DNA damage. New evidence is emerging for lesion-specific and tissue-specific functions of DNA polymerases. Many point mutations that occur in cancer cells arise from the error-generating activities of DNA polymerases. However, the ability of some of these enzymes to bypass DNA damage may actually defend against chromosome instability in cells and at least one DNA polymerase, POLζ, is a suppressor of spontaneous tumorigenesis. Because DNA polymerases can help cancer cells tolerate DNA damage, some of these enzymes may be viable targets for therapeutic strategies. PMID:21258395

  8. Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches.

    PubMed

    Ahmad, Irshad; Ahmad, Ajaz; Ahmad, Masood

    2016-03-01

    Pendimethalin (PND) is a systemic herbicide widely used on rice, cotton, peas, wheat, potatoes, fruits, nuts and other residential and non-residential crops; however, it concurrently exerts toxic effects on beneficial organisms like earthworms, aquatic invertebrates and other non-targeted animals including humans. Most likely, the genotoxicity of agrochemicals/drugs is modulated through cellular distribution of bound DNA. Therefore, the in vitro interaction of PND with calf thymus DNA (ctDNA) has been investigated using various sensitive biophysical techniques to ascertain its binding mechanism. UV-visible absorption and fluorescence spectra suggested the formation of a complex between PND and ctDNA. The binding constant of the PND-ctDNA complex was found to be around 10(4) M(-1) using steady state fluorescence titration. The calculated positive values of enthalpy and entropy changes suggested that the binding reaction was predominantly driven by hydrophobic interactions. Competitive displacement studies using acridine orange (AO), ethidium bromide (EB) and Hoechst dye suggested intercalation of PND molecules into the double helix of ctDNA by replacing the bound AO and EB probes. An increase in the viscosity and melting temperature of ctDNA and a decrease in iodine-quenching also support the intercalative binding of PND with ctDNA. Molecular docking analysis further confirmed the specific binding mode of PND between adjacent 'G-C' base pairs of ctDNA. PMID:26862600

  9. LDEF: Dosimetric measurement results (AO 138-7 experiment)

    NASA Technical Reports Server (NTRS)

    Bourrieau, J.

    1992-01-01

    One of the objectives of the AO 138-7 experiment on board the LDEF was a total dose measurement with Thermo Luminescent Detectors (TLD 100). Two identical cases, both including 5 TLDs inside various aluminum shields, are exposed to the space environment in order to obtain the absorbed dose profile induced. Radiation fluence received during the total mission length was computed, taking into account the trapped particles (solar maximum and solar minimum periods) and the cosmic rays; due to the magnetospheric shielding, the solar proton fluences are negligible on the LDEF orbit. The total dose induced by these radiations inside a semi-infinite plane shield of Al are computed with radiation transport codes. TLD reading are performed after flight; due to the mission duration increase, a post-flight calibration was necessary in order to cover the range of the flight induced dose. The results obtained, similar (+ or - 30 pct.) in both cases, are compared with the dose profile computation. In practice, these LDEF results, with less than a factor 1.4 between measurements and forecasts, reinforce the validity of the computation methods and models used for the long term evaluation of space radiation intensity on low inclination Earth orbits.

  10. Atomic oxygen effects on LDEF experiment AO171

    NASA Technical Reports Server (NTRS)

    Whitaker, Ann F.; Kamenetzky, Rachel R.; Finckenor, Miria M.; Norwood, Joseph K.

    1993-01-01

    The Solar Array Materials Passive Long Duration Exposure Facility (LDEF) Experiment (SAMPLE), AO171, contained in total approximately 100 materials and materials processes with a 300 specimen complement. With the exception of experiment solar cell and solar cell modules, all test specimens were weighed before flight, thus allowing an accurate determination of mass loss as a result of space exposure. Since almost all of the test specimens were thermal vacuum baked before flight, the mass loss sustained can be attributed principally to atomic oxygen attack. The atomic oxygen effects observed and measured in five classes of materials is documented. The atomic oxygen reactivity values generated for these materials are compared to those values derived for the same materials from exposures on short term shuttle flights. An assessment of the utility of predicting long term atomic oxygen effects from short term exposures is given. This experiment was located on Row 8 position A which allowed all experiment materials to be exposed to an atomic oxygen fluence of 6.93 x 10(exp 21) atoms/cm(sup 2) as a result of being positioned 38 degrees off the RAM direction.

  11. LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray G10

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray G10 The flight/on-orbit photograph of the G10 experi ment tray was taken from the Orbiter aft flight deck during the LDEF retrieval. A light brown stain can be seen on the experiment tray flanges and to a lesser degree on the IDE Chemglaze Z tained their integrity. A light tan stain on the solar sensor base plate, located in the center of the tray, is more easily seen than that on the IDE mounting plate. Surface defects are highly visible due to the lighting conditions existing at the time the photograph was taken. The lighting angle is such that many impact craters can be seen. Two (2) detectors, located in the twenty (20) detector layout in the lower left corner of the tray, seem to have defects. A triangular shaped discoloration appears on the second detector from the left and in the second row from the bottom. Another irregular shaped discoloration can be seen on the fourth detector from the left and in the third row from the bottom. These discolorations appear to be due to material and/or fabrication defects and not reflected light. The blue colors on the detector's mirror like surface are caused by reflections of the LDEF surroundings.

  12. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray G10

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray G10 The IDE experiment appears to be in excellent condition in the postflight photograph. All bond joints seem to have survived the space environment and the experiment hardware seems to be intact. The direction and intensity of the artificial light source has caused hot spots and reflections that tend to wash out the brown stain on the exposed surfaces. A close inspection of individual detectors reveal locations where impacts have occurred and damage is present. In the detector layout in the lower left corner of the tray, two detectors continue to show the discolorations observed in the flight photograph. A triangular shape can be seen in the detector located in the second horizontal row from the bottom and the second vertical row from the left. The other detector, located in the third horizontal row from the bottom and the fourth vertical row from the left has an irregular shaped, very faint, discolora tion. The blue color in the detectors metallic surface is caused by reflections of the surrounding area.

  13. Ruled and holographic experiment (AO 138-5)

    NASA Technical Reports Server (NTRS)

    Bonnemason, Francis

    1993-01-01

    The AO 138-5 experiment was designed, via the FRECOPA (FRench COoperative PAyload) experiment with the aim to study the optical behavior of different diffraction gratings submitted to space vacuum long exposure and solar irradiation. Samples were ruled and holographic gratings, masters or replica, and some additional control mirrors with various coatings. The experiment was located on the B3, trailing edge of the LDEF and was protected against Atomic Oxygen flux. The experienced thermal cycling was evaluated from -23 C to 66 C during the flight, 34,000 orbits. The samples (two batches of four pieces) were located on a dedicated plate, by a pair of equivalent gratings or mirrors; optical faces were located on the external side. The plate was inside a canister, which had been opened in space for ten months. When the satellite returned to Kennedy Space Center, the remaining vacuum in the canister was still correct. The analysis focused on the triple point characterization including light efficiency, wavefront flatness quality and stray light level. Tests were conducted on control mirrors and gratings (rules and holographic master or replica) loaded but not exposed to cosmic dust or direct solar irradiations. They did not show any significant variations. Solar exposure had damaged the coating (aluminum and platinum) reflectivity in the Ultra-Violet region; the degradation is higher with the gratings, in terms of efficiency. However, wavefront flatness quality and stray light level tests revealed no additional changes.

  14. Four year experience with the AO Anterior Thoracolumbar Locking Plate.

    PubMed

    Thalgott, J S; Kabins, M B; Timlin, M; Fritts, K; Giuffre, J M

    1997-05-01

    For decades spinal surgeons have attempted to design simple, single stage anterior internal fixation systems for the thoracic and lumbar spine. Early devices presented both biomechanical and technical problems. The AO Anterior Thoracolumbar Locking Plate (ATLP) was designed to solve some of the problems encountered with early anterior instrumentation. The ATLP system is constructed in Commercially Pure titanium. It is a low profile device indicated for use for unstable burst fractures in the anterior column; metastatic tumor management; and degenerative diseases of the thoracolumbar spine between levels T10 and L5. Implantation of the device involves direct anterior decompression with sagittal reduction and corpectomy. This is followed by grafting reconstruction, and plate fixation. This device has been implanted in 25 patients with an average follow-up of 38 months. There were five (5) broken screws in three (3) patients, and no broken plates. Implant related postoperative complications included two misplaced screws. Preliminary results indicate that the ATLP system seems to be a safe, low profile, MRI/CT compatible device that provides definitive single stage fixation of the anterior spinal column. PMID:9160452

  15. Ruled and holographic experiment (AO 138-5)

    NASA Astrophysics Data System (ADS)

    Bonnemason, Francis

    1993-04-01

    The AO 138-5 experiment was designed, via the FRECOPA (FRench COoperative PAyload) experiment with the aim to study the optical behavior of different diffraction gratings submitted to space vacuum long exposure and solar irradiation. Samples were ruled and holographic gratings, masters or replica, and some additional control mirrors with various coatings. The experiment was located on the B3, trailing edge of the LDEF and was protected against Atomic Oxygen flux. The experienced thermal cycling was evaluated from -23 C to 66 C during the flight, 34,000 orbits. The samples (two batches of four pieces) were located on a dedicated plate, by a pair of equivalent gratings or mirrors; optical faces were located on the external side. The plate was inside a canister, which had been opened in space for ten months. When the satellite returned to Kennedy Space Center, the remaining vacuum in the canister was still correct. The analysis focused on the triple point characterization including light efficiency, wavefront flatness quality and stray light level. Tests were conducted on control mirrors and gratings (rules and holographic master or replica) loaded but not exposed to cosmic dust or direct solar irradiations. They did not show any significant variations. Solar exposure had damaged the coating (aluminum and platinum) reflectivity in the Ultra-Violet region; the degradation is higher with the gratings, in terms of efficiency. However, wavefront flatness quality and stray light level tests revealed no additional changes.

  16. DNA Nanotechnology-- Architectures Designed with DNA

    NASA Astrophysics Data System (ADS)

    Han, Dongran

    As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.

  17. Communication: Origin of the contributions to DNA structure in phages

    PubMed Central

    Myers, Christopher G.; Pettitt, B. Montgomery

    2013-01-01

    Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies. PMID:23444988

  18. Communication: Origin of the contributions to DNA structure in phages

    NASA Astrophysics Data System (ADS)

    Myers, Christopher G.; Pettitt, B. Montgomery

    2013-02-01

    Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.

  19. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  20. Patterns of Impairments in AOS and Mechanisms of Interaction between Phonological and Phonetic Encoding

    ERIC Educational Resources Information Center

    Laganaro, Marina

    2012-01-01

    Purpose: One reason why the diagnosis of apraxia of speech (AOS) and its underlying impairment are often debated may lie in the fact that most patients do not display pure patterns of AOS. Mixed patterns are clearly acknowledged at other levels of impairment (e.g., lexical-semantic and lexical-phonological), and they have contributed to debate…

  1. SCExAO as a precursor to an ELT exoplanet direct imaging instrument

    NASA Astrophysics Data System (ADS)

    Jovanovic, Nemanja; Guyon, Olivier; Martinache, Frantz; Clergeon, Christophe; Singh, Garima; Vievard, Sebastien; Kudo, Tomoyuki; Garrel, Vincent; Norris, Barnaby; Tuthill, Peter; Stewart, Paul; Huby, Elsa; Perrin, Guy; Lacour, Sylvestre

    2013-12-01

    The Subaru Coronagraphic Extreme AO (SCExAO) instrument consists of a high performance Phase Induced Amplitude Apodisation (PIAA) coronagraph combined with an extreme Adaptive Optics (AO) system operating in the near-infrared (H band). The extreme AO system driven by the 2000 element deformable mirror will allow for Strehl ratios>90% to be achieved in the H-band when it goes closed loop. This makes the SCExAO instrument a powerful platform for high contrast imaging down to angular separations of the order of 1 lambda/D and an ideal testbed for exploring coronagraphic techniques for ELTs. In this paper we report on the recent progress in regards to the development of the instrument, which includes the addition of a visible bench that makes use of the light at shorter wavelengths not currently utilized by SCExAO and closing the loop on the tip/tilt wavefront sensor. We will also discuss several exciting guest instruments which will expand the capabilities of SCExAO over the next few years; namely CHARIS which is a integral field spectrograph as well as VAMPIRES, a visible aperture masking experiment based on polarimetric analysis of circumstellar disks. In addition we will elucidate the unique role extreme AO systems will play in enabling high precision radial velocity spectroscopy for the detection of small companions.

  2. MagAO: Status and on-sky performance of the Magellan adaptive optics system

    NASA Astrophysics Data System (ADS)

    Morzinski, Katie M.; Close, Laird M.; Males, Jared R.; Kopon, Derek; Hinz, Phil M.; Esposito, Simone; Riccardi, Armando; Puglisi, Alfio; Pinna, Enrico; Briguglio, Runa; Xompero, Marco; Quirós-Pacheco, Fernando; Bailey, Vanessa; Follette, Katherine B.; Rodigas, T. J.; Wu, Ya-Lin; Arcidiacono, Carmelo; Argomedo, Javier; Busoni, Lorenzo; Hare, Tyson; Uomoto, Alan; Weinberger, Alycia

    2014-07-01

    MagAO is the new adaptive optics system with visible-light and infrared science cameras, located on the 6.5-m Magellan "Clay" telescope at Las Campanas Observatory, Chile. The instrument locks on natural guide stars (NGS) from 0th to 16th R-band magnitude, measures turbulence with a modulating pyramid wavefront sensor binnable from 28×28 to 7×7 subapertures, and uses a 585-actuator adaptive secondary mirror (ASM) to provide at wavefronts to the two science cameras. MagAO is a mutated clone of the similar AO systems at the Large Binocular Telescope (LBT) at Mt. Graham, Arizona. The high-level AO loop controls up to 378 modes and operates at frame rates up to 1000 Hz. The instrument has two science cameras: VisAO operating from 0.5-1μm and Clio2 operating from 1-5 μm. MagAO was installed in 2012 and successfully completed two commissioning runs in 2012-2013. In April 2014 we had our first science run that was open to the general Magellan community. Observers from Arizona, Carnegie, Australia, Harvard, MIT, Michigan, and Chile took observations in collaboration with the MagAO instrument team. Here we describe the MagAO instrument, describe our on-sky performance, and report our status as of summer 2014.

  3. DNA Deformations near Charged Surfaces: Electron and Atomic Force Microscopy Views

    PubMed Central

    Faas, F.G.A.; Rieger, B.; van Vliet, L.J.; Cherny, D.I.

    2009-01-01

    Abstract DNA is a very important cell structural element, which determines the level of expression of genes by virtue of its interaction with regulatory proteins. We use electron (EM) and atomic force microscopy (AFM) to characterize the flexibility of double-stranded DNA (∼150–950 nm long) close to a charged surface. Automated procedures for the extraction of DNA contours (∼10–120 nm for EM data and ∼10–300 nm for AFM data) combined with new statistical chain descriptors indicate a uniquely two-dimensional equilibration of the molecules on the substrate surface regardless of the procedure of molecule mounting. However, in contrast to AFM, the EM mounting leads to a noticeable decrease in DNA persistence length together with decreased kurtosis. Analysis of local bending on short length scales (down to 6 nm in the EM study) shows that DNA flexibility behaves as predicted by the wormlike chain model. We therefore argue that adhesion of DNA to a charged surface may lead to additional static bending (kinking) of ∼5 degrees per dinucleotide step without impairing the dynamic behavior of the DNA backbone. Implications of this finding are discussed. PMID:19686663

  4. Visualization of Bacteriophage T3 Capsids with DNA Incompletely Packaged In Vivo

    PubMed Central

    Fang, Ping-An; Wright, Elena T.; Weintraub, Susan T.; Hakala, Kevin; Wu, Weimin; Serwer, Philip; Jiang, Wen

    2009-01-01

    The tightly packaged dsDNA genome in the mature particles of many tailed bacteriophages has been shown to form multiple concentric rings when reconstructed from cryo-electron micrographs. However, recent single-particle DNA packaging force measurements have suggested that incompletely packaged DNA (ipDNA) is less ordered when it is shorter than ∼25% of the full genome length. The study presented here initially achieves both the isolation and the ipDNA length-based fractionation of ipDNA-containing T3 phage capsids (ipDNA-capsids) produced by DNA packaging in vivo; some ipDNA has quantized lengths, as judged by high-resolution gel electrophoresis of expelled DNA. This is the first isolation of such particles among the tailed dsDNA bacteriophages. The ipDNA-capsids are a minor component (containing ∼10-4 of packaged DNA in all particles) and are initially detected by non-denaturing gel electrophoresis after partial purification by buoyant density centrifugation. The primary contaminants are aggregates of phage particles and empty capsids. This study then investigates ipDNA conformations by the first cryo-electron microscopy (cryo-EM) of ipDNA-capsids produced in vivo. The 3-D structures of DNA-free capsids, ipDNA-capsids with various lengths of ipDNA, and mature bacteriophage are reconstructed, which reveals the typical T=7l icosahedral shell of many tailed dsDNA bacteriophages. Though the icosahedral shell structures of these capsids are indistinguishable at the current resolution for the protein shell (∼15 Å), the conformations of the DNA inside the shell are drastically different. T3 ipDNA-capsids with 10.6 kb or shorter dsDNA (<28% of total genome) have an ipDNA conformation indistinguishable from random. However, T3 ipDNA-capsids with 22 kb DNA (58% of total genome) forms a single DNA ring next to the inner surface of the capsid shell. In contrast, dsDNA fully packaged (38.2 kb) in mature T3 phage particles forms multiple concentric rings like those seen

  5. OV-Wav: um novo pacote para análise multiescalar em astronomia

    NASA Astrophysics Data System (ADS)

    Pereira, D. N. E.; Rabaça, C. R.

    2003-08-01

    Wavelets e outras formas de análise multiescalar têm sido amplamente empregadas em diversas áreas do conhecimento, sendo reconhecidamente superiores a técnicas mais tradicionais, como as análises de Fourier e de Gabor, em certas aplicações. Embora a teoria dos wavelets tenha começado a ser elaborada há quase trinta anos, seu impacto no estudo de imagens astronômicas tem sido pequeno até bem recentemente. Apresentamos um conjunto de programas desenvolvidos ao longo dos últimos três anos no Observatório do Valongo/UFRJ que possibilitam aplicar essa poderosa ferramenta a problemas comuns em astronomia, como a remoção de ruído, a detecção hierárquica de fontes e a modelagem de objetos com perfis de brilho arbitrários em condições não ideais. Este pacote, desenvolvido para execução em plataforma IDL, teve sua primeira versão concluída recentemente e está sendo disponibilizado à comunidade científica de forma aberta. Mostramos também resultados de testes controlados ao quais submetemos os programas, com a sua aplicação a imagens artificiais, com resultados satisfatórios. Algumas aplicações astrofísicas foram estudadas com o uso do pacote, em caráter experimental, incluindo a análise da componente de luz difusa em grupos compactos de galáxias de Hickson e o estudo de subestruturas de nebulosas planetárias no espaço multiescalar.

  6. Robo-AO: Initial results from the first autonomous laser guide star adaptive optics instrument

    NASA Astrophysics Data System (ADS)

    Riddle, R. L.; Baranec, C.; Law, N. M.; Ramaprakash, A. N.; Tendulkar, S.; Hogstrom, K.; Bui, K.; Burse, M.; Chordia, P.; Das, H.; Dekany, R.; Kulkarni, S.; Punnadi, S.; Smith, R.

    2014-12-01

    Large surveys are discovering thousands of objects which require further characterization at high angular resolution. The demands on space-based observatories and large telescopes with AO systems leave them generally unavailable for large high angular resolution surveys. To address this gap, we have developed Robo-AO, the first robotic laser AO system, as an economical and efficient imaging instrument for 1-3 m class telescopes. Observations of over 200 stellar objects per night have routinely been performed, with target-to-target observation overheads of less than 1.5 minutes. Scientific programs of several thousands of targets can be executed in mere weeks, and Robo-AO has already completed the three largest AO surveys to date.

  7. AO-308: the high-order adaptive optics system at Big Bear Solar Observatory

    NASA Astrophysics Data System (ADS)

    Shumko, Sergey; Gorceix, Nicolas; Choi, Seonghwan; Kellerer, Aglaé; Cao, Wenda; Goode, Philip R.; Abramenko, Volodymyr; Richards, Kit; Rimmele, Thomas R.; Marino, Jose

    2014-08-01

    In this paper we present Big Bear Solar Observatory's (BBSO) newest adaptive optics system - AO-308. AO-308 is a result of collaboration between BBSO and National Solar Observatory (NSO). AO-308 uses a 357 actuators deformable mirror (DM) from Xinetics and its wave front sensor (WFS) has 308 sub-apertures. The WFS uses a Phantom V7.3 camera which runs at 2000 Hz with the region of interest of 416×400 pixels. AO-308 utilizes digital signal processors (DSPs) for image processing. AO-308 has been successfully used during the 2013 observing season. The system can correct up to 310 modes providing diffraction limited images at all wavelengths of interest.

  8. Multi-conjugate AO for the European Solar Telescope

    NASA Astrophysics Data System (ADS)

    Montilla, I.; Béchet, C.; Le Louarn, M.; Tallon, M.; Sánchez-Capuchino, J.; Collados Vera, M.

    2012-07-01

    The European Solar Telescope (EST) will be a 4-meter diameter world-class facility, optimized for studies of the magnetic coupling between the deep photosphere and upper chromosphere. It will specialize in high spatial resolution observations and therefore it has been designed to incorporate an innovative built-in Multi-Conjugate Adaptive Optics system (MCAO). It combines a narrow field high order sensor that will provide the information to correct the ground layer and a wide field low order sensor for the high altitude mirrors used in the MCAO mode. One of the challenging particularities of solar AO is that it has to be able to correct the turbulence for a wide range of observing elevations, from zenith to almost horizon. Also, seeing is usually worse at day-time, and most science is done at visible wavelengths. Therefore, the system has to include a large number of high altitude deformable mirrors. In the case of the EST, an arrangement of 4 high altitude DMs is used. Controlling such a number of mirrors makes it necessary to use fast reconstruction algorithms to deal with such large amount of degrees of freedom. For this reason, we have studied the performance of the Fractal Iterative Method (FriM) and the Fourier Transform Reconstructor (FTR), to the EST MCAO case. Using OCTOPUS, the end-to-end simulator of the European Southern Observatory, we have performed several simulations with both algorithms, being able to reach the science requirement of a homogeneous Strehl higher that 50% all over the 1 arcmin field of view.

  9. A reflective Gaussian coronagraph for ExAO: laboratory performance

    NASA Astrophysics Data System (ADS)

    Park, Ryeojin; Close, Laird M.; Siegler, Nick; Nielsen, Eric L.; Stalcup, Thomas

    2006-06-01

    We report laboratory results of a coronagraphic testbed to assess the intensity reduction differences between a "Gaussian" tapered focal plane coronagraphic mask and a classical hard-edged "Top Hat" function mask at Extreme Adaptive Optics (ExAO) Strehl ratios of ~94%. However, unlike a traditional coronagraph design, we insert a reflective focal plane mask at 45 ° to the optical axis and used a "spot of Arago blocker" (axicon stop) before a final image in order to block additional mask edge-diffracted light. The testbed simulates the optical train of ground-based telescopes (in particular the 8.1m Gemini North telescope) and includes one spider vane and different mask radii (r= 1.9λ/D, 3.7λ/D, 7.4λ/D) and two types of reflective focal plane masks (hard-edged "Top Hat" and "Gaussian" tapered profiles). In order to investigate the performance of these competing coronagraphic designs with regard to extra-solar planet detection sensitivity, we utilize the simulation of realistic extra-solar planet populations (Nielsen et al. 2006). With an appropriate translation of our laboratory results to expected telescope performance, a "Gaussian" tapered mask radius of 3.7λ/D with an axicon stop performs best (highest planet detection sensitivity). For a full survey with this optimal design, the simulation predicts ~30% more planets detected compared to a similar sized "Top Hat" function mask with an axicon stop. Using the best design, the "point contrast ratio" between the stellar PSF peak and the coronagraphic PSF at 10λ/D (0.4" in H band if D = 8.1m) is 1.4 x 10 6. This is ~10 times higher than a classical Lyot "Top Hat" coronagraph.

  10. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray B12

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray B12 The postflight photograph shows little change of the exposed surfaces when compared with the prelaunch photograph. Although not noticable in the photograph, a light coating of contamination was seen on all experiment surfaces in this location. The difference in colors of the IDE detectors, located on the right hand mounting plate, is a result of the reflected surroundings and not related to space exposure. A close observation of the detector surfaces reveal that some damage has occured from meteroid and/or debris impacts. One impact crater can be seen, upper right quadrant, on the detector located in the sixth (6th) row down from the top and the fifth (5th) row from the right. Other impacts, smaller in size, show as small white dots on the detector surface. The solar sensor seems to have changed little, if any. However, the color of the solar array baseplate, showing indications of contamination, appears to be darker than the detector mounting plate. The center section cover plate shows little change when compared with the pre-launch photograph. However, during inspection, a light coat of the brown contamination has been observed on all surfaces. The color of the bonding material (RTV) used to secure several thin specimen, sapphire, to individual mounting plates has changed from pink to gold. At one location, that of a single specimen, the bonding material is more gray than gold in color. This has been attributed to the specimen being considerably thicker. The EPDS thermal cover in the right hand side of the tray shows a light coating of brown contamination on the Chemglaze II A-276 white paint.

  11. AO Capabilities at the MMT for the User

    NASA Astrophysics Data System (ADS)

    Lloyd-Hart, Michael M.

    2009-05-01

    The MMT operates a facility natural guide star (NGS) AO system. Diffraction limited imaging and medium and high resolution spectroscopy in the near IR are offered over the full isoplanatic field with the ARIES instrument.The system also offers imaging with unique sensitivity in the thermal IR from 3 to 10 microns thanks to its use of an adaptive secondary mirror. L and M band imaging is offered with Clio which has a 12x15 arcsec field of view with Nyquist sampling if the diffraction limt. Recent M band images from Clio show the planetary system around HR8799. In addition, 10 - 25 micron imaging is offered with the MIRAC camera, which may also be operated as a Bracewell nulling interferometer. In this mode, two large subapertures are defined within the pupil. Light from the two is combined so as to cancel the light from an unresolved star through destructive interference, while the environs are imaged in constructive interference. In this way, dust disks and planetary systems may be imaged with greatly improved contrast. The MMT also operates the first astronomical adaptive optics system to employ multiple laser guide stars (LGS). Its initial operational mode, ground-layer adaptive optics (GLAO), provides uniform stellar wavefront correction within the 2 arcmin diameter laser beacon constellation, routinely reducing the stellar image widths to < 0.3 arcsec in the J - K bands. An imaging camera,PISCES, is available for these bands with 2 arcmin field of view sampled at 0.1 arcsec/pixel. In addition, L and M band imaging will be available with Clio in the fall of 2009, opening up near all-sky coverage with near-diffraction limited image quality and emissivity of just 7%.

  12. Determinação de regiões de órbitas diretas estáveis ao redor da Lua

    NASA Astrophysics Data System (ADS)

    de Melo, C. F.; Winter, O. C.; Vieira Neto, E.

    2003-08-01

    Neste Trabalho estamos investigando regiões do sistema Terra-Lua que contêm órbitas diretas estáveis ao redor da Lua visando a utilização destas órbitas em futuras missões de veículos espaciais como alternativas de trajetórias com baixo custo de manutenção. Adotando-se o problema restrito de três corpos, Terra-Lua-partícula, a localização e a extensão destas regiões de estabilidade foram investigadas numericamente considerando como estável toda órbita que permanece ao redor a Lua por, no mínimo, 1000 dias com energia de dois corpos da partícula em relação à Lua negativa. A estabilidade de tais regiões está associada a duas famílias de órbitas periódicas simples H1 e H2 e a órbitas quase-periódicas associadas a elas. Uma vez identificadas as regiões de estabilidade passamos a analisá-las introduzindo, paulatinamente, outras interações relevantes ao sistema como as perturbações do Sol (via problema restrito de quatro corpos), das marés, da pressão de radiação e do achatamento terrestre. Os resultados encontrados até o momento mostram que a perturbação do Sol é a única que reduz significativamente o tamanho das regiões de estabilidade. Também estamos investigando o comportamento de tais regiões quando características intrínsecas do sistema como as excentricidades das órbitas da Terra e da Lua e a inclinação da órbita Lua são consideradas. Com este estudo estamos reunindo informações que nos permitirão compreender a evolução das regiões de estabilidade no sistema Terra-Lua, bem como estabelecer parâmetros adequados para a utilização das trajetórias estáveis em futuras missões espaciais. Agradecimentos: Este projeto conta com o apoio do CNPq, da Capes e da Fapesp.

  13. Aquisição de Estreptococos Mutans e Desenvolvimento de Cárie Dental em Primogênitos

    PubMed Central

    NOCE, Erica; RUBIRA, Cassia Maria Fischer; da Silva ROSA, Odila Pereira; da SILVA, Salete Moura Bonifácio; BRETZ, Walter Antonio

    2011-01-01

    Objetivo Avaliar o momento de aquisição de estreptococos mutans (EM), desenvolvimento de cárie dental e as variáveis a eles associadas no decorrer de 23 meses, em primogênitos de famílias de baixo nível socioeconômico, desde os sete meses de idade. Método A amostra foi selecionada com base em mães densamente colonizadas por EM, incluindo todos os membros de 14 famílias que conviviam na mesma casa. Foram envolvidos no estudo 14 mães, pais e primogênitos e 8 parentes, na maioria avós. Exames clínicos e radiográficos iniciais determinaram os índices de cárie e condição periodontal dos adultos. Contagens de EM foram feitas em todos os adultos nas duas primeiras visitas. Nas crianças foram avaliados os níveis de EM, o número de dentes e de cáries, em quatro visitas. Resultados A prevalência de EM nos adultos foi alta, estando ausente em apenas um dos pais. EM foram detectados em 1, 2, 3 e 10 crianças, respectivamente nas visitas #1, 2, 3 e 4. A cárie dental foi detectada em apenas três crianças na última visita (aos 30 meses de idade), as quais apresentaram escores de EM significantemente maiores que as crianças sem cárie, na mesma visita. Conclusão Exclusivamente a condição social de baixa renda e mães densamente colonizadas por EM não são sinônimo de colonização precoce e alta atividade de cárie em crianças cuidadas em casa. O desenvolvimento de cárie está significantemente associado a escores elevados de EM nas crianças. PMID:22022218

  14. LDEF: Dosimetric measurement results (AO 138-7 experiment)

    NASA Technical Reports Server (NTRS)

    Bourrieau, J.

    1993-01-01

    One of the objectives of the AO 138-7 experiment on board the Long Duration Exposure Facility (LDEF) was a total dose measurement with Thermo Luminescent Detectors (TLD 100). Two identical packages, both of them including five TLD's inside various aluminum shields, are exposed to the space environment in order to obtain the absorbed dose profile. Radiation fluence received during the total mission length was computed, taking into account the trapped particles (AE8 and AP8 models during solar maximum and minimum periods) and the cosmic rays; due to the magnetospheric shielding the solar proton fluences are negligible on the LDEF orbit. The total dose induced by these radiations inside a semi infinite plane shield of aluminum are computed with the radiation transport codes available at DERTS. The dose profile obtained is in good agreement with the evaluation by E.V. Benton. TLD readings are performed after flight; due to the mission duration increase a post flight calibration was necessary in order to cover the range of the in flight induced dose. The results obtained, similar (plus or minus 30 percent) for both packages, are compared with the dose profile computation. For thick shields it seems that the measurements exceed the forecast (about 40 percent). That can be due to a cosmic ray and trapped proton contributions coming from the backside (assumed as perfectly shielded by the LDEF structure in the computation), or to an underestimate of the proton or cosmic ray fluences. A fine structural shielding analysis should be necessary in order to determine the origin of this slight discrepancy between forecast and in flight measurements. For the less shielded dosimeters, mainly exposed to the trapped electron flux, a slight overestimation of the dose (less than 40 percent) appears. Due to the dispersion of the TLD's response, this cannot be confirmed. In practice these results obtained on board LDEF, with less than a factor 1.4 between measurements and forecast

  15. Bringing the visible universe into focus with Robo-AO.

    PubMed

    Baranec, Christoph; Riddle, Reed; Law, Nicholas M; Ramaprakash, A N; Tendulkar, Shriharsh P; Bui, Khanh; Burse, Mahesh P; Chordia, Pravin; Das, Hillol K; Davis, Jack T C; Dekany, Richard G; Kasliwal, Mansi M; Kulkarni, Shrinivas R; Morton, Timothy D; Ofek, Eran O; Punnadi, Sujit

    2013-01-01

    a high-power laser beam in the direction of the astronomical target to create an artificial reference of known shape, also known as a 'laser guide star'. The Robo-AO laser adaptive optics system, employs a 10-W ultraviolet laser focused at a distance of 10 km to generate a laser guide star. Wavefront sensor measurements of the laser guide star drive the adaptive optics correction resulting in diffraction-limited images that have an angular resolution of ~0.1 arc seconds on a 1.5-m telescope. PMID:23426078

  16. Bringing the Visible Universe into Focus with Robo-AO

    PubMed Central

    Baranec, Christoph; Riddle, Reed; Law, Nicholas M.; Ramaprakash, A.N.; Tendulkar, Shriharsh P.; Bui, Khanh; Burse, Mahesh P.; Chordia, Pravin; Das, Hillol K.; Davis, Jack T.C.; Dekany, Richard G.; Kasliwal, Mansi M.; Kulkarni, Shrinivas R.; Morton, Timothy D.; Ofek, Eran O.; Punnadi, Sujit

    2013-01-01

    focus a high-power laser beam in the direction of the astronomical target to create an artificial reference of known shape, also known as a 'laser guide star'. The Robo-AO laser adaptive optics system2,3 employs a 10-W ultraviolet laser focused at a distance of 10 km to generate a laser guide star. Wavefront sensor measurements of the laser guide star drive the adaptive optics correction resulting in diffraction-limited images that have an angular resolution of ~0.1 arc seconds on a 1.5-m telescope. PMID:23426078

  17. LCAT DNA shearing.

    PubMed

    Okabe, Yuka; Lee, Abraham P

    2014-04-01

    We present a novel method to fragment DNA by using lateral cavity acoustic transducers (LCATs). DNA solution is placed within a microfluidic device containing LCATs. The LCATs cause microstreaming, which fragments DNA within the solution without any need for purification or downstream processing. The LCAT-based DNA fragmentation method offers an easy-to-use, low-cost, low-energy way to fragment DNA that is amenable to integration on microfluidic platforms to further automate DNA processing. Furthermore, the LCAT microdevice requires less than 10 µL of sample, and no external equipment is needed besides a piezoelectric transducer. PMID:23850863

  18. emGain: Determination of EM gain of CCD

    NASA Astrophysics Data System (ADS)

    Daigle, Olivier; Carignan, Claude; Blais-Ouellette, Sebastien

    2012-01-01

    The determination of the EM gain of the CCD is best done by fitting the histogram of many low-light frames. Typically, the dark+CIC noise of a 30ms frame itself is a sufficient amount of signal to determine accurately the EM gain with about 200 512x512 frames. The IDL code emGain takes as an input a cube of frames and fit the histogram of all the pixels with the EM stage output probability function. The function returns the EM gain of the frames as well as the read-out noise and the mean signal level of the frames.

  19. Calibration of a curvature sensor/bimorph mirror AO system: interaction matrix measurement on MACAO systems

    NASA Astrophysics Data System (ADS)

    Oberti, Sylvain; Bonnet, Henri; Fedrigo, Enrico; Ivanescu, Liviu; Kasper, Markus E.; Paufique, Jerome

    2004-10-01

    The accurate calibration of an AO system is fundamental in order to reach the top performance expected from design. To improve this aspect, we propose procedures for calibrating a curvature AO system in view of optimizing performances and robustness, based on the experience accumulated by the ESO AO team through the development of MACAO systems for VLTI and SINFONI. The approach maximizes the quality of the Interaction Matrix (IM) while maintaining the system in its linear regime and minimizing noise and bias on the measurement.

  20. Structural Organization of DNA.

    ERIC Educational Resources Information Center

    Banfalvi, Gaspar

    1986-01-01

    Explains the structural organization of DNA by providing information on the primary, secondary, tertiary, and higher organization levels of the molecule. Also includes illustrations and descriptions of sign-inversion and rotating models for supercoiling of DNA. (ML)

  1. Modeling DNA Replication.

    ERIC Educational Resources Information Center

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  2. HPV DNA test

    MedlinePlus

    The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...

  3. DNA tagged microparticles

    DOEpatents

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  4. LDEF (Prelaunch), AO201 : Interplanetary Dust Experiment, Tray B12

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO201 : Interplanetary Dust Experiment, Tray B12 The prelaunch photograph shows the six (6) inch deep Interplanetary Dust Experiment (IDE) master control tray. The tray has three (3) mounting/cover plates elevated on fiberglass stand-offs to provide clearance and protection for hardware and electronics located underneath. The stand-offs also raise the plates to a level that minimizes shading of detectors by the tray sidewalls. The mounting plate located at the left hand end of the tray is populated with eighty (80) metaloxide-silicon (MOS) capacitor-type impact sensors and one (1) solar sensor that is located approximately in the center of the mounting plate. The IDE sensors are two (2) inch diameter MOS capacitor structures approximately 250 um thick. The detectors are formed by growing either 0.4um or 1.0um thick silicon oxide, SiO2, layer on the 250um thick, B-doped polished silicon wafer. The top metal contact, the visible surface, was formed by vapor deposition of 1000A of aluminum on the SiO2 surface. Aluminum was also vapor deposited on the backside to form the contact with the silicon substrate. Gold wires are bonded to the front and back aluminum layers for use in connecting the detectors to the circuits. The complete wafers, IDE detectors, are mounted on chromic anodized aluminum frames by bonding the detector backside to the aluminum frame with a space qualified RTV silicon adhesive, de-volatized RTV-511. The difference in colors of the detectors is caused by reflections in the metallized surfaces. A reflection of one of the technicians is visible in the three (3) rows of detector on the left hand side of the mounting plate. The solar sensor, located at the mounting plate center, consist of four (4) silicon solar cells connected in series and associated circuity bonded to an aluminum baseplate. The solar sensor registered each orbital sunrise independant of LDEF orientation at the time of sunrise. When IDE solar sensor data from the six

  5. Is DNA a language?

    PubMed

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1997-01-01

    DNA sequences usually involve local construction rules that affect different scales. As such their "dictionary" may not follow Zipf's law (a power law) which is followed in every natural language. Indeed, analysis of many DNA sequences suggests that no linguistics connections to DNA exist and that even though it has structure DNA is not a language. Computer simulations and a biological approach to this problem further support these results. PMID:9039397

  6. DNAzymes in DNA Nanomachines and DNA Analysis

    NASA Astrophysics Data System (ADS)

    He, Yu; Tian, Ye; Chen, Yi; Mao, Chengde

    This chapter discusses our efforts in using DNAzymes in DNA nano-machines and DNA analysis systems. 10-23 DNAzymes can cleave specific phos-phodiester bonds in RNA. We use them to construct an autonomous DNA-RNA chimera nanomotor, which constantly extracts chemical energy from RNA substrates and transduces the energy into a mechanical motion: cycles of contraction and extension. The motor's motion can be reversibly turned on and off by a DNA analogue (brake) of the RNA substrate. Addition and removal of the brake stops and restarts, respectively, the motor's motion. Furthermore, when the RNA substrates are preorganized into a one-dimensional track, a DNAzyme can continuously move along the track so long as there are substrates available ahead. Based on a similar mechanism, a novel DNA detection system has been developed. A target DNA activates a DNAzyme to cleave RNA-containing molecular beacons (MB), which generates an enhanced fluorescence signal. A following work integrates two steps of signal amplifications: a rolling-circle amplification (RCA) to synthesize multiple copies of DNAzymes, and the DNAzymes catalyze a chemical reaction to generate a colorimetric signal. This method allows detection of DNA analytes whose concentration is as low as 1 pM.

  7. East Asian winter temperature variation associated with the combined effects of AO and WP pattern

    NASA Astrophysics Data System (ADS)

    Park, Hye-Jin; Ahn, Joong-Bae

    2016-04-01

    The combined effects of the Arctic Oscillation (AO) and Western Pacific (WP) teleconnection pattern on the East Asian winter monsoon (EAWM) over the last 56 years (1958/59-2013/2014) were investigated using NCEP/NCAR reanalysis data (Park and Ahn, 2015). The study results revealed that the effect of the AO on winter temperature in East Asia could be changed depending on the phases of the WP pattern in the North Pacific. The negative relationship between the EAWM and the AO increased when the AO and WP were in-phase with each other. Hence, when winter negative (positive) AO was accompanied by negative (positive) WP, negative (positive) temperature anomalies were dominant across the entire East Asia region. Conversely, when the AO and WP were of-of-phase, the winter temperature anomaly in East Asia did not show distinct changes. Furthermore, from the perspective of stationary planetary waves, the zonal wavenumber-2 patterns of sea level pressure and geopotential height at 500hPa circulation strengthened when the AO and WP were in-phase but were not significant for the out-of-phase condition. It explained the possible mechanism of the combined effects of the AO and WP on the circulation related to EAWM. Reference Park, H.-J., and J.-B. Ahn (2015) Combined effect of the Arctic Oscillation and the Western Pacific pattern on East Asia winter temperature, Clim. Dyn. DOI:10.1007/s00382-015-2763-2. Acknowledgements This work was funded by the Korea Meteorological Administration Research and Development Program under grant KMIPA2015-2081.

  8. The Many Sides of DNA.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1997-01-01

    Explores the meaning of DNA. Discusses histories of DNA, literature on DNA, the contributions of Max Delbruck and Barbara McClintock, life, views of control, current research, and the language of DNA. Contains 24 references. (JRH)

  9. Building a reliable, scalable and affordable RTC for AO instruments on ELTs

    NASA Astrophysics Data System (ADS)

    Gratadour, Damien; Sevin, Arnaud; Perret, Denis; Brule, Julien

    2013-12-01

    Addressing the unprecedented amount of computing power needed by the ELTs AO instruments real-time controllers (RTC) is one of the key technological developments required for the design of the next generation AO systems. Throughput oriented architectures such as GPUs, providing orders of magnitude greater computational performance than high-end CPUs, have recently appeared as attractive and economically viable candidates since the fast emergence of devices capable of general purpose computing. However, using for real-time applications a I/0 device which cannot be scheduled nor controlled internally by the operating system but is sent commands through a closed source driver comes with a number of challenges. Building on the experience of almost real-time end-to-end simulations using GPUs, and relying on the development of the COMPASS platform, a unified and optimized framework for AO simulations and real-time control, our team has engaged into the development of a scalable, heterogeneous GPU-based prototype for an AO RTC. In this paper, we review the main challenges arising when utilizing GPUs in real-time systems for AO and rank them in terms of impact significance and available solutions. We present our strategy, to mitigate these issues including the general architecture of our prototype, the real-time core and additional dedicated components for data acquisition and distribution. Finally, we discuss the expected performance in terms of latency and jitter on the basis of realistic benchmarks and focusing on the dimensioning of the MICADO AO module RTC.

  10. Robo-AO: Initial results from the first autonomous laser guide star adaptive optics instrument

    NASA Astrophysics Data System (ADS)

    Riddle, R.; Baranec, C.; Law, N. M.; Ramaprakash, A. N.; Tendulkar, S.; Hogstrom, K.; Bui, K.; Burse, M.; Chordia, P.; Das, H.; Dekany, R.; Kulkarni, S.; Punnadi, S.; Smith, R.

    2014-03-01

    Large surveys, such as the Kepler mission and Palomar Transient Factory, are discovering upwards of thousands of objects which require further characterization at angular resolutions significantly finer than normally allowed by atmospheric seeing. The demands on precious space-based observatories (i.e. Hubble Space Telescope) and large telescopes with adaptive optics (AO) systems (i.e. Keck, VLT, Gemini) leave them generally unavailable for high angular resolution surveys of more than a few hundred targets at a time. To address the gap between scientific objects and available telescopes, we have developed Robo-AO, the first robotic laser AO system, as an economical and efficient imaging instrument for the more readily available 1-3 m class telescopes. The Robo-AO system system demonstrates angular resolutions approaching the visible diffraction limit of the Palomar 60-inch telescope. Observations of over 200 stellar objects per night have routinely been performed, with target-to-target observation overheads of less than 1.5 minutes. Scientific programs requiring high-resolution follow-up characterization of several thousands of targets can thus be executed in mere weeks, and Robo-AO has already completed the three largest AO surveys to date.

  11. Parameterising E-ELT AO PSFs for detailed science simulations for HARMONI

    NASA Astrophysics Data System (ADS)

    Zieleniewski, Simon; Thatte, Niranjan

    2013-12-01

    With the first ELTs around the corner it is becoming ever more important to determine observational strategies and assess the prospective success of observing programs prior to making the observations. To this end, scientific simulations need to become more refined to understand the criteria required for a specific science case. We address the science simulations for HARMONI, an AO assisted first light integral field spectrograph (IFS) for the E-ELT. AO PSFs vary markedly as a function of wavelength and type of AO system used, so there is need to create detailed PSFs across all IFS wavelength channels for accurate simulations. Detailed AO simulations have shown that for LTAO on the E-ELT, Strehl ratios can vary from 0.5E-3 in V-band up to 0.5 in K-band. Using a single PSF for an entire datacube (especially with large instantaneous wavelength coverage) could introduce misleading features into simulated observations using HARMONI. We have developed a method to parameterize detailed PSFs using analytical models, which can then be interpolated as a function of wavelength. This allows us to create accurate, but computationally inexpensive, AO PSF datacubes for HARMONI simulations. This shall be developed to cover LTAO, SCAO and GLAO/no-AO PSFs for a range of observing parameters.

  12. DNA Sequencing apparatus

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  13. DNA in Nanoscale Electronics

    NASA Astrophysics Data System (ADS)

    Slinker, Jason

    2012-10-01

    DNA, the quintessential molecule of life, possesses a number of attractive properties for use in nanoscale circuits. Charge transport (CT) through DNA itself is of both fundamental and practical interest. Fundamentally, DNA has a unique configuration of π-stacked bases in a well ordered, double helical structure. Given its unparalleled importance to life processes and its arrangement of conjugated subunits, DNA has been a compelling target of conductivity studies. In addition, further understanding of DNA CT will elucidate the biological implications of this process and advance its use in sensing technologies. We have investigated the fundamentals of DNA CT by measuring the electrochemistry of DNA monolayers under biologically-relevant conditions. We have uncovered both fundamental kinetic parameters to distinguish between competing models of operation as well as the practical implications of DNA CT for sensing. Furthermore, we are leveraging our studies of DNA conductivity for the manufacture of nanoscale circuits. We are investigating the electrical properties and self-assembly of DNA nanowires containing artificial base pair surrogates, which can be prepared through low cost and high throughput automated DNA synthesis. This unique and economically viable approach will establish a new paradigm for the scalable manufacture of nanoscale semiconductor devices.

  14. DNA structure and function.

    PubMed

    Travers, Andrew; Muskhelishvili, Georgi

    2015-06-01

    The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase. PMID:25903461

  15. The EM Earthquake Precursor

    NASA Astrophysics Data System (ADS)

    Jones, K. B., II; Saxton, P. T.

    2013-12-01

    Many attempts have been made to determine a sound forecasting method regarding earthquakes and warn the public in turn. Presently, the animal kingdom leads the precursor list alluding to a transmission related source. By applying the animal-based model to an electromagnetic (EM) wave model, various hypotheses were formed, but the most interesting one required the use of a magnetometer with a differing design and geometry. To date, numerous, high-end magnetometers have been in use in close proximity to fault zones for potential earthquake forecasting; however, something is still amiss. The problem still resides with what exactly is forecastable and the investigating direction of EM. After the 1989 Loma Prieta Earthquake, American earthquake investigators predetermined magnetometer use and a minimum earthquake magnitude necessary for EM detection. This action was set in motion, due to the extensive damage incurred and public outrage concerning earthquake forecasting; however, the magnetometers employed, grounded or buried, are completely subject to static and electric fields and have yet to correlate to an identifiable precursor. Secondly, there is neither a networked array for finding any epicentral locations, nor have there been any attempts to find even one. This methodology needs dismissal, because it is overly complicated, subject to continuous change, and provides no response time. As for the minimum magnitude threshold, which was set at M5, this is simply higher than what modern technological advances have gained. Detection can now be achieved at approximately M1, which greatly improves forecasting chances. A propagating precursor has now been detected in both the field and laboratory. Field antenna testing conducted outside the NE Texas town of Timpson in February, 2013, detected three strong EM sources along with numerous weaker signals. The antenna had mobility, and observations were noted for recurrence, duration, and frequency response. Next, two

  16. Human DNA repair genes.

    PubMed

    Wood, R D; Mitchell, M; Sgouros, J; Lindahl, T

    2001-02-16

    Cellular DNA is subjected to continual attack, both by reactive species inside cells and by environmental agents. Toxic and mutagenic consequences are minimized by distinct pathways of repair, and 130 known human DNA repair genes are described here. Notable features presently include four enzymes that can remove uracil from DNA, seven recombination genes related to RAD51, and many recently discovered DNA polymerases that bypass damage, but only one system to remove the main DNA lesions induced by ultraviolet light. More human DNA repair genes will be found by comparison with model organisms and as common folds in three-dimensional protein structures are determined. Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process. PMID:11181991

  17. "Turn off-on" phosphorescent biosensors for detection of DNA based on quantum dots/acridine orange.

    PubMed

    Miao, Yanming; Li, Yuting; Zhang, Zhifeng; Yan, Guiqin; Bi, Yi

    2015-04-15

    A "turn off-on" switch mode was established by using the interaction between acridine orange (AO) and DNA as an input signal and using the room temperature phosphorescence (RTP) reversible change of 3-mercaptopropionic acid (MPA)-capped Mn-doped ZnS quantum dots (QDs) as an output signal in biological fluids. AO was absorbed into the surface of Mn-doped ZnS QDs via electrostatic attraction and, thus, formed a ground-state complex through photoinduced electron transfer (PIET). This complex quenched the phosphorescence of Mn-doped ZnS QDs and then rendered the system into the "turn-off" mode. Along with the addition of DNA and embedded binding with DNA, AO was competitively induced to fall off from the surface of Mn-doped ZnS QDs and embed into the double helix structure of DNA. As a result, the RTP of Mn-doped ZnS QDs was recovered and the system consequently was rendered into "turn-on" mode. In this case, a new biosensor for DNA detection was built and has a detection limit of 0.033mgL(-1) and a detection range from 0.033 to 20mgL(-1). What is more, this kind of biosensor does not require complex pretreatments and is free from the interference from autofluorescence and scattering light. Thus, this biosensor can be used to detect DNA in biological fluids. PMID:25637306

  18. Constitutive activation of the fucAO operon and silencing of the divergently transcribed fucPIK operon by an IS5 element in Escherichia coli mutants selected for growth on L-1,2-propanediol.

    PubMed Central

    Chen, Y M; Lu, Z; Lin, E C

    1989-01-01

    L-1,2-Propanediol is an irretrievable end product of L-fucose fermentation by Escherichia coli. Selection for increased aerobic growth rate on propanediol results in the escalation of basal synthesis of the NAD+-linked oxidoreductase encoded by fucO, a member of the fuc regulon for the utilization of L-fucose. In general, when fucO becomes constitutively expressed, two other simultaneous changes occur: the fucA gene encoding fuculose-1-phosphate aldolase becomes constitutively expressed and the fucPIK operon encoding fucose permease, fucose isomerase, and fuculose kinase becomes noninducible. In the present study, we show that fucO and fucA form an operon which is divergently transcribed from the adjacent fucPIK operon. In propanediol-positive and fucose-negative mutants the cis-controlling region shared by the operons fucAO and fucPIK is lengthened by 1.2 kilobases. DNA hybridization identified the insertion element to be IS5. This element, always oriented in the same direction with the left end (the BglII end) proximal to fucA, apparently causes constitutive expression of fucAO and noninducibility of fucPIK. The DNA of the fucAO operon and a part of the adjacent fucP was sequenced. Images PMID:2553671

  19. Estudo comparativo entre estrelas centrais de nebulosas planetárias deficientes em hidrogênio

    NASA Astrophysics Data System (ADS)

    Marcolino, W. L. F.; de Araújo, F. X.

    2003-08-01

    Apresentamos neste trabalho o resultado de um estudo das principais características espectrais das estrelas centrais de nebulosas planetárias (ECNP) deficientes em hidrogênio. A origem e a evolução dessas estrelas ainda constitui um problema em aberto na evolução estelar. Geralmente esses objetos são divididos em [WCE], [WCL] e [WELS]. Os tipos [WCE] e [WCL] apresentam um espectro típico de uma estrela Wolf-Rayet carbonada de população I e as [WELS] apresentam linhas fracas de carbono e oxigênio em emissão. Existem evidências que apontam a seguinte sequência evolutiva : [WCL] = > [WCE] = > [WELS] = > PG 1159 (pré anã-branca). No entanto, tal cenário apresenta falhas como por exemplo a falta de ECNP entre os tipos [WCL] e [WCE]. Baseados em uma amostra de 24 objetos obtida no telescópio de 1.52m em La Silla, Chile (acordo ESO/ON), ao longo do ano 2000, apresentamos os resultados da comparação das larguras equivalentes de diversas linhas relevantes entre os tipos [WCL], [WCE] e [WELS]. Verificamos que nossos dados estão de acordo com a sequência evolutiva. Baseado nas linhas de C IV, conseguimos dividir pela primeira vez as [WELS] em dois grupos principais. Além disso, os dados reforçam a afirmação de que as [WCE] são as estrelas que possuem a maior temperatura entre as ECNP deficientes em hidrogênio. Discutimos ainda, a escassez de dados disponíveis na literatura e a necessidade da obtenção de parametros físicos para estes objetos.

  20. Bioterrorism awareness for EMS.

    PubMed

    Patrick, Richard W

    2004-04-01

    It is important to understand that the issues surrounding bioterrorism and all weapons of mass destruction are complex. In an effort to enhance response to such events, EMS should handle all incidents from the perspective of an all-hazards approach. Prevention, preparation, response and recovery are essential to the safe mitigation of all incidents. Organizations must be prepared. Plan now for a safer tomorrow. Your personnel and communities depend on you. PMID:15131906

  1. DNA methylation in plants.

    PubMed

    Vanyushin, B F

    2006-01-01

    DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA

  2. Forensic DNA analysis.

    PubMed

    McDonald, Jessica; Lehman, Donald C

    2012-01-01

    Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

  3. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  4. DNA profiles from fingermarks.

    PubMed

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success. PMID:25391915

  5. Electrocatalysis in DNA Sensors.

    PubMed

    Furst, Ariel; Hill, Michael G; Barton, Jacqueline K

    2014-12-14

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  6. DNA Media Storage

    PubMed Central

    Bogard, Christy M.; Rouchka, Eric C.

    2010-01-01

    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors. PMID:20622994

  7. DNA Media Storage.

    PubMed

    Bogard, Christy M; Rouchka, Eric C

    2007-09-01

    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors. PMID:20622994

  8. Ribonucleotides in Bacterial DNA

    PubMed Central

    Schroeder, Jeremy W.; Randall, Justin R.; Matthews, Lindsay A.; Simmons, Lyle A.

    2014-01-01

    In all living cells, DNA is the storage medium for genetic information. Being quite stable, DNA is well-suited for its role in storage and propagation of information, but RNA is also covalently included in DNA through various mechanisms. Recent studies also demonstrate useful aspects of including ribonucleotides in the genome during repair. Therefore, our understanding of the consequences of RNA inclusion into bacterial genomic DNA is just beginning, but with its high frequency of occurrence the consequences and potential benefits are likely to be numerous and diverse. In this review, we discuss the processes that cause ribonucleotide inclusion in genomic DNA, the pathways important for ribonucleotide removal and the consequences that arise should ribonucleotides remain nested in genomic DNA. PMID:25387798

  9. Electrocatalysis in DNA Sensors

    PubMed Central

    Furst, Ariel; Hill, Michael G.; Barton, Jacqueline K.

    2014-01-01

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  10. Requirements Modeling with the Aspect-oriented User Requirements Notation (AoURN): A Case Study

    NASA Astrophysics Data System (ADS)

    Mussbacher, Gunter; Amyot, Daniel; Araújo, João; Moreira, Ana

    The User Requirements Notation (URN) is a recent ITU-T standard that supports requirements engineering activities. The Aspect-oriented URN (AoURN) adds aspect-oriented concepts to URN, creating a unified framework that allows for scenario-based, goal-oriented, and aspect-oriented modeling. AoURN is applied to the car crash crisis management system (CCCMS), modeling its functional and non-functional requirements (NFRs). AoURN generally models all use cases, NFRs, and stakeholders as individual concerns and provides general guidelines for concern identification. AoURN handles interactions between concerns, capturing their dependencies and conflicts as well as the resolutions. We present a qualitative comparison of aspect-oriented techniques for scenario-based and goal-oriented requirements engineering. An evaluation carried out based on the metrics adapted from literature and a task-based evaluation suggest that AoURN models are more scalable than URN models and exhibit better modularity, reusability, and maintainability.

  11. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications. PMID:24647836

  12. [Discussion on academic origin of Ao shi shang han jin jing lu (Ao's Records of golden mirror on cold pathogenic diseases].

    PubMed

    Liang, Rong; Wang, Zhaoping

    2002-07-01

    Ao shi shang han jin jing lu (Ao's Records of Golden Mirror on Cold Pathogenic Diseases) is the extant first work of lingual diagnosis. It is demonstrated that the author of this book is categorized under the school of Liu Wansu based on the location of disease, the nature of disease, therapies and drugs, and pathogenesis in pathological lingual pictures described in this book. The lingual diagnosis was based on Liu Wansu's theory of fire - heat, and used for diagnosing warm diseases. Intuitionistic vision was used in this book to prove the direct relation between red tongue and heat syndrome, which was the important joint for the theory of warm diseases to derive from the theory of cold pathogenic diseases. At the same time, the set up of the model of diagnosis and treatment for red tongue - inner heat syndrome, and clearing inner heat is established. PMID:12639446

  13. Immune protection of microneme 7 (EmMIC7) against Eimeria maxima challenge in chickens.

    PubMed

    Huang, Jingwei; Zhang, Zhenchao; Li, Menghui; Song, Xiaokai; Yan, Ruofeng; Xu, Lixin; Li, Xiangrui

    2015-10-01

    In the present study, the immune protective effects of recombinant microneme protein 7 of Eimeria maxima (rEmMIC7) and a DNA vaccine encoding this antigen (pVAX1-EmMIC7) on experimental challenge were evaluated. Two-week-old chickens were randomly divided into five groups. Experimental groups of chickens were immunized with 100 μg DNA vaccine pVAX1-MIC7 or 200 μg rEmMIC7, while control groups of chickens were injected with pVAX1 plasmid or sterile phosphate buffered saline (PBS). The results showed that the anti-EmMIC7 antibody titres in chickens of both rEmMIC7 and pVAX1-MIC7 groups were significantly higher as compared to PBS and pVAX1 control (P < .05). The splenocytes from both vaccinated groups of chickens displayed significantly greater proliferation response compared with the controls (P < .05). Serum from chickens immunized with pVAX1-MIC7 and rEmMIC7 displayed significantly high levels of interleukin-2, interferon-γ, IL-10, IL-17, tumour growth factor-β and IL-4 (P < .05) compared to those of negative controls. The challenge experiment results showed that both the recombinant antigen and the DNA vaccine could obviously alleviate jejunum lesions, body weight loss and enhance oocyst decrease ratio. The anti-coccidial index (ACI) of the pVAX1-MIC7 group was 167.84, higher than that of the recombinant MIC7 protein group, 167.10. Our data suggested that immunization with EmMIC7 was effective in imparting partial protection against E. maxima challenge in chickens and it could be an effective antigen candidate for the development of new vaccines against E. maxima. PMID:26181095

  14. Carbon stable isotope composition of DNA isolated from an incipient paleosol

    NASA Astrophysics Data System (ADS)

    Jahren, A. Hope; Kelm, Kellie; Wendland, Beverly; Petersen, Gitte; Seberg, Ole

    2006-05-01

    We determined the carbon isotope (δ13C) value of double-stranded DNA (dsDNA) isolated from the organic horizons of a Delaware soil that is actively being covered by an encroaching sand dune. The soil belongs to a Nymphaea odorataem> Ait. (water lily) wetland, and we regard its active acquisition of a thick (˜24 cm) surface mantle to embody the process of paleopedogenesis; therefore, we have termed it an “incipient paleosol.” In this study, we compared the δ13C value of paleosol dsDNA to the bulk δ13C value of N. odorataem>, as well as to the δ13C value of plants that had colonized the surface mantle. The isotopic offset between paleosol δ13CdsDNA and N. odorataem> δ13Ctissue was identical to the relationship between δ13CdsDNA and δ13Ctissue for tracheophytes, which we had previously determined. In contrast, the isotopic offset between paleosol δ13CdsDNA and the δ13Ctissue of plants colonizing the surface mantle differed from this relationship by as much as 4‰. Similarly, the δ13C value of bulk paleosol organic matter was extremely heterogeneous and varied across 6‰. All paleosol DNA polymerase chain reaction (PCR) products produced clear, sharp, 350 base-pair (bp) fragments of rbcLem>, a gene shared by all photosynthetic organisms. These results open the exciting possibility that stable isotope analysis of dsDNA isolated from paleosol organic matter can be used to infer the δ13C value of the plant that dominated the nucleic acid contribution.

  15. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  16. Tiny telomere DNA

    PubMed Central

    Ren, Jinsong; Qu, Xiaogang; Trent, John O.; Chaires, Jonathan B.

    2002-01-01

    We describe the design, synthesis and biophysical characterization of a novel DNA construct in which a folded quadruplex structure is joined to a standard double helix. Circular dichroism, gel electrophoresis, three-dimensional UV melting and differential scanning calorimetry were all used to characterize the structure. Rigorous molecular dynamics simulations were used to build a plausible atomic-level structural model of the DNA construct. This novel DNA construct provides a model for the duplex–quadruplex junction region at the end of chromosomal DNA and offers a system for the study of structure-selective ligand binding. PMID:12034817

  17. DNA Damage Response

    PubMed Central

    Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

    2011-01-01

    Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damage can occur at any time on any genomic location, a specialized spatio-temporal orchestration of this defense apparatus is required. PMID:20980439

  18. Replication of single-stranded DNA templates by primase-polymerase complexes of the yeast, Saccharomyces cerevisiae.

    PubMed Central

    Biswas, E E; Biswas, S B

    1988-01-01

    A partially purified primase-polymerase complex from the yeast, Saccharomyces cerevisiae, was capable of replicating a single stranded circular phage DNA into a replicative form with high efficiency. The primase-polymerase complex exhibited primase activity and polymerase activity on singly primed circular ssDNA as well as on gapped DNA. In addition, it was able to replicate an unprimed, single-stranded, circular phage DNA through a coupled primase-polymerase action. On Biogel A-O.5m filtration the primase-polymerase activities appeared in the void volume, demonstrating a mass of greater than 500 kilodaltons. Primase and various primase-polymerase complexes synthesized unique primers on single stranded DNA templates and the size distribution of primers was dependent on the structure of the DNA and the nature of the primase-polymerase assembly. Images PMID:3041377

  19. Optical-X-ray Observations of BL Lacertae Object AO 0235+164

    NASA Astrophysics Data System (ADS)

    Howard, Emily S.; Webb, James R.; Balonek, Thomas J.; McGrath, Elizabeth; Shrader, Chris R.

    1998-11-01

    The BL Lacertea object AO 0235+164 dramatically increased in brightness on October 20, 1997. This outburst was observed with the 1 meter SARA (Southeastern Association for Research in Astronomy) telescope located at Kitt Peak National Observatory (KPNO) located southwest of Tucson, Arizona. As a result of our observations, AO 0235+164 was also observed during the outbust by the Rossi X-ray Timing Experiment (RXTE) and Foggy Bottom Observaotry, Colgate Univserity, New York as a part of a Target of Opportunity (TOO) program. We present here the historical lightcurve of AO 0235+164, Optical observations during the ourtburst from the SARA and Foggy Bottom Observatories and X-ray observations from RXTE. Also, we present multifrequency data during this period and compare the variability of the Optical and X-ray bands.

  20. Replicative DNA polymerases.

    PubMed

    Johansson, Erik; Dixon, Nicholas

    2013-06-01

    In 1959, Arthur Kornberg was awarded the Nobel Prize for his work on the principles by which DNA is duplicated by DNA polymerases. Since then, it has been confirmed in all branches of life that replicative DNA polymerases require a single-stranded template to build a complementary strand, but they cannot start a new DNA strand de novo. Thus, they also depend on a primase, which generally assembles a short RNA primer to provide a 3'-OH that can be extended by the replicative DNA polymerase. The general principles that (1) a helicase unwinds the double-stranded DNA, (2) single-stranded DNA-binding proteins stabilize the single-stranded DNA, (3) a primase builds a short RNA primer, and (4) a clamp loader loads a clamp to (5) facilitate the loading and processivity of the replicative polymerase, are well conserved among all species. Replication of the genome is remarkably robust and is performed with high fidelity even in extreme environments. Work over the last decade or so has confirmed (6) that a common two-metal ion-promoted mechanism exists for the nucleotidyltransferase reaction that builds DNA strands, and (7) that the replicative DNA polymerases always act as a key component of larger multiprotein assemblies, termed replisomes. Furthermore (8), the integrity of replisomes is maintained by multiple protein-protein and protein-DNA interactions, many of which are inherently weak. This enables large conformational changes to occur without dissociation of replisome components, and also means that in general replisomes cannot be isolated intact. PMID:23732474

  1. Many Ways to Loop DNA

    PubMed Central

    Griffith, Jack D.

    2013-01-01

    In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675

  2. Deep-water sponges (Porifera) from Bonaire and Klein Curaçao, Southern Caribbean.

    PubMed

    Van Soest, Rob W M; Meesters, Erik H W G; Becking, Leontine E

    2014-01-01

    Four submersible dives off the coast of Bonaire (Caribbean Netherlands) and Klein Curaçao (Curaçao) to depths of 99.5-242 m, covering lower mesophotic and upper dysphotic zones, yielded 52 sponge specimens belonging to 31 species. Among these we identified 13 species as new to science. These are Plakinastrella stinapa n. sp., Pachastrella pacoi n. sp., Characella pachastrelloides n. sp., Geodia curacaoensis n. sp., Caminus carmabi n. sp., Discodermia adhaerens n. sp., Clathria (Microciona) acarnoides n. sp., Antho (Acarnia) pellita n. sp., Parahigginsia strongylifera n. sp., Calyx magnoculata n. sp., Neopetrosia dutchi n. sp., Neopetrosia ovata n. sp. and Neopetrosia eurystomata n. sp. We also report an euretid hexactinellid, which belongs to the rare genus Verrucocoeloidea, recently described (2014) as V. liberatorii Reiswig & Dohrmann. The remaining 18 already known species are all illustrated by photos of the habit, either in situ or 'on deck', but only briefly characterized in an annotated table to confirm their occurrence in the Southern Caribbean. The habitat investigated-steep limestone rocks, likely representing Pleistocene fossil reefs--is similar to deep-water fossil reefs at Barbados of which the sponges were sampled and studied by Van Soest and Stentoft (1988). A comparison is made between the two localities, showing a high degree of similarity in sponge composition: 53% of the present Bonaire-Klein Curaçao species were also retrieved at Barbados. At the level of higher taxa (genera, families) Bonaire-Klein Curaçao shared approximately 80% of its lower mesophotic and upper dysphotic sponge fauna with Barbados, despite a distance between them of 1000 km, indicating high faunal homogeneity. We also preliminarily compared the shallow-water (euphotic) sponge fauna of Curaçao with the combined data available for the Barbados, Bonaire and Klein Curaçao mesophotic and upper dysphotic sponges, which resulted in the conclusion that the two faunas show only

  3. Nanoparticle bridge DNA biosensor

    NASA Astrophysics Data System (ADS)

    Huang, Hong-Wen

    A new DNA sensing method is demonstrated in which DNA hybridization events lead to the formation of nanoparticle satellites that bridge two electrodes and are detected electrically. The hybridization events are exclusively carried out only on specific locations, the surfaces of C-ssDNA modified 50 nm GNPs. The uniqueness of this work is that only a small number of T-ccDNA molecules (<10) is required to form the nanoparticle satellites, allowing ultra-sensitive DNA sensing. The principle of this new DNA sensing technique has been demonstrated using target DNA and three-base-pair-mismatched DNA in 20nM concentrations. Three single-stranded DNA (ssDNA) system is used in our experiment which includes Capture-ssDNA (C-ssDNA), Target-ssDNA (T-ssDNA) and Probe-ssDNA (P-ssDNA). Both C-ssDNA and P-ssDNA are modified by a thiol group and can hybridize with different portions of T-ssDNA. T-ssDNA requires no modification in three ssDNA system, which is beneficial in many applications. C-ssDNA modified 50nm gold nanoparticle (C-50au) and P-ssDNA modified 30nm gold nanoparticle (P-30au) are prepared through the reaction of thiol-gold chemical bonding between thiolated ssDNA and gold nanoparticle (GNP) (C-ssDNA with 50nm GNP, P-ssDNA with 30nm GNP). We controllably place the C-50au only on the SiO2 band surface (˜ 90nm width) between two gold electrodes (source and drain electrodes) by forming positively- and negatively-charged self-assembled monolayers (SAMs) on SiO2 and gold surface, respectively. DNA modified GNP is negatively charged due to ionization of phosphate group on DNA back bone. C-50au therefore is negatively charged and can only be attracted toward SiO2 area (repelled by negatively charged gold electrode surface). The amine group of positively-charged SAMs on SiO2 surface is then passivated by converting to non-polar methyl functional group after C-50au placement. P-30au is first hybridized with T-ssDNA in the solution phase (T-P- 30au formed) and is introduced

  4. [Study on Provenance of Kraak Porcelains from "Nan'ao I" Shipwreck].

    PubMed

    Du, Jing-nan; Chen, Yue; Li, Nai-sheng; Ming, Chao-fang; Zhu, Jian; Luo, Wu-gan

    2015-06-01

    The "Kraak Porcelain" was a kind of Blue and White Porcelain which exported from China to Europe in Ming and Qing period. The study of Kraak Porcelain is a focus issue in international field of porcelain research. In 2007, the discovery of "Nan'ao I" Shipwreck of Ming Dynasty and the porcelains loaded in it, provided precious materials for the research on Kraak Porcelain. In this paper, we explored the provenance of 10 Kraak Porcelain samples from Nan'ao I, using both traditional visual method and WDXRF. PMID:26601402

  5. Curating DNA specimens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA data are used in a variety of ethnobiological disciplines including archaeology, conservation, ecology, medicinal plants and natural products research, taxonomy and systematics, crop evolution and domestication, and genetic diversity. It frequently is convenient to store and share DNA among coop...

  6. Routine DNA testing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

  7. Recombinant DNA for Teachers.

    ERIC Educational Resources Information Center

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  8. MICROWAVE RESONANCES IN DNA

    EPA Science Inventory

    This report describes spectroscopic studies of DNA which were undertaken to better understand a physical basis for microwave absorption by this molecule. hree types of studies are described. ) The low frequency scattered light spectrum of DNA was studied by two methods. irst, Ram...

  9. Replicating repetitive DNA.

    PubMed

    Tognetti, Silvia; Speck, Christian

    2016-05-27

    The function and regulation of repetitive DNA, the 'dark matter' of the genome, is still only rudimentarily understood. Now a study investigating DNA replication of repetitive centromeric chromosome segments has started to expose a fascinating replication program that involves suppression of ATR signalling, in particular during replication stress. PMID:27230530

  10. Hydrogels: DNA bulks up

    NASA Astrophysics Data System (ADS)

    Labean, Thom

    2006-10-01

    Since the 1940s DNA has been known as the genetic material connected to heredity, and from the early 1980s it has also been considered as a potential structural material for nanoscale construction. Now, a hydrogel made entirely of DNA brings this molecule into the realm of bulk materials.

  11. Translesion DNA synthesis

    PubMed Central

    Vaisman, Alexandra; McDonald, John P.; Woodgate, Roger

    2014-01-01

    All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell’s replicase. Under these situations, cells are forced to choose between recombination-mediated “damage avoidance” pathways, or use a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions, but also downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival. Escherichia coli and Salmonella typhimurium possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases. PMID:26442823

  12. Characterization of muntjac DNA

    SciTech Connect

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  13. DNA as information.

    PubMed

    Wills, Peter R

    2016-03-13

    This article reviews contributions to this theme issue covering the topic 'DNA as information' in relation to the structure of DNA, the measure of its information content, the role and meaning of information in biology and the origin of genetic coding as a transition from uninformed to meaningful computational processes in physical systems. PMID:26857666

  14. DNA-cell conjugates

    DOEpatents

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  15. Human DNA repair and recombination genes

    SciTech Connect

    Thompson, L.H.; Weber, C.A.; Jones, N.J.

    1988-09-01

    Several genes involved in mammalian DNA repair pathways were identified by complementation analysis and chromosomal mapping based on hybrid cells. Eight complementation groups of rodent mutants defective in the repair of uv radiation damage are now identified. At least seven of these genes are probably essential for repair and at least six of them control the incision step. The many genes required for repair of DNA cross-linking damage show overlap with those involved in the repair of uv damage, but some of these genes appear to be unique for cross-link repair. Two genes residing on human chromosome 19 were cloned from genomic transformants using a cosmid vector, and near full-length cDNA clones of each gene were isolated and sequenced. Gene ERCC2 efficiently corrects the defect in CHO UV5, a nucleotide excision repair mutant. Gene XRCC1 normalizes repair of strand breaks and the excessive sister chromatid exchange in CHO mutant EM9. ERCC2 shows a remarkable /approximately/52% overall homology at both the amino acid and nucleotide levels with the yeast RAD3 gene. Evidence based on mutation induction frequencies suggests that ERCC2, like RAD3, might also be an essential gene for viability. 100 refs., 4 tabs.

  16. Premeltons in DNA.

    PubMed

    Sobell, Henry M

    2016-03-01

    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review

  17. Advances in DNA photonics

    NASA Astrophysics Data System (ADS)

    Heckman, Emily M.; Aga, Roberto S.; Fehrman Cory, Emily M.; Ouchen, Fahima; Lesko, Alyssa; Telek, Brian; Lombardi, Jack; Bartsch, Carrie M.; Grote, James G.

    2012-10-01

    In this paper we present our current research in exploring a DNA biopolymer for photonics applications. A new processing technique has been adopted that employs a modified soxhlet-dialysis (SD) rinsing technique to completely remove excess ionic contaminants from the DNA biopolymer, resulting in a material with greater mechanical stability and enhanced performance reproducibility. This newly processed material has been shown to be an excellent material for cladding layers in poled polymer electro-optic (EO) waveguide modulator applications. Thin film poling results are reported for materials using the DNA biopolymer as a cladding layer, as are results for beam steering devices also using the DNA biopolymer. Finally, progress on fabrication of a Mach Zehnder EO modulator with DNA biopolymer claddings using nanoimprint lithography techniques is reported.

  18. Archaeal DNA replication.

    PubMed

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  19. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  20. DNA damage by smoke: Protection by turmeric and other inhibitors of ROS

    SciTech Connect

    Srinivas, L.; Shalini, V.K. )

    1991-01-01

    Twigs-dry leaves smoke condensate (TDS), as a source of clastogenic ROS and carcinogenic PAH, was investigated for its in vitro DNA-damaging effect in calf thymus DNA and human peripheral lymphocytes. An aqueous turmeric component--Aq.T--with an established antioxidant activity, was tested as a DNA protectant. TDS induced 13-fold damage to calf thymus DNA as judged by the emergence of a DNA damage specific, fluorescent product (em: 405 nm). Aq.T at 800 ng/microL extended 69% protection to calf thymus DNA and was comparable to the other protectants such as curcumin, BHA, vitamin E, SOD, and CAT. In human peripheral lymphocytes, TDS induced extensive DNA damage in comparison with the tumor promoter TPA, as judged by FADU. Aq.T at 300 ng/microL extended 90% protection to human lymphocyte DNA against TDS-induced damage, and was more effective than the other protectants--DABCO, D-mannitol, sodium benzoate, vitamin E (ROS quenchers), SOD, CAT (antioxidant enzymes), tannic acid, flufenamic acid, BHA, BHT, n-PG, curcumin and quercetin (antioxidants). Aq.T offered 65% protection to human lymphocyte DNA against TPA-induced damage and was comparable to SOD. The above results indicate that TDS induces substantial DNA damage in calf thymus DNA and human lymphocytes and Aq.T is an efficient protectant.

  1. Identified EM Earthquake Precursors

    NASA Astrophysics Data System (ADS)

    Jones, Kenneth, II; Saxton, Patrick

    2014-05-01

    Many attempts have been made to determine a sound forecasting method regarding earthquakes and warn the public in turn. Presently, the animal kingdom leads the precursor list alluding to a transmission related source. By applying the animal-based model to an electromagnetic (EM) wave model, various hypotheses were formed, but the most interesting one required the use of a magnetometer with a differing design and geometry. To date, numerous, high-end magnetometers have been in use in close proximity to fault zones for potential earthquake forecasting; however, something is still amiss. The problem still resides with what exactly is forecastable and the investigating direction of EM. After a number of custom rock experiments, two hypotheses were formed which could answer the EM wave model. The first hypothesis concerned a sufficient and continuous electron movement either by surface or penetrative flow, and the second regarded a novel approach to radio transmission. Electron flow along fracture surfaces was determined to be inadequate in creating strong EM fields, because rock has a very high electrical resistance making it a high quality insulator. Penetrative flow could not be corroborated as well, because it was discovered that rock was absorbing and confining electrons to a very thin skin depth. Radio wave transmission and detection worked with every single test administered. This hypothesis was reviewed for propagating, long-wave generation with sufficient amplitude, and the capability of penetrating solid rock. Additionally, fracture spaces, either air or ion-filled, can facilitate this concept from great depths and allow for surficial detection. A few propagating precursor signals have been detected in the field occurring with associated phases using custom-built loop antennae. Field testing was conducted in Southern California from 2006-2011, and outside the NE Texas town of Timpson in February, 2013. The antennae have mobility and observations were noted for

  2. Studying DNA in the Classroom.

    ERIC Educational Resources Information Center

    Zarins, Silja

    1993-01-01

    Outlines a workshop for teachers that illustrates a method of extracting DNA and provides instructions on how to do some simple work with DNA without sophisticated and expensive equipment. Provides details on viscosity studies and breaking DNA molecules. (DDR)

  3. Simple & Safe Genomic DNA Isolation.

    ERIC Educational Resources Information Center

    Moss, Robert; Solomon, Sondra

    1991-01-01

    A procedure for purifying DNA using either bacteria or rat liver is presented. Directions for doing a qualitative DNA assay using diphenylamine and a quantitative DNA assay using spectroscopy are included. (KR)

  4. Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit.

    PubMed

    Sawatani, Yoshito; Kashiwazaki, Gengo; Chandran, Anandhakumar; Asamitsu, Sefan; Guo, Chuanxin; Sato, Shinsuke; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2016-08-15

    With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds. PMID:27301681

  5. Estudo em microondas do aprisionamento e precipitação de elétrons em explosões solares

    NASA Astrophysics Data System (ADS)

    Rosal, A. C.; Costa, J. E. R.

    2003-08-01

    Uma explosão solar é uma variação rápida e intensa do brilho que ocorre nas chamadas regiões ativas da atmosfera, constituídas por um plasma magnetizado com intensa indução magnética. Os modelos de explosões solares atuais, discutidos na literatura, apresentam características de aprisionamento e precipitação de elétrons em ambientes magnéticos simplificados. Neste trabalho, nos propusemos a separar a emissão dos elétrons aprisionados da emissão dos elétrons em precipitação apenas a partir da emissão em microondas, melhorando portanto o controle sobre o conjunto de parâmetros inferidos. A emissão em microondas da população em precipitação é bastante fraca e portanto da nossa base de dados de 130 explosões observadas pelo Rádio Polarímetro de Nobeyama, em sete freqüências, apenas para 32 foi possível separar as duas componentes de emissão com uma boa razão sinal/ruído. A partir de estudos das escalas de tempo das emissões devidas à variação gradual da emissão no aprisionamento e da variação rápida da emissão dos elétrons em precipitação foi possível obter a separação utilizando um filtro temporal nas emissões resultantes. Em nossa análise destas explosões estudamos os espectros girossincrotrônicos da emissão gradual, a qual associamos provir do topo dos arcos magnéticos e da emissão de variação rápida associada aos elétrons em precipitação. Estes espectros foram calculados e dos quais inferimos que a indução magnética efetiva do topo e dos pés foi em média, Btopo = 236 G e Bpés = 577 G, inferidas das freqüências de pico dos espectros em ntopo = 11,8 GHz e npés = 14,6 GHz com leve anisotropia (pequeno alargamento espectral). O índice espectral da distribuição não-térmica de elétrons d, inferido do índice espectral de fótons da emissão em regime opticamente fino, foi de dtopo = 3,3 e dpés = 3,9. Estes parâmetros são típicos da maioria das análises realizadas em ambiente único de

  6. SWAS-AOS: the first acousto-optical spectrometer in space

    NASA Astrophysics Data System (ADS)

    Frerick, Johannes; Klumb, Markus; Schieder, Rudolf; Tolls, Volker; Winnewisser, Gisbert F.

    1999-12-01

    On December 5, 1998, the Submillimeter Wave Astronomy Satellite has been launched with a PEGASUS carrier after more than 3 years delay. SWAS is observing molecular line signals (H2O, 13CO, Cl, O2 and H2 18O) from astronomical sources at frequencies between 487 and 557 GHz. SWAS is the first sub-millimeter heterodyne space mission, and, for the spectral analysis of the received signals, it carries the first acousto-optical spectrometer (AOS) in space. The AOS has been built at University of Cologne, and it covers 1.4 GHz bandwidth with approximately 1400 frequency channels. The total weight is 7.5 kg and the power consumption is 5.5 Watts only. The very stable temperature conditions on SWAS allow longtime integrations at total observing times far above 100 hours still with radiometric performance. So far, the AOS- spectra have not been degraded by particle hits, particularly the CCD detector of the AOS does not exhibit any visible effect due to cosmic rays. SWAS has already observed many interstellar sources in our galaxy. Emission of water is seen to be very abundant, while signals of molecular oxygen seem to be too weak to be observable.

  7. Performance of a MEMS-based AO-OCT system using Fourier Reconstruction

    SciTech Connect

    Evans, J; Zawadzki, R; Jones, S; Olivier, S; Werner, J S

    2009-01-21

    Adaptive optics (AO) and optical coherence tomography (OCT) are powerful imaging modalities that, when combined, can provide high-resolution (3.5 {micro}m isotropic), 3-D images of the retina. The AO-OCT system at UC Davis has demonstrated the utility of this technology for microscopic, volumetric, in vivo retinal imaging. The current system uses an AOptix bimorph deformable mirror (DM) for low-order, high-stroke correction and a 140-actuator Boston Micromachines DM for high-order correction. Developments to improve performance or functionality of the instrument are on-going. Based on previous work in system characterization we have focused on improved AO control. We present preliminary results and remaining challenges for a newly implemented Fourier transform reconstructor (FTR). The previously reported error budget analysis is also reviewed and updated, with consideration of how to improve both the amount of residual error and the robustness of the system. Careful characterization of the AO system will lead to improved performance and inform the design of future systems.

  8. GPS-Based Navigation And Orbit Determination for the AMSAT AO-40 Satellite

    NASA Technical Reports Server (NTRS)

    Davis, George; Moreau, Michael; Carpenter, Russell; Bauer, Frank

    2002-01-01

    The AMSAT OSCAR-40 (AO-40) spacecraft occupies a highly elliptical orbit (HEO) to support amateur radio experiments. An interesting aspect of the mission is the attempted use of GPS for navigation and attitude determination in HEO. Previous experiences with GPS tracking in such orbits have demonstrated the ability to acquire GPS signals, but very little data were produced for navigation and orbit determination studies. The AO-40 spacecraft, flying two Trimble Advanced Navigation Sensor (TANS) Vector GPS receivers for signal reception at apogee and at perigee, is the first to demonstrate autonomous tracking of GPS signals from within a HEO with no interaction from ground controllers. Moreover, over 11 weeks of total operations as of June 2002, the receiver has returned a continuous stream of code phase, Doppler, and carrier phase measurements useful for studying GPS signal characteristics and performing post-processed orbit determination studies in HEO. This paper presents the initial efforts to generate AO-40 navigation solutions from pseudorange data reconstructed from the TANS Vector code phase, as well as to generate a precise orbit solution for the AO-40 spacecraft using a batch filter.

  9. Improvement of phase diversity algorithm for non-common path calibration in extreme AO context

    NASA Astrophysics Data System (ADS)

    Robert, Clélia; Fusco, Thierry; Sauvage, Jean-François; Mugnier, Laurent

    2008-07-01

    Exoplanet direct imaging with a ground-based telescope needs a very high performance adaptive optics (AO) system, so-called eXtreme AO (XAO), a coronagraph device, and a smart imaging process. One limitation of AO system in operation remains the Non Common Path Aberrations (NCPA). To achieve the ultimate XAO performance, these aberrations have to be measured with a dedicated wavefront sensor placed in the imaging camera focal plane, and then pre-compensated using the AO closed loop process. In any events, the pre-compensation should minimize the aberrations at the coronagraph focal plane mask. An efficient way for the NCPA measurement is the phase diversity technique. A pixel-wise approach is well-suited to estimate NCPA on large pupils and subsequent projection on the deformable mirror with Cartesian geometry. However it calls for a careful regularization for optimal results. The weight of the regularization is written in close-form for un-supervised tuning. The accuracy of NCPA pre-compensation is below 8 nm for a wide range of conditions. Point-by-point phase estimation improves the accuracy of the Phase Diversity method. The algorithm is validated in simulation and experimentally. It will be implemented in SAXO, the XAO system of the second generation VLT instrument: SPHERE.

  10. Development of vibration source requirements for TMT to ensure AO performance

    NASA Astrophysics Data System (ADS)

    MacMartin, Doug; Thompson, Hugh

    2013-12-01

    In order for TMT to deliver the required adaptive optics (AO) image quality, vibrationsources throughout the observatory need to be understood and their resulting optical response characterized.The sensitivity to vibration has been determined using a finite element model of the telescopestructure and mirror segments coupled to optical models. Frequency dependent models of the AO, activeoptics and mount control systems are included allowing end-to-end assessment of vibration sourceson AO-corrected image quality; future work will improve estimates of the propagation of vibrationsfrom equipment in the summit support building and enclosure to the telescope pier. Modeling separatelypredicts effects on image jitter caused by relative rigid body motion of main optical elements, and thedynamic motion of the 492 individual primary mirror segments. These results have been used to developallocated requirements on source amplitudes at different locations and as a function of frequency, whichwill lead to subsystem design requirements (e.g. for isolation systems at various locations both in thesupport building and enclosure and on the telescope structure). In order to meet an aggressive target forthis contribution to the AO error budget, vibration forces on the telescope itself must be limited to a fewNewtons in the most sensitive frequency range of 5-20Hz; larger forces of order 100N can be toleratedfor equipment mounted off the telescope in the summit facilities building.

  11. Effects of adrenergic agents on the expression of zebrafish (Danio rerio) vitellogenin Ao1

    SciTech Connect

    Yin Naida; Jin Xia; He Jiangyan; Yin Zhan

    2009-07-01

    Teleost vitellogenins (VTGs) are large multidomain apolipoproteins, traditionally considered to be estrogen-responsive precursors of the major egg yolk proteins, expressed and synthesized mainly in hepatic tissue. The inducibility of VTGs has made them one of the most frequently used in vivo and in vitro biomarkers of exposure to estrogen-active substances. A significant level of zebrafish vtgAo1, a major estrogen responsive form, has been unexpectedly found in heart tissue in our present studies. Our studies on zebrafish cardiomyopathy, caused by adrenergic agonist treatment, suggest a similar protective function of the cardiac expressed vtgAo1. We hypothesize that its function is to unload surplus intracellular lipids in cardiomyocytes for 'reverse triglyceride transportation' similar to that found in lipid transport proteins in mammals. Our results also demonstrated that zebrafish vtgAo1 mRNA expression in heart can be suppressed by both {alpha}-adrenergic agonist, phenylephrine (PE) and {beta}-adrenergic agonist, isoproterenol (ISO). Furthermore, the strong stimulation of zebrafish vtgAo1 expression in plasma induced by the {beta}-adrenergic antagonist, MOXIsylyl, was detected by Enzyme-Linked ImmunoSorbent Assay (ELISA). Such stimulation cannot be suppressed by taMOXIfen, an antagonist to estrogen receptors. Thus, our present data indicate that the production of teleost VTG in vivo can be regulated not only by estrogenic agents, but by adrenergic signals as well.

  12. An Infrared Optimized AO System for a 15 - 20m Class Telescope

    NASA Astrophysics Data System (ADS)

    Brandl, Bernhard R.; Eikenberry, Stephen S.; Herter, Terry L.; Kulkarni, Jayant

    2003-02-01

    Despite the relatively large number of proposed 'extremely large telescopes' very few of them concentrate on the thermal infrared as their main operating wavelengths. An IR-optimized large telescope located in the Atacama dessert at about 5500m altitude, where many atmospheric windows in the mid-IR open up, would be ideal to study astronomical targets that are either intrinsically red or heavily obscured by dust. A large aperture in the order of 15 - 20m requires adaptive optics correction out to λ<= 20 μm with the least possible thermal emission from the instrument itself. Here we discuss a specialized, integrated AO system that provides diffraction-limited performance in the thermal infrared (at λ>=2.5 μm). This approach is very different from the AO systems proposed for other 10m+ class telescopes. We present the basic concept of such an IR-optimized AO system, based on a 2m chopping adaptive secondary. We derive its technical specifications: configuration, bandwidth, and degrees of freedom show its predicted performance for typical seeing in terms of Strehl ratio as a function of limiting guide star magnitude, wavelength and corrected field-of-view. We also briefly address the science that this AO system/telescope would be ideal for.

  13. Outcome of Surgical Treatment of AO Type C Pelvic Ring Injury

    PubMed Central

    Moon, Do Hyeon; Kim, Nam Ki; Won, Jun Sung; Kim, Dong Hyun

    2014-01-01

    Purpose To evaluate the radiologic and clinical outcomes of AO type C pelvic ring injury and identify the prognostic factors. Materials and Methods We studied 53 patients who were treated for AO type C pelvic ring injury from January 2002 to February 2010. Mean age and mean follow-up duration were 42.4 years and 14 months, respectively. We had 8 cases of AO type C1-1, 19 cases of C1-2, 11 cases of C1-3, 6 cases of C2 and 9 cases of C3 injury. We analyzed type of fracture, displacement, method of fixation and associated injuries. Radiologic outcome was evaluated with Matta and Saucedo criteria and clinical outcome was evaluated using Majeed score. Results The average Majeed score was 86.2 distributing as 36 excellent cases, 15 good cases and 2 fair cases. Using radiologic Matta and Saucedo criteria, patients were divided as 31 excellent cases, 17 good cases and 5 fair cases. There was no significant difference between the outcomes of anterior, posterior and antero-posterior fixation. Neurologic injury was the reason for an unsatisfactory functional outcome. We identified two cases with complication, one with postoperative infection and the other with nonunion following anterior-posterior fixation. Conclusion Satisfactory radiologic and clinical outcomes were obtained with open reduction and internal fixation in the management of AO type C pelvic ring injuries. Neurologic injuries affected the clinical outcome.

  14. Quantitive DNA Fiber Mapping

    SciTech Connect

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  15. Reversible DNA compaction.

    PubMed

    González-Pérez, Alfredo

    2014-01-01

    In this review we summarize and discuss the different methods we can use to achieve reversible DNA compaction in vitro. Reversible DNA compaction is a natural process that occurs in living cells and viruses. As a result these process long sequences of DNA can be concentrated in a small volume (compacted) to be decompacted only when the information carried by the DNA is needed. In the current work we review the main artificial compacting agents looking at their suitability for decompaction. The different approaches used for decompaction are strongly influenced by the nature of the compacting agent that determines the mechanism of compaction. We focus our discussion on two main artificial compacting agents: multivalent cations and cationic surfactants that are the best known compacting agents. The reversibility of the process can be achieved by adding chemicals like divalent cations, alcohols, anionic surfactants, cyclodextrins or by changing the chemical nature of the compacting agents via pH modifications, light induced conformation changes or by redox-reactions. We stress the relevance of electrostatic interactions and self-assembly as a main approach in order to tune up the DNA conformation in order to create an on-off switch allowing a transition between coil and compact states. The recent advances to control DNA conformation in vitro, by means of molecular self-assembly, result in a better understanding of the fundamental aspects involved in the DNA behavior in vivo and serve of invaluable inspiration for the development of potential biomedical applications. PMID:24444152

  16. Purification of mammalian DNA repair protein XRCC1

    SciTech Connect

    Chen, I.

    1995-11-01

    Malfunctioning DNA repair systems lead to cancer mutations, and cell death. XRCC1 (X-ray Repair Cross Complementing) is a human DNA repair gene that has been found to fully correct the x-ray repair defect in Chinese hamster ovary (CHO) cell mutant EM9. The corresponding protein (XRCC1) encoded by this gene has been linked to a DNA repair pathway known as base excision repair, and affects the activity of DNA ligase III. Previously, an XRCC1 cDNA minigene (consisting of the uninterrupted coding sequence for XRCC1 protein followed by a decahistidine tag) was constructed and cloned into vector pET-16b for the purpose of: (1) overproduction of XRCC1 in both prokaryotic and eukaryotic cells; and (2) to facilitate rapid purification of XRCC1 from these systems. A vector is basically a DNA carrier that allows recombinant protein to be cloned and overexpressed in host cells. In this study, XRCC1 protein was overexpressed in E. coli and purified by immobilized metal affinity chromatography. Currently, the XRCC1 minigene is being inserted into a new vector [pET-26b(+)] in hopes to increase overexpression and improve purification. Once purified XRCC1 can be crystallized for structural studies, or studied in vitro for its biological function.

  17. Cheminformatics methods for novel nanopore analysis of HIV DNA termini

    PubMed Central

    Winters-Hilt, Stephen; Landry, Matthew; Akeson, Mark; Tanase, Maria; Amin, Iftekhar; Coombs, Amy; Morales, Eric; Millet, John; Baribault, Carl; Sendamangalam, Srikanth

    2006-01-01

    Background Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis. Results HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus. PMID:17118144

  18. Tracking Mitochondrial DNA In Situ.

    PubMed

    Ligasová, Anna; Koberna, Karel

    2016-01-01

    The methods of the detection of (1) non-labeled and (2) BrdU-labeled mitochondrial DNA (mtDNA) are described. They are based on the production of singlet oxygen by monovalent copper ions and the subsequent induction of DNA gaps. The ends of interrupted DNA serve as origins for the labeling of mtDNA by DNA polymerase I or they are utilized by exonuclease that degrades DNA strands, unmasking BrdU in BrdU-labeled DNA. Both methods are sensitive approaches without the need of additional enhancement of the signal or the use of highly sensitive optical systems. PMID:26530676

  19. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  20. Improved tilt sensing in an LGS-based tomographic AO system based on instantaneous PSF estimation

    NASA Astrophysics Data System (ADS)

    Veran, Jean-Pierre

    2013-12-01

    Laser guide star (LGS)-based tomographic AO systems, such as Multi-Conjugate AO (MCAO), Multi-Object AO (MOAO) and Laser Tomography AO (LTAO), require natural guide stars (NGSs) to sense tip-tilt (TT) and possibly other low order modes, to get rid of the LGS-tilt indetermination problem. For example, NFIRAOS, the first-light facility MCAO system for the Thirty Meter Telescope requires three NGSs, in addition to six LGSs: two to measure TT and one to measure TT and defocus. In order to improve sky coverage, these NGSs are selected in a so-called technical field (2 arcmin in diameter for NFIRAOS), which is much larger than the on-axis science field (17x17 arcsec for NFIRAOS), on which the AO correction is optimized. Most times, the NGSs are far off-axis and thus poorly corrected by the high-order AO loop, resulting in spots with low contrast and high speckle noise. Accurately finding the position of such spots is difficult, even with advanced methods such as matched-filtering or correlation, because these methods rely on the knowledge of an average spot image, which is quite different from the instantaneous spot image, especially in case of poor correction. This results in poor tilt estimation, which, ultimately, impacts sky coverage. We propose to improve the estimation of the position of the NGS spots by using, for each frame, a current estimate of the instantaneous spot profile instead of an average profile. This estimate can be readily obtained by tracing wavefront errors in the direction of the NGS through the turbulence volume. The latter is already computed by the tomographic process from the LGS measurements as part of the high order AO loop. Computing such a wavefront estimate has actually already been proposed for the purpose of driving a deformable mirror (DM) in each NGS WFS, to optically correct the NGS spot, which does lead to improved centroiding accuracy. Our approach, however, is much simpler, because it does not require the complication of extra DMs

  1. DNA-PK assay

    DOEpatents

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  2. Recent progress with the DNA repair mutants of Chinese hamster ovary cells

    SciTech Connect

    Thompson, L.H.; Salazar, E.P.; Brookman, K.W.; Collins, C.C.; Stewart, S.A.; Busch, D.B.; Weber, C.A.

    1986-04-02

    Repair deficient mutants of Chinese hamster ovary (CHO) cells are being used to identify human genes that correct the repair defects and to study mechanisms of DNA repair and mutagenesis. Five independent tertiary DNA transformants were obtained from the EM9 mutant. In these clones a human DNA sequence was identified that correlated with the resistance of the cells to CldUrd. After Eco RI digestion, Southern transfer, and hybridization of transformant DNAs with the BLUR-8 Alu family sequence, a common fragment of 25 to 30 kb was present. 37 refs., 4 figs., 3 tabs.

  3. DNA Mismatch Repair

    PubMed Central

    MARINUS, M. G.

    2014-01-01

    DNA mismatch repair functions to correct replication errors in newly synthesized DNA and to prevent recombination between related, but not identical (homeologous), DNA sequences. The mechanism of mismatch repair is best understood in Escherichia coli and is the main focus of this review. The early genetic studies of mismatch repair are described as a basis for the subsequent biochemical characterization of the system. The effects of mismatch repair on homologous and homeologous recombination are described. The relationship of mismatch repair to cell toxicity induced by various drugs is included. The VSP (Very Short Patch) repair system is described in detail. PMID:26442827

  4. Focus: DNA probes

    SciTech Connect

    Not Available

    1986-11-01

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  5. Binding of the wheat basic leucine zipper protein EmBP-1 to nucleosomal binding sites is modulated by nucleosome positioning.

    PubMed Central

    Niu, X; Adams, C C; Workman, J L; Guiltinan, M J

    1996-01-01

    To investigate interactions of the basic leucine zipper transcription factor EmBP-1 with its recognition sites in nucleosomal DNA, we reconstituted an abscisic acid response element and a high-affinity binding site for EmBP-1 into human and wheat nucleosome cores in vitro. DNA binding studies demonstrated that nucleosomal elements can be bound by EmBP-1 at reduced affinities relative to naked DNA. EmBP-1 affinity was lowest when the recognition sites were positioned near the center of the nucleosome. Binding was achieved with a truncated DNA binding domain; however, binding of full-length EmBP-1 caused additional strong DNase I hypersensitivity flanking the binding sites. Similar results were observed with nucleosomes reconstituted with either human or wheat histones, demonstrating a conserved mechanism of transcription factor-nucleosome interactions. We conclude that positioning of recognition sequences on a nucleosome may play an important role in regulating interactions of EmBP-1 with its target sites in plant cells. PMID:8837510

  6. Modulation of the chaperone DnaK allosterism by the nucleotide exchange factor GrpE.

    PubMed

    Melero, Roberto; Moro, Fernando; Pérez-Calvo, María Ángeles; Perales-Calvo, Judit; Quintana-Gallardo, Lucía; Llorca, Oscar; Muga, Arturo; Valpuesta, José María

    2015-04-17

    Hsp70 chaperones comprise two domains, the nucleotide-binding domain (Hsp70NBD), responsible for structural and functional changes in the chaperone, and the substrate-binding domain (Hsp70SBD), involved in substrate interaction. Substrate binding and release in Hsp70 is controlled by the nucleotide state of DnaKNBD, with ATP inducing the open, substrate-receptive DnaKSBD conformation, whereas ADP forces its closure. DnaK cycles between the two conformations through interaction with two cofactors, the Hsp40 co-chaperones (DnaJ in Escherichia coli) induce the ADP state, and the nucleotide exchange factors (GrpE in E. coli) induce the ATP state. X-ray crystallography showed that the GrpE dimer is a nucleotide exchange factor that works by interaction of one of its monomers with DnaKNBD. DnaKSBD location in this complex is debated; there is evidence that it interacts with the GrpE N-terminal disordered region, far from DnaKNBD. Although we confirmed this interaction using biochemical and biophysical techniques, our EM-based three-dimensional reconstruction of the DnaK-GrpE complex located DnaKSBD near DnaKNBD. This apparent discrepancy between the functional and structural results is explained by our finding that the tail region of the GrpE dimer in the DnaK-GrpE complex bends and its tip contacts DnaKSBD, whereas the DnaKNBD-DnaKSBD linker contacts the GrpE helical region. We suggest that these interactions define a more complex role for GrpE in the control of DnaK function. PMID:25739641

  7. A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication

    SciTech Connect

    Evrin, C.; Li, H.; Clarke, P.; Zech, J.; Lurz, R.; Sun, J.; Uhle, S.; Stillman, B.; Speck, C.

    2009-12-01

    During pre-replication complex (pre-RC) formation, origin recognition complex (ORC), Cdc6, and Cdt1 cooperatively load the 6-subunit mini chromosome maintenance (MCM2-7) complex onto DNA. Loading of MCM2-7 is a prerequisite for DNA licensing that restricts DNA replication to once per cell cycle. During S phase MCM2-7 functions as part of the replicative helicase but within the pre-RC MCM2-7 is inactive. The organization of replicative DNA helicases before and after loading onto DNA has been studied in bacteria and viruses but not eukaryotes and is of major importance for understanding the MCM2-7 loading mechanism and replisome assembly. Lack of an efficient reconstituted pre-RC system has hindered the detailed mechanistic and structural analysis of MCM2-7 loading for a long time. We have reconstituted Saccharomyces cerevisiae pre-RC formation with purified proteins and showed efficient loading of MCM2-7 onto origin DNA in vitro. MCM2-7 loading was found to be dependent on the presence of all pre-RC proteins, origin DNA, and ATP hydrolysis. The quaternary structure of MCM2-7 changes during pre-RC formation: MCM2-7 before loading is a single hexamer in solution but is transformed into a double-hexamer during pre-RC formation. Using electron microscopy (EM), we observed that loaded MCM2-7 encircles DNA. The loaded MCM2-7 complex can slide on DNA, and sliding is not directional. Our results provide key insights into mechanisms of pre-RC formation and have important implications for understanding the role of the MCM2-7 in establishment of bidirectional replication forks.

  8. Environmental toxicants cause sperm DNA fragmentation as detected by the Sperm Chromatin Structure Assay (SCSA[reg])

    SciTech Connect

    Evenson, Donald P. . E-mail: scsa@brookings.net; Wixon, Regina

    2005-09-01

    Studies over the past two decades have clearly shown that reproductive toxicants cause sperm DNA fragmentation. This DNA fragmentation can usually be detected prior to observing alterations of metaphase chromosomes in embryos. Thus, Sperm Chromatin Structure Assay (SCSA)-detected DNA damage is viewed as the molecular precursor to later gross chromosome damage observed under the light microscope. SCSA measurements of animal or human sperm consist of first obtaining a fresh or flash frozen neat semen sample in LN2 or dry ice. Samples are then sent to a SCSA diagnostic laboratory where the samples are thawed, diluted to {approx}1-2 x 106 sperm/ml, treated for 30 s with a pH 1.2 detergent buffer and then stained with acridine orange (AO). The low pH partially denatures DNA at the sites of DNA strand breaks and the AO-ssDNA fluoresces red while the AO-dsDNA fluoresces green. Flow cytometry measurements of 5000 sperm/sample provide statistically robust data on the ratio of red to green sperm, the extent of the DNA fragmentation and the standard deviations of measures. Numerous experiments on rodents treated with reproductive toxicants clearly showed that SCSA measures are highly dose responsive and have a very low CV. Different agents that act on germ cells at various stages of development usually showed sperm DNA fragmentation when that germ cell fraction arrived in the epididymis or ejaculate. Some of these treated samples were capable of successful in vitro fertilization but with frequent embryo failure. A 2-year longitudinal study of men living a valley town with a reported abnormal level of infertility and spontaneous miscarriages and also a seasonal atmospheric smog pollution, showed, for the first time, that SCSA measurements of human sperm DNA fragmentation were detectable and correlated with dosage of air pollution while the classical semen measures were not correlated. Also, young men spraying pesticides without protective gear are at an increased risk for

  9. Astronomia para/com crianças carentes em Limeira

    NASA Astrophysics Data System (ADS)

    Bretones, P. S.; Oliveira, V. C.

    2003-08-01

    Em 2001, o Instituto Superior de Ciências Aplicadas (ISCA Faculdades de Limeira) iniciou um projeto pelo qual o Observatório do Morro Azul empreendeu uma parceria com o Centro de Promoção Social Municipal (CEPROSOM), instituição mantida pela Prefeitura Municipal de Limeira para atender crianças e adolescentes carentes. O CEPROSOM contava com dois projetos: Projeto Centro de Convivência Infantil (CCI) e Programa Criança e Adolescente (PCA), que atendiam crianças e adolescentes em Centros Comunitários de diversas áreas da cidade. Esses projetos têm como prioridades estabelecer atividades prazerosas para as crianças no sentido de retirá-las das ruas. Assim sendo, as crianças passaram a ter mais um tipo de atividade - as visitas ao observatório. Este painel descreve as várias fases do projeto, que envolveu: reuniões de planejamento, curso de Astronomia para as orientadoras dos CCIs e PCAs, atividades relacionadas a visitas das crianças ao Observatório, proposta de construção de gnômons e relógios de Sol nos diversos Centros Comunitários de Limeira e divulgação do projeto na imprensa. O painel inclui discussões sobre a aprendizagem de crianças carentes, relatos que mostram a postura das orientadoras sobre a pertinência do ensino de Astronomia, relatos do monitor que fez o atendimento no Observatório e o que o número de crianças atendidas representou para as atividades da instituição desde o início de suas atividades e, em particular, em 2001. Os resultados são baseados na análise de relatos das orientadoras e do monitor do Observatório, registros de visitas e matérias da imprensa local. Conclui com uma avaliação do que tal projeto representou para as Instituições participantes. Para o Observatório, em particular, foi feita uma análise com relação às outras modalidades de atendimentos que envolvem alunos de escolas e público em geral. Também é abordada a questão do compromisso social do Observatório na educação do

  10. Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures.

    PubMed

    Pike, Ashley C W; Gomathinayagam, Shivasankari; Swuec, Paolo; Berti, Matteo; Zhang, Ying; Schnecke, Christina; Marino, Francesca; von Delft, Frank; Renault, Ludovic; Costa, Alessandro; Gileadi, Opher; Vindigni, Alessandro

    2015-04-01

    RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration. PMID:25831490

  11. Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures

    PubMed Central

    Pike, Ashley C. W.; Gomathinayagam, Shivasankari; Swuec, Paolo; Berti, Matteo; Schnecke, Christina; Marino, Francesca; von Delft, Frank; Renault, Ludovic; Costa, Alessandro; Vindigni, Alessandro

    2015-01-01

    RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration. PMID:25831490

  12. Interaction of DNA and DNA-anti-DNA complexes to fibronectin

    SciTech Connect

    Gupta, R.C.; Simpson, W.A.; Raghow, R.; Hasty, K.

    1986-03-01

    Fibronectin (Fn) is a large multidomain glycoprotein found in the basement membrane, on cell surface and in plasma. The interactions of Fn with DNA may be significant in glomerular deposition of DNA-anti-DNA complexes in patients with systemic lupus erythematosus (SLE). The authors examined the binding of DNA and DNA-anti-DNA complexes to Fn by a solid phase assay in which Fn was coated to microtiter plates and reacted with (/sup 3/H)DNA or DNA complexes with a monoclonal anti-DNA antibody. The optimal interaction of DNA with Fn occurs at <0.1M NaCl suggesting that the binding is charge dependent; the specificity of this binding was shown by competitive inhibition and locking experiments using anti-Fn. The binding was maximum at pH 6.5 and in the absence of Ca/sup 2 +/. The addition of Clq enhanced the binding of DNA and DNA-anti-DNA complexes to Fn, whereas heparan sulfate inhibited such binding. The monomeric or aggregated IgC did not bind Fn but aggregated IgG bound to Fn in the presence of Clq. Furthermore, DNA-anti-DNA complexes in sera from active SLE patients bound Fn which was enhanced in the presence of Clq; DNase abolished this binding indicating that the interaction of these complexes was mediated by DNA. These observations may partially explain the molecular mechanism(s) of the deposition of DNA-anti-DNA complexes in basement membrane.

  13. Expansion of the DNA Alphabet beyond Natural DNA Recognition.

    PubMed

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2016-07-15

    Simple and inexpensive DNA fibres: New, stable DNA structures are created by the binding of a small molecule to poly(A). Because these DNA fibres are formed from inexpensive materials by using very simple methods, DNA materials suitable for practical use such as information storage should be possible in the near future. PMID:27061868

  14. DNA computing in microreactors

    NASA Astrophysics Data System (ADS)

    Wagler, Patrick; van Noort, Danny; McCaskill, John S.

    2001-11-01

    The goal of this research is to improve the modular stability and programmability of DNA-based computers and in a second step towards optical programmable DNA computing. The main focus here is on hydrodynamic stability. Clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT. This work demonstrates by construction how one micro-reactor design can be programmed to solve any instance of Maximum Clique up to its given maximum size (N). It reports on an implementation of the architecture proposed previously. This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. In this pilot study we are tackling a graph for the Maximum Clique problem with NDNA solution space will be presented, which is symbolized by a set of bit-strings (words).

  15. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  16. Close encounters with DNA

    PubMed Central

    Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

    2014-01-01

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

  17. FBI's DNA analysis program

    NASA Astrophysics Data System (ADS)

    Brown, John R.

    1994-03-01

    Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

  18. Making DNA Fingerprints.

    ERIC Educational Resources Information Center

    Nunley, Kathie F.

    1996-01-01

    Presents an activity to simulate electrophoresis using everyday items. Uses adding machine paper to construct a set of DNA fingerprints that can be used to solve crime cases designed by students in any biology class. (JRH)

  19. Harnessing DNA intercalation.

    PubMed

    Persil, Ozgül; Hud, Nicholas V

    2007-10-01

    Numerous small molecules are known to bind to DNA through base pair intercalation. Fluorescent dyes commonly used for nucleic acid staining, such as ethidium, are familiar examples. Biological and physical studies of DNA intercalation have historically been motivated by mutation and drug discovery research. However, this same mode of binding is now being harnessed for the creation of novel molecular assemblies. Recent studies have used DNA scaffolds and intercalators to construct supramolecular assemblies that function as fluorescent 'nanotags' for cell labeling. Other studies have demonstrated how intercalators can be used to promote the formation of otherwise unstable nucleic acid assemblies. These applications illustrate how intercalators can be used to facilitate and expand DNA-based nanotechnology. PMID:17825446

  20. DNA damage tolerance.

    PubMed

    Branzei, Dana; Psakhye, Ivan

    2016-06-01

    Accurate chromosomal DNA replication is fundamental for optimal cellular function and genome integrity. Replication perturbations activate DNA damage tolerance pathways, which are crucial to complete genome duplication as well as to prevent formation of deleterious double strand breaks. Cells use two general strategies to tolerate lesions: recombination to a homologous template, and trans-lesion synthesis with specialized polymerases. While key players of these processes have been outlined, much less is known on their choreography and regulation. Recent advances have uncovered principles by which DNA damage tolerance is regulated locally and temporally - in relation to replication timing and cell cycle stage -, and are beginning to elucidate the DNA dynamics that mediate lesion tolerance and influence chromosome structure during replication. PMID:27060551

  1. Multiplex analysis of DNA

    DOEpatents

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

    This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

  2. Patterning nanocrystals using DNA

    SciTech Connect

    Williams, Shara Carol

    2003-09-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than

  3. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex.

    PubMed

    Witosch, Justine; Wolf, Eva; Mizuno, Naoko

    2014-11-10

    The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. PMID:25348395

  4. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex

    PubMed Central

    Witosch, Justine; Wolf, Eva; Mizuno, Naoko

    2014-01-01

    The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. PMID:25348395

  5. Supercoiled DNA wraps around the bacteriophage phi 29 head-tail connector.

    PubMed Central

    Turnquist, S; Simon, M; Egelman, E; Anderson, D

    1992-01-01

    Supercoiled pBR322 DNA wraps around the outside of the isolated Bacillus subtilis bacteriophage phi 29 head-tail connector, the crux of the DNA packaging machine of the viral precursor capsid or prohead. The contour length of the supercoiled DNA, determined by EM, decreased by approximately 180 base pairs for each connector bound. Mass and radial density determinations by scanning transmission EM showed that the increased mass of the connector-DNA complex relative to the connector alone was equivalent to approximately 170 base pairs of DNA and was located around the outside of the connector. Topoisomerase I treatment of the complexes followed by deproteinization suggested that supercoils were restrained by the connectors. Connectors bound linear and open-circular plasmid DNAs inefficiently but were not wrapped by these DNAs. The wrapping of supercoiled DNA around the isolated phi 29 connector is hypothesized to reflect the initiation phase of the normal process of DNA packaging. Packaging substrates would be supercoiled, wrapped by the connector, linearized, and translocated by rotation of the connector relative to the viral capsid with the aid of ATP hydrolysis. Images PMID:1438237

  6. Das DNA-Puzzle

    NASA Astrophysics Data System (ADS)

    Kirchner, Stefan

    Im Jahre 1953 wurde von James Watson und Francis Crick erstmalig der strukturelle Aufbau der sogenannten DNA (Desoxyribonukleinsäure) beschrieben, welche das Erbgut jedes Lebewesens enthält. Der wesentliche Teil des Erbguts wird dabei durch eine sehr lange Folge der vier Basen Adenin (A), Cytosin (C), Guanin (G) und Thymin (T) codiert. Seit einigen Jahren ist es möglich, die Folge der vier Basen zu einer gegebenen DNA zu bestimmen. Biologen bezeichnen diesen Vorgang als Sequenzierung.

  7. DNA-Nanoparticle Tinkertoys.

    PubMed

    Chandrasekaran, Arun Richard

    2016-06-16

    Nanoparticle superlattices can be self-assembled by using DNA linkers, which gives control over their size, shape, and composition. Recently, such programmable atom equivalents have been tailored to respond to chemical stimuli and result in specific crystalline lattices. Moreover, the molecular recognition properties and the robustness of designed DNA nanostructures have been used in combination with metallic nanoparticles for the production of the elusive diamond superlattice. PMID:27080095

  8. Ribonucleotide triggered DNA damage and RNA-DNA damage responses

    PubMed Central

    Wallace, Bret D; Williams, R Scott

    2014-01-01

    Research indicates that the transient contamination of DNA with ribonucleotides exceeds all other known types of DNA damage combined. The consequences of ribose incorporation into DNA, and the identity of protein factors operating in this RNA-DNA realm to protect genomic integrity from RNA-triggered events are emerging. Left unrepaired, the presence of ribonucleotides in genomic DNA impacts cellular proliferation and is associated with chromosome instability, gross chromosomal rearrangements, mutagenesis, and production of previously unrecognized forms of ribonucleotide-triggered DNA damage. Here, we highlight recent findings on the nature and structure of DNA damage arising from ribonucleotides in DNA, and the identification of cellular factors acting in an RNA-DNA damage response (RDDR) to counter RNA-triggered DNA damage. PMID:25692233

  9. Probing Protein-DNA Interactions by Unzipping DNA

    NASA Astrophysics Data System (ADS)

    Wang, Michelle

    2003-03-01

    Protein-DNA interactions are essential to cellular processes. In replication, transcription, recombination, DNA repair, and DNA packaging, proteins bind to DNA as activators or repressors, to recruit other proteins, or to carry out various catalytic activities. I will present Unzipping Force Analysis of Protein Association (UFAPA) as a novel and versatile method for detection of the position and dynamic nature of protein-DNA interactions. A single DNA double helix was unzipped in the presence of DNA-binding proteins using a feedback-enhanced optical trap. When the unzipping fork in a DNA reached a bound protein molecule, we observed a dramatic increase in the tension in the DNA, followed by a sudden tension reduction. Analysis of the unzipping force throughout an unbinding "event" revealed information about the spatial location and dynamic nature of the protein-DNA complex.

  10. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-01-01

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

  11. Safety evaluation of pectin-derived acidic oligosaccharides (pAOS): genotoxicity and sub-chronic studies.

    PubMed

    Garthoff, Jossie A; Heemskerk, Suzanne; Hempenius, Rixta A; Lina, Ben A R; Krul, Cyrille A M; Koeman, Jan H; Speijers, Gerrit J A

    2010-06-01

    Pectin-derived acidic oligosaccharides (pAOS) are non-digestible carbohydrates to be used in infant formulae and medical nutrition. To support its safety, the genotoxic potential of pAOS was evaluated. pAOS was not mutagenic in the Ames test. Positive results were obtained in the chromosome aberration test only at highly cytotoxic concentrations. The effects obtained in the mouse lymphoma test were equivocal; pAOS was not mutagenic in vivo. A sub-chronic dietary study, preceded by 4-week parental and in utero exposure phase, investigated general safety. Administration of pAOS did not affect parental health nor pup characteristics. No effects specific for acidic oligosaccharides were observed in the subsequent sub-chronic study. Slight diffuse hyperplasia of epithelial layer of the urinary bladder was noted to result from concurrently elevated urinary sodium, due to high sodium in pAOS, and elevated urinary pH. This phenomenon was confirmed in a mechanistic (sub-chronic) study. In contrast, in rats fed pAOS in combination with NH(4)Cl, an acidifying agent, the induced low urinary pH completely prevented the development of urothelial hyperplasia. Hyperplasia induced by this mechanism in rats is considered not relevant to man. Based on the current knowledge we consider pAOS safe for human consumption under its intended use. PMID:20026148

  12. 76 FR 52972 - United States v. Regal Beloit Corp. and A.O. Smith Corp.; Proposed Final Judgment and Competitive...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-24

    ... Columbia in United States v. Regal Beloit Corporation. and A.O. Smith Corporation., Civil Action No. 1:11... acquisition by Regal Beloit Corporation (``RBC'') of the electric motor business of A.O. Smith Corporation...., Suite 8700, Washington, DC 20530, Plaintiff, v. Regal Beloit Corporation, 200 State Street,...

  13. DNA biosensors that reason.

    PubMed

    Sainz de Murieta, Iñaki; Rodríguez-Patón, Alfonso

    2012-08-01

    Despite the many designs of devices operating with the DNA strand displacement, surprisingly none is explicitly devoted to the implementation of logical deductions. The present article introduces a new model of biosensor device that uses nucleic acid strands to encode simple rules such as "IF DNA_strand(1) is present THEN disease(A)" or "IF DNA_strand(1) AND DNA_strand(2) are present THEN disease(B)". Taking advantage of the strand displacement operation, our model makes these simple rules interact with input signals (either DNA or any type of RNA) to generate an output signal (in the form of nucleotide strands). This output signal represents a diagnosis, which either can be measured using FRET techniques, cascaded as the input of another logical deduction with different rules, or even be a drug that is administered in response to a set of symptoms. The encoding introduces an implicit error cancellation mechanism, which increases the system scalability enabling longer inference cascades with a bounded and controllable signal-noise relation. It also allows the same rule to be used in forward inference or backward inference, providing the option of validly outputting negated propositions (e.g. "diagnosis A excluded"). The models presented in this paper can be used to implement smart logical DNA devices that perform genetic diagnosis in vitro. PMID:22406690

  14. Ancient dirt DNA

    NASA Astrophysics Data System (ADS)

    Willerslev, E.

    2007-12-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole genomic studies of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the discoveries of DNA preserved in ancient sediments, coprolites, and fossil ice (Ancient Dirt DNA). These findings promise to make possible the reconstructions of entire ecosystems through time and allow for studies of past population genetics in cases where fossils are rare. The advantages and pitfalls connected to the Ancient Dirt DNA approach will be discussed as will recently obtained data relating to Greenland environmental history, long-term bacterial survival and the first human migration into the Americas.

  15. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  16. Vibrational structure of DNA

    NASA Astrophysics Data System (ADS)

    Gómez C, S.; Rey-González, R. R.

    2003-10-01

    DNA has been object of more extensive research in last years. Human genome may be the main work. On the other hand, DNA has been used as physical system in opposite to its biological character. Examples of this are electronic, thermally and Ramman spectroscopy studies, in others. However, some DNA physical features are unclear, they deserve more work in a effort to understand them. In this work we are interesting on the vibrational properties of DNA. We model it as a lineal chain constituted by three different mass. We use two different constant forces into the Dynamical Matrix formalism. Two masses represent the real mass of DNA bases plus the glucose mass and the third represents the phosphate mass. In this model, DNA unit cell is composed by four masses The dispersion relation shows one acoustical and three optical branches. Also, there is a wide gap between the first and second optical branches. These features are confirmed by the density of states. Also we consider disorder effects in the proposal to do a more realistic model. In this case our results suggest a behavior as diatomic chain where the central and wide gap is preserved.

  17. EPA LABORATORIES IMPLEMENT EMS PROGRAM

    EPA Science Inventory

    This paper highlights the breadth and magnitude of carrying out an effective Environmental Management System (EMS) program at the U.S. EPA's research and development laboratories. Federal research laboratories have unique operating challenges compared to more centralized industr...

  18. Supramolecular Complexes of DNA

    NASA Astrophysics Data System (ADS)

    Zuber, G.; Scherman, D.

    Deoxyribose nucleic acid or DNA is a linear polymer in the form of a double strand, synthesised by sequential polymerisation of a large number of units chosen from among the nucleic bases called purines (adenosine A and guanosine G) and pyrimidines (cytosine C and thymidine T). DNA contains all the genetic information required for life. It exists in the form of a limited number (a few dozen) of very big molecules, called chromosomes. This genetic information is first of all transcribed. In this process, a restricted fragment of the DNA called a gene is copied in the form of ribonucleic acid, or RNA. This RNA is itself a polymer, but with a single strand in which the sequence of nucleic acids is schematically analogous to the sequence on one of the two strands of the transcribed DNA. Finally, this RNA is translated into a protein, yet another linear polymer. The proteins make up the main part of the active constituents ensuring the survival of the cell. Any loss of information, either by mutation or by deletion of the DNA, will cause an imbalance in the cell's metabolism that may in turn lead to incurable pathologies. Several strategies have been developed to reduce the consequences of such genetic deficiencies or, more generally, to act, by amplifying or suppressing them, on the mechanisms leading from the reading of the genetic information to the production of proteins: Strategies aiming to introduce synthetic DNA or RNA, which selectively block the expression of certain genes, are now being studied by an increasing number of research scientists and pharmacologists. They use antisense oligodeoxyribonucleotides or interfering oligoribonucleotides and they already have clinical applications. This kind of therapy is often called gene pharmacology. Other, more ambitious strategies aim to repair in situ mutated or incomplete DNA within the chromosomes themselves, by introducing short sequences of DNA or RNA which recognise and take the place of mutations. This is the

  19. DNA Knots: Theory and Experiments

    NASA Astrophysics Data System (ADS)

    Sumners, D. W.

    Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

  20. Observações simultâneas no óptico e infravermelho próximo dos BL Lacs PKS 2005-489 e PKS 2155-304 em diversas escalas de tempo

    NASA Astrophysics Data System (ADS)

    Dominici, T. P.; Abraham, Z.; Galo, A. L.

    2003-08-01

    A existência de variações rápidas de brilho em alguns blazares é um fenômeno bem comprovado, mas até agora não sabemos ao certo quais são os mecanismos físicos envolvidos. A maior dificuldade é a ausência de observações multibanda simultâneas que poderiam fornecer vínculos aos modelos. Buscando colaborar com a discussão estudamos o comportamento de dois BL Lacs, PKS 2005-489 e PKS 2155-304, em relação à variabilidade em diversas escalas de tempo, de poucos minutos até vários meses, com observações simultâneas em seis bandas espectrais (óptico e infravermelho próximo). Para tanto dois telescópios do LNA foram utilizados em conjunto nas campanhas observacionais realizadas em 2001 e 2002, cujos resultados são apresentados aqui. As duas fontes apresentaram características bastante diferentes, inclusive em relação à existência de variabilidade nos índices espectrais. Particularmente, registramos a primeira detecção de variações em escalas de tempo da ordem de poucos minutos em PKS 2005-489, com evidências da presença de um atraso entre as curvas de luz nas bandas V e R e a variação em R ocorrendo antes (o contrário do esperado no modelo de shock-in-jet). Em PKS 2155-304 detectamos pela primeira vez variabilidade em escalas de tempo de poucos minutos no infravermelho em um AGN. As observações indicam que as variações de brilho em blazares são o resultado da ação de mais de um fenômeno, especialmente em escalas de tempo muito curtas. Alguns cenários físicos são sugeridos para explicar os resultados observacionais.

  1. Forensic DNA Profiling and Database

    PubMed Central

    Panneerchelvam, S.; Norazmi, M.N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

  2. Patterned Thread-like Micelles and DNA-Tethered Nanoparticles: A Structural Study of PEGylated Cationic Liposome–DNA Assemblies

    PubMed Central

    Majzoub, Ramsey N.; Ewert, Kai K.; Jacovetty, Erica L.; Carragher, Bridget; Potter, Clinton S.; Li, Youli; Safinya, Cyrus R.

    2015-01-01

    The self-assembly of oppositely charged biomacromolecules has been extensively studied due to its pertinence in the design of functional nanomaterials. Using cryo electronic microscopy (cryo-EM), optical light scattering and fluorescence microscopy, we investigated the structure and phase behavior of PEGylated (PEG: poly(ethylene-glycol)) cationic liposome–DNA nanoparticles (CL–DNA NPs) as a function of DNA length, topology (linear and circular) and ρchg (the molar charge ratio of cationic lipid to anionic DNA). Although all NPs studied showed a lamellar internal nanostructure, NPs formed with short (~ 2 kbps), linear, polydisperse DNA were defect-rich and contained smaller domains. Unexpectedly, we found distinctly different equilibrium structures away from the isoelectric point. At ρchg > 1, in the excess cationic lipid regime, thread-like micelles rich in PEG-lipid were found to coexist with NPs, cationic liposomes and spherical micelles. At high concentrations these PEGylated thread-like micelles formed a well-ordered, patterned morphology with highly uniform inter-micellar spacing. At ρchg < 1, in the excess DNA regime and with no added salt, individual NPs were tethered together via long, linear DNA (48 kbps λ-phage DNA) into a biopolymer-mediated floc. Our results provide insight on what equilibrium nanostructures can form when oppositely charged macromolecules self-assemble in aqueous media. Self-assembled, well-ordered thread-like micelles and tethered nanoparticles may have a broad range of applications in bionanotechnology, including nanoscale lithograpy and the development of lipid-based multi-functional nanoparticle networks. PMID:26048043

  3. Patterned Threadlike Micelles and DNA-Tethered Nanoparticles: A Structural Study of PEGylated Cationic Liposome-DNA Assemblies.

    PubMed

    Majzoub, Ramsey N; Ewert, Kai K; Jacovetty, Erica L; Carragher, Bridget; Potter, Clinton S; Li, Youli; Safinya, Cyrus R

    2015-06-30

    The self-assembly of oppositely charged biomacromolecules has been extensively studied due to its pertinence in the design of functional nanomaterials. Using cryo electron microscopy (cryo-EM), optical light scattering, and fluorescence microscopy, we investigated the structure and phase behavior of PEGylated (PEG: poly(ethylene glycol)) cationic liposome-DNA nanoparticles (CL-DNA NPs) as a function of DNA length, topology (linear and circular), and ρ(chg) (the molar charge ratio of cationic lipid to anionic DNA). Although all NPs studied exhibited lamellar internal nanostructure, NPs formed with short (∼2 kbps), linear, polydisperse DNA were defect-rich and contained smaller domains. Unexpectedly, we found distinctly different equilibrium structures away from the isoelectric point. At ρ(chg) > 1, in the excess cationic lipid regime, threadlike micelles rich in PEG-lipid were found to coexist with NPs, cationic liposomes, and spherical micelles. At high concentrations these PEGylated threadlike micelles formed a well-ordered, patterned morphology with highly uniform intermicellar spacing. At ρ(chg) < 1, in the excess DNA regime and with no added salt, individual NPs were tethered together via long, linear DNA (48 kbps λ-phage DNA) into a biopolymer-mediated floc. Our results provide insight into what equilibrium nanostructures can form when oppositely charged macromolecules self-assemble in aqueous media. Self-assembled, well-ordered threadlike micelles and tethered nanoparticles may have a broad range of applications in bionanotechnology, including nanoscale lithograpy and the development of lipid-based multifunctional nanoparticle networks. PMID:26048043

  4. Human DNA polymerase α in binary complex with a DNA:DNA template-primer

    PubMed Central

    Coloma, Javier; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.

    2016-01-01

    The Polα/primase complex assembles the short RNA-DNA fragments for priming of lagging and leading strand DNA replication in eukaryotes. As such, the Polα polymerase subunit encounters two types of substrates during primer synthesis: an RNA:DNA helix and a DNA:DNA helix. The engagement of the polymerase subunit with the DNA:DNA helix has been suggested as the of basis for primer termination in eukaryotes. However, there is no structural information on how the Polα polymerase subunit actually engages with a DNA:DNA helix during primer synthesis. We present here the first crystal structure of human Polα polymerase subunit in complex with a DNA:DNA helix. Unexpectedly, we find that portion of the DNA:DNA helix in contact with the polymerase is not in a B-form but in a hybrid A-B form. Almost all of the contacts observed previously with an RNA primer are preserved with a DNA primer – with the same set of polymerase residues tracking the sugar-phosphate backbone of the DNA or RNA primer. Thus, rather than loss of specific contacts, the free energy cost of distorting DNA from B- to hybrid A-B form may augur the termination of primer synthesis in eukaryotes. PMID:27032819

  5. The 384-channel prototype of DM Electronics for ELT AO systems

    NASA Astrophysics Data System (ADS)

    Caputa, Kris; Atwood, Jenny; Herriot, Glen; Veran, Jean-Pierre; Spanò, Paolo; Zielinski, Adam

    2014-08-01

    High order AO subsystems of the ELT require technological advancements in the Deformable Mirror (DM) construction and corresponding improvements in the drive electronics. Advanced prototyping is currently under way at NSI-Herzberg to reduce risks of deploying untried technology in the TMT AO subsystem NFIRAOS. We have developed a 96-channel output module and constructed a sub-scale DM Electronics prototype NDME384 with 384 output channels based on 4 such modules. French DM vendor Cilas has fabricated the NFIRAOS DM Breadoboard with 360 piezoelectric actuators in a 60×6 matrix, to demonstrate the DM technology to be deployed in NFIRAOS wavefront correctors. We present the results of testing our NDME384 prototype while driving the NFIRAOS DM Breadoboard.

  6. Identification and calibration of the interaction matrix parameters for AO and MCAO systems

    NASA Astrophysics Data System (ADS)

    Neichel, Benoit; Parisot, Amelie; Petit, Cyril; Fusco, Thierry; Rigaut, François

    2012-07-01

    New tomographic Adaptive Optics (AO) concepts require a good knowledge of the system geometry and characteristics. These parameters are used to feed the tomographic reconstructors. In this paper we present a method to precisely identify the parameters required to construct an accurate synthetic set of models such as inuence functions, mis-registrations, directions of analysis or altitude of the DMs. The method is based on a multiparameter t of the interaction matrix. This identication method nds also its application in high contrast AO systems, such as SPHERE : in that case it is used as a diagnostic tool in order to precisely realign the system. The method has been tested and successfully implemented on HOMER, SPHERE and GeMS. Experimental results for these three systems are presented.

  7. CANARY phase B: on-sky open-loop tomographic LGS AO results

    NASA Astrophysics Data System (ADS)

    Morris, Tim; Gendron, Eric; Basden, Alastair; Martin, Olivier; Osborn, James; Henry, David; Hubert, Zoltan; Sivo, Gaetano; Gratadour, Damien; Chemla, Fanny; Sevin, Arnaud; Cohen, Matthieu; Younger, Eddy; Vidal, Fabrice; Wilson, Richard; Butterley, Tim; Bitenc, Urban; Reeves, Andrew; Bharmal, Nazim; Raynaud, Henri-François; Kulcsar, Caroline; Conan, Jean-Marc; Huet, Jean-Michel; Perret, Denis; Dickson, Colin; Atkinson, David; Bailie, Tom; Longmore, Andy; Todd, Stephen; Talbot, Gordon; Morris, Simon; Rousset, Gérard; Myers, Richard

    2014-07-01

    CANARY is an on-sky Laser Guide Star (LGS) tomographic AO demonstrator that has been in operation at the 4.2m William Herschel Telescope (WHT) in La Palma since 2010. In 2013, CANARY was upgraded from its initial configuration that used three off-axis Natural Guide Stars (NGS) through the inclusion of four off-axis Rayleigh LGS and associated wavefront sensing system. Here we present the system and analysis of the on-sky results obtained at the WHT between May and September 2014. Finally we present results from the final `Phase C' CANARY system that aims to recreate the tomographic configuration to emulate the expected tomographic AO configuration of both the AOF at the VLT and E-ELT.

  8. Dynamic Modulation of DNA Hybridization Using Allosteric DNA Tetrahedral Nanostructures.

    PubMed

    Song, Ping; Li, Min; Shen, Juwen; Pei, Hao; Chao, Jie; Su, Shao; Aldalbahi, Ali; Wang, Lihua; Shi, Jiye; Song, Shiping; Wang, Lianhui; Fan, Chunhai; Zuo, Xiaolei

    2016-08-16

    The fixed dynamic range of traditional biosensors limits their utility in several real applications. For example, viral load monitoring requires the dynamic range spans several orders of magnitude; whereas, monitoring of drugs requires extremely narrow dynamic range. To overcome this limitation, here, we devised tunable biosensing interface using allosteric DNA tetrahedral bioprobes to tune the dynamic range of DNA biosensors. Our strategy takes the advantage of the readily and flexible structure design and predictable geometric reconfiguration of DNA nanotechnology. We reconfigured the DNA tetrahedral bioprobes by inserting the effector sequence into the DNA tetrahedron, through which, the binding affinity of DNA tetrahedral bioprobes can be tuned. As a result, the detection limit of DNA biosensors can be programmably regulated. The dynamic range of DNA biosensors can be tuned (narrowed or extended) for up to 100-fold. Using the regulation of binding affinity, we realized the capture and release of biomolecules by tuning the binding behavior of DNA tetrahedral bioprobes. PMID:27435955

  9. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect

    Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L.

    2012-05-14

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

  10. Efficient control schemes with limited computation complexity for Tomographic AO systems on VLTs and ELTs

    NASA Astrophysics Data System (ADS)

    Petit, C.; Le Louarn, M.; Fusco, T.; Madec, P.-Y.

    2011-09-01

    Various tomographic control solutions have been proposed during the last decades to ensure efficient or even optimal closed-loop correction to tomographic Adaptive Optics (AO) concepts such as Laser Tomographic AO (LTAO), Multi-Conjugate AO (MCAO). The optimal solution, based on Linear Quadratic Gaussian (LQG) approach, as well as suboptimal but efficient solutions such as Pseudo-Open Loop Control (POLC) require multiple Matrix Vector Multiplications (MVM). Disregarding their respective performance, these efficient control solutions thus exhibit strong increase of on-line complexity and their implementation may become difficult in demanding cases. Among them, two cases are of particular interest. First, the system Real-Time Computer architecture and implementation is derived from past or present solutions and does not support multiple MVM. This is the case of the AO Facility which RTC architecture is derived from the SPARTA platform and inherits its simple MVM architecture, which does not fit with LTAO control solutions for instance. Second, considering future systems such as Extremely Large Telescopes, the number of degrees of freedom is twenty to one hundred times bigger than present systems. In these conditions, tomographic control solutions can hardly be used in their standard form and optimized implementation shall be considered. Single MVM tomographic control solutions represent a potential solution, and straightforward solutions such as Virtual Deformable Mirrors have been already proposed for LTAO but with tuning issues. We investigate in this paper the possibility to derive from tomographic control solutions, such as POLC or LQG, simplified control solutions ensuring simple MVM architecture and that could be thus implemented on nowadays systems or future complex systems. We theoretically derive various solutions and analyze their respective performance on various systems thanks to numerical simulation. We discuss the optimization of their performance and

  11. Real-time control for the high order, wide field DRAGON AO test bench

    NASA Astrophysics Data System (ADS)

    Basden, Alastair; Bharmal, Nazim A.; Bitenc, Urban; Dipper, Nigel; Morris, Tim; Myers, Richard; Reeves, Andrew; Younger, Eddy

    2014-07-01

    DRAGON is a high order, wide field AO test-bench at Durham. A key feature of DRAGON is the ability to be operated at real-time rates, i.e. frame rates of up to 1kHz, with low latency to maintain AO performance. Here, we will present the real-time control architecture for DRAGON, which includes two deformable mirrors, eight wavefront sensors and thousands of Shack-Hartmann sub-apertures. A novel approach has been taken to allow access to the wavefront sensor pixel stream, reducing latency and peak computational load, and this technique can be implemented for other similar wavefront sensor cameras with no hardware costs. We report on experience with an ELT-suitable wavefront sensor camera. DRAGON will form the basis for investigations into hardware acceleration architectures for AO real-time control, and recent work on GPU and many-core systems (including the Xeon Phi) will be reported. Additionally, the modular structure of DRAGON, its remote control capabilities, distribution of AO telemetry data, and the software concepts and architecture will be reported. Techniques used in DRAGON for pixel processing, slope calculation and wavefront reconstruction will be presented. This will include methods to handle changes in CN2 profile and sodium layer profile, both of which can be modelled in DRAGON. DRAGON software simulation techniques linking hardware-in-the-loop computer models to the DRAGON real-time system and control software will also be discussed. This tool allows testing of the DRAGON system without requiring physical hardware and serves as a test-bed for ELT integration and verification techniques.

  12. Inter- and intra-observer agreement of the AO classification for operatively treated distal radius fractures.

    PubMed

    van Buijtenen, Jesse M; van Tunen, Mischa L C; Zuidema, Wietse P; Heilbron, Emile A; de Haan, Jeroen; de Vet, Henrica C W; Derksen, Robert J

    2015-11-01

    The reproducibility of the AO classification for distal radius fractures remains a topic of debate. Previous studies showed variable reproducibility results. Important treatment decisions depend on correct classification, especially in comminuted, intra-articular fractures. Therefore, reliable reproducibility results need to be undisputedly determined. Hence, the study objective was to assess inter- and intra-observer agreement of the AO classification for operatively treated distal radius fractures. A database of 54 radiographs of all AO types (A, B and C) and groups (A2-3, B1-3, and C1-3) of distal radius fractures was assessed in twofold. Likewise, a subset of 152 radiographs of solely C-type groups (C1-3) was assessed. All fractures were classified by six observers with different experience levels: three consultant trauma surgeons, one sixth-year trauma surgery resident, a consultant trauma radiologist, and an intern with limited experienced. The inter-observer agreement of both main types and groups was moderate (κ = 0.49 resp. κ = 0.48) in combination with a good intra-observer agreement (κ = 0.68 resp. κ = 0.70). The inter-observer agreement of the subset C-type fractures group was fair (κ = 0.27) with moderate intra-observer agreement (κ = 0.43). According to these results, the reproducibility of the AO classification of main types and groups of distal radius fractures based on conventional radiographs is insufficient (κ < 0.50), especially at group level of C-type fractures. PMID:26614083

  13. World-wide deployment of Robo-AO visible-light robotic laser adaptive optics systems

    NASA Astrophysics Data System (ADS)

    Baranec, Christoph; Riddle, Reed; Law, Nicholas Michael; Lu, Jessica R.; Tonry, John; Tully, R. Brent; Wright, Shelley; Kulkarni, Shrinivas; Severson, Scott; Choi, Philip; Ramaprakash, A.; Chun, Mark; Connelley, Mike; Tokunaga, Alan; Hall, Donald

    2015-08-01

    In the next few years, several modest-sized telescopes around the world will be upgraded with autonomous laser adaptive optics systems based on the Robo-AO prototype deployed at the Palomar Observatory 1.5-m telescope. The prototype commenced scientific operations in June 2012 and more than 19,000 observations have since been performed at the ~0.12" visible-light diffraction limit. We are planning to move the prototype system to the 2.1-m telescope at Kitt Peak for a 3-year deployment which will serve a consortium of users including Caltech, the University of Hawai`i, IUCAA, NCU and institutions in China. Additionally, 2 months per year will be made available to the US astronomical community.New Robo-AO systems are in various stages of development: a clone by IUCAA for the 2-m IGO telescope in India; a natural guide star variant, KAPAO, by Pomona College at the 1-m Table Mountain telescope in California; and second generation Robo-AO systems are planned for the 3-m IRTF and 2.2-m University of Hawai'i telescopes on Maunakea, Hawai`i. The latter will exploit Maunakea's excellent observing conditions to provide higher Strehl ratios, sharper imaging, ~0.07", and correction to lambda = 400 nm. An additional infrared integral-field spectrograph will be fed by the UH 2.2-m Robo-AO system to quickly classify transients, such as supernovae and asteroids, discovered by the ATLAS system in Hawai`i.

  14. Enabling technologies for visible adaptive optics: the Magellan adaptive secondary VisAO camera

    NASA Astrophysics Data System (ADS)

    Kopon, Derek; Males, Jared; Close, Laird M.; Gasho, Victor

    2009-08-01

    Since its beginnings, diffraction-limited ground-based adaptive optics (AO) imaging has been limited to wavelengths in the near IR (λ>1μm) and longer. Visible AO (λ>1μm) has proven to be difficult because shorter wavelengths require wavefront correction on very short spatial and temporal scales. The pupil must be sampled very finely, which requires dense actuator spacing and fine wavefront sampling with large dynamic range. In addition, atmospheric dispersion is much more significant in the visible than in the near-IR. Imaging over a broad visible band requires a very good Atmospheric Dispersion Corrector (ADC). Even with these technologies, our AO simulations using the CAOS code, combined with the optical and site parameters for the 6.5m Magellan telescope, demonstrate a large temporal variability of visible (λ=0.7μm) Strehl on timescales of 50 ms. Over several hundred milliseconds, the visible Strehl can be as high at 50% and as low as 10%. Taking advantage of periods of high Strehl requires either the ability to read out the CCD very fast, thereby introducing significant amounts of read-noise, or the use of a fast asynchronous shutter that can block the low-Strehl light. Our Magellan VisAO camera will use an advanced ADC, a high-speed shutter, and our 585 actuator adaptive secondary to achieve broadband (0.5-1.0 μm) diffraction limited images on the 6.5m Magellan Clay telescope in Chile at Las Campanas Observatory. These will be the sharpest and deepest visible direct images taken to date with a resolution of 17 mas, a factor of 2.7 better than the diffraction limit of the Hubble Space Telescope.

  15. Active DNA demethylation by DNA repair: Facts and uncertainties.

    PubMed

    Schuermann, David; Weber, Alain R; Schär, Primo

    2016-08-01

    Pathways that control and modulate DNA methylation patterning in mammalian cells were poorly understood for a long time, although their importance in establishing and maintaining cell type-specific gene expression was well recognized. The discovery of proteins capable of converting 5-methylcytosine (5mC) to putative substrates for DNA repair introduced a novel and exciting conceptual framework for the investigation and ultimate discovery of molecular mechanisms of DNA demethylation. Against the prevailing notion that DNA methylation is a static epigenetic mark, it turned out to be dynamic and distinct mechanisms appear to have evolved to effect global and locus-specific DNA demethylation. There is compelling evidence that DNA repair, in particular base excision repair, contributes significantly to the turnover of 5mC in cells. By actively demethylating DNA, DNA repair supports the developmental establishment as well as the maintenance of DNA methylation landscapes and gene expression patterns. Yet, while the biochemical pathways are relatively well-established and reviewed, the biological context, function and regulation of DNA repair-mediated active DNA demethylation remains uncertain. In this review, we will thus summarize and critically discuss the evidence that associates active DNA demethylation by DNA repair with specific functional contexts including the DNA methylation erasure in the early embryo, the control of pluripotency and cellular differentiation, the maintenance of cell identity, and the nuclear reprogramming. PMID:27247237

  16. Programmable Quantitative DNA Nanothermometers.

    PubMed

    Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis

    2016-07-13

    Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology. PMID:27058370

  17. Electroeluting DNA fragments.

    PubMed

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation. PMID:20834225

  18. Dynamical Behavior of DNA

    NASA Astrophysics Data System (ADS)

    Kumar, Shankar

    1990-01-01

    The crystal structure of the DNA-EcoRI complex (Kim et al., 1990) revealed the existence of a 'kink' (or a disruption of the helical symmetry) in the DNA. Part of this work was an investigation of whether or not the kinked structure is a physically meaningful metastable state that is intrinsic to DNA. By using the "All Atom" hamiltonian of Weiner et al (1986) it has been found that the kink is not a metastable feature of the DNA. Rapid scanning of conformational space is indispensable in statistical mechanical studies of proteins and DNA. The Quasi-Optimized-Monte-Carlo (or QOMC) method is more efficient than the conventional Metropolis Monte Carlo method in the simulated annealing calculations reported here. It is also shown here that using altered masses in Molecular Dynamics calculations enhances sampling efficiency. The Multiple Histogram technique (Ferrenberg, 1989) has been applied for the first time on complex biomolecular hamiltonians. This method is superior to the classical perturbation and multistage sampling techniques for calculating free energy differences and generating potential of mean force profiles for suitably chosen reaction coordinates. This was demonstrated by using the multiple histogram method to generate the potential of mean force for the pseudorotation phase angle of the sugar ring in adenosine.

  19. Chromatin and DNA replication.

    PubMed

    MacAlpine, David M; Almouzni, Geneviève

    2013-08-01

    The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program. PMID:23751185

  20. A predicted T4 secretion system and conserved DNA-repeats identified in a subset of related Arthrobacter plasmids.

    PubMed

    Mihăşan, Marius; Brandsch, Roderich

    2016-10-01

    BLAST analysis of pAO1 ORFs of Arthrobacter nicotinovorans revealed 12 ORFs, including the ORF of a transcriptional regulator, predicted to encode the components of a T4-secretion system involved in bacterial conjugation. These ORFs were conserved and showed synteny among 14 Arthrobacter plasmids. A DNA repeat of about 370 nucleotides was found to be present 5' to the pAO1 ORFs of DUF4192-, DprA- and ParB-like proteins. Similar repeats were present in identical positions on 12 additional Arthrobacter plasmids. The DNA repeats on a particular plasmid are highly identical duplications. The DNA repeats contain alternating GC and AT reach sequences, potential protein DNA-binding sites and purine reach stretches. The sequences end with 5'ATG.AAC3' which results in the amino terminal sequence methionine (M) and asparagine (N) for all predicted DprA, DUF4192 and ParB proteins. The presences of conserved ORFs of a T4-secretion system and of similar DNA repeats suggest that these Arthrobacter plasmids are related and evolved from a common ancestor. The functional significance of the DNA repeats in a coordinated common mechanism of regulation of expression of the dprA-(involved in natural competence), parB- (involved in plasmid partitioning) and duf4192- (unknown function in plasmid life cycle) genes remains to be established. PMID:27524651

  1. AO modelling for wide-field E-ELT instrumentation using Monte-Carlo simulation

    NASA Astrophysics Data System (ADS)

    Basden, Alastair; Morris, Simon; Morris, Tim; Myers, Richard

    2014-08-01

    Extensive simulations of AO performance for several E-ELT instruments (including EAGLE, MOSAIC, HIRES and MAORY) have been ongoing using the Monte-Carlo Durham AO Simulation Package. We present the latest simulation results, including studies into DM requirements, dependencies of performance on asterism, detailed point spread function generation, accurate telescope modelling, and studies of laser guide star effects. Details of simulations will be given, including the use of optical models of the E-ELT to generate wave- front sensor pupil illumination functions, laser guide star modelling, and investigations of different many-layer atmospheric profiles. We discuss issues related to ELT-scale simulation, how we have overcome these, and how we will be approaching forthcoming issues such as modelling of advanced wavefront control, multi-rate wavefront sensing, and advanced treatment of extended laser guide star spots. We also present progress made on integrating simulation with AO real-time control systems. The impact of simulation outcomes on instrument design studies will be discussed, and the ongoing work plan presented.

  2. SCExAO: the most complete instrument to characterize exoplanets and stellar environments

    NASA Astrophysics Data System (ADS)

    Lozi, Julien; Guyon, Olivier; Jovanovic, Nemanja; Singh, Garima; Doughty, Danielle; Pathak, Prashant; Goebel, Sean; Kudo, Tomoyuki

    2015-12-01

    The Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) instrument, currently under development for the Subaru Telescope, optimally combines state-of-the-art technologies to directly study exoplanets and stellar environments at the diffraction limit, both in visible and infrared light (0.6 to 2.4 um). The instrument already includes an ultra-fast visible pyramid wavefront sensor operating at 3.5 kHz, a 2k-actuator deformable mirror, a set of optimal coronagraphs that can work as close as 1 l/D, a low-order wavefront sensor, a high-speed speckle control, and two visible interferometric modules, VAMPIRES and FIRST. Stability of the wavefront correction has already been demonstrated on sky, and SCExAO is already producing scientific results. After the integration of the Integral Field Spectrograph (IFS) CHARIS and a Microwave Kinetic Inductance Detector (MKID) in 2016, SCExAO will be one of the most powerful and effective tools for characterizing exoplanets and disks.

  3. Using the Fingerprinting Method to Customize RTLS Based on the AoA Ranging Technique

    PubMed Central

    Jachimczyk, Bartosz; Dziak, Damian; Kulesza, Wlodek J.

    2016-01-01

    Real-time Locating Systems (RTLSs) have the ability to precisely locate the position of things and people in real time. They are needed for security and emergency applications, but also for healthcare and home care appliances. The research aims for developing an analytical method to customize RTLSs, in order to improve localization performance in terms of precision. The proposed method is based on Angle of Arrival (AoA), a ranging technique and fingerprinting method along with an analytically defined uncertainty of AoA, and a localization uncertainty map. The presented solution includes three main concerns: geometry of indoor space, RTLS arrangement, and a statistical approach to localization precision of a pair of location sensors using an AoA signal. An evaluation of the implementation of the customized RTLS validates the analytical model of the fingerprinting map. The results of simulations and physical experiments verify the proposed method. The research confirms that the analytically established fingerprint map is the valid representation of RTLS’ performance in terms of precision. Furthermore, the research demonstrates an impact of workspace geometry and workspace layout onto the RTLS’ performance. Moreover, the studies show how the size and shape of a workspace and the placement of the calibration point affect the fingerprint map. Withal, the performance investigation defines the most effective arrangement of location sensors and its influence on localization precision. PMID:27314354

  4. AO/NAO Response to Climate Change. 1; Respective Influences of Stratospheric and Tropospheric Climate Changes

    NASA Technical Reports Server (NTRS)

    Rind, D.; Perlwitz, J.; Lonergan, P.

    2005-01-01

    We utilize the GISS Global Climate Middle Atmosphere Model and 8 different climate change experiments, many of them focused on stratospheric climate forcings, to assess the relative influence of tropospheric and stratospheric climate change on the extratropical circulation indices (Arctic Oscillation, AO; North Atlantic Oscillation, NAO). The experiments are run in two different ways: with variable sea surface temperatures (SSTs) to allow for a full tropospheric climate response, and with specified SSTs to minimize the tropospheric change. The results show that tropospheric warming (cooling) experiments and stratospheric cooling (warming) experiments produce more positive (negative) AO/NAO indices. For the typical magnitudes of tropospheric and stratospheric climate changes, the tropospheric response dominates; results are strongest when the tropospheric and stratospheric influences are producing similar phase changes. Both regions produce their effect primarily by altering wave propagation and angular momentum transports, but planetary wave energy changes accompanying tropospheric climate change are also important. Stratospheric forcing has a larger impact on the NAO than on the AO, and the angular momentum transport changes associated with it peak in the upper troposphere, affecting all wavenumbers. Tropospheric climate changes influence both the A0 and NAO with effects that extend throughout the troposphere. For both forcings there is often vertical consistency in the sign of the momentum transport changes, obscuring the difference between direct and indirect mechanisms for influencing the surface circulation.

  5. Microwelding of various metallic materials under ultravacuum (AO 138-10)

    NASA Technical Reports Server (NTRS)

    Assie, Jean Pierre; Conde, Eric

    1991-01-01

    The first finding from the AO 138-10 is that cold welding never occurred, and that microwelds didn't even affect the reference (presumably microweld prone) pairs of metals consisting of gold, silver, and chromium. The scientific disappointment from these results must be tempered by the notion of a static AO 138-10 experiment, reflecting the passive character of the global Long Duration Exposure Facility (LDEF) flight. Thus far, it has been theorized that cold welding results from the peeling of the oxide layer, that is formed in an earth environment, by the space environment since such a layer no longer grows in space. In fact, such stripping of the oxide layer supposes relative motion of the contacting materials. In the absence of such motion, as in this experiment, oxidation will preserve its integrity and continue to prevent microwelding. More bewildering is that there was no microwelding of the reference pairs. Even though AO 138-10 failed scientific expectations, as did the LDEF structure with cold welding, the positive, functional aspect to keep in mind is the safe operation of single-shot (appendage releasing and/or latching) mechanisms, unhindered by microwelding in a space vacuum, as now demonstrated by the statically representative pairs of materials. Other aspects of the experiment are discussed.

  6. Using the Fingerprinting Method to Customize RTLS Based on the AoA Ranging Technique.

    PubMed

    Jachimczyk, Bartosz; Dziak, Damian; Kulesza, Wlodek J

    2016-01-01

    Real-time Locating Systems (RTLSs) have the ability to precisely locate the position of things and people in real time. They are needed for security and emergency applications, but also for healthcare and home care appliances. The research aims for developing an analytical method to customize RTLSs, in order to improve localization performance in terms of precision. The proposed method is based on Angle of Arrival (AoA), a ranging technique and fingerprinting method along with an analytically defined uncertainty of AoA, and a localization uncertainty map. The presented solution includes three main concerns: geometry of indoor space, RTLS arrangement, and a statistical approach to localization precision of a pair of location sensors using an AoA signal. An evaluation of the implementation of the customized RTLS validates the analytical model of the fingerprinting map. The results of simulations and physical experiments verify the proposed method. The research confirms that the analytically established fingerprint map is the valid representation of RTLS' performance in terms of precision. Furthermore, the research demonstrates an impact of workspace geometry and workspace layout onto the RTLS' performance. Moreover, the studies show how the size and shape of a workspace and the placement of the calibration point affect the fingerprint map. Withal, the performance investigation defines the most effective arrangement of location sensors and its influence on localization precision. PMID:27314354

  7. PHOTOMETRIC EVOLUTION OF SNe Ib/c 2004ao, 2004gk, AND 2006gi

    SciTech Connect

    Elmhamdi, Abouazza; Kordi, Ayman; Tsvetkov, Dmitry; Danziger, I. John

    2011-04-20

    Photometric observations of three core collapse supernovae (SNe 2004ao, 2004gk, and 2006gi), covering about 200 days of evolution, are presented and analyzed. The photometric behavior of the three objects is consistent with their membership in the envelope-stripped Type Ib/c class. Pseudobolometric light curves are constructed. The corresponding measured e-folding times are found to be faster compared to the {sup 56}Co decay (i.e., 111.3 days), suggesting that a proportion of {gamma}-rays increasing with time have escaped without thermalization, owing to the low-mass nature of the ejecta. SN 2006gi has almost identical post-maximum decline phase luminosities as SN 1999ex and found to be similar to both SNe 1999dn and 1999ex in terms of the quasi-bolometric shape, placing it among the fast decliner Ib objects. SN 2004ao appears to fit within the slow decliner Ib SNe. SNe 2004ao and 2004gk display almost identical luminosities in the [50-100] day time interval, similar to SN 1993J. A preliminary simplified {gamma}-ray deposition model is described and applied to the computed pseudobolometric light curves, allowing one to find a range in the ejecta and {sup 56}Ni masses. The optical and quasi-bolometric light curves and the B - V color evolution of SN 2004gk are found to show a sudden drop after day 150. Correlating this fact to dust formation is premature and requires further observational evidence.

  8. Detecção inesperada de efeitos de lentes fracas em grupos de galáxias pouco luminosos em raios-X

    NASA Astrophysics Data System (ADS)

    Carrasco, R.; Mendes de Oliveira, C.; Sodrã©, L., Jr.; Lima Neto, G. B.; Cypriano, E. S.; Lengruber, L. L.; Cuevas, H.; Ramirez, A.

    2003-08-01

    Obtivemos, como parte do programa de verificação científica do GMOS Sul, imagens profundas de três grupos de galáxias: G97 e G102 (z~0,4) e G124 (z = 0,17). Esses alvos foram selecionados a partir do catálogo de fontes extensas de Vikhlinin (1998), por terem luminosidades em raios X menores que 3´1043 ergs s-1, valor cerca de uma ou duas ordens de grandeza inferior ao de aglomerados de galáxias. O objetivo primário dessas observações é o estudo da evolução de galáxias em grupos. Grupos são ambientes menos densos que aglomerados, contêm a grande maioria das galáxias do Universo mas que, até o momento, foram estudados detalhadamente apenas no Universo local (z~0). Com esses dados efetuamos uma análise estatística da distorção na forma das galáxias de fundo (lentes gravitacionais fracas) como forma de inferir o conteúdo e a distribuição de massa nesses grupos apesar de que, em princípio, esse efeito não deveria ser detectado uma vez que os critérios de seleção adotados previlegiam sistemas de baixa massa. De fato, para G124 obtivemos apenas um limite superior para sua massa que é compatível com sua luminosidade em raios X. De modo contrário e surpreendente, os objetos G102 e G097, aparentam ter massas que resultariam em dispersões de velocidade maiores que 1000 km s-1, muito maiores do que se espera para grupos de galáxias. Com efeito, para G097 obtivemos, a partir de dados do satélite XMM, uma estimativa para a temperatura do gás intragrupo de kT = 2,6 keV, que é tipica de sistemas com dispersões de velocidade de ~ 600 km s-1, bem característica de grupos. Essas contradições aparentes entre lentes fracas e raios X podem ser explicadas de dois modos: i) a massa obtida por lentes estaria sobreestimada devido à superposição de estruturas massivas ao longo da linha de visada ou ii) a temperatura do gás do meio intra-grupo reflete o potencial gravitacional de estruturas menores que estariam se fundindo para formar uma

  9. Tunnelling microscopy of DNA

    NASA Astrophysics Data System (ADS)

    Selci, Stefano; Cricenti, Antonio

    1991-01-01

    Uncoated DNA molecules marked with an activated tris (1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with a high resolution Scanning Tunnelling Microscope (STM). The STM operated simultaneously in the constant-current and gap-modulated mode. Highly reproducible STM images have been obtained and interpreted in terms of expected DNA structure. The main periodicity, regularly presented in molecules several hundred Ångstrom long, ranges from 25 Å to 35 Å with an average diameter of 22 Å. Higher resolution images of the minor groove have revealed the phosphate groups along the DNA backbones. Constant-current images of TAPO deposited on gold show a crystalline structure of rows of molecules with a side-by-side spacing of 3 Å.

  10. Transposon facilitated DNA sequencing

    SciTech Connect

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  11. DNA sequencing: chemical methods

    SciTech Connect

    Ambrose, B.J.B.; Pless, R.C.

    1987-01-01

    Limited base-specific or base-selective cleavage of a defined DNA fragment yields polynucleotide products, the length of which correlates with the positions of the particular base (or bases) in the original fragment. Sverdlov and co-workers recognized the possibility of using this principle for the determination of DNA sequences. In 1977 a fully elaborated method was introduced based on this principle, which allowed routine analysis of DNA sequences over distances greater than 100 nucleotide unite from a defined, radiolabeled terminus. Six procedures for partial cleavage were described. Simultaneous parallel resolution of an appropriate set of partial cleavage mixtures by polyacrylamide gel electrophoresis, followed by visualization of the radioactive bands by autoradiography, allows the deduction of nucleotide sequence.

  12. [DNA methylation in obesity].

    PubMed

    Pokrywka, Małgorzata; Kieć-Wilk, Beata; Polus, Anna; Wybrańska, Iwona

    2014-01-01

    The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes), have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA) synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described. PMID:25531701

  13. Adaptive Optics at Optical Wavelengths: Test Observations of Kyoto 3DII Connected to Subaru Telescope AO188

    NASA Astrophysics Data System (ADS)

    Matsubayashi, K.; Sugai, H.; Shimono, A.; Akita, A.; Hattori, T.; Hayano, Y.; Minowa, Y.; Takeyama, N.

    2016-09-01

    Adaptive optics (AO) enables us to observe objects with high spatial resolution, which is important in most astrophysical observations. Most AO systems are operational at near-infrared wavelengths but not in the optical range, because optical observations require a much higher performance to obtain the same Strehl ratio as near-infrared observations. Therefore, to enable AO-assisted observations at optical wavelengths, we connected the Kyoto Tridimensional Spectrograph II (Kyoto 3DII), which can perform integral field spectroscopy, to the second generation AO system of the Subaru Telescope (AO188). We developed a new beam-splitter that reflects light below 594 nm for the wavefront sensors of AO188 and transmits above 644 nm for Kyoto 3DII. We also developed a Kyoto 3DII mount at the Nasmyth focus of the Subaru Telescope. In test observations, the spatial resolution of the combined AO188–Kyoto 3DII was higher than that in natural seeing conditions, even at 6500 Å. The full width at half maximum of an undersampled (1.5 spaxels) bright guide star (7.0 mag in the V-band) was 0.″12.

  14. Mitogen-activated protein kinase signal transduction and DNA repair network are involved in aluminum-induced DNA damage and adaptive response in root cells of Allium cepa L.

    PubMed Central

    Panda, Brahma B.; Achary, V. Mohan M.

    2014-01-01

    In the current study, we studied the role of signal transduction in aluminum (Al3+)-induced DNA damage and adaptive response in root cells of Allium cepa L. The root cells in planta were treated with Al3+ (800 μM) for 3 h without or with 2 h pre-treatment of inhibitors of mitogen-activated protein kinase (MAPK), and protein phosphatase. Also, root cells in planta were conditioned with Al3+ (10 μM) for 2 h and then subjected to genotoxic challenge of ethyl methane sulfonate (EMS; 5 mM) for 3 h without or with the pre-treatment of the aforementioned inhibitors as well as the inhibitors of translation, transcription, DNA replication and repair. At the end of treatments, roots cells were assayed for cell death and/or DNA damage. The results revealed that Al3+ (800 μM)-induced significant DNA damage and cell death. On the other hand, conditioning with low dose of Al3+ induced adaptive response conferring protection of root cells from genotoxic stress caused by EMS-challenge. Pre-treatment of roots cells with the chosen inhibitors prior to Al3+-conditioning prevented or reduced the adaptive response to EMS genotoxicity. The results of this study suggested the involvement of MAPK and DNA repair network underlying Al-induced DNA damage and adaptive response to genotoxic stress in root cells of A. cepa. PMID:24926302

  15. Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity.

    PubMed

    Shen, Qingming; Fan, Mengxing; Yang, Yin; Zhang, Hui

    2016-08-31

    DNA demethylation and demethylase activity play important roles in DNA self-repair, and their detection is key to early diagnosis of fatal diseases. Herein, a facile electrochemical DNA (E-DNA) sensor was developed for the sensitive detection of DNA demethylation and demethylase activity based on an enzyme cleavage strategy. The thiol modified hemi-methylated hairpin probe DNA (pDNA) was self-assembled on a Au electrode surface through the formation of AuS bonds. The hemi-methylated pDNA served as the substrate of DNA demethylase (using methyl-CpG-binding domain protein 2 (MBD2) as an example). Following demethylation, the hairpin stem was then recognized and cleaved by BstUI endonuclease. The ferrocene carboxylic acid (FcA)-tagged pDNA strands were released into the buffer solution from the electrode surface, resulting in a significant decrease of electrochemical signal and providing a means to observe DNA demethylation. The activity of DNA demethylase was analyzed in the concentration ranging from 0.5 to 500 ng mL(-1) with a limit of detection as low as 0.17 ng mL(-1). With high specificity and sensitivity, rapid response, and low cost, this simple E-DNA sensor provides a unique platform for the sensitive detection of DNA demethylation, DNA demethylase activity, and related molecular diagnostics and drug screening. PMID:27506345

  16. DNA templated magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Kinsella, Joseph M.

    Recent discoveries in nanoscience are predicted to potentially revolutionize future technologies in an extensive number of fields. These developments are contingent upon discovering new and often unconventional methods to synthesize and control nanoscale components. Nature provides several examples of working nanotechnology such as the use of programmed self assembly to build and deconstruct complex molecular systems. We have adopted a method to control the one dimensional assembly of magnetic nanoparticles using DNA as a scaffold molecule. With this method we have demonstrated the ability to organize 5 nm particles into chains that stretch up to ˜20 mum in length. One advantage of using DNA compared is the ability of the molecule to interact with other biomolecules. After assembling particles onto DNA we have been able to cleave the molecule into smaller fragments using restriction enzymes. Using ligase enzymes we have re-connected these fragments, coated with either gold or iron oxide, to form long one-dimensional arrangements of the two different types of nanoparticles on a single molecular guide. We have also created a sensitive magnetic field sensor by incorporating magnetic nanoparticle coated DNA strands with microfabricated electrodes. The IV characteristics of the aligned nanoparticles are dependant on the magnitude of an externally applied magnetic field. This transport phenomenon known as tunneling magnetoresistance (TMR) shows room temperature resistance of our devices over 80% for cobalt ferrite coated DNA when a field of 20 kOe is applied. In comparison, studies using two dimensional nanoparticle films of irox oxides xii only exhibit a 35% MR effect. Confinement into one dimension using the DNA guide produces a TMR mechanism which produces significant increases in magnetoresistance. This property can be utilized for applications in magnetic field sensing, data storage, and logic elements.

  17. Automated DNA sequencing.

    PubMed

    Wallis, Yvonne; Morrell, Natalie

    2011-01-01

    Fluorescent cycle sequencing of PCR products is a multistage process and several methodologies are available to perform each stage. This chapter will describe the more commonly utilised dye-terminator cycle sequencing approach using BigDye® terminator chemistry (Applied Biosystems) ready for analysis on a 3730 DNA genetic analyzer. Even though DNA sequencing is one of the most common and robust techniques performed in molecular laboratories it may not always produce desirable results. The causes of the most common problems will also be discussed in this chapter. PMID:20938839

  18. Ancient human DNA.

    PubMed

    Kirsanow, Karola; Burger, Joachim

    2012-01-20

    The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements. PMID:22169595

  19. Rigidity of melting DNA.

    PubMed

    Pal, Tanmoy; Bhattacharjee, Somendra M

    2016-05-01

    The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation. PMID:27300825

  20. Rigidity of melting DNA

    NASA Astrophysics Data System (ADS)

    Pal, Tanmoy; Bhattacharjee, Somendra M.

    2016-05-01

    The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.

  1. Extraktion von DNA

    NASA Astrophysics Data System (ADS)

    Pöpping, Bert; Unterberger, Claudia

    Eine DNA-gestützte Analytik spielt im Lebensmittelbereich eine große Rolle. So wird die PCR bzw. die Real Time PCR z. B. für den Nachweis von Krankheitserreger in Lebensmitteln, zur Tier- und Pflanzenartendifferenzierung und den Nachweis von gentechnologisch veränderten Organismen eingesetzt [1]. Grundvoraussetzung für die sehr sensitiven molekularbiologischen Methoden ist eine saubere und kontaminationsfreie Nukleinsäure [2]. Die Qualität der Nukleinsäure entscheidet über Erfolg und Misserfolg der anschließenden molekularbiologischen Analytik. Deshalb werden im Bereich der Lebensmittelanalytik hohe Anforderungen an das jeweilige DNA-Extraktionsprotokoll gestellt. Durch die Anwendung eines geeigneten Extraktionsverfahrens soll die nachzuweisende DNA möglichst in hochmolekularer Form und frei von die nachfolgende Analytik hemmenden Substanzen vorliegen [1]. Gerade hier stellt die Natur der Lebensmittelmatrix eine besondere Herausforderung dar. Matrixkomponenten wie Fette, Zucker, Proteine und sekundäre Inhaltsstoffe erschweren die DNA-Extraktion und können, wenn sie nicht durch die Extraktion vollständig entfernt werden, zu einer Inhibierung der PCR führen [3]. Des Weiteren müssen auf der Matrixoberfläche vorhandene DNA-abbauende Enzyme gehemmt werden [1]. Daneben spielt der Einfluss verschiedener chemischer und physikalischer Parameter (pH-Wert, Temperatur, Enzyme, Scherkräfte) bei der Lebensmittelproduktion eine große Rolle für die Qualität der extrahierten DNA. So führen z. B. hohe Temperaturen und saure pH-Werte während der Lebensmittelverarbeitung zu einer Fragmentierung der DNA. Auch die physikalischen und chemischen Bedingungen der verwendeten Extraktionsmethode beeinflussen die Qualität der DNA [2]. Bleiben nach der Extraktion organische Lösungsmittel (Phenol, Ethanol), Enzyme, Proteine oder Salze zurück, können diese ebenfalls eine nachfolgende PCR inhibieren. Um eine Inhibition der PCR auszuschließen, sollten in der

  2. DNA banking and DNA databanking by academic and commercial laboratories

    SciTech Connect

    McEwen, J.E. |; Reilly, P.R.

    1994-09-01

    The advent of DNA-based testing is giving rise to DNA banking (the long-term storage of cells, transformed cell lines, or extracted DNA for subsequent retrieval and analysis) and DNA data banking (the indefinite storage of information derived from DNA analysis). Large scale acquisition and storage of DNA and DNA data has important implications for the privacy rights of individuals. A survey of 148 academically based and commercial DNA diagnostic laboratories was conducted to determine: (1) the extent of their DNA banking activities; (2) their policies and experiences regarding access to DNA samples and data; (3) the quality assurance measures they employ; and (4) whether they have written policies and/or depositor`s agreements addressing specific issues. These issues include: (1) who may have access to DNA samples and data; (2) whether scientists may have access to anonymous samples or data for research use; (3) whether they have plans to contact depositors or retest samples if improved tests for a disorder become available; (4) disposition of samples at the end of the contract period if the laboratory ceases operations, if storage fees are unpaid, or after a death or divorce; (5) the consequence of unauthorized release, loss, or accidental destruction of samples; and (6) whether depositors may share in profits from the commercialization of tests or treatments developed in part from studies of stored DNA. The results suggest that many laboratories are banking DNA, that many have already amassed a large number of samples, and that a significant number plan to further develop DNA banking as a laboratory service over the next two years. Few laboratories have developed written policies governing DNA banking, and fewer still have drafted documents that define the rights and obligations of the parties. There may be a need for increased regulation of DNA banking and DNA data banking and for better defined policies with respect to protecting individual privacy.

  3. Ethanolic extract of the Goldenseal, Hydrastis canadensis, has demonstrable chemopreventive effects on HeLa cells in vitro: Drug-DNA interaction with calf thymus DNA as target.

    PubMed

    Saha, Santu Kumar; Sikdar, Sourav; Mukherjee, Avinaba; Bhadra, Kakali; Boujedaini, Naoual; Khuda-Bukhsh, Anisur Rahman

    2013-07-01

    This study tested chemotherapeutic potential of Hydrastis canadensis (HC) extract in HeLa cells in vitro, with emphasis on its drug-DNA interaction and apoptosis induction ability. Nuclear uptake of HC by DAPI, Ao/Eb staining and internucleosomal DNA damage by comet assay was studied through fluorescence microscopy. Possible changes in MMP and apoptotic signalling events were critically analyzed. Cell cycle progression studied through FACS and fragmented DNA through "TUNEL" assay were critically analyzed. RT-PCR studies were conducted for analyzing Cyt-C and Bax translocation in mitochondrial and cytosolic extracts, and Caspase 3 in whole cell lysate. Role of p53-mediated regulation of NF-κβ and TNF-α was elucidated by Western blot analysis. Data of CD and Tm profile of CT-DNA were analyzed. Overall results indicated anti-cancer potential of HC through its ability to induce apoptosis, and interaction with CT-DNA that changed structural conformation of DNA, proving HC to be a promising candidate for chemoprevention. PMID:23628949

  4. DNA Nanotechnology for Cancer Therapy

    PubMed Central

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

  5. DNA Nanotechnology for Cancer Therapy.

    PubMed

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

  6. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOEpatents

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  7. Quantification of human mitochondrial DNA using synthesized DNA standards.

    PubMed

    Kavlick, Mark F; Lawrence, Helen S; Merritt, R Travis; Fisher, Constance; Isenberg, Alice; Robertson, James M; Budowle, Bruce

    2011-11-01

    Successful mitochondrial DNA (mtDNA) forensic analysis depends on sufficient quantity and quality of mtDNA. A real-time quantitative PCR assay was developed to assess such characteristics in a DNA sample, which utilizes a duplex, synthetic DNA to ensure optimal quality assurance and quality control. The assay's 105-base pair target sequence facilitates amplification of degraded DNA and is minimally homologous to nonhuman mtDNA. The primers and probe hybridize to a region that has relatively few sequence polymorphisms. The assay can also identify the presence of PCR inhibitors and thus indicate the need for sample repurification. The results show that the assay provides information down to 10 copies and provides a dynamic range spanning seven orders of magnitude. Additional experiments demonstrated that as few as 300 mtDNA copies resulted in successful hypervariable region amplification, information that permits sample conservation and optimized downstream PCR testing. The assay described is rapid, reliable, and robust. PMID:21883207

  8. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  9. Is EMS communicating with the FCC?

    PubMed

    Johnson, M S; VanCott, C; Glass, C; Anderson, P B

    1989-07-01

    Radio communication problems in EMS run the spectrum from annoying to deadly. Dedicated radio frequencies for EMS, much like those exclusive to police and fire departments, are long overdue. PMID:10293680

  10. Impact of Alternative DNA Structures on DNA Damage, DNA Repair, and Genetic Instability

    PubMed Central

    Wang, Guliang; Vasquez, Karen M.

    2014-01-01

    Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability. PMID:24767258

  11. População nuclear e extranuclear em rádio-galáxias

    NASA Astrophysics Data System (ADS)

    Raimann, D. I.; Storchi-Bergmann, T.; Quintana, H.; Alloin, D.; Hunstead, R.; Wisotzki, L.

    2003-08-01

    A natureza do contínuo UV/ótico em rádio-galáxias é muito importante para o seu entendimento. Em baixos redshifts existem evidências de que muitas delas são dominadas no ótico por luz de estrelas velhas, características de galáxias early-type e em altos redshifts a característica dominante é um excesso de luz no UV, freqüentemente associado com estruturas que estão alinhadas aos eixos das estruturas rádio em grande escala. Inicialmente esse excesso foi interpretado como devido a episódios intensos de formação estelar nas galáxias hospedeiras. Entretanto, as descobertas dos alinhamentos entre as estruturas UV e rádio modificaram essa idéia. Foi proposto que a formação estelar é iniciada pela passagem do jato rádio através do meio interestelar das galáxias hospedeiras. A natureza do excesso UV começou a ser compreendida em um estudo detalhado do continuo ótico da 3C321, onde se concluiu que o contínuo desta galáxia tem origem multicomponente, com contribuições de populações velhas e intermediárias, de luz espalhada oriunda de um quasar obscurecido e do contínuo nebular. No presente trabalho estudamos a população nuclear e extranuclear de uma amostra de 24 rádio-galáxias, utilizando espectros óticos de fenda longa, com alta razão sinal/ruído. Através do método de síntese espectral de populações estelares, foram estimadas as contribuições de populações estelares de diferentes idades (e de um contínuo tipo lei de potência devido a um AGN, FC) para a luz integrada das galáxias, em 4020Å. As principais conclusões deste trabalho são: apenas quatro dos objetos estudados têm contribuições significativas (maiores do que 10%) das populações de 100 milhões de anos ou mais jovens (ou de FC) ao longo da região espacial estudada (6 kpc centrais); nenhuma das rádio-galáxias de tipo FRI estudadas tem contribuição significativa destas populações ao longo desta região; duas (de oito) de tipo FRII tem contribui

  12. Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits.

    PubMed

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2016-08-22

    Modern electronic microprocessors use semiconductor logic gates organized on a silicon chip to enable efficient inter-gate communication. Here, arrays of communicating DNA logic gates integrated on a single DNA tile were designed and used to process nucleic acid inputs in a reusable format. Our results lay the foundation for the development of a DNA nanoprocessor, a small and biocompatible device capable of performing complex analyses of DNA and RNA inputs. PMID:27430161

  13. DNA Methylation in Osteoarthritis

    PubMed Central

    den Hollander, Wouter; Meulenbelt, Ingrid

    2015-01-01

    Osteoarthritis (OA) is a prevalent disease of articular joints and primarily characterized by degradation and calcification of articular cartilage. Presently, no effective treatment other than pain relief exists and patients ultimately need to undergo replacement surgery of the affected joint. During disease progression articular chondrocytes, the single cell type present in articular cartilage, show altered transcriptional profiles and undergo phenotypic changes that resemble the terminal differentiation route apparent in growth plate chondrocytes. Hence, given its prominent function in both regulating gene expression and maintaining cellular phenotypes, DNA methylation of CpG dinucleotides is intensively studied in the context of OA. An increasing number of studies have been published that employed a targeted approach on genes known to play a role in OA pathophysiology. As of such, it has become clear that OA responsive DNA methylation changes seem to mediate disease associated aberrant gene expression. Furthermore, established OA susceptibility alleles such as GDF5 and DIO2 appear to confer OA risk via DNA methylation and respective pathophysiological expression changes. In more recent years, genome wide profiling of DNA methylation in OA affected articular cartilage has emerged as a powerful tool to address the epigenetic changes in their entirety, which has resulted in the identification of putative patient subgroups as well as generic OA associated pathways. PMID:27019616

  14. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  15. TRANSFECTION WITH BACULOVIRUS DNA

    EPA Science Inventory

    Purified DNA from the nuclear polyhedrosis viruses of Autographa californica (AcM NPV) and Rachiplusia ou (RoM NPV) were found to be infectious in TN-368 cells employing the calcium phosphate precipitation technique (F.L. Graham and A.J. van der Eb, Virology, 52, 456-467, 1973). ...

  16. DNA Replication Origins

    PubMed Central

    Leonard, Alan C.; Méchali, Marcel

    2013-01-01

    The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin environment in origin selection and the mechanisms used by initiators to recognize replication origins. Close examination of bacterial and archaeal replication origins reveals an array of DNA sequence motifs that position individual initiator protein molecules and promote initiator oligomerization on origin DNA. Conversely, the need for specific recognition sequences in eukaryotic replication origins is relaxed. In fact, the primary rule for origin selection appears to be flexibility, a feature that is modulated either by structural elements or by epigenetic mechanisms at least partly linked to the organization of the genome for gene expression. PMID:23838439

  17. DNA Methylation in Osteoarthritis.

    PubMed

    den Hollander, Wouter; Meulenbelt, Ingrid

    2015-12-01

    Osteoarthritis (OA) is a prevalent disease of articular joints and primarily characterized by degradation and calcification of articular cartilage. Presently, no effective treatment other than pain relief exists and patients ultimately need to undergo replacement surgery of the affected joint. During disease progression articular chondrocytes, the single cell type present in articular cartilage, show altered transcriptional profiles and undergo phenotypic changes that resemble the terminal differentiation route apparent in growth plate chondrocytes. Hence, given its prominent function in both regulating gene expression and maintaining cellular phenotypes, DNA methylation of CpG dinucleotides is intensively studied in the context of OA. An increasing number of studies have been published that employed a targeted approach on genes known to play a role in OA pathophysiology. As of such, it has become clear that OA responsive DNA methylation changes seem to mediate disease associated aberrant gene expression. Furthermore, established OA susceptibility alleles such as GDF5 and DIO2 appear to confer OA risk via DNA methylation and respective pathophysiological expression changes. In more recent years, genome wide profiling of DNA methylation in OA affected articular cartilage has emerged as a powerful tool to address the epigenetic changes in their entirety, which has resulted in the identification of putative patient subgroups as well as generic OA associated pathways. PMID:27019616

  18. DNA-coated microcrystals.

    PubMed

    Kreiner, Michaela; Fuglevand, Geeta; Moore, Barry D; Parker, Marie-Claire

    2005-06-01

    Coprecipitation leads to self-assembly of bioactive DNA on the surface of salt, sugar or amino-acid crystals and provides a rapid inexpensive immobilization method suitable for preparing dry-powder formulations of nucleic acids, useful for storage, imaging and drug delivery. PMID:15917916

  19. Nutrients and DNA Methylation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Epigenetics is a new mechanism responsible for development, aging, and disease process such as cancer development. One major epigenetic phenomenon is DNA methylation, which attributes to gene expression and integrity. Deepening the knowledge on one-carbon metabolism is very important to understandin...

  20. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  1. Field Deployable DNA analyzer

    SciTech Connect

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  2. DNA tagged microparticles

    DOEpatents

    Farquar, George R.; Leif, Roald N.; Wheeler, Elizabeth

    2016-03-22

    In one embodiment, a product includes a plurality of particles, each particle including: a carrier that includes a non-toxic material; and at least one DNA barcode coupled to the carrier, where the particles each have a diameter in a range from about 1 nanometer to about 100 microns.

  3. Making environmental DNA count.

    PubMed

    Kelly, Ryan P

    2016-01-01

    The arc of reception for a new technology or method--like the reception of new information itself--can pass through predictable stages, with audiences' responses evolving from 'I don't believe it', through 'well, maybe' to 'yes, everyone knows that' to, finally, 'old news'. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. 'Macrobial' biologists and ecologists--those accustomed to dealing with species they can see and count--have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. (2015) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species' biomasses. The strength and slope of this association vary for each species and each primer set--further evidence that there is no universal parameter linking recovered DNA to species abundance--but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: 'Yes, but how many are there?' PMID:26768195

  4. Twist-Induced Defects of the P-SSP7 Genome Revealed by Modeling the Cryo-EM Density

    PubMed Central

    Wang, Qian; Myers, Christopher G.

    2015-01-01

    We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing. PMID:25793549

  5. Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.

    PubMed

    Wang, Qian; Myers, Christopher G; Pettitt, B Montgomery

    2015-04-16

    We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing. PMID:25793549

  6. Emerging roles of DNA-PK besides DNA repair.

    PubMed

    Kong, Xianming; Shen, Ying; Jiang, Na; Fei, Xin; Mi, Jun

    2011-08-01

    The DNA-dependent protein kinase (DNA-PK) is a DNA-activated serine/threonine protein kinase, and abundantly expressed in almost all mammalian cells. The roles of DNA-PK in DNA-damage repair pathways, including non-homologous end-joining (NHEJ) repair and homologous recombinant (HR) repair, have been studied intensively. However, the high levels of DNA-PK in human cells are somewhat paradoxical in that it does not impart any increased ability to repair DNA damage. If DNA-PK essentially exceeds the demand for DNA damage repair, why do human cells universally express such high levels of this huge complex? DNA-PK has been recently reported to be involved in metabolic gene regulation in response to feeding/insulin stimulation; our studies have also suggested a role of DNA-PK in the regulation of the homeostasis of cell proliferation. These novel findings expand our horizons about the importance of DNA-PK. PMID:21514376

  7. Borrowing nuclear DNA helicases to protect mitochondrial DNA.

    PubMed

    Ding, Lin; Liu, Yilun

    2015-01-01

    In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA) mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer's disease, premature aging‎ and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4), petite integration frequency 1 (PIF1), DNA replication helicase/nuclease 2 (DNA2) and suppressor of var1 3-like protein 1 (SUV3). Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases. PMID:25984607

  8. DNA computing on surfaces

    NASA Astrophysics Data System (ADS)

    Liu, Qinghua; Wang, Liman; Frutos, Anthony G.; Condon, Anne E.; Corn, Robert M.; Smith, Lloyd M.

    2000-01-01

    DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the `NP-complete' or non-deterministic polynomial time complete problems). The principle of the technique has been demonstrated experimentally for a simple example of the hamiltonian path problem (in this case, finding an airline flight path between several cities, such that each city is visited only once). DNA computational approaches to the solution of other problems have also been investigated. One technique involves the immobilization and manipulation of combinatorial mixtures of DNA on a support. A set of DNA molecules encoding all candidate solutions to the computational problem of interest is synthesized and attached to the surface. Successive cycles of hybridization operations and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions. Upon completion of all the multi-step cycles, the solution to the computational problem is identified using a polymerase chain reaction to amplify the remaining molecules, which are then hybridized to an addressed array. The advantages of this approach are its scalability and potential to be automated (the use of solid-phase formats simplifies the complex repetitive chemical processes, as has been demonstrated in DNA and protein synthesis). Here we report the use of this method to solve a NP-complete problem. We consider a small example of the satisfiability problem (SAT), in which the values of a set of boolean variables satisfying certain logical constraints are determined.

  9. MAMMALIAN DNA IN PCR REAGENTS

    EPA Science Inventory

    Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high- cycle PCR amplification t...

  10. Mouse models of DNA polymerases.

    PubMed

    Menezes, Miriam R; Sweasy, Joann B

    2012-12-01

    In 1956, Arthur Kornberg discovered the mechanism of the biological synthesis of DNA and was awarded the Nobel Prize in Physiology or Medicine in 1959 for this contribution, which included the isolation and characterization of Escherichia coli DNA polymerase I. Now there are 15 known DNA polymerases in mammalian cells that belong to four different families. These DNA polymerases function in many different cellular processes including DNA replication, DNA repair, and damage tolerance. Several biochemical and cell biological studies have provoked a further investigation of DNA polymerase function using mouse models in which polymerase genes have been altered using gene-targeting techniques. The phenotypes of mice harboring mutant alleles reveal the prominent role of DNA polymerases in embryogenesis, prevention of premature aging, and cancer suppression. PMID:23001998

  11. The Dynamics of DNA Sequencing.

    ERIC Educational Resources Information Center

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  12. Structural diversity of supercoiled DNA

    NASA Astrophysics Data System (ADS)

    Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

    2015-10-01

    By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

  13. An Introduction to DNA Fingerprinting.

    ERIC Educational Resources Information Center

    Hepfer, Carol Ely; And Others

    1993-01-01

    Provides background information on DNA fingerprinting, and describes exercises for introducing general biology students at the high school or college level to the methodology and applications of DNA fingerprinting. (PR)

  14. Mitochondrial DNA Damage and Diseases

    PubMed Central

    Singh, Gyanesh; Pachouri, U C; Khaidem, Devika Chanu; Kundu, Aman; Chopra, Chirag; Singh, Pushplata

    2015-01-01

    Various endogenous and environmental factors can cause mitochondrial DNA (mtDNA) damage.  One of the reasons for enhanced mtDNA damage could be its proximity to the source of oxidants, and lack of histone-like protective proteins. Moreover, mitochondria contain inadequate DNA repair pathways, and, diminished DNA repair capacity may be one of the factors responsible for high mutation frequency of the mtDNA. mtDNA damage might cause impaired mitochondrial function, and, unrepaired mtDNA damage has been frequently linked with several diseases. Exploration of mitochondrial perspective of diseases might lead to a better understanding of several diseases, and will certainly open new avenues for detection, cure, and prevention of ailments.

  15. Structural diversity of supercoiled DNA

    PubMed Central

    Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

    2015-01-01

    By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function. PMID:26455586

  16. Chemical approaches to DNA nanotechnology.

    PubMed

    Endo, Masayuki; Sugiyama, Hiroshi

    2009-10-12

    Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials. PMID:19714700

  17. Closed-loop tomographic control on HOMER wide-field AO bench: experimental results and identification issues

    NASA Astrophysics Data System (ADS)

    Parisot, Amelie; Costille, Anne; Petit, Cyril; Fusco, Thierry

    2010-07-01

    Adaptive Optics (AO) has a limited corrected field of view because of the anisoplanatism effect. Wide Field AO (WFAO) concepts, such as Multi-Conjugate AO (MCAO), have been developed to overcome this limitation. These complex WFAO systems raise critical challenges such as tomographic control and calibrations. We present new results obtained in closed-loop configuration with the laboratory bench HOMER which is devoted to implementation and validation of these WFAO concepts in the perspective of future VLT/ELT AO systems. Turbulence is generated with rotating phase screens and multi-directional analysis is performed. Tomographic control relies on Linear Quadratic Gaussian control (LQG). The correction can be applied thanks to two Deformable Mirrors (DM). We also focus on calibration issues and models identification. We investigate in particular identification of relative geometry of the wave front sensors, DM altitude and asterism and its impact on performance.

  18. Increasing Efficiency at the NTF by Optimizing Model AoA Positioning

    NASA Technical Reports Server (NTRS)

    Crawford, Bradley L.; Spells, Courtney

    2006-01-01

    The National Transonic Facility (NTF) at NASA Langley Research Center (LaRC) is a national resource for aeronautical research and development. The government, military and private industries rely on the capability of this facility for realistic flight data. Reducing the operation costs and keeping the NTF affordable is essential for aeronautics research. The NTF is undertaking an effort to reduce the time between data points during a pitch polar. This reduction is being driven by the operating costs of a cryogenic facility. If the time per data point can be reduced, a substantial cost savings can be realized from a reduction in liquid nitrogen (LN2) consumption. It is known that angle-of-attack (AoA) positioning is the longest lead-time item between points. In January 2005 a test was conducted at the NTF to determine the cause of the long lead-time so that an effort could be made to improve efficiency. The AoA signal at the NTF originates from onboard instrumentation then travels through a number of different systems including the signal conditioner, digital voltmeter, and the data system where the AoA angle is calculated. It is then fed into a closed loop control system that sets the model position. Each process along this path adds to the time per data point affecting the efficiency of the data taking process. Due to the nature of the closed loop feed back AoA control and the signal path, it takes approximately 18 seconds to take one pitch pause point with a typical AoA increment. Options are being investigated to reduce the time delay between points by modifying the signal path. These options include: reduced signal filtering, using analog channels instead of a digital volt meter (DVM), re-routing the signal directly to the AoA control computer and implementing new control algorithms. Each of these has potential to reduce the positioning time and together the savings could be significant. These timesaving efforts are essential but must be weighed against

  19. Defined DNA/nanoparticle conjugates.

    PubMed

    Ackerson, Christopher J; Sykes, Michael T; Kornberg, Roger D

    2005-09-20

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. PMID:16155122

  20. Introductory experiments in recombinant DNA.

    PubMed

    Tait, R C

    2000-07-01

    Nine practical exercises demonstrate the basic principles in recombinant DNA. The exercises explain the principles that DNA equals genes and that changes in DNA cause changes in genetic properties. The aim is to provide a teaching resource that can be used to illustrate the theory and applications of molecular biology to highschool students, undergraduate students, medics, dentists, doctors, nurses, life scientists, and anyone learning the basics of DNA technology. PMID:11471559

  1. DNA Electrophoresis on Nanopatterned surfaces

    NASA Astrophysics Data System (ADS)

    Luo, Haobin; Gersappe, Dilip

    2002-03-01

    Conventional electrophoretic methods for DNA separation use topological restriction such as the network point in a gel to separate DNA. Here, we present a new approach to DNA electrophoresis using a nanopatterned surface. We exploit the conformational differences that arise when chains of different length are adsorbed onto a flat nanopatterned surface. We use a MD simulation to determine conditions that will optimize separation and present guidelines for the design of nanopatterned surfaces that can separate DNA in a broad size range.

  2. Alveolar Echinococcosis: Characterization of Diagnostic Antigen Em18 and Serological Evaluation of Recombinant Em18

    PubMed Central

    Sako, Yasuhito; Nakao, Minoru; Nakaya, Kazuhiro; Yamasaki, Hiroshi; Gottstein, Bruno; Lightowers, Marshall W.; Schantz, Peter M.; Ito, Akira

    2002-01-01

    The Echinococcus multilocularis protein Em18 is one of the most promising antigens for use in serodiagnosis of alveolar echinococcosis in human patients. Here we identify an antigenic relationship between Em18 and a 65-kDa immunodominant E. multilocularis surface protein previously identified as either EM10 or EmII/3. The NH2-terminal sequence of native Em18 was determined, revealing it to be a fragment of EM10. Experiments were undertaken to investigate the effect of proteinase inhibitors on the degradation of EM10 in crude extracts of E. multilocularis protoscoleces. Em18 was found to be the product of degradation of EM10 by cysteine proteinase. A recombinant Em18 (RecEm18, derived from 349K to 508K of EM10) was successfully expressed by using Escherichia coli expression system and then evaluated for use in serodiagnosis of alveolar echinococcosis. RecEm18 was recognized by 27 (87.1%) and 28 (90.3%) of 31 serum samples from clinically and/or pathologically confirmed alveolar echinococcosis patients by enzyme-linked immunosorbent assay and immunoblotting, respectively. Of 33 serum samples from cystic echinococcosis patients, 1 was recorded as having a weak positive reaction to RecEm18; however, none of the serum samples which were tested from neurocysticercosis patients (n = 10) or healthy people (n = 15) showed positive reactions. RecEm18 has the potential for use in the differential serodiagnosis of alveolar echinococcosis. PMID:12149326

  3. Effects of The NAO/ao Fluctuations Upon Precipitation Over Sardinia In The 20th Century.

    NASA Astrophysics Data System (ADS)

    Delitala, A.

    The effects at regional scale of decadal fluctuation of the NAO/AO on the 20th cen- tury precipitation over Sardinia will be analyzed. Decadal variations of precipitation will initially be described, by use of the Standardized Anomaly Index (Katz &Glantz, 1986) based on two indicators: the cumulated precipitation (the classical approach) and the number of rainy days. A clear decreasing trend in the last two deacdes, statis- tically significant at the 1% level, will be highlighted. A short survey of connections with MSLP and 500hPA Geopotential Height fields will be used to give an overview of dependence of Sardinia (regional) precipitation on synoptic-scale and planetary scale features. In the following part, three different paradigms of the NAO/AO will be used: the classical two point obscillation, the PCA analysis of MSLP (Thompson &Wallace, 1998) and the centers of action approach (Machel et al., 1998). The results of the anal- ysis of the effects of NAO/AO (described in the former three ways) on precipitation will enable to discuss how such a teleconnection influences regional precipitation on this part of the Mediterranean. Statistical significance of each result will be provided during the presentation. Katz, R., Glantz, M., 1986. "Anatomy of a Rainfall Index". Mon. Wea. Rev., 114, 764-771. Mächel, M., Kapala, A., Flohn, H., 1998. "Behaviour of the Centers of Action above the Atlantic since 1881. Part I: Characteristics of seasonal and interannual Variability". Int. Jou. of Climatol., 18, 1-22. Thopson, D. W. J., Wallace, J. M., 1998. "The Arctic Oscillation signature in the wintertime geopotential height and temperature fields". Geoph. Res. Let., 25, 1297- 1300.

  4. LDEF (Prelaunch), AO135 : Effect of Space Exposure on Pyroelectric Infrared Detectors, Tray E05

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO135 : Effect of Space Exposure on Pyroelectric Infrared Detectors, Tray E05 The prelaunch photograph was taken in SAEF II at KSC prior to installation of the integrated tray on the LDEF. The Space Exposure on Pyroelectric Infrared Detectors Experiment (AO135) consist of twenty detectors of three different types of materials, lithium-tantalate, strontium-barium-niobate and triglycine-sulfide. The Pyroelectric infrered detector experiment is an integral part of the Active Optical System Component Experiment (S0050) that contains 136 test specimen and is located in a six (6) inch deep LDEF peripheral experiment tray. The experiment tray is divided into six sections, each consisting of a 1/4 inch thick chromic anodized aluminum base plate and a 1/16th inch thick aluminum hat shaped structure for mounting the test specimen. The test specimen are typi- cally placed in fiberglass-epoxy retainer strip assemblies prior to installation on the hat shaped mounting structure. Five of the six sections are covered by a 1/8 inch thick anodized aluminum sun screen with openings that allowed 56 percent transmission over the central region. Two subexperiments, The Optical Materials and UV Detectors Experiment (S0050-01) consist of 15 optical windows, filters and detectors and occupies one of the trays six sub-sections and The Optical Substrates and Coatings Experiment (S0050-02 ) that includes 12 substrates and coatings and a secondary experiment, The Holographic Data Storage Crystal Experiment (AO044) with four crystals, are also mounted in the integrated tray. The experiment structure was assembled with non-magnetic stainless steel fasteners.

  5. A method to capture large DNA fragments from genomic DNA.

    PubMed

    Ball, Geneviève; Filloux, Alain; Voulhoux, Romé

    2014-01-01

    The gene capture technique is a powerful tool that allows the cloning of large DNA regions (up to 80 kb), such as entire genomic islands, without using restriction enzymes or DNA amplification. This technique takes advantage of the high recombinant capacity of the yeast. A "capture" vector containing both ends of the target DNA region must first be constructed. The target region is then captured by co-transformation and recombination in yeast between the "capture" vector and appropriate genomic DNA. The selected recombinant plasmid can be verified by sequencing and transferred in the bacteria for multiple applications. This chapter describes a protocol specifically adapted for Pseudomonas aeruginosa genomic DNA capture. PMID:24818928

  6. LDEF (Postflight), AO180 : The Effect of Space Environment Exposure on the Properties of Polymer Mat

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO180 : The Effect of Space Environment Exposure on the Properties of Polymer Matrix Composite Materials, Tray D12 The postflight photograph was taken in the SAEF-II facility prior to removal of experiment trays from the LDEF. The Polymer Matrix Composite Materials experiment appears the same as in the flight photograph. The composite containing the aramid (Kevlar) fibers has changed from a yellow to a light brown color and the cylinderical tubes containing the boron and carbon fiber materials have changed from a light green tint to a brown color. The experiment mounting hardware and fasteners seem to be intact and in very good condition.

  7. Optical Photometry of the flaring gamma-ray blazar AO 0235+164

    NASA Astrophysics Data System (ADS)

    Pursimo, Tapio; Losada, Illa R.; Messa, Matteo; Gafton, Emanuel; Ojha, Roopesh

    2016-03-01

    We report optical photometry of the blazar AO 0235+164 obtained with the 2.56m Nordic Optical Telescope in La Palma to look for any enhanced optical activity associated with a recent flare in the daily averaged gamma-ray flux seen in the public lightcurve of the Fermi/LAT instrument: http://fermi.gsfc.nasa.gov/FTP/glast/data/lat/catalogs/asp/current/lightcurves/0235+164_86400.png Fermi/LAT first reported a detection of gamma-ray activity from this source in Sep, 2008 (ATel#1744) and a short timescale flare in Oct 14, 2008 (ATel#1784).

  8. Tomographic separation of composite spectra - The components of the O-star spectroscopic binary AO Cassiopeiae

    NASA Technical Reports Server (NTRS)

    Bagnuolo, William G., Jr.; Gies, Douglas R.

    1991-01-01

    The UV photospheric lines of the short-period, double-lined O-star spectroscopic binary AO Cas are analyzed. Archival data from IUE (16 spectra uniformly distributed in orbital phase) were analyzed with a tomography algorithm to produce the separate spectra of the two stars in six spectral regions. The spectral classifications of the primary and secondary, O9.5 III and O8 V, respectively, were estimated through a comparison of UV line ratios with those in spectral standard stars. An intensity ratio of 0.5-0.7 (primary brighter) at 1600 A is compatible with the data.

  9. Monitoring Io volcanism with AO telescopes during and after the NH flyby

    NASA Astrophysics Data System (ADS)

    Marchis, F.; Spencer, J. R.; Lopes, R. M.; Davies, A. G.; Dumas, C.

    2007-12-01

    To support the New Horizons (NH) Jupiter encounter we monitored Io's volcanic activity using high angular resolution images in the near infrared (1-5 microns) provided by adaptive optics (AO) systems available on 8-10m class telescopes. We initiated the campaign on Feb. 25 2007 with data obtained with the VLT-Yepun telescope (ESO, Paranal, Chile), just before NH closest approach. We continued monitoring with the Gemini North telescope (Hawaii, USA). The last observation was taken on May 28 2007. Numerous active volcanoes are visible in the data but the Tvashtar eruption is by far the most energetic. Extremely high angular resolution data from NH revealed fine detail of the eruption, such as the presence of an active plume [1]. This volcano has an interesting past history. It was seen as a powerful eruption from Nov. 26 1999 during the Galileo I25 [2] flyby to Feb. 19 2001 from the ground [3]. It was dormant or below our ground-based limit of detection (T<330 K assuming an area of 460 km2) between Dec 2001 and May 2004 [4,5]. The re-awakening of the volcano was reported by Laver et al. [6] in April 2006 based on Keck Adaptive Optics (AO) observations. Our last Gemini AO observation taken on May 26 shows that Tvashtar was still very active. Based on the previous behavior of this volcano [7] it is very likely that the activity reported in 2007 is a continuation of the Tvashtar-2006 eruption. Other hot spots, such as Loki Patera, Pele, and a new hot spot located north of Loki Patera, were seen in our data. We will describe the global picture of Io's volcanic activity derived from our observations, comparing it with previous observations from the Galileo spacecraft and using ground-based AO. 1. Spencer et al., AGU, this session, 2007 2. McEwen et al., Science, 288, 1193-1198, 2000 3. Marchis et al. Icarus, 160, 124-131, 2002 4. Marchis et al., Icarus, 176, 1, 2005 5. Marchis et al., AGU Fall meeting, V33C-1483, 2004 6. Laver et al., Icarus, in press, 2006 7. Milazzo et

  10. Preliminary results from the chemistry of micrometeoroid experiment (AO 187-1)

    NASA Technical Reports Server (NTRS)

    Horz, Friedrich; Bernhard, R. P.; See, Thomas H.; Warren, J.; Brownlee, Don E.; Laurance, M.

    1991-01-01

    The purpose of experiment AO 187-1 was to expose high purity substrates of suitable cratering properties to obtain detailed crater statistics that may be converted into projectile masses and fluxes and to chemically characterize as many impactors as possible. The latter information would hopefully reveal distinct classes of natural and man-made particles in low-Earth orbit. It was found that crater that yield residues show that natural and man-made impactors may be differentiated and that diversity exists within each group. 'Chondritic' compositions dominate among natural particles, yet some craters contain unmelted fragments of minerals (Olivine and pyroxene).

  11. The optical periodic analysis of BL Lac object AO 0235+164

    NASA Astrophysics Data System (ADS)

    Wang, Hongtao

    2014-05-01

    BL Lac object AO 0235+164 is a well-known object. We collect a large number of effective observation in B, V, R and I band from historical literatures. The possible periods are analyzed by means of discrete correlation function (DCF) method, structure function (SF) method and Jurkevich (J-K) method. The results show that there are possible periodic variations of 2.63-2.66 years in B band, 2.79-2.84 years in V band, 2.57-2.87 years in R band, 2.62-2.88 years in I band, respectively.

  12. LDEF (Prelaunch), AO187-01 : The Chemistry of Micrometeoroids, Tray A03

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO187-01 : The Chemistry of Micrometeoroids, Tray A03 The prelaunch photograph shows the two (2) clam shell type canisters in their closed position. The canister shells are made of aluminum sheet material with end caps of diecast aluminum. The baseplate and support structure are fabricated from 6000 series aluminum. Fasteners are non-magnetic stainless steel. The electrical box and the stainless steel tubing located on the baseplate protect the drive system wiring. The experiment contains a timing mechanism that provides the intelligence to open the canisters after the Orbiter has departed the area and any initial outgassing or offgassing has occurred.

  13. DNA Oligonucleotide 3'-Phosphorylation by a DNA Enzyme.

    PubMed

    Camden, Alison J; Walsh, Shannon M; Suk, Sarah H; Silverman, Scott K

    2016-05-10

    T4 polynucleotide kinase is widely used for 5'-phosphorylation of DNA and RNA oligonucleotide termini, but no natural protein enzyme is capable of 3'-phosphorylation. Here, we report the in vitro selection of deoxyribozymes (DNA enzymes) capable of DNA oligonucleotide 3'-phosphorylation, using a 5'-triphosphorylated RNA transcript (pppRNA) as the phosphoryl donor. The basis of selection was the capture, during each selection round, of the 3'-phosphorylated DNA substrate terminus by 2-methylimidazole activation of the 3'-phosphate (forming 3'-MeImp) and subsequent splint ligation with a 5'-amino DNA oligonucleotide. Competing and precedented DNA-catalyzed reactions were DNA phosphodiester hydrolysis or deglycosylation, each also leading to a 3'-phosphate but at a different nucleotide position within the DNA substrate. One oligonucleotide 3'-kinase deoxyribozyme, obtained from an N40 random pool and named 3'Kin1, can 3'-phosphorylate nearly any DNA oligonucleotide substrate for which the 3'-terminus has the sequence motif 5'-NKR-3', where N denotes any oligonucleotide sequence, K = T or G, and R = A or G. These results establish the viabilty of in vitro selection for identifying DNA enzymes that 3'-phosphorylate DNA oligonucleotides. PMID:27063020

  14. Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

    PubMed Central

    Sharma, Nynne; Cai, Yujia; Bak, Rasmus O; Jakobsen, Martin R; Schrøder, Lisbeth Dahl; Mikkelsen, Jacob Giehm

    2013-01-01

    DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB) DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs) devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system. PMID:23443502

  15. DNA Sequential Logic Gate Using Two-Ring DNA.

    PubMed

    Zhang, Cheng; Shen, Linjing; Liang, Chao; Dong, Yafei; Yang, Jing; Xu, Jin

    2016-04-13

    Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize "before" and "after" triggering sequences of DNA signals. By taking advantage of a "loop-open" mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by "interlocked" two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems. PMID:26990044

  16. Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips.

    SciTech Connect

    Proudnikov, D.; Timofeev, E.; Mirzabekov, A.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology

    1998-05-15

    Activated DNA was immobilized in aldehyde-containing polyacrylamide gel for use in manufacturing the MAGIChip (microarrays of gel-immobilized compounds on a chip). First, abasic sites were generated in DNA by partial acidic depurination. Amino groups were then introduced into the abasic sites by reaction with ethylenediamine and reduction of the aldimine bonds formed. It was found that DNA could be fragmented at the site of amino group incorporation or preserved mostly unfragmented. In similar reactions, both amino-DNA and amino-oligonucleotides were attached through their amines to polyacrylamide gel derivatized with aldehyde groups. Single- and double-stranded DNA of 40 to 972 nucleotides or base pairs were immobilized on the gel pads to manufacture a DNA microchip. The microchip was hybridized with fluorescently labeled DNA-specific oligonucleotide probes. This procedure for immobilization of amino compounds was used to manufacture MAGIChips containing both DNA and oligonucleotides.

  17. The European Mobile System (EMS)

    NASA Technical Reports Server (NTRS)

    Jongejans, A.; Rogard, R.; Mistretta, I.; Ananasso, F.

    1993-01-01

    The European Space Agency is presently procuring an L band payload in order to promote a regional European L band system coping with the specific needs of the European market. The payload, and the two communications systems to be supported, are described below. The potential market for EMS in Europe is discussed.

  18. Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool

    NASA Astrophysics Data System (ADS)

    Meylan, S.; Vimont, U.; Incerti, S.; Clairand, I.; Villagrasa, C.

    2016-07-01

    Several DNA representations are used to study radio-induced complex DNA damages depending on the approach and the required level of granularity. Among all approaches, the mechanistic one requires the most resolved DNA models that can go down to atomistic DNA descriptions. The complexity of such DNA models make them hard to modify and adapt in order to take into account different biological conditions. The DnaFabric project was started to provide a tool to generate, visualise and modify such complex DNA models. In the current version of DnaFabric, the models can be exported to the Geant4 code to be used as targets in the Monte Carlo simulation. In this work, the project was used to generate two DNA fibre models corresponding to two DNA compaction levels representing the hetero and the euchromatin. The fibres were imported in a Geant4 application where computations were performed to estimate the influence of the DNA compaction on the amount of calculated DNA damage. The relative difference of the DNA damage computed in the two fibres for the same number of projectiles was found to be constant and equal to 1.3 for the considered primary particles (protons from 300 keV to 50 MeV). However, if only the tracks hitting the DNA target are taken into account, then the relative difference is more important for low energies and decreases to reach zero around 10 MeV. The computations were performed with models that contain up to 18,000 DNA nucleotide pairs. Nevertheless, DnaFabric will be extended to manipulate multi-scale models that go from the molecular to the cellular levels.

  19. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    PubMed Central

    Vlijm, Rifka; v.d. Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  20. Tops and Writhing DNA

    NASA Astrophysics Data System (ADS)

    Samuel, Joseph; Sinha, Supurna

    2011-04-01

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

  1. Fleet DNA (Presentation)

    SciTech Connect

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  2. DNA waves and water

    NASA Astrophysics Data System (ADS)

    Montagnier, L.; Aissa, J.; Del Giudice, E.; Lavallee, C.; Tedeschi, A.; Vitiello, G.

    2011-07-01

    Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We discuss this phenomenon in the framework of quantum field theory. A scheme able to account for the observations is proposed. The reported phenomenon could allow to develop highly sensitive detection systems for chronic bacterial and viral infections.

  3. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center (ESTSC)

    1995-07-27

    The program controls the operation of various hardware components of an automatic 12-channel parrallel oligosynthesizer. This involves accepting information regarding the DNA sequence to be generated and converting this into a series of instructions to I/O ports to actuate the appropriate hardware components. The design and function of the software is specific to a particular hardware platform and has no utility for controlling other configurations.

  4. DNA degradation and its defects.

    PubMed

    Kawane, Kohki; Motani, Kou; Nagata, Shigekazu

    2014-06-01

    DNA is one of the most essential molecules in organisms, containing all the information necessary for organisms to live. It replicates and provides a mechanism for heredity and evolution. Various events cause the degradation of DNA into nucleotides. DNA also has a darker side that has only recently been recognized; DNA that is not properly degraded causes various diseases. In this review, we discuss four deoxyribonucleases that function in the nucleus, cytosol, and lysosomes, and how undigested DNA causes such diseases as cancer, cataract, and autoinflammation. Studies on the biochemical and physiological functions of deoxyribonucleases should continue to increase our understanding of cellular functions and human diseases. PMID:24890510

  5. DNA nanotechnology and fluorescence applications.

    PubMed

    Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Woehrstein, Johannes B; Jungmann, Ralf

    2016-06-01

    Structural DNA nanotechnology allow researchers to use the unique molecular recognition properties of DNA strands to construct nanoscale objects with almost arbitrary complexity in two and three dimensions. Abstracted as molecular breadboards, DNA nanostructures enable nanometer-precise placement of guest molecules such as proteins, fluorophores, or nanoparticles. These assemblies can be used to study biological phenomena with unprecedented control over number, spacing, and molecular identity. Here, we give a general introduction to structural DNA nanotechnology and more specifically discuss applications of DNA nanostructures in the field of fluorescence and plasmonics. PMID:26773303

  6. DNA Degradation and Its Defects

    PubMed Central

    Kawane, Kohki; Motani, Kou; Nagata, Shigekazu

    2014-01-01

    DNA is one of the most essential molecules in organisms, containing all the information necessary for organisms to live. It replicates and provides a mechanism for heredity and evolution. Various events cause the degradation of DNA into nucleotides. DNA also has a darker side that has only recently been recognized; DNA that is not properly degraded causes various diseases. In this review, we discuss four deoxyribonucleases that function in the nucleus, cytosol, and lysosomes, and how undigested DNA causes such diseases as cancer, cataract, and autoinflammation. Studies on the biochemical and physiological functions of deoxyribonucleases should continue to increase our understanding of cellular functions and human diseases. PMID:24890510

  7. Actions of human DNA glycosylases on uracil-containing DNA, methylated DNA and their reconstituted chromatins.

    PubMed

    Ishiwata, K; Oikawa, A

    1979-07-26

    Extracts of human lymphoblastoid cells catalyzed complete release of uracil (Ura) from PBS1 DNA, which contains Ura instead of thymine as a normal component (Ura-DNA), and 3-methyladenine (3-MeAde) from DNA methylated with methyl methanesulfonate (Me-DNA). These two activities, Ura-DNA glycosylase and 3-MeAde-DNA glycosylase, differed in heat stability. Cell extracts released Ura more rapidly and 3-MeAde more slowly from alkali-denatured preparations of Ura- and Me-DNA, respectively, than from native DNA's. On incubation with reconstituted chromatins, prepared from Ura-DNA and Me-DNA, respectively, with calf thymus chromosomal protein by salt gradient dialysis, cell extracts released all the Ura but only about half of the 3-MeAde residues, although both these chromatins were degraded by micrococcal nuclease until about half of the nucleotides became acid soluble. The activities of Ura-DNA and 3-MeAde-DNA glycosylase of xeroderma pigmentosum cells were similar to those of normal cells. PMID:465495

  8. Compressive Sensing DNA Microarrays

    PubMed Central

    2009-01-01

    Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed. PMID:19158952

  9. Breathing Dynamics in Heteropolymer DNA

    PubMed Central

    Ambjörnsson, Tobias; Banik, Suman K.; Krichevsky, Oleg; Metzler, Ralf

    2007-01-01

    While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged basepair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs. PMID:17237209

  10. Reversible fluorescence photoswitching in DNA.

    PubMed

    Smith, Darren A; Holliger, Philipp; Flors, Cristina

    2012-08-30

    We describe the engineering of reversible fluorescence photoswitching in DNA with high-density substitution, and its applications in advanced fluorescence microscopy methods. High-density labeling of DNA with cyanine dyes can be achieved by polymerase chain reaction using a modified DNA polymerase that has been evolved to efficiently incorporate Cy3- and Cy5-labeled cytosine base analogues into double-stranded DNA. The resulting biopolymer, "CyDNA", displays hundreds of fluorophores per DNA strand and is strongly colored and highly fluorescent, although previous observations suggest that fluorescence quenching at such high density might be a concern, especially for Cy5. Herein, we first investigate the mechanisms of fluorescence quenching in CyDNA and we suggest that two different mechanisms, aggregate formation and resonance energy transfer, are responsible for fluorescence quenching at high labeling densities. Moreover, we have been able to re-engineer CyDNA into a reversible fluorescence photoswitchable biopolymer by using the properties of the Cy3-Cy5 pair. This novel biopolymer constitutes a new class of photoactive DNA-based nanomaterial and is of great interest for advanced microscopy applications. We show that reversible fluorescence photoswitching in CyDNA can be exploited in optical lock-in detection imaging. It also lays the foundations for improved and sequence-specific super-resolution fluorescence microscopy of DNA. PMID:22861666

  11. Archaeal DNA polymerases in biotechnology.

    PubMed

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Huang, Yanchao

    2015-08-01

    DNA polymerase (pol) is a ubiquitous enzyme that synthesizes DNA strands in all living cells. In vitro, DNA pol is used for DNA manipulation, including cloning, PCR, site-directed mutagenesis, sequencing, and several other applications. Family B archaeal DNA pols have been widely used for molecular biological methods. Biochemical and structural studies reveal that each archaeal DNA pol has different characteristics with respect to fidelity, processivity and thermostability. Due to their high fidelity and strong thermostability, family B archaeal DNA pols have the extensive application on high-fidelity PCR, DNA sequencing, and site-directed mutagenesis while family Y archaeal DNA pols have the potential for error-prone PCR and random mutagenesis because of their low fidelity and strong thermostability. This information combined with mutational analysis has been used to construct novel DNA pols with altered properties that enhance their use as biotechnological reagents. In this review, we focus on the development and use of family B archaeal DNA pols. PMID:26150245

  12. Risk Factors Associated with Campylobacter jejuni Infections in Curaçao, Netherlands Antilles

    PubMed Central

    Endtz, Hubert P.; van West, Hanneke; Godschalk, Peggy C. R.; de Haan, Lidewij; Halabi, Yaskara; van den Braak, Nicole; Kesztyüs, Barbara I.; Leyde, Ewald; Ott, Alewijn; Verkooyen, Roel; Price, Lawrence J.; Woodward, David L.; Rodgers, Frank G.; Ang, C. Wim; van Koningsveld, Rinske; van Belkum, Alex; Gerstenbluth, Izzy

    2003-01-01

    A steady increase in the incidence of Guillain-Barré syndrome (GBS) with a seasonal preponderance, almost exclusively related to Campylobacter jejuni, and a rise in the incidence of laboratory-confirmed Campylobacter enteritis have been reported from Curaçao, Netherlands Antilles. We therefore investigated possible risk factors associated with diarrhea due to epidemic C. jejuni. Typing by pulsed-field gel electrophoresis identified four epidemic clones which accounted for almost 60% of the infections. One hundred six cases were included in a case-control study. Infections with epidemic clones were more frequently observed in specific districts in Willemstad, the capital of Curaçao. One of these clones caused infections during the rainy season only and was associated with the presence of a deep well around the house. Two out of three GBS-related C. jejuni isolates belonged to an epidemic clone. The observations presented point toward water as a possible source of Campylobacter infections. PMID:14662945

  13. OCam with CCD220, the Fastest and Most Sensitive Camera to Date for AO Wavefront Sensing

    NASA Astrophysics Data System (ADS)

    Feautrier, Philippe; Gach, Jean-Luc; Balard, Philippe; Guillaume, Christian; Downing, Mark; Hubin, Norbert; Stadler, Eric; Magnard, Yves; Skegg, Michael; Robbins, Mark; Denney, Sandy; Suske, Wolfgang; Jorden, Paul; Wheeler, Patrick; Pool, Peter; Bell, Ray; Burt, David; Davies, Ian; Reyes, Javier; Meyer, Manfred; Baade, Dietrich; Kasper, Markus; Arsenault, Robin; Fusco, Thierry; Diaz Garcia, José Javier

    2011-03-01

    For the first time, subelectron readout noise has been achieved with a camera dedicated to astronomical wavefront-sensing applications. The OCam system demonstrated this performance at a 1300 Hz frame rate and with 240 × 240 pixel frame size. ESO and JRA2 OPTICON jointly funded e2v Technologies to develop a custom CCD for adaptive optics (AO) wavefront-sensing applications. The device, called CCD220, is a compact Peltier-cooled 240 × 240 pixel frame-transfer eight-output back-illuminated sensor using the EMCCD technology. This article demonstrates, for the first time, subelectron readout noise at frame rates from 25 Hz to 1300 Hz and dark current lower than 0.01 e- pixel-1 frame-1. It reports on the quantitative performance characterization of OCam and the CCD220, including readout noise, dark current, multiplication gain, quantum efficiency, and charge transfer efficiency. OCam includes a low-noise preamplifier stage, a digital board to generate the clocks, and a microcontroller. The data acquisition system includes a user-friendly timer file editor to generate any type of clocking scheme. A second version of OCam, called OCam2, has been designed to offer enhanced performance, a completely sealed camera package, and an additional Peltier stage to facilitate operation on a telescope or environmentally challenging applications. New features of OCam2 are presented in this article. This instrumental development will strongly impact the performance of the most advanced AO systems to come.

  14. Closed-loop focal plane wavefront control with the SCExAO instrument

    NASA Astrophysics Data System (ADS)

    Martinache, Frantz; Jovanovic, Nemanja; Guyon, Olivier

    2016-09-01

    Aims: This article describes the implementation of a focal plane based wavefront control loop on the high-contrast imaging instrument SCExAO (Subaru Coronagraphic Extreme Adaptive Optics). The sensor relies on the Fourier analysis of conventional focal-plane images acquired after an asymmetric mask is introduced in the pupil of the instrument. Methods: This absolute sensor is used here in a closed-loop to compensate for the non-common path errors that normally affects any imaging system relying on an upstream adaptive optics system.This specific implementation was used to control low-order modes corresponding to eight zernike modes (from focus to spherical). Results: This loop was successfully run on-sky at the Subaru Telescope and is used to offset the SCExAO deformable mirror shape used as a zero-point by the high-order wavefront sensor. The paper details the range of errors this wavefront-sensing approach can operate within and explores the impact of saturation of the data and how it can be bypassed, at a cost in performance. Conclusions: Beyond this application, because of its low hardware impact, the asymmetric pupil Fourier wavefront sensor (APF-WFS) can easily be ported in a wide variety of wavefront sensing contexts, for ground- as well space-borne telescopes, and for telescope pupils that can be continuous, segmented or even sparse. The technique is powerful because it measures the wavefront where it really matters, at the level of the science detector.

  15. LDEF (Prelaunch), AO076 : Cascade Variable-Conductance Heat Pipe, Tray F09

    NASA Technical Reports Server (NTRS)

    1983-01-01

    LDEF (Prelaunch), AO076 : Cascade Variable-Conductance Heat Pipe, Tray F09 EL-1994-00302 LDEF (Prelaunch), AO076 : Cascade Variable-Conductance Heat Pipe, Tray F09 The prelaunch photograph was taken in SAEF II at KSC prior to installation of the Cascade Variable Conductance Heat Pipe Experiment (CVCHPE) on the LDEF. The Cascade Variable Conductance Heat Pipe Experiment (CVCHPE) occupies a 6 inch deep LDEF peripheral experiment tray and consist of two series connected variable conductance heatpipes, a black chrome solar collector panel and a silvered TEFLON® radiator panel, a power source to support six thermistor-type temperature monitoring sensors and actuations of two valves. Fiberglass standoffs and internal insulation blankets thermally isolated the experiment from the experiment tray and the LDEF interior. The outside of the CVCHPE, except the collector and radiator panels, was covered with an aluminumized Kapton multilayer insulation (MLI) blanket with an outer layer of 0.076 mm thick Kapton. The two patches of thin film materials, part of Experiment S1001 by NASA GSFC, were attached to the cover of the external thermal blanket with Kapton tape. The experiment was assembled and mounted in the experiment tray with non-magnetic stainless steel fasteners.

  16. LDEF (Flight), AO187-01 : The Chemistry of Micrometeoroids, Tray A03

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Flight), AO187-01 : The Chemistry of Micrometeoroids, Tray A03 EL-1994-00680 LDEF (Flight), AO187-01 : The Chemistry of Micrometeoroids, Tray A03 The flight photograph was taken with the LDEF on the Orbiter's RMS arm prior to berthing the spacecraft in the cargo bay. The canisters are in their open condition (they were expected to open about two (2) weeks after launch and close about eleven (11) months into the mission) with three (3) full panels and 3/4th of the fourth panel covered with a highly reflective gold foil (>99.99 percent pure).The remaining area is covered with strips of other detector materials: zirconium, beryllium, titanium, platium, aluminum, carbon, Kapton, polyethylene and TEFLON®. The exposed fasteners are non-magnetic stainless steel. All of the exposed materials seem to be secure and no damage is evident. The contamination stain that has changed the white paint dot on the tray clamp blocks to brown also coats the tray flanges and the aluminum canister hardware. The end support beam scuff plate in the photograph was a bright yellow prior to launch but is a much darker, mustard yellow after the space exposure.

  17. Tc-99m complexes of new functionalized propylene amine oxime (PnAO) ligands

    SciTech Connect

    Pillai, M.R.A.; Kothari, K.; Ramamoorthy, N.

    1994-05-01

    Three new functionalized PnAO ligands, 3,3,9,9-tetra-methyl-6-R-4, 8-diazaundecane-2,10-dionedioxime (R=benzyl, p-nitrobenzyl and p-aminobenzyl) were synthesised. Tc-99m complexes of these ligands were prepared by direct reduction of Tc-99m O{sub 4}{sup -} using stannous tartrate in the presence of ligands at pH 9.0. Complexation yields were greater than 95% at 1h and 24h post preparation as assessed by ITLC, HPLC and extraction into CHCl3. All three of the complexes were neutral and lipophilic (logP > 2.0) and eluted as single peak from a RP HPLC column. Biodistribution studies of the Tc-99m complexes of the benzyl and the nitrobenzyl derivatives were done in Wistar rats. Both complexes showed brain uptake but were washed out of the brain similar to the behavior of Tc-99m PnAO.

  18. Spiromastixones A-O, antibacterial chlorodepsidones from a deep-sea-derived Spiromastix sp. fungus.

    PubMed

    Niu, Siwen; Liu, Dong; Hu, Xinxin; Proksch, Peter; Shao, Zhongzhe; Lin, Wenhan

    2014-04-25

    Fifteen new depsidone-based analogues named spiromastixones A-O (1-15) were isolated from the fermentation broth of a deep-sea Spiromastix sp. fungus. Their structures were elucidated on the basis of extensive NMR and mass spectroscopic analysis in association with chemical conversion. Spiromastixones A-O are classified into two subtypes based on the orientation of ring C relative to ring A, while the n-propyl substituents on rings A and C are rarely seen in natural products. Most analogues are substituted by various numbers of chlorine atoms. All compounds exhibited significant inhibition against Gram-positive bacteria including Staphylococcus aureus, Bacillus thuringiensis, and Bacillus subtilis with MIC values ranging from 0.125 to 8.0 μg/mL. In addition, compounds 6-10 displayed potent inhibitory effects against methicillin-resistant bacterial strains of S. aureus (MRSA) and S. epidermidis (MRSE), while 10 also inhibited the growth of the vancomycin-resistant bacteria Enterococcus faecalis and E. faecium (VRE). The structure-activity relationships are discussed. PMID:24571273

  19. DNA adducts-chemical addons.

    PubMed

    Rajalakshmi, T R; AravindhaBabu, N; Shanmugam, K T; Masthan, K M K

    2015-04-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers. PMID:26015708

  20. Cinnamate-based DNA photolithography

    PubMed Central

    Romulus, Joy; Li, Minfeng; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin

    2013-01-01

    As demonstrated by means of DNA nanoconstructs[1], as well as DNA functionalization of nanoparticles[2-4] and micrometre-scale colloids[5-8], complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage[9]. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction[10]. Here, we show that the substitution of a pair of complementary bases by a cinnamate group provides an efficient, addressable, UV light-based method to covalently bond complementary DNA. To show the potential of this approach, we wrote micrometre-scale patterns on a surface via UV light and demonstrate the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multi-step, specific binding in self-assembly processes. PMID:23685865

  1. DNA Templating of Au Nanowires

    NASA Astrophysics Data System (ADS)

    Wood, David; Braun, Gary; Inagaki, Katsuhiko

    2005-03-01

    We have developed a process for fabricating nanoscale wires using DNA templates. The templates were subsequently decorated with gold nanoparticles to make metallic wires. We have successfully deposited linear, straight sections of random (λ-phage) and regular-repeat sequences of DNA, of various lengths, on oxidized silicon substrates. We have also successfully deposited thiolated DNA on gold electrodes, allowing the DNA to electrically bridge gaps between electrode pairs. Electrode gaps ranged from 50 nm to 300 nm, fabricated using electron beam lithography. We decorated the DNA with gold nanoparticles with diameters in the range of 1-13 nm, and have used the nanoparticles as nucleation sites for the growth of continuous gold wires. We have performed AFM characterization of all surfaces and structures. In addition, we have performed current-voltage measurements on the undecorated DNA, the nanoparticle-decorated DNA, and the gold nanowires.

  2. Forensic trace DNA: a review

    PubMed Central

    2010-01-01

    DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements. PMID:21122102

  3. DNA adducts-chemical addons

    PubMed Central

    Rajalakshmi, T. R.; AravindhaBabu, N.; Shanmugam, K. T.; Masthan, K. M. K.

    2015-01-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers. PMID:26015708

  4. [DNA biobanks. Establishment and maintenance].

    PubMed

    Henriksen, F L; Hørder, M

    1998-08-24

    The need for extraction, purification and storage of DNA in biobanks is increasing. DNA may be obtained from mouth brush water, guthrie cards, tissue biopsies or venous blood. Sampling conditions depend on the method used for procurement of DNA, e.g. DNA extraction or Ebstein Barr Virus transformation. Exact knowledge about the validity and stability of DNA stored in buffer is still insufficient. Biobanks at hospitals and at research departments are regulated by the Danish Private Registers, etc. Act. Research projects based on DNA biobanks should be notified to the Danish Data Protection Agency and approved by the local ethical committee. Discount, economic, and business class set-ups are different practical and financial models for the structure of DNA biobanking. PMID:9739602

  5. Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2.

    PubMed

    Leung, Kevin K K; Shilton, Brian H

    2015-12-29

    Quinone reductase 2 (NQO2) is an enzyme that might have intracellular signaling functions. NQO2 can exist in either an oxidized state or a reduced state, and binding of compounds to one or both of these states inhibits enzymatic activity and could also affect intracellular signaling. A wide range of planar aromatic compounds bind NQO2, and we have identified three DNA-intercalating agents [ethidium bromide, acridine orange (AO), and doxorubicin] as novel nanomolar inhibitors of NQO2. Ethidium and AO, which carry a positive charge in their aromatic ring systems, bound reduced NQO2 with an affinity 50-fold higher than that of oxidized NQO2, while doxorubicin bound only oxidized NQO2. Crystallographic analyses of oxidized NQO2 in complex with the inhibitors indicated that the inhibitors were situated deep in the active site. The aromatic faces were sandwiched between the isoalloxazine ring of FAD and the phenyl ring of F178, with their edges making direct contact with residues lining the active site. In reduced NQO2, ethidium and AO occupied a more peripheral position in the active site, allowing several water molecules to interact with the polar end of the negatively charged isoalloxazine ring. We also showed that AO inhibited NQO2 at a nontoxic concentration in cells while ethidium was less effective at inhibiting NQO2 in cells. Together, this study shows that reduced NQO2 has structural and electrostatic properties that yield a preference for binding of planar, aromatic, and positively charged molecules that can also function as DNA-intercalating agents. PMID:26636353

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

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    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.

  7. Sequence and Structure Dependent DNA-DNA Interactions

    NASA Astrophysics Data System (ADS)

    Kopchick, Benjamin; Qiu, Xiangyun

    Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

  8. Touch DNA-The prospect of DNA profiles from cables.

    PubMed

    Lim, Sharon; Subhani, Zuhaib; Daniel, Barbara; Frascione, Nunzianda

    2016-05-01

    Metal theft in the railroad industry poses significant challenges to transport investigators. Cable sheaths left behind at crime scenes, if appropriately analysed, could provide valuable evidence in a forensic investigation, but attempts at recovering DNA are not routinely made. Experiments were set up to ascertain the success in DNA recovery from the surface of cable sheaths after deposition of (a) sweat, (b) extracted DNA and (c) fingermarks. Since investigators try to collect fingermarks and often treat the cables with cyanoacrylate fuming (CNA fuming) or wet powder suspensions (WPS) to enhance the marks this study investigated the recovery of DNA from fingermarks pre- and post-enhancement. The double-swab technique and mini-taping were compared as options to recover DNA from the cable sheaths. Results demonstrate that generally, there is no significant difference between using swabs or mini-tapes to recover the DNA from the non-porous cables (p>0.05). It was also illustrated that CNA fuming performed better than WPS in terms of subsequent recovery and profiling of DNA. CNA fuming resulted in an average increase in DNA recovered via swabbing and taping (more than 4× and 8×, respectively), as compared to no treatment, with 50% of the DNA recovered after CNA fuming generating full DNA profiles. PMID:27162019

  9. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  10. Resposta do detector de ondas gravitacionais Mario Schenberg ao "ringdown" de buraco negros

    NASA Astrophysics Data System (ADS)

    Costa, C. A.; Aguiar, O. D.; Magalhães, N. S.

    2003-08-01

    Acredita-se que quando duas estrelas de nêutrons coalescem, elas, eventualmente, formam um buraco negro com massa igual a soma das massas dos objetos originais. Durante a formação do buraco negro, o espaço-tempo em torno do sistema sofre perturbações que se propagam na forma de radiação gravitacional. A forma de onda associada a radiação gravitacional, durante este estágio, aproxima-se a uma senóide exponencialmente amortecida. Este tipo de sinal é conhecido como "ringdown", e seu comportamento e parametrização são muito bem conhecidos. Neste trabalho, simulamos computacionalmente sinais provenientes do "ringdown" de buracos negros, com a finalidade de testar o desempenho do detector de ondas gravitacionais Mario Schenberg em observá-los, quando entrar em funcionamento. Este primeiro teste teórico ajudou-nos a criar estratégias de detecção de sinais imersos no ruído instrumental. Calculamos a relação sinal-ruído como uma função da frequência, bem como sua integral dentro da faixa de sensibilidade do detector. Os resultados obtidos mostraram que o detector Schenberg terá sensibilidade suficiente para detectar este tipo de sinal, proveniente de fontes astrofísicas localizadas dentro de um raio de ~100kpc.

  11. The MeJA-inducible copper amine oxidase AtAO1 is expressed in xylem tissue and guard cells

    PubMed Central

    Ghuge, Sandip A; Carucci, Andrea; Rodrigues-Pousada, Renato A; Tisi, Alessandra; Franchi, Stefano; Tavladoraki, Paraskevi; Angelini, Riccardo; Cona, Alessandra

    2015-01-01

    Copper amine oxidases oxidize the polyamine putrescine to 4-aminobutanal with the production of the plant signal molecule hydrogen peroxide (H2O2) and ammonia. The Arabidopsis (Arabidopsis thaliana) gene At4g14940 (AtAO1, previously referred to as ATAO1) encodes an apoplastic copper amine oxidase expressed in lateral root cap cells and developing xylem, especially in root protoxylem and metaxylem precursors. In our recent study, we demonstrated that AtAO1 expression is strongly induced in the root vascular tissues by the wound-signal hormone methyl jasmonate (MeJA). Furthermore, we also demonstrated that the H2O2 derived by the AtAO1-driven oxidation of putrescine, mediates the MeJA–induced early protoxylem differentiation in Arabidopsis roots. H2O2 may contribute to protoxylem differentiation by signaling developmental cell death and by acting as co-substrate in peroxidase-mediated cell wall stiffening and lignin polymerization. Here, by the means of AtAO1 promoter::green fluorescent protein-β-glucuronidase (AtAO1::GFP-GUS) fusion analysis, we show that a strong AtAO1 gene expression occurs also in guard cells of leaves and flowers. The high expression levels of AtAO1 in tissues or cell types regulating water supply and water loss may suggest a role of the encoded protein in water balance homeostasis, by modulating coordinated adjustments in anatomical and functional features of xylem tissue and guard cells during acclimation to adverse environmental conditions. PMID:26241131

  12. Acetylation of Werner syndrome protein (WRN): relationships with DNA damage, DNA replication and DNA metabolic activities

    PubMed Central

    Lozada, Enerlyn; Yi, Jingjie; Luo, Jianyuan; Orren, David K.

    2014-01-01

    Loss of WRN function causes Werner Syndrome, characterized by increased genomic instability, elevated cancer susceptibility and premature aging. Although WRN is subject to acetylation, phosphorylation and sumoylation, the impact of these modifications on WRN’s DNA metabolic function remains unclear. Here, we examined in further depth the relationship between WRN acetylation and its role in DNA metabolism, particularly in response to induced DNA damage. Our results demonstrate that endogenous WRN is acetylated somewhat under unperturbed conditions. However, levels of acetylated WRN significantly increase after treatment with certain DNA damaging agents or the replication inhibitor hydroxyurea. Use of DNA repair-deficient cells or repair pathway inhibitors further increase levels of acetylated WRN, indicating that induced DNA lesions and their persistence are at least partly responsible for increased acetylation. Notably, acetylation of WRN correlates with inhibition of DNA synthesis, suggesting that replication blockage might underlie this effect. Moreover, WRN acetylation modulates its affinity for and activity on certain DNA structures, in a manner that may enhance its relative specificity for physiological substrates. Our results also show that acetylation and deacetylation of endogenous WRN is a dynamic process, with sirtuins and other histone deacetylases contributing to WRN deacetylation. These findings advance our understanding of the dynamics of WRN acetylation under unperturbed conditions and following DNA damage induction, linking this modification not only to DNA damage persistence but also potentially to replication stalling caused by specific DNA lesions. Our results are consistent with proposed metabolic roles for WRN and genomic instability phenotypes associated with WRN deficiency. PMID:24965941

  13. Novel applications of DNA materials

    NASA Astrophysics Data System (ADS)

    Ogata, Naoya; Yamaoka, Kanji; Yoshida, Junichi

    2009-08-01

    This paper describes preparations of innovative photonic devices based on high purity DNA molecules which are obtained from Salmon roe. DNA molecules have characteristic features of double helical chain structures where aromatic compounds can intercalate into the stacked layers so that various optically active aromatic dyes indicate strong enhancement effects of photonic activities. Thus, various DNA photonic devices have been developed in the world in terms of optical switches, electro-luminescence (EL), lasers and so on. However, these DNA photonic devices adsorb moisture in the air because of hydrophilic character of DNA molecules, leading to decrease photonic activities. Nevertheless, it was found by my group that a novel hybridization method of the dye-intercalated DNA molecules by means of so-called so-gel process increased stabilities and durability of DNA photonic devices under environmental changes. Also, hybridization of dye-intercalated DNA devices with synthetic polymers including fluorinated poly(methylmethacrylate ) or polycarbonates was successfully carried out by solution blending method, followed by casting the solution to obtain these films which showed stability and durability increases of these DNA photonic devices. DNA-lipid complexes showed a very strong fluorescence amplification by chelating with rare earth metals such as Europium or Telbiumu compounds. This paper also describes the chelate effects of rare earth metal compounds for light amplifications.

  14. Topological Behavior of Plasmid DNA

    PubMed Central

    Higgins, N. Patrick; Vologodskii, Alexander V.

    2015-01-01

    The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells. PMID:26104708

  15. DNA reviews: the national DNA database of the United Kingdom.

    PubMed

    Graham, E A M

    2007-12-01

    The national DNA database in United Kingdom has now been operational for over 10 years. This review looks at the history and development of this investigative resource. From the development of commercial DNA profiling kits to the current statistics for matches obtained in relation to criminal investigation in the United Kingdom, before moving onto discussing potential future direction that national DNA databases might take, including international collaboration on a European and global scale. PMID:25869270

  16. DNA-based watermarks using the DNA-Crypt algorithm

    PubMed Central

    Heider, Dominik; Barnekow, Angelika

    2007-01-01

    Background The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. Results The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein. Conclusion The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms. PMID:17535434

  17. Using DNA looping to measure sequence dependent DNA elasticity

    NASA Astrophysics Data System (ADS)

    Kandinov, Alan; Raghunathan, Krishnan; Meiners, Jens-Christian

    2012-10-01

    We are using tethered particle motion (TPM) microscopy to observe protein-mediated DNA looping in the lactose repressor system in DNA constructs with varying AT / CG content. We use these data to determine the persistence length of the DNA as a function of its sequence content and compare the data to direct micromechanical measurements with constant-force axial optical tweezers. The data from the TPM experiments show a much smaller sequence effect on the persistence length than the optical tweezers experiments.

  18. Aluminium-induced DNA damage and adaptive response to genotoxic stress in plant cells are mediated through reactive oxygen intermediates.

    PubMed

    Murali Achary, V Mohan; Panda, Brahma B

    2010-03-01

    Experiments employing growing root cells of Allium cepa were conducted with a view to elucidate the role of reactive oxygen intermediates (ROI) in aluminium (Al)-induced DNA damage, cell death and adaptive response to genotoxic challenge imposed by ethyl methanesulphonate (EMS) or methyl mercuric chloride (MMCl). In a first set of experiments, root cells in planta were treated with Al at high concentrations (200-800 microM) for 3 h without or with pre-treatments of dihydroxybenzene disulphonic acid (Tiron) and dimethylthiourea (DMTU) for 2 h that trap O(2)(.-)and hydrogen peroxide (H(2)O(2)), respectively. At the end of treatments, generation of O(2)(.-) and H(2)O(2), cell death and DNA damage were determined. In a second set of experiments, root cells in planta were conditioned by Al at low concentrations (5 or 10 microM) for 2 h and after a 2 h intertreatment interval challenged by MMCl or EMS for 3 h without or with a pre-treatment of Tiron or DMTU. Conditioning treatments, in addition, included two oxidative agents viz rose bengal and H(2)O(2) for comparison. Following treatments, root cells in planta were allowed to recover in tap water. Genotoxicity and DNA damage were evaluated by micronucleus (MN), chromosome aberration (CA) or spindle aberration (SA) and comet assays at different hours (0-30 h) of recovery. The results demonstrated that whereas Al at high concentrations induced DNA damage and cell death, in low concentrations induced adaptive response conferring genomic protection from genotoxic challenge imposed by MMCl, EMS and Al. Pre-treatments of Tiron and DMTU prevented Al-induced DNA damage, cell death, as well as genotoxic adaptation to MMCl and EMS, significantly. The findings underscored the biphasic (hormetic) mode of action of Al that at high doses induced DNA damage and at low non-toxic doses conferred genomic protection, both of which were mediated through ROI but perhaps involving different networks. PMID:19955331

  19. Cryo-EM reveals a novel octameric integrase structure for β-retroviral intasome function

    PubMed Central

    Ballandras-Colas, Allison; Brown, Monica; Cook, Nicola J.; Dewdney, Tamaria G.; Demeler, Borries; Cherepanov, Peter; Lyumkis, Dmitry; Engelman, Alan N.

    2016-01-01

    Retroviral integrase (IN) catalyzes the integration of viral DNA (vDNA) into host target (tDNA), which is an essential step in the lifecycle of all retroviruses1. Prior structural characterization of IN-vDNA complexes, or intasomes, from the spumavirus prototype foamy virus (PFV) revealed a functional IN tetramer2–5, and it is generally believed that intasomes derived from other retroviral genera will employ tetrameric IN6–9. However, the intasomes of orthoretroviruses, which include all known pathogenic species, have not been characterized structurally. Using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography, we determine here an unexpected octameric IN architecture for the β-retrovirus mouse mammary tumor virus (MMTV) intasome. The structure is composed of two core IN dimers, which interact with the vDNA ends and structurally mimic the PFV IN tetramer, and two flanking IN dimers that engage the core structure via their IN C-terminal domains (CTDs). Contrary to the belief that tetrameric IN components are sufficient to catalyze integration, the flanking IN dimers were necessary for MMTV IN activity. The IN octamer solves a conundrum for the β- as well as α-retroviruses by providing critical CTDs to the intasome core that cannot be provided in cis due to evolutionarily restrictive catalytic core domain (CCD)-CTD linker regions. The octameric architecture of the MMTV intasome provides a new paradigm for the structural basis of retroviral DNA integration. PMID:26887496

  20. Strandwise translocation of a DNA glycosylase on undamaged DNA.

    PubMed

    Qi, Yan; Nam, Kwangho; Spong, Marie C; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L

    2012-01-24

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA. PMID:22219368

  1. Mechanism for priming DNA synthesis by yeast DNA Polymerase α

    PubMed Central

    Perera, Rajika L; Torella, Rubben; Klinge, Sebastian; Kilkenny, Mairi L; Maman, Joseph D; Pellegrini, Luca

    2013-01-01

    The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate in the production of RNA-DNA oligonucleotides that prime synthesis of new DNA. Here we report crystal structures of the catalytic core of yeast Pol α in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with deoxynucleotides. We combine the structural analysis with biochemical and computational data to demonstrate that Pol α specifically recognizes the A-form RNA/DNA helix and that the ensuing synthesis of B-form DNA terminates primer synthesis. The spontaneous release of the completed RNA-DNA primer by the Pol α/primase complex simplifies current models of primer transfer to leading- and lagging strand polymerases. The proposed mechanism of nucleotide polymerization by Pol α might contribute to genomic stability by limiting the amount of inaccurate DNA to be corrected at the start of each Okazaki fragment. DOI: http://dx.doi.org/10.7554/eLife.00482.001 PMID:23599895

  2. Applications of mass spectrometry to DNA fingerprinting and DNA sequencing

    SciTech Connect

    Jacobson, K.B.; Buchanan, M.V.; Chen, C.H.; Doktycz, M.J.; McLuckey, S.A. ); Arlinghaus, H.F. )

    1993-01-01

    DNA fingerprinting and sequencing rely on polyacrylamide gel electrophoresis to determine the sizes of the DNA fragments. Innovative altematives to polyacrylamide gel electrophoresis are under investigation for characterization of such fingerprinting and sequencing. One method uses stable isotopes of tin and other elements to label the DNAwhereas other procedures do not require labels. The detectors in each case are mass spectrometers that detect either the stable isotopes or the DNA fragments themselves. If successful, these methods will speed up the rate of DNA analysis by one or two orders of magnitude.

  3. Applications of mass spectrometry to DNA fingerprinting and DNA sequencing

    SciTech Connect

    Jacobson, K.B.; Buchanan, M.V.; Chen, C.H.; Doktycz, M.J.; McLuckey, S.A.; Arlinghaus, H.F.

    1993-06-01

    DNA fingerprinting and sequencing rely on polyacrylamide gel electrophoresis to determine the sizes of the DNA fragments. Innovative altematives to polyacrylamide gel electrophoresis are under investigation for characterization of such fingerprinting and sequencing. One method uses stable isotopes of tin and other elements to label the DNAwhereas other procedures do not require labels. The detectors in each case are mass spectrometers that detect either the stable isotopes or the DNA fragments themselves. If successful, these methods will speed up the rate of DNA analysis by one or two orders of magnitude.

  4. Foldback intercoil DNA and the mechanism of DNA transposition.

    PubMed

    Kim, Byung-Dong

    2014-09-01

    Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180° and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed. PMID:25317106

  5. Slowing DNA Transport Using Graphene–DNA Interactions

    PubMed Central

    Banerjee, Shouvik; Wilson, James; Shim, Jiwook; Shankla, Manish; Corbin, Elise A.

    2015-01-01

    Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 dielectric layers in stacked membrane structures are fabricated. Slow translocations of ssDNA in nanopores drilled in membranes with layers of graphene are reported. The increased hydrophobic interactions between the ssDNA and the graphene layers could explain this phenomenon. Further confirmation of the hydrophobic origins of these interactions is obtained through reporting significantly faster translocations of dsDNA through these graphene layered membranes. Molecular dynamics simulations confirm the preferential interactions of DNA with the graphene layers as compared to the dielectric layer verifying the experimental findings. Based on our findings, we propose that the integration of multiple stacked graphene layers could slow down DNA enough to enable the identification of nucleobases. PMID:26167144

  6. The DNA Files

    SciTech Connect

    1998-06-09

    The DNA Files is a radio documentary which disseminates genetics information over public radio. The documentaries explore subjects which include the following: How genetics affects society. How human life began and how it evolved. Could new prenatal genetic tests hold the key to disease prevention later in life? Would a national genetic data base sacrifice individual privacy? and Should genes that may lead to the cure for cancer be privately owned? This report serves as a project update for the second quarter of 1998. It includes the spring/summer 1998 newsletter, the winter 1998 newsletter, the program clock, and the latest flyer.

  7. DNA helicases: 'inching forward'.

    PubMed

    Soultanas, P; Wigley, D B

    2000-02-01

    Recently determined crystal structures of PcrA helicase complexed with a DNA substrate have revealed details of the helicase mechanism. PcrA and UvrD helicases have been shown to be functional as monomers, challenging previous suggestions that all helicases are required to be oligomeric. Crystal structures of the hexameric helicases RepA and T7 gene 4 explain the formation of hexameric assemblies from identical monomers with RecA-like folds, but their molecular mechanism remains elusive. PMID:10679457

  8. Switchable catalytic DNA catenanes.

    PubMed

    Hu, Lianzhe; Lu, Chun-Hua; Willner, Itamar

    2015-03-11

    Two-ring interlocked DNA catenanes are synthesized and characterized. The supramolecular catenanes show switchable cyclic catalytic properties. In one system, the catenane structure is switched between a hemin/G-quadruplex catalytic structure and a catalytically inactive state. In the second catenane structure the catenane is switched between a catalytically active Mg(2+)-dependent DNAzyme-containing catenane and an inactive catenane state. In the third system, the interlocked catenane structure is switched between two distinct catalytic structures that include the Mg(2+)- and the Zn(2+)-dependent DNAzymes. PMID:25642796

  9. The new Arecibo Observatory Remote Optical Facility (AO-ROF) in Culebra Island, Puerto Rico: Current Status and Future Projects

    NASA Astrophysics Data System (ADS)

    Santos, P. T.

    2015-12-01

    The idea of establishing the Arecibo Observatory Remote Optical Facility (AO-ROF) in the island of Culebra is a solution to mitigate the ever cumulative quantity of cloud, fog, and rain that has distressed observations at the Arecibo Observatory (AO) during major optical campaigns and observations. Given Culebra Island's favorable geographical and climatological characteristics as its low elevation and geographic location, it appears to have more steady weather conditions than Arecibo, so therefore it provides more availability for optical observations. Placed on Culebra, optical instruments can observe the same thermospheric volume over AO sampled by the Incoherent Scatter Radar (ISR). This capability will become especially important during the High Frequency (HF) facility is on operation. Small and large scale irregularities created by that HF can be readily observed and tracked from the Culebra site, and simultaneous observations from AO of the same atmospheric volume will permit direct vector measurements of dynamical evolution of the irregularities. This work presents a discussion of the current status of AO-ROF facility, as well the future projects.

  10. GOALS, STRATEGIES AND FIRST DISCOVERIES OF AO327, THE ARECIBO ALL-SKY 327 MHz DRIFT PULSAR SURVEY

    SciTech Connect

    Deneva, J. S.; Stovall, K.; Martinez, J. G.; Jenet, F.; McLaughlin, M. A.; Bates, S. D.; Bagchi, M.; Freire, P. C. C.

    2013-09-20

    We report initial results from AO327, a drift survey for pulsars with the Arecibo telescope at 327 MHz. The first phase of AO327 will cover the sky at declinations of –1° to 28°, excluding the region within 5° of the Galactic plane, where high scattering and dispersion make low-frequency surveys sub-optimal. We record data from a 57 MHz bandwidth with 1024 channels and 125 μs sampling time. The 60 s transit time through the AO327 beam means that the survey is sensitive to very tight relativistic binaries even with no acceleration searches. To date we have detected 44 known pulsars with periods ranging from 3 ms to 2.21 s and discovered 24 new pulsars. The new discoveries include 3 ms pulsars, three objects with periods of a few tens of milliseconds typical of young as well as mildly recycled pulsars, a nuller, and a rotating radio transient. Five of the new discoveries are in binary systems. The second phase of AO327 will cover the sky at declinations of 28°-38°. We compare the sensitivity and search volume of AO327 to the Green Bank North Celestial Cap survey and the GBT350 drift survey, both of which operate at 350 MHz.

  11. DNA damage protective effect of honey-sweetened cashew apple nectar in Drosophila melanogaster.

    PubMed

    Silva, Robson Alves da; Dihl, Rafael Rodrigues; Dias, Lucas Pinheiro; Costa, Maiane Papke; Abreu, Bianca Regina Ribas de; Cunha, Kênya Silva; Lehmann, Mauricio

    2016-01-01

    Fruits and derivatives, such as juices, are complex mixtures of chemicals, some of which may have mutagenic and/or carcinogenic potential, while others may have antimutagenic and/or anticancer activities. The modulating effects of honey-sweetened cashew apple nectar (HSCAN), on somatic mutation and recombination induced by ethyl methanesulfonate (EMS) and mitomycin C (MMC) were evaluated with the wing spot test in Drosophila melanogaster using co- and post-treatment protocols. Additionally, the antimutagenic activity of two HSCAN components, cashew apple pulp and honey, in MMC-induced DNA damage was also investigated. HSCAN reduced the mutagenic activity of both EMS and MMC in the co-treatment protocol, but had a co-mutagenic effect when post-administered. Similar results were also observed with honey on MMC mutagenic activity. Cashew apple pulp was effective in exerting protective or enhancing effects on the MMC mutagenicity, depending on the administration protocol and concentration used. Overall, these results indicate that HSCAN, cashew apple and honey seem capable of modulating not only the events that precede the induced DNA damages, but also the Drosophila DNA repair processes involved in the correction of EMS and MMC-induced damages. PMID:27560988

  12. DNA damage protective effect of honey-sweetened cashew apple nectar in Drosophila melanogaster.

    PubMed

    Silva, Robson Alves da; Dihl, Rafael Rodrigues; Dias, Lucas Pinheiro; Costa, Maiane Papke; Abreu, Bianca Regina Ribas de; Cunha, Kênya Silva; Lehmann, Mauricio

    2016-07-25

    Fruits and derivatives, such as juices, are complex mixtures of chemicals, some of which may have mutagenic and/or carcinogenic potential, while others may have antimutagenic and/or anticancer activities. The modulating effects of honey-sweetened cashew apple nectar (HSCAN), on somatic mutation and recombination induced by ethyl methanesulfonate (EMS) and mitomycin C (MMC) were evaluated with the wing spot test in Drosophila melanogaster using co- and post-treatment protocols. Additionally, the antimutagenic activity of two HSCAN components, cashew apple pulp and honey, in MMC-induced DNA damage was also investigated. HSCAN reduced the mutagenic activity of both EMS and MMC in the co-treatment protocol, but had a co-mutagenic effect when post-administered. Similar results were also observed with honey on MMC mutagenic activity. Cashew apple pulp was effective in exerting protective or enhancing effects on the MMC mutagenicity, depending on the administration protocol and concentration used. Overall, these results indicate that HSCAN, cashew apple and honey seem capable of modulating not only the events that precede the induced DNA damages, but also the Drosophila DNA repair processes involved in the correction of EMS and MMC-induced damages. PMID:27459259

  13. DNA damage protective effect of honey-sweetened cashew apple nectar in Drosophila melanogaster

    PubMed Central

    da Silva, Robson Alves; Dihl, Rafael Rodrigues; Dias, Lucas Pinheiro; Costa, Maiane Papke; de Abreu, Bianca Regina Ribas; Cunha, Kênya Silva; Lehmann, Mauricio

    2016-01-01

    Abstract Fruits and derivatives, such as juices, are complex mixtures of chemicals, some of which may have mutagenic and/or carcinogenic potential, while others may have antimutagenic and/or anticancer activities. The modulating effects of honey-sweetened cashew apple nectar (HSCAN), on somatic mutation and recombination induced by ethyl methanesulfonate (EMS) and mitomycin C (MMC) were evaluated with the wing spot test in Drosophila melanogaster using co- and post-treatment protocols. Additionally, the antimutagenic activity of two HSCAN components, cashew apple pulp and honey, in MMC-induced DNA damage was also investigated. HSCAN reduced the mutagenic activity of both EMS and MMC in the co-treatment protocol, but had a co-mutagenic effect when post-administered. Similar results were also observed with honey on MMC mutagenic activity. Cashew apple pulp was effective in exerting protective or enhancing effects on the MMC mutagenicity, depending on the administration protocol and concentration used. Overall, these results indicate that HSCAN, cashew apple and honey seem capable of modulating not only the events that precede the induced DNA damages, but also the Drosophila DNA repair processes involved in the correction of EMS and MMC-induced damages. PMID:27560988

  14. Interannual variations of the blocking high over the Ural Mountains and its association with the AO/NAO in boreal winter

    NASA Astrophysics Data System (ADS)

    Li, Chao; Zhang, Qingyun; Ji, Liren; Peng, Jingbei

    2012-04-01

    This paper analyzes interannual variations of the blocking high over the Ural Mountains in the boreal winter and their association with the Arctic Oscillation/North Atlantic Oscillation (AO/NAO). In January, the relationship between the Ural blocking high (UR) and the AO index is statistically significant. The UR tends to occur more frequently and with greater strength during negative AO periods. Some strong URs also occur during positive AO phases (positive UR-AO events), as in January 2008. This paper discusses the characteristics of atmospheric circulation in the cases of positive UR-AO events and contrast cases (negative UR-AO events). The eastward extending of the Icelandic Low (IL) center and the associated NAO dipole anomaly pattern in the upstream region may play a more important role for the UR-AO events. When the center of the IL shifts eastward to 30°W, the amplitude of zonal wavenumber 2 (wavenumber 3) is intensified in the positive (negative) UR-AO events, which favors positive (negative) height anomalies over the Urals. Further analyses indicate that the intensified zonal wind in high latitudes and weakened zonal wind in midlatitudes over the North Atlantic Ocean render the eastward shift of the IL and the NAO dipole anomaly pattern. The Ural blocking in January 2008 bears similar characteristics to the positive UR-AO events.

  15. Ancient DNA and human history

    PubMed Central

    Slatkin, Montgomery; Racimo, Fernando

    2016-01-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. PMID:27274045

  16. Charge transport in desolvated DNA

    NASA Astrophysics Data System (ADS)

    Wolter, Mario; Elstner, Marcus; Kubař, Tomáš

    2013-09-01

    The conductivity of DNA in molecular junctions is often probed experimentally under dry conditions, but it is unclear how much of the solvent remains attached to the DNA and how this impacts its structure, electronic states, and conductivity. Classical MD simulations show that DNA is unstable if the solvent is removed completely, while a micro-hydrated system with few water molecules shows similar charge transport properties as fully solvated DNA does. This surprising effect is analyzed in detail by mapping the density functional theory-based electronic structure to a tight-binding Hamiltonian, allowing for an estimate of conductivity of various DNA sequences with snapshot-averaged Landauer's approach. The characteristics of DNA charge transport turn out to be determined by the nearest hydration shell(s), and the removal of bulk solvent has little effect on the transport.

  17. Cryptography with DNA binary strands.

    PubMed

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H

    2000-06-01

    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'. PMID:10963862

  18. DNA vaccine for cancer immunotherapy

    PubMed Central

    Yang, Benjamin; Jeang, Jessica; Yang, Andrew; Wu, T C; Hung, Chien-Fu

    2015-01-01

    DNA vaccination has emerged as an attractive immunotherapeutic approach against cancer due to its simplicity, stability, and safety. Results from numerous clinical trials have demonstrated that DNA vaccines are well tolerated by patients and do not trigger major adverse effects. DNA vaccines are also very cost effective and can be administered repeatedly for long-term protection. Despite all the practical advantages, DNA vaccines face challenges in inducing potent antigen specific cellular immune responses as a result of immune tolerance against endogenous self-antigens in tumors. Strategies to enhance immunogenicity of DNA vaccines against self-antigens have been investigated including encoding of xenogeneic versions of antigens, fusion of antigens to molecules that activate T cells or trigger associative recognition, priming with DNA vectors followed by boosting with viral vector, and utilization of immunomodulatory molecules. This review will focus on discussing strategies that circumvent immune tolerance and provide updates on findings from recent clinical trials. PMID:25625927

  19. Ancient DNA and human history.

    PubMed

    Slatkin, Montgomery; Racimo, Fernando

    2016-06-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. PMID:27274045

  20. DNA denaturation in ionic solution

    NASA Astrophysics Data System (ADS)

    Maity, Arghya; Singh, Amar; Singh, Navin

    2016-05-01

    Salt or cations, present in solution play an important role in DNA denaturation and folding kinetics of DNA helix. In this work we study the thermal melting of double stranded DNA (dsDNA) molecule using Peyrard Bishop Dauxois (PBD) model. We modify the potential of H-bonding between the bases of the complimentary strands to introduce the salt and solvent effect. We choose different DNA sequences having different contents of GC pairs and calculate the melting temperatures. The melting temperature increases logarithmically with the salt concentration of the solution. The more GC base pairs in the chain enhance the stability of DNA chain at a fix salt concentration. The obtained results are in good accordance with experimental findings.

  1. Interaction of chlorpromazine with DNA.

    PubMed

    Motohashi, N; Kamata, K; Meyer, R

    1990-01-01

    The mechanism of the potential anticancer agent chlorpromazine hydrochloride (CPZ) with DNA was investigated by the techniques of high-performance liquid chromatography (HPLC), viscosity and Raman spectroscopy. It has been suggested from HPLC work that DNA nucleotides (except nucleosides) from either a CPZ-DNA system or a CPZ-nucleotide system. Furthermore, the shear stress of the viscosity of the CPZ-DNA system and the CPZ-nucleotide systems ware shown to be apparently the higher increasing than that of DNA and nucleotide alone. These systems had non-Newtonian properties for the formation of the CPZ-DNA and the CPZ-nucleotide systems under experimental conditions. The Raman spectra showed a dramatic difference at 982 cm-1 due to the symmetric P-O stretching vibration of the PO4(2-) group between dGMP and the CPZ-dGMP system. PMID:2285233

  2. Methods of DNA methylation detection

    NASA Technical Reports Server (NTRS)

    Maki, Wusi Chen (Inventor); Filanoski, Brian John (Inventor); Mishra, Nirankar (Inventor); Rastogi, Shiva (Inventor)

    2010-01-01

    The present invention provides for methods of DNA methylation detection. The present invention provides for methods of generating and detecting specific electronic signals that report the methylation status of targeted DNA molecules in biological samples.Two methods are described, direct and indirect detection of methylated DNA molecules in a nano transistor based device. In the direct detection, methylated target DNA molecules are captured on the sensing surface resulting in changes in the electrical properties of a nano transistor. These changes generate detectable electronic signals. In the indirect detection, antibody-DNA conjugates are used to identify methylated DNA molecules. RNA signal molecules are generated through an in vitro transcription process. These RNA molecules are captured on the sensing surface change the electrical properties of nano transistor thereby generating detectable electronic signals.

  3. LDEF (Flight), AO180 : The Effect of Space Environment Exposure on the Properties of Polymer Matrix

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Flight), AO180 : The Effect of Space Environment Exposure on the Properties of Polymer Matrix Composite Materials, Tray D12 The flight photograph was taken from the Orbiter aft flight deck during the LDEF retrieval. During the mission, the tray surface was at an angle of approximately ninety-eight (98) degrees to the orbital velocity vector and therefore exposed to a lower atomic oxygen flux than if parallel with the velocity vector. A very light stain is present on white paint dots on experiment tray clamps along the lower edge of the tray. The Polymer Matrix Composite Materials experiment has several changes to material colors. The composite containing the aramid (Kevlar) fibers has changed from a yellow to a light brown color and the cylindrical tubes containing the boron and carbon fiber materials have changed from a light green tint to a brown color.

  4. Toward a large lightweight mirror for AO: development of a 1m Ni coated CFRP mirror

    NASA Astrophysics Data System (ADS)

    Thompson, S. J.; Doel, A. P.; Brooks, D.; Strangwood, M.

    2008-07-01

    We present our recent developments towards the construction of a large, thin, single-piece mirror for adaptive optics (AO). Our current research program aims to have completed fabrication and testing of a 1m diameter, nickel coated carbon-fibre reinforced cyanate ester resin mirror by the last quarter of 2009. This composite mirror material is being developed to provide a lightweight and robust alternative to thin glass shell mirrors, with the challenge of future large deformable mirrors such as the 2.5m M4 on the E-ELT in mind. A detailed analysis of the material properties of test mirror samples is being performed at the University of Birmingham (UK), the first results of which are discussed and presented here. We discuss the project progress achieved so far, including fabrication of the 1m flat moulds for the replication process, manufacturing and testing methods for 20 cm diameter sample mirrors and system simulations.

  5. ShaneAO: wide science spectrum adaptive optics system for the Lick Observatory

    NASA Astrophysics Data System (ADS)

    Gavel, Donald; Kupke, Renate; Dillon, Daren; Norton, Andrew; Ratliff, Chris; Cabak, Jerry; Phillips, Andrew; Rockosi, Connie; McGurk, Rosalie; Srinath, Srikar; Peck, Michael; Deich, William; Lanclos, Kyle; Gates, John; Saylor, Michael; Ward, Jim; Pfister, Terry

    2014-07-01

    A new high-order adaptive optics system is now being commissioned at the Lick Observatory Shane 3-meter telescope in California. This system uses a high return efficiency sodium beacon and a combination of low and high-order deformable mirrors to achieve diffraction-limited imaging over a wide spectrum of infrared science wavelengths covering 0.8 to 2.2 microns. We present the design performance goals and the first on-sky test results. We discuss several innovations that make this system a pathfinder for next generation AO systems. These include a unique woofer-tweeter control that provides full dynamic range correction from tip/tilt to 16 cycles, variable pupil sampling wavefront sensor, new enhanced silver coatings developed at UC Observatories that improve science and LGS throughput, and tight mechanical rigidity that enables a multi-hour diffraction-limited exposure in LGS mode for faint object spectroscopy science.

  6. Sub-rubble communities of Curaçao and Bonaire coral reefs

    NASA Astrophysics Data System (ADS)

    Meesters, E.; Knijn, R.; Willemsen, P.; Pennartz, R.; Roebers, G.; van Soest, R. W. M.

    1991-12-01

    The distribution and abundance of sessile organisms under coral rubble has been studied at Bonaire and Curaçao, Netherlands Antilles. Species richness under rubble is extremely high with at least 367 species of which sponges, tunicates and bryozoans are the most important. Shallow sub-rubble communities can be considered refuges as the majority of these species are crypt-obligate. Sub-rubble communities may also have a preserve function for sponges, but do not harbour enough corals to ensure a quick coral recolonization of the reef surface after a major disaster. Cryptic community composition is affected by depth and pollution, and differs substantially between the two neighbouring islands, possibly as a result of different bottom characteristics. Biomass of the sub-rubble communities may contribute considerably to total reef biomass. Diversity varies inversely with increased depth and increased rubble size, possibly indicating abiotic control (e.g. physical disturbance by wave action and reef slope substrate collapse).

  7. Analysis of Optical Variations of BL Lac Object AO 0235+164

    NASA Astrophysics Data System (ADS)

    Hong-tao, Wang

    2014-03-01

    Historical optical BVRI band data are combined on the BL Lac object AO 0235 + 164. In order to examine the possible existence of lags and correlations between variations in different optical bands from this source, a statistical analysis is performed through the Discrete Correlation Function (DCF) method. Monte Carlo simulations called Flux Redistribution/Random Subset Selection (FR/RSS) are performed to obtain statistically meaningful values for the cross-correlation time lags and their related uncertainties. The analysis confirms that the variations in different optical light curves are strongly correlated, with no or very weak lag within the errors. Long term variability of color indices are also analysed. No color variabilities are found.

  8. Selected Examples of Solar and Extra-Solar Planetary Science with AO

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Lenzen, Rainer; Biller, Beth; Brandner, Wolfgang; Hartung, Markus

    High spatial resolution planetary science has seen a large boost from AO observations complementing space missions. Adaptive optics is particularly well suited for planetary astronomy since solar system bodies have temporal behavior well suited to multiple epochs of observation. Here we will just highlight some very recent examples: Uranus's rings (de Pater et al. 2002), volcanoes on Io (Marchis et al. 2002), the surface of 3 Juno (Baliunas et al. 2003), and binary asteroids (Merline et al. 2002). In addition, we will present "first light" sensitivities from a high contrast simultaneous differential imager (SDI) device. This device (called NACO SDI) can detect an extrasolar planet 25,000 times fainter just 0.5" from its parent star in 40 min of VLT time at 6 sigma. These are the highest contrast astronomical images taken to date.

  9. Eutrophication threatens Caribbean seagrasses - An example from Curaçao and Bonaire.

    PubMed

    Govers, Laura L; Lamers, Leon P M; Bouma, Tjeerd J; de Brouwer, Jan H F; van Katwijk, Marieke M

    2014-12-15

    Seagrass beds are globally declining due to human activities in coastal areas. We here aimed to identify threats from eutrophication to the valuable seagrass beds of Curaçao and Bonaire in the Caribbean, which function as nursery habitats for commercial fish species. We documented surface- and porewater nutrient concentrations, and seagrass nutrient concentrations in 6 bays varying in nutrient loads. Water measurements only provided a momentary snapshot, due to timing, tidal stage, etc., but Thalassia testudinum nutrient concentrations indicated long-term nutrient loads. Nutrient levels in most bays did not raise any concern, but high leaf % P values of Thalassia in Piscadera Bay (∼0.31%) and Spanish Water Bay (∼0.21%) showed that seagrasses may be threatened by eutrophication, due to emergency overflow of waste water and coastal housing. We thus showed that seagrasses may be threatened and measures should be taken to prevent loss of these important nursery areas due to eutrophication. PMID:25256296

  10. FlyEyes: integrating CCID-35 into PUEO AO system at CFHT

    NASA Astrophysics Data System (ADS)

    Ho, Kevin K. Y.; Cuillandre, Jean-Charles; Lin, Chueh-Jen; Benedict, Tom; Lai, Olivier; Ward, Jeff; Salmon, Derrick; Luppino, Gerry; Beletic, James; Dorn, Reinhold; Puget, Pascal; Burke, Barry; Wang, Shiang-Yu

    2006-06-01

    A project to upgrade PUEO, the CFHT AO system, was first proposed in 2002. As part of the upgrade effort, a technology project was conceived to evaluate and characterize the backside-illuminated CCID-35 detector as suitable a replacement for the array of avalanche photo diode modules (APDs) in the curvature wavefront sensor. The CCID-35 was envisioned to replace an array of expensive APDs thus providing a cost-effective means of upgrading PUEO to a higher-order system. Work on the project, dubbed FlyEyes, occurred sporadically until Oct 2005 but substantial progress has been made since. This paper was intended to report on the performance of FlyEyes in PUEO but unfortunately the instrument was not ready for tests at the time of this writing. This paper summarizes the progress made on the project thus far and touches upon some of the difficulties encountered.

  11. LDEF (Postflight), AO187-02 : Chemical and Isotropic Measurements of Micrometeoroids by Secondary Io

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO187-02 : Chemical and Isotropic Measurements of Micrometeoroids by Secondary Ion Mass Spectrometry, Tray E08 This postflight photograph shows an experiment that has been severely degraded due to orbital exposure on the leading edge of the LDEF. The metallic coated thin Mylar film has been lost on each of the capture cells. As the thin Mylar film failed, the material curled tightly into small conical shapes and can be seen still attached to the aluminum mounting structure edges of many capture cells. Close examination of capture cells near the tray center clearly show the four individual high purity germanium plates with some of the bonding material exposed between plates. The green tint on the germanium plate at the right edge of the experiment tray is a reflection from the lights in the high bay area of SAEF II at KFC. Dim reflections from various sources can be seen on other sections of the experiment.

  12. Development and operation of an off-limb solar AO system

    NASA Astrophysics Data System (ADS)

    Taylor, Gregory Edward

    An Adaptive Optics system capable of locking-on to off-limb prominence structure has been proven successful. It has been shown to allow for diffraction limited spectroscopy and polarimetry of prominence structure. Spectroscopic data obtained using the Off-Limb AO system have been shown to contain a trove of information regarding the nature of solar prominences. In particular a Rayleigh-Taylor instability was seen in part of this data set. Such instabilities, and the rising plumes that result from them, are thought to be critical clues to the longterm persistence of quiescent solar prominences. This adaptive optics system will allow scientists to come one step closer to understanding the true nature of solar prominences.

  13. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States

    SciTech Connect

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom

    2010-09-13

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a 'jackknife model' in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.

  14. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.

    PubMed

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A; Tomkinson, Alan E; Ellenberger, Tom

    2010-07-27

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a "jackknife model" in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers. PMID:20518483

  15. Stability of mRNA/DNA and DNA/DNA Duplexes Affects mRNA Transcription

    PubMed Central

    Kraeva, Rayna I.; Krastev, Dragomir B.; Roguev, Assen; Ivanova, Anna; Nedelcheva-Veleva, Marina N.; Stoynov, Stoyno S.

    2007-01-01

    Nucleic acids, due to their structural and chemical properties, can form double-stranded secondary structures that assist the transfer of genetic information and can modulate gene expression. However, the nucleotide sequence alone is insufficient in explaining phenomena like intron-exon recognition during RNA processing. This raises the question whether nucleic acids are endowed with other attributes that can contribute to their biological functions. In this work, we present a calculation of thermodynamic stability of DNA/DNA and mRNA/DNA duplexes across the genomes of four species in the genus Saccharomyces by nearest-neighbor method. The results show that coding regions are more thermodynamically stable than introns, 3′-untranslated regions and intergenic sequences. Furthermore, open reading frames have more stable sense mRNA/DNA duplexes than the potential antisense duplexes, a property that can aid gene discovery. The lower stability of the DNA/DNA and mRNA/DNA duplexes of 3′-untranslated regions and the higher stability of genes correlates with increased mRNA level. These results suggest that the thermodynamic stability of DNA/DNA and mRNA/DNA duplexes affects mRNA transcription. PMID:17356699

  16. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    PubMed Central

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  17. Exons, Introns, and DNA Thermodynamics

    NASA Astrophysics Data System (ADS)

    Carlon, Enrico; Malki, Mehdi Lejard; Blossey, Ralf

    2005-05-01

    The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e., stretches of DNA which do not carry useful information for protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights into the physical mechanisms underlying the evolution of genes.

  18. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  19. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor

    PubMed Central

    Reyes-Aldrete, Emilio; Sherman, Michael B.; Woodson, Michael; Atz, Rockney; Grimes, Shelley; Jardine, Paul J.; Morais, Marc C.

    2016-01-01

    SUMMARY Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring, and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate. PMID:26904950

  20. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.

    PubMed

    Mao, Huzhang; Saha, Mitul; Reyes-Aldrete, Emilio; Sherman, Michael B; Woodson, Michael; Atz, Rockney; Grimes, Shelley; Jardine, Paul J; Morais, Marc C

    2016-03-01

    Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate. PMID:26904950

  1. User perceptions on coastal resource state and management options in Curaçao.

    PubMed

    Debrot, A O; Nagelkerken, I

    2000-12-01

    Public environmental awareness and support for management measures are key determinants of the scope for successful implementation of natural resource management. To assess user perceptions and opinions on resource state and potential management options for the coastal zone of Curaçao, we queried 250 coastal resource users from around the island (sport divers, part-time artisanal fishermen and recreational boaters) using questionnaires. There is wide awareness of a long-term decline in coastal resource condition as measured by various indicators. Even among fishermen there was wide awareness of anthropogenic contributors to the decline, broad agreement of management measures required and a general willingness to contribute to management by means of annual license fees. Some of the more salient findings include the endorsement by fishermen of the current ban on spearfishing (81%), the regulation of the beach seine fishery for scad (77%), the introduction of fish reserves (72%), special protection for sea turtles (90%), conch (82%), and lobsters (72%), and notable support for gradual elimination of trap fisheries (45%). Also, both divers (65%) and boaters (92%) expressed the importance to them of an attractive coastline, with both groups expressing preference for natural (un-built) coastline (>74%) above other categories. Management based on the concept "user pays", as already implemented in the Netherlands Antilles on Saba and Bonaire, is well supported by the resource user public. A review of other main constraints such as finances and institutional capacity, shows that conditions are quite favorable for implementation of new legislation. Modem coral reef management is urgently needed in Curaçao to safeguard a key natural resource and concerted action is called for on the part of government agencies, legislators and elected officials. PMID:15266797

  2. Robotic laser adaptive optics imaging of 715 Kepler exoplanet candidates using Robo-AO

    SciTech Connect

    Law, Nicholas M.; Ziegler, Carl; Morton, Tim; Riddle, Reed; Tendulkar, Shriharsh P.; Bui, Khanh; Dekany, Richard G.; Kulkarni, Shrinivas; Punnadi, Sujit; Baranec, Christoph; Ravichandran, Ganesh; Johnson, John Asher; Burse, Mahesh P.; Das, H. K.; Ramaprakash, A. N.

    2014-08-10

    The Robo-AO Kepler Planetary Candidate Survey is observing every Kepler planet candidate host star with laser adaptive optics imaging to search for blended nearby stars, which may be physically associated companions and/or responsible for transit false positives. In this paper, we present the results from the 2012 observing season, searching for stars close to 715 Kepler planet candidate hosts. We find 53 companions, 43 of which are new discoveries. We detail the Robo-AO survey data reduction methods including a method of using the large ensemble of target observations as mutual point-spread-function references, along with a new automated companion-detection algorithm designed for large adaptive optics surveys. Our survey is sensitive to objects from ≈0.''15 to 2.''5 separation, with magnitude differences up to Δm ≈ 6. We measure an overall nearby-star probability for Kepler planet candidates of 7.4% ± 1.0%, and calculate the effects of each detected nearby star on the Kepler-measured planetary radius. We discuss several Kepler Objects of Interest (KOIs) of particular interest, including KOI-191 and KOI-1151, which are both multi-planet systems with detected stellar companions whose unusual planetary system architecture might be best explained if they are 'coincident multiple' systems, with several transiting planets shared between the two stars. Finally, we find 98% confidence evidence that short-period giant planets are two to three times more likely than longer-period planets to be found in wide stellar binaries.

  3. Interdecadal changes in the Asian winter monsoon variability and its relationship with ENSO and AO

    NASA Astrophysics Data System (ADS)

    Yun, Kyung-Sook; Seo, Ye-Won; Ha, Kyung-Ja; Lee, June-Yi; Kajikawa, Yoshiyuki

    2014-08-01

    Interdecadal changes in the Asian winter monsoon (AWM) variability are investigated using three surface air temperature datasets for the 55-year period of 1958-2012 from (1) the National Centers for Environmental Prediction-National Center for Atmospheric Research reanalysis 1 (NCEP), (2) combined datasets from the European Centre for Medium-range Weather Forecasts (ECMWF) 40-yr reanalysis and interim data (ERA), and (3) Japanese 55-year reanalysis (JRA). Particular attention has been paid to the first four empirical orthogonal function (EOF) modes of the AWM temperature variability that together account for 64% of the total variance and have been previously identified as predictable modes. The four modes are characterized as follows: the first mode by a southern warming over the Indo-western Pacific Ocean associated with a gradually increasing basin-wide warming trend; the second mode by northern warming with the interdecadal change after the late 1980s; the third and fourth modes by north-south triple pattern, which reveal a phase shift after the late 1970s. The three reanalyses agree well with each other when producing the first three modes, but show large discrepancy in capturing both spatial and temporal characteristics of the fourth mode. It is therefore considered that the first three leading modes are more reliable than the rest higher modes. Considerable interdecadal changes are found mainly in the first two modes. While the first mode shows gradually decreasing variance, the second mode exhibits larger interannual variance during the recent decade. In addition, after the late 1970s, the first mode has a weakening relationship with the El Niño-Southern Oscillation (ENSO) whereas the second mode has strengthening association with the Artic Oscillation (AO). This indicates an increasing role of AO but decreasing role of ENSO on the AWM variability. A better understanding of the interdecadal change in the dominant modes would contribute toward advancing in

  4. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  5. DNA Damage, Homology-Directed Repair, and DNA Methylation

    PubMed Central

    Angrisano, Tiziana; Morano, Annalisa; Lee, Bongyong; Pardo, Alba Di; Messina, Samantha; Iuliano, Rodolfo; Fusco, Alfredo; Santillo, Maria R; Muller, Mark T; Chiariotti, Lorenzo; Gottesman, Max E; Avvedimento, Enrico V

    2007-01-01

    To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES) cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP) genes (DR-GFP). A total of 2%–4% of the cells generated a functional GFP by homology-directed repair (HR) and gene conversion. However, ~50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2′-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments. PMID:17616978

  6. Intralymphatic immunization enhances DNA vaccination

    NASA Astrophysics Data System (ADS)

    Maloy, Kevin J.; Erdmann, Iris; Basch, Veronique; Sierro, Sophie; Kramps, Thomas A.; Zinkernagel, Rolf M.; Oehen, Stefan; Kündig, Thomas M.

    2001-03-01

    Although DNA vaccines have been shown to elicit potent immune responses in animal models, initial clinical trials in humans have been disappointing, highlighting a need to optimize their immunogenicity. Naked DNA vaccines are usually administered either i.m. or intradermally. The current study shows that immunization with naked DNA by direct injection into a peripheral lymph node enhances immunogenicity by 100- to 1,000-fold, inducing strong and biologically relevant CD8+ cytotoxic T lymphocyte responses. Because injection directly into a lymph node is a rapid and easy procedure in humans, these results have important clinical implications for DNA vaccination.

  7. Synthesis of chemically modified DNA.

    PubMed

    Shivalingam, Arun; Brown, Tom

    2016-06-15

    Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion. PMID:27284032

  8. DNA Methylation Screening and Analysis

    PubMed Central

    Sant, Karilyn E.; Nahar, Muna S.; Dolinoy, Dana C.

    2013-01-01

    DNA methylation is an epigenetic form of gene regulation that is universally important throughout the life course, especially during in utero and postnatal development. DNA methylation aids in cell cycle regulation and cellular differentiation processes. Previous studies have demonstrated that DNA methylation profiles may be altered by diet and the environment, and that these profiles are especially vulnerable during development. Thus, it is important to understand the role of DNA methylation in developmental governance and subsequent disease progression. A variety of molecular methods exist to assay for global, gene-specific, and epigenome-wide methylation. Here we describe these methods and discuss their relative strengths and limitations. PMID:22669678

  9. DNA nanotechnology-enabled biosensors.

    PubMed

    Chao, Jie; Zhu, Dan; Zhang, Yinan; Wang, Lianhui; Fan, Chunhai

    2016-02-15

    Biosensors employ biological molecules to recognize the target and utilize output elements which can translate the biorecognition event into electrical, optical or mass-sensitive signals to determine the quantities of the target. DNA-based biosensors, as a sub-field to biosensor, utilize DNA strands with short oligonucleotides as probes for target recognition. Although DNA-based biosensors have offered a promising alternative for fast, simple and cheap detection of target molecules, there still exist key challenges including poor stability and reproducibility that hinder their competition with the current gold standard for DNA assays. By exploiting the self-recognition properties of DNA molecules, researchers have dedicated to make versatile DNA nanostructures in a highly rigid, controllable and functionalized manner, which offers unprecedented opportunities for developing DNA-based biosensors. In this review, we will briefly introduce the recent advances on design and fabrication of static and dynamic DNA nanostructures, and summarize their applications for fabrication and functionalization of DNA-based biosensors. PMID:26212206

  10. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  11. Piezoresistivity in single DNA molecules

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-09-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes.

  12. Piezoresistivity in single DNA molecules.

    PubMed

    Bruot, Christopher; Palma, Julio L; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  13. Stabbing simulations and DNA transfer.

    PubMed

    Samie, Lydie; Hicks, Tacha; Castella, Vincent; Taroni, Franco

    2016-05-01

    Technical developments have made it possible to analyze very low amounts of DNA. This has many advantages, but the drawback of this technological progress is that interpretation of the results becomes increasingly complex: the number of mixed DNA profiles increased relatively to single source DNA profiles and stochastic effects in the DNA profile, such as drop-in and drop-out, are more frequently observed. Moreover, the relevance of low template DNA material regarding the activities alleged is not as straightforward as it was a few years ago, when for example large quantities of blood were recovered. The possibility of secondary and tertiary transfer is now becoming an issue. The purpose of this research is twofold: first, to study the transfer of DNA from the handler and secondly, to observe if handlers would transfer DNA from persons closely connected to them. We chose to mimic cases where the offender would attack a person with a knife. As a first approach, we envisaged that the defense would not give an alternative explanation for the origin of the DNA. In our transfer experiments (4 donors, 16 experiments each, 64 traces), 3% of the traces were single DNA profiles. Most of the time, the DNA profile of the person handling the knife was present as the major profile: in 83% of the traces the major contributor profile corresponded to the stabber's DNA profile (in single stains and mixtures). Mixture with no clear major/minor fraction (12%) were observed. 5% of the traces were considered of insufficient quality (more than 3 contributors, presence of a few minor peaks). In that case, we considered that the stabber's DNA was absent. In our experiments, no traces allowed excluding the stabber, however it must be noted that precautions were taken to minimize background DNA as knives were cleaned before the experiments. DNA profiles of the stabber's colleagues were not observed. We hope that this study will allow for a better understanding of the transfer mechanism and

  14. Unusual monoclonal DNA binding immunoglobulin.

    PubMed

    Sawada, S; Iijima, S; Kuwana, K; Nishinarita, S; Takeuchi, J; Shida, M; Karasaki, M; Amaki, I

    1983-03-01

    The monoclonal antibodies directed against DNA were produced by somatic cell hybridization with parental cells (SP-2) and spleen cells from nonimmunized autoimmune MRL/lpr mice. The immunoglobulins were recovered from the culture supernatant from hybridoma by a solid immunoadsorbent and antibody immunoprecipitation. The results from the specificities of DNA binding monoclonal immunoglobulins suggest that the antibodies to DNA have the antibody combining sites for both epitope of double stranded helix and base of DNA and support the concept of the multiple antigen binding potentials of the hybridoma autoantibodies. PMID:6857646

  15. Defined DNA/nanoparticle conjugates

    NASA Astrophysics Data System (ADS)

    Ackerson, Christopher J.; Sykes, Michael T.; Kornberg, Roger D.

    2005-09-01

    Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content. Freely available online through the PNAS open access option.

  16. DNA attachment to support structures

    DOEpatents

    Balhorn, Rodney L.; Barry, Christopher H.

    2002-01-01

    Microscopic beads or other structures are attached to nucleic acids (DNA) using a terminal transferase. The transferase adds labeled dideoxy nucleotide bases to the ends of linear strands of DNA. The labels, such as the antigens digoxigenin and biotin, bind to the antibody compounds or other appropriate complementary ligands, which are bound to the microscopic beads or other support structures. The method does not require the synthesis of a synthetic oligonucleotide probe. The method can be used to tag or label DNA even when the DNA has an unknown sequence, has blunt ends, or is a very large fragment (e.g., >500 kilobase pairs).

  17. Bioremediation of bisphenol-A polluted soil by Sphingomonas bisphenolicum AO1 and the microbial community existing in the soil.

    PubMed

    Matsumura, Yoshinobu; Akahira-Moriya, Ayako; Sasaki-Mori, Miho

    2015-01-01

    Bisphenol A (BPA, 2,2'-Bis (4-hydroxyphenyl) propane) is an artificial pollutant that is easily detected in soil and water environments. BPA decomposition and removal from the environment is relatively difficult due to its stability. This study evaluated the BPA decomposition and removal activities of the microbial community existing in the soil with or without Sphingomonas bisphenolicum AO1, and revealed the toxic effects of BPA towards the microbial community. The microbial community in soil was able to degrade BPA at 1.0 mg·g(-1) soil or lower, although its degradation was slow. On the other hand, BPA at more than 10 mg·g(-1) soil was not only degraded by the microbial community but also decreased its diversity, suggesting that BPA is harmful to many microorganisms. PCR-TTGE analysis and the cloned 16S rRNA gene sequence analysis indicated that Sphingomonadales, Xanthomonadales, Burkholderiales and Pseudomonadales in the microbial community might independently or cooperatively degrade BPA. On the other hand, supplementation with strain AO1 was able to significantly improve the BPA decomposition activity of the microbial community in soil even at 10 mg BPA·g(-1) soil, although BPA at 100 mg·g(-1) soil overwhelmed the BPA decomposition activity of strain AO1. Furthermore, it was also concluded that strain AO1 could not inhabit BPA purified soil after decomposition of BPA by strain AO1 and the soil microbial community, suggesting that the application of strain AO1 could be a low-burden method for the decomposition and removal of BPA from the natural environment. PMID:25817811

  18. The Magellan Adaptive Secondary VisAO Camera: diffraction-limited broadband visible imaging and 20mas fiber array IFU

    NASA Astrophysics Data System (ADS)

    Kopon, Derek; Close, Laird M.; Males, Jared; Gasho, Victor; Follette, Katherine

    2010-07-01

    The Magellan Adaptive Secondary AO system, scheduled for first light in the fall of 2011, will be able to simultaneously perform diffraction limited AO science in both the mid-IR, using the BLINC/MIRAC4 10μm camera, and in the visible using our novel VisAO camera. The VisAO camera will be able to operate as either an imager, using a CCD47 with 8.5 mas pixels, or as an IFS, using a custom fiber array at the focal plane with 20 mas elements in its highest resolution mode. In imaging mode, the VisAO camera will have a full suite of filters, coronagraphic focal plane occulting spots, and SDI prism/filters. The imaging mode should provide ~20% mean Strehl diffraction-limited images over the band 0.5-1.0 μm. In IFS mode, the VisAO instrument will provide R~1,800 spectra over the band 0.6-1.05 μm. Our unprecedented 20 mas spatially resolved visible spectra would be the highest spatial resolution achieved to date, either from the ground or in space. We also present lab results from our recently fabricated advanced triplet Atmospheric Dispersion Corrector (ADC) and the design of our novel wide-field acquisition and active optics lens. The advanced ADC is designed to perform 58% better than conventional doublet ADCs and is one of the enabling technologies that will allow us to achieve broadband (0.5-1.0μm) diffraction limited imaging and wavefront sensing in the visible.

  19. ANIMAL DNA IN PCR REAGENTS PLAGUES ANCIENT DNA RESEARCH

    EPA Science Inventory

    Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high-cycle PCR amplification targ...

  20. Pea amyloplast DNA is qualitatively similar to pea chloroplast DNA

    NASA Technical Reports Server (NTRS)

    Gaynor, J. J.

    1984-01-01

    Amyloplast DNA (apDNA), when subjected to digestion with restriction endonucleases, yields patterns nearly identical to that of DNA from mature pea chloroplasts (ctDNA). Southern transfers of apDNA and ctDNA, probed with the large subunit (LS) gene of ribulose-1,5-bisphosphate carboxylase (Rubisco), shows hybridization to the expected restriction fragments for both apDNA and ctDNA. However, Northern transfers of total RNA from chloroplasts and amyloplasts, probed again with the LS gene of Rubisco, shows that no detectable LS meggage is found in amyloplasts although LS expression in mature chloroplasts is high. Likewise, two dimensional polyacrylamide gel electrophoresis of etiolated gravisensitive pea tissue shows that both large and small subunits of Rubisco are conspicuously absent; however, in greening tissue these two constitute the major soluble proteins. These findings suggest that although the informational content of these two organelle types is equivalent, gene expression is quite different and is presumably under nuclear control.

  1. Structure and Energetics of Encapsidated DNA in Bacteriophage HK97 Studied by Scanning Calorimetry and Cryo-electron Microscopy

    PubMed Central

    Duda, Robert L.; Ross, Philip D.; Cheng, Naiqian; Firek, Brian A.; Hendrix, Roger W.; Conway, James F.; Steven, Alasdair C.

    2009-01-01

    Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-EM and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When scanned in buffer containing 1mM [Mg++], filled capsids exhibit a complex thermal profile between 82° and 96°, to which DNA melting and capsid denaturation both contribute. In the absence of (unbound) [Mg++], DNA melting shifts to lower temperatures and the two events are resolved. Filled capsids release their DNA at temperatures well below the onset of DNA melting or capsid denaturation. On heating, the internal pressure increases, causing the DNA to exit – probably, via the portal vertex; the capsid, although largely intact, sustains local damage that leads to an earlier onset of thermal denaturation. Filled capsids differ structurally from empty capsids in the curvature of their protein shell, a change attributable to outwards pressure exerted by the DNA. We propose that this transition is sensed by the portal which is embedded in the capsid wall, whereupon the portal's structure and its interactions with terminase, the packaging enzyme, are altered, thus signaling that packaging is at or approaching completion. PMID:19540242

  2. Enhancement of DNA vaccine potency through coadministration of CIITA DNA with DNA vaccines via gene gun.

    PubMed

    Kim, Daejin; Hoory, Talia; Monie, Archana; Ting, Jenny Pan-Yun; Hung, Chien-Fu; Wu, T-C

    2008-05-15

    Administration of DNA vaccines via gene gun has emerged as an important form of Ag-specific immunotherapy. The MHC CIITA is a master regulator of MHC class II expression and also induces expression of class I molecules. We reasoned that the gene gun administration of CIITA DNA with DNA vaccines employing different strategies to improve MHC I and II processing could enhance DNA vaccine potency. We observed that DC-1 cells transfected with CIITA DNA lead to higher expression of MHC I and II molecules, leading to enhanced Ag presentation through the MHC I/II pathways. Furthermore, our data suggested that coadministration of DNA-encoding calreticulin (CRT) linked to human papillomavirus (HPV) 16 E6 Ag (CRT/E6) with CIITA DNA leads to enhanced E6-specific CD8(+) T cell immune responses in vaccinated mice. In addition, coadministration of the combination of CRT/E6 DNA with CIITA DNA and DNA encoding the invariant chain (Ii) linked to the pan HLA-DR-reactive epitope (Ii-PADRE) further enhanced E6-specific CD8(+) T cell immune responses in vaccinated mice. Treatment with the combination vaccine was also shown to enhance the antitumor effects and to prolong survival in TC-1 tumor-bearing mice. Vaccination with the combination vaccine also led to enhanced E6-specific CD8(+) memory T cells and to long-term protection against TC-1 tumors and prolonged survival in vaccinated mice. Thus, our findings suggest that the combination of CIITA DNA with CRT/E6 and Ii-PADRE DNA vaccines represents a potentially effective means to combat tumors in the clinical setting. PMID:18453624

  3. Authentication of forensic DNA samples.

    PubMed

    Frumkin, Dan; Wasserstrom, Adam; Davidson, Ariane; Grafit, Arnon

    2010-02-01

    Over the past twenty years, DNA analysis has revolutionized forensic science, and has become a dominant tool in law enforcement. Today, DNA evidence is key to the conviction or exoneration of suspects of various types of crime, from theft to rape and murder. However, the disturbing possibility that DNA evidence can be faked has been overlooked. It turns out that standard molecular biology techniques such as PCR, molecular cloning, and recently developed whole genome amplification (WGA), enable anyone with basic equipment and know-how to produce practically unlimited amounts of in vitro synthesized (artificial) DNA with any desired genetic profile. This artificial DNA can then be applied to surfaces of objects or incorporated into genuine human tissues and planted in crime scenes. Here we show that the current forensic procedure fails to distinguish between such samples of blood, saliva, and touched surfaces with artificial DNA, and corresponding samples with in vivo generated (natural) DNA. Furthermore, genotyping of both artificial and natural samples with Profiler Plus((R)) yielded full profiles with no anomalies. In order to effectively deal with this problem, we developed an authentication assay, which distinguishes between natural and artificial DNA based on methylation analysis of a set of genomic loci: in natural DNA, some loci are methylated and others are unmethylated, while in artificial DNA all loci are unmethylated. The assay was tested on natural and artificial samples of blood, saliva, and touched surfaces, with complete success. Adopting an authentication assay for casework samples as part of the forensic procedure is necessary for maintaining the high credibility of DNA evidence in the judiciary system. PMID:20129467

  4. A chiroptical photoswitchable DNA complex.

    PubMed

    Mammana, Angela; Carroll, Gregory T; Areephong, Jetsuda; Feringa, Ben L

    2011-10-13

    The interesting structural, electronic, and optical properties of DNA provide fascinating opportunities for developing nanoscale smart materials by integrating DNA with opto-electronic components. In this article we demonstrate the electrostatic binding of an amine-terminated dithienylethene (DET) molecular switch to double-stranded synthetic polynucleotides. The DET switch can undergo photochemical ring-closure and opening reactions. Circular dichroism (CD) and UV-vis spectroscopy show that both the open, 1o, and the closed, 1c, forms of the switch bind to DNA. Upon addition of DNA to a solution of 1o or 1c, the UV-vis spectrum displays a hypochromic effect, indicative of an interaction between the switch and the DNA. The chirality of the DNA double-helix is transmitted to the switching unit which displays a well-defined CD signal upon supramolecular complexation to the DNA. Additionally, the CD signal of the DNA attenuates, demonstrating that both components of the complex mutually influence each other's structure; the DNA induces chirality in the switch, and the switch modifies the structure of the DNA. Modulation of the chiroptical properties of the complex is achieved by photochemically switching the DET between its ring open and closed isomers. A pH dependence study of the binding shows that when the pH is increased the switches lose their binding ability, indicating that electrostatic interactions between protonated amines and the negatively charged phosphate backbone are the dominant driving force for binding to the DNA. A comparison of poly(deoxyguanylic-deoxycytidylic) acid [poly(dGdC)(2)] polynucleotides with poly(deoxyadenylic-deoxythymidylic) acid [poly(dAdT)(2)] shows distinct differences in the CD spectra of the complexes. PMID:21879715

  5. Eimeria maxima microneme protein 2 delivered as DNA vaccine and recombinant protein induces immunity against experimental homogenous challenge.

    PubMed

    Huang, Jingwei; Zhang, Zhenchao; Li, Menghui; Song, Xiaokai; Yan, Ruofeng; Xu, Lixin; Li, Xiangrui

    2015-10-01

    E. maxima is one of the seven species of Eimeria that infects chicken. Until now, only a few antigenic genes of E. maxima have been reported. In the present study, the immune protective effects against E. maxima challenge of recombinant protein and DNA vaccine encoding EmMIC2 were evaluated. Two-week-old chickens were randomly divided into five groups. The experimental group of chickens was immunized with 100 μg DNA vaccine pVAX1-MIC2 or 200 μg rEmMIC2 protein while the control group of chickens was injected with pVAX1 plasmid or sterile PBS. The results showed that the anti-EmMIC2 antibody titers of both rEmMIC2 protein and pVAX1-MIC2 groups were significantly higher as compared to PBS and pVAX1 control (P<0.05). The splenocytes from both vaccinated groups of chickens displayed significantly greater proliferation compared with the controls (P<0.05). Serum from chickens immunized with pVAX1-MIC2 and rEmMIC2 protein displayed significantly high levels of IL-2, IFN-γ, IL-10, IL-17, TGF-β and IL-4 (P<0.05) compared to those of negative controls. The challenge experiment results showed that both the recombinant protein and the DNA vaccine could obviously alleviate jejunum lesions, body weight loss, increase oocyst, decrease ratio and provide ACIs of more than 165. All the above results suggested that immunization with EmMIC2 was effective in imparting partial protection against E. maxima challenge and it could be an effective antigen candidate for the development of new vaccines against E. maxima. PMID:26072304

  6. Method for assaying clustered DNA damages

    DOEpatents

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  7. Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes

    PubMed Central

    Li, Fuyang; Papworth, Monika; Minczuk, Michal; Rohde, Christian; Zhang, Yingying; Ragozin, Sergei; Jeltsch, Albert

    2007-01-01

    Gene silencing by targeted DNA methylation has potential applications in basic research and therapy. To establish targeted methylation in human cell lines, the catalytic domains (CDs) of mouse Dnmt3a and Dnmt3b DNA methyltransferases (MTases) were fused to different DNA binding domains (DBD) of GAL4 and an engineered Cys2His2 zinc finger domain. We demonstrated that (i) Dense DNA methylation can be targeted to specific regions in gene promoters using chimeric DNA MTases. (ii) Site-specific methylation leads to repression of genes controlled by various cellular or viral promoters. (iii) Mutations affecting any of the DBD, MTase or target DNA sequences reduce targeted methylation and gene silencing. (iv) Targeted DNA methylation is effective in repressing Herpes Simplex Virus type 1 (HSV-1) infection in cell culture with the viral titer reduced by at least 18-fold in the presence of an MTase fused to an engineered zinc finger DBD, which binds a single site in the promoter of HSV-1 gene IE175k. In short, we show here that it is possible to direct DNA MTase activity to predetermined sites in DNA, achieve targeted gene silencing in mammalian cell lines and interfere with HSV-1 propagation. PMID:17151075

  8. DNA Extraction Techniques for Use in Education

    ERIC Educational Resources Information Center

    Hearn, R. P.; Arblaster, K. E.

    2010-01-01

    DNA extraction provides a hands-on introduction to DNA and enables students to gain real life experience and practical knowledge of DNA. Students gain a sense of ownership and are more enthusiastic when they use their own DNA. A cost effective, simple protocol for DNA extraction and visualization was devised. Buccal mucosal epithelia provide a…

  9. DNA: Polymer and molecular code

    NASA Astrophysics Data System (ADS)

    Shivashankar, G. V.

    1999-10-01

    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  10. Tumorigenic DNA viruses

    SciTech Connect

    Klein, G.

    1989-01-01

    The eighth volume of Advances in Viral Oncology focuses on the three major DNA virus groups with a postulated or proven tumorigenic potential: papillomaviruses, animal hepatitis viruses, and the Epstein-Bar virus. In the opening chapters, the contributors analyze the evidence that papillomaviruses and animal hepatitis viruses are involved in tumorigenesis and describe the mechanisms that trigger virus-host cell interactions. A detailed section on the Epstein-Barr virus (EBV) - comprising more than half the book - examines the transcription and mRNA processing patterns of the virus genome; the mechanisms by which EBV infects lymphoid and epithelial cells; the immunological aspects of the virus; the actions of EBV in hosts with Acquired Immune Deficiency Syndrome; and the involvement of EBV in the etiology of Burkitt's lymphoma.

  11. Condensation of circular DNA

    NASA Astrophysics Data System (ADS)

    Starostin, E. L.

    2013-04-01

    A simple model of a circularly closed double-stranded DNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.

  12. Sense antisense DNA strand?

    PubMed

    Boldogkói, Z; Kaliman, A V; Murvai, J; Fodor, I

    1994-01-01

    Recent evidence indicates that alphaherpesviruses express latency associated transcripts (LATs) from the antisense strand of immediate-early (IE) genes of the viral genome. It has been suggested that LATs containing extended open reading frames (ORFs), might be translated into (a) protein product(s). We found that a salient feature of some herpesvirus DNAs is a high GC preference at the third codon positions. The consequence of this feature is that the probability of a stop-codon appearing at two of the six reading frames of the DNA strand is very low. Therefore, the presence of an extended ORF does not necessarily mean that it is relevant to real translation. PMID:7810418

  13. A distribuição de velocidades na linha de visada em galáxias barradas vistas de face

    NASA Astrophysics Data System (ADS)

    Gadotti, D. A.; de Souza, R. E.

    2003-08-01

    Com o objetivo de realizar um estudo cinemático da componente vertical de barras em galáxias, obtivemos espectros de fenda longa de alta razão S/N ao longo dos eixos maior e menor de 14 galáxias barradas vistas de face, nos telescópios de 1.52m do ESO em La Silla, Chile, e de 2.3m do Steward Observatory em Kitt Peak, Arizona. Estes dados nos permitiram determinar a distribuição de velocidades das estrelas ao longo do eixo vertical das barras e discos destes sistemas, tanto no centro como em pontos que distam cerca de 5 e 20 segundos de arco do núcleo, correspondendo a distâncias de cerca de 0.7 e 2.8 kpc, respectivamente. Desta forma, a variação radial da distribuição de velocidades também pôde ser avaliada. Este tipo de análise tem raros exemplos na literatura por ser caro em termos de tempo de telescópio. Entretanto, é de fácil justificativa, considerando que traz novas informações que podem ser utilizadas para aperfeiçoar modelos teóricos acerca da formação e evolução de galáxias. Um algoritmo por nós desenvolvido foi utilizado para obter as distribuições de velocidades como Gaussianas generalizadas (polinômios de Gauss-Hermite), o que traz um ingrediente a mais neste tipo de estudo que, tradicionalmente, se utiliza de Gaussianas puras, uma hipótese nem sempre razoável. Apresentaremos os resultados deste trabalho, que incluem um diagnóstico para a identificação de barras recém formadas, e testes para o modelo isotérmico de discos. Mostraremos que: (i) a escolha das estrelas padrão em velocidade, e dos parâmetros da Gaussiana, deve ser muito bem justificada já que tem influência significativa nos resultados; (ii) muitas galáxias apresentam uma depressão na dispersão de velocidades na região central, que pode estar associada a um disco interno; e (iii) a dispersão de velocidades é constante ao longo da barra, nos eixos maior e menor, mas cai substancialmente quando se passa da barra para o disco.

  14. DOE/EM Criticality Safety Needs Assessment

    SciTech Connect

    Westfall, Robert Michael; Hopper, Calvin Mitchell

    2011-02-01

    The issue of nuclear criticality safety (NCS) in Department of Energy Environmental Management (DOE/EM) fissionable material operations presents challenges because of the large quantities of material present in the facilities and equipment that are committed to storage and/or material conditioning and dispositioning processes. Given the uncertainty associated with the material and conditions for many DOE/EM fissionable material operations, ensuring safety while maintaining operational efficiency requires the application of the most-effective criticality safety practices. In turn, more-efficient implementation of these practices can be achieved if the best NCS technologies are utilized. In 2002, DOE/EM-1 commissioned a survey of criticality safety technical needs at the major EM sites. These needs were documented in the report Analysis of Nuclear Criticality Safety Technology Supporting the Environmental Management Program, issued May 2002. Subsequent to this study, EM safety management personnel made a commitment to applying the best and latest criticality safety technology, as described by the DOE Nuclear Criticality Safety Program (NCSP). Over the past 7 years, this commitment has enabled the transfer of several new technologies to EM operations. In 2008, it was decided to broaden the basis of the EM NCS needs assessment to include not only current needs for technologies but also NCS operational areas with potential for improvements in controls, analysis, and regulations. A series of NCS workshops has been conducted over the past years, and needs have been identified and addressed by EM staff and contractor personnel. These workshops were organized and conducted by the EM Criticality Safety Program Manager with administrative and technical support by staff at Oak Ridge National Laboratory (ORNL). This report records the progress made in identifying the needs, determining the approaches for addressing these needs, and assimilating new NCS technologies into EM

  15. DNA nanotechnology: a future perspective

    NASA Astrophysics Data System (ADS)

    Zahid, Muniza; Kim, Byeonghoon; Hussain, Rafaqat; Amin, Rashid; Park, Sung Ha

    2013-03-01

    In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.

  16. Isothermal amplification of insect DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The loop-mediated isothermal amplification of DNA (LAMP) method can amplify a target DNA sequence at a constant temperature in about 1 hour. LAMP has broad application in agriculture and medicine because of the need for rapid and inexpensive diagnoses. The power of LAMP is being used by researchers ...

  17. Improved ethanol precipitation of DNA.

    PubMed

    Fregel, Rosa; González, Ana; Cabrera, Vicente M

    2010-04-01

    In this Short Communication, a shorter version of the standard DNA ethanol precipitation and purification protocol is described. It uses a mixture of 70% ethanol, 75 mM ammonium acetate and different concentrations of different carriers to perform DNA precipitation and washing in only one step. PMID:20336673

  18. Isothermal Amplification of Insect DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The loop-mediated isothermal amplification of DNA (LAMP) method can amplify a target DNA sequence at a constant temperature in about one hour. LAMP has broad application in agriculture and medicine because of the need for rapid and inexpensive diagnoses. LAMP eliminates the need for temperature cycl...

  19. DNA repair in mammalian embryos.

    PubMed

    Jaroudi, Souraya; SenGupta, Sioban

    2007-01-01

    Mammalian cells have developed complex mechanisms to identify DNA damage and activate the required response to maintain genome integrity. Those mechanisms include DNA damage detection, DNA repair, cell cycle arrest and apoptosis which operate together to protect the conceptus from DNA damage originating either in parental gametes or in the embryo's somatic cells. DNA repair in the newly fertilized preimplantation embryo is believed to rely entirely on the oocyte's machinery (mRNAs and proteins deposited and stored prior to ovulation). DNA repair genes have been shown to be expressed in the early stages of mammalian development. The survival of the embryo necessitates that the oocyte be sufficiently equipped with maternal stored products and that embryonic gene expression commences at the correct time. A Medline based literature search was performed using the keywords 'DNA repair' and 'embryo development' or 'gametogenesis' (publication dates between 1995 and 2006). Mammalian studies which investigated gene expression were selected. Further articles were acquired from the citations in the articles obtained from the preliminary Medline search. This paper reviews mammalian DNA repair from gametogenesis to preimplantation embryos to late gestational stages. PMID:17141556

  20. Fabrication of patterned DNA surfaces.

    PubMed Central

    Chrisey, L A; O'Ferrall, C E; Spargo, B J; Dulcey, C S; Calvert, J M

    1996-01-01

    Two photolithographic methods are described for the formation of patterned single or multiple DNA species on SiO2 substrates. In the first approach, substrates are treated with a photochemically labile organosilane monolayer film. Irradiation of these surfaces with patterned deep UV (193 nm) light results in patterned chemically reactive groups which are then reacted with heterobifunctional crosslinking molecules. Covalent attachment of modified synthetic DNA oligomers to the crosslinker results in stable DNA patterns. Alternatively, a photoresist is spin-coated over a silane film which had been previously modified with the heterobifunctional crosslinker. Upon patterned irradiation and subsequent development, the underlying crosslinker-modified layer is revealed, and is then reacted with a chemically modified DNA. Feature dimensions to 1 micron are observed when a single fluorescent DNA is attached to the surface. By performing sequential exposures, we have successfully immobilized two distinguishable DNA oligomers on a single surface. Synthetic DNA immobilized in this manner retains the ability to hybridize to its complementary strand, suggesting that these approaches may find utility in the development of miniaturized DNA-based biosensors. PMID:8760891

  1. DNA nanotechnology: a future perspective

    PubMed Central

    2013-01-01

    In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology. PMID:23497147

  2. Methods of DNA methylation analysis.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purpose of this review was to provide guidance for investigators who are new to the field of DNA methylation analysis. Epigenetics is the study of mitotically heritable alterations in gene expression potential that are not mediated by changes in DNA sequence. Recently, it has become clear that n...

  3. DNA/chitosan electrostatic complex.

    PubMed

    Bravo-Anaya, Lourdes Mónica; Soltero, J F Armando; Rinaudo, Marguerite

    2016-07-01

    Up to now, chitosan and DNA have been investigated for gene delivery due to chitosan advantages. It is recognized that chitosan is a biocompatible and biodegradable non-viral vector that does not produce immunological reactions, contrary to viral vectors. Chitosan has also been used and studied for its ability to protect DNA against nuclease degradation and to transfect DNA into several kinds of cells. In this work, high molecular weight DNA is compacted with chitosan. DNA-chitosan complex stoichiometry, net charge, dimensions, conformation and thermal stability are determined and discussed. The influence of external salt and chitosan molecular weight on the stoichiometry is also discussed. The isoelectric point of the complexes was found to be directly related to the protonation degree of chitosan. It is clearly demonstrated that the net charge of DNA-chitosan complex can be expressed in terms of the ratio [NH3(+)]/[P(-)], showing that the electrostatic interactions between DNA and chitosan are the main phenomena taking place in the solution. Compaction of DNA long chain complexed with low molar mass chitosan gives nanoparticles with an average radius around 150nm. Stable nanoparticles are obtained for a partial neutralization of phosphate ionic sites (i.e.: [NH3(+)]/[P(-)] fraction between 0.35 and 0.80). PMID:27050113

  4. Wireframe and tensegrity DNA nanostructures.

    PubMed

    Simmel, Stephanie S; Nickels, Philipp C; Liedl, Tim

    2014-06-17

    CONSPECTUS: Not only can triangulated wireframe network and tensegrity design be found in architecture, but it is also essential for the stability and organization of biological matter. Whether the scaffolding material is metal as in Buckminster Fuller's geodesic domes and Kenneth Snelson's floating compression sculptures or proteins like actin or spectrin making up the cytoskeleton of biological cells, wireframe and tensegrity construction can provide great stability while minimizing the material required. Given the mechanical properties of single- and double-stranded DNA, it is not surprising to find many variants of wireframe and tensegrity constructions in the emerging field of DNA nanotechnology, in which structures of almost arbitrary shape can be built with nanometer precision. The success of DNA self-assembly relies on the well-controlled hybridization of complementary DNA strands. Consequently, understanding the fundamental physical properties of these molecules is essential. Many experiments have shown that double-stranded DNA (in its most commonly occurring helical form, the B-form) behaves in a first approximation like a relatively stiff cylindrical beam with a persistence length of many times the length of its building blocks, the base pairs. However, it is harder to assign a persistence length to single-stranded DNA. Here, normally the Kuhn length is given, a measure that describes the length of individual rigid segments in a freely jointed chain. This length is on the order of a few nucleotides. Two immediate and important consequences arise from this high flexibility: single-stranded DNA is almost always present in a coiled conformation, and it behaves, just like all flexible polymers in solution, as an entropic spring. In this Account, we review the relation between the mechanical properties of DNA and design considerations for wireframe and tensegrity structures built from DNA. We illustrate various aspects of the successful evolution of DNA

  5. Fuzzy logic sensing of G-quadruplex DNA and its cleavage reagents based on reduced graphene oxide.

    PubMed

    Huang, Wei Tao; Zhang, Jian Rong; Xie, Wan Yi; Shi, Yan; Luo, Hong Qun; Li, Nian Bing

    2014-07-15

    Herein, by combining the merits of nanotechnology and fuzzy logic theory, we develop a simple, label-free, and general strategy based on an organic dye-graphene hybrid system for fluorescence intelligent sensing of G-quadruplexes (G4) formation, hydroxyl radical (HO∙), and Fe(2+) in vitro. By exploiting acridine orange (AO) dyes-graphene as a nanofilter and nanoswitch and the ability of graphene to interact with DNA with different structures, our approach can efficiently distinguish, quantitatively detect target analytes. In vitro assays with G4DNA demonstrated increases in fluorescence intensity of the AO-rGO system with a linear range of 16-338 nM and a detection limit as low as 2.0 nM. The requenched fluorescence of the G4TBA-AO-rGO system has a non-linear response to Fenton reagent. But this requenching reduces the fluorescence intensity in a manner proportional to the logarithm to the base 10 of the concentration of Fenton reagent in the range of 0.1-100 μM and 100-2000 μM, respectively. Furthermore, we develop a novel and intelligent sensing method based on fuzzy logic which mimics human reasoning, solves complex and non-linear problems, and transforms the numerical output into the language description output for potential application in biochemical systems, environmental monitoring systems, and molecular-level fuzzy logic computing system. PMID:24561526

  6. DNA vaccines in veterinary use

    PubMed Central

    Redding, Laurel; Werner, David B

    2015-01-01

    DNA vaccines represent a new frontier in vaccine technology. One important application of this technology is in the veterinary arena. DNA vaccines have already gained a foothold in certain fields of veterinary medicine. However, several important questions must be addressed when developing DNA vaccines for animals, including whether or not the vaccine is efficacious and cost effective compared with currently available options. Another important question to consider is how to apply this developing technology in a wide range of different situations, from the domestic pet to individual fish in fisheries with several thousand animals, to wildlife programs for disease control. In some cases, DNA vaccines represent an interesting option for vaccination, while in others, currently available options are sufficient. This review will examine a number of diseases of veterinary importance and the progress being made in DNA vaccine technology relevant to these diseases, and we compare these with the conventional treatment options available. PMID:19722897

  7. Graphene nanodevices for DNA sequencing.

    PubMed

    Heerema, Stephanie J; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology. PMID:26839258

  8. Graphene nanodevices for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  9. DNA signals at isoform promoters

    PubMed Central

    Dai, Zhiming; Xiong, Yuanyan; Dai, Xianhua

    2016-01-01

    Transcriptional heterogeneity is extensive in the genome, and most genes express variable transcript isoforms. However, whether variable transcript isoforms of one gene are regulated by common promoter elements remain to be elucidated. Here, we investigated whether isoform promoters of one gene have separated DNA signals for transcription and translation initiation. We found that TATA box and nucleosome-disfavored DNA sequences are prevalent in distinct transcript isoform promoters of one gene. These DNA signals are conserved among species. Transcript isoform has a RNA-determined unstructured region around its start site. We found that these DNA/RNA features facilitate isoform transcription and translation. These results suggest a DNA-encoded mechanism by which transcript isoform is generated. PMID:27353836

  10. Single-Molecule DNA Analysis

    NASA Astrophysics Data System (ADS)

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  11. Future of DNA diagnostic testing

    NASA Astrophysics Data System (ADS)

    Petersen, Kurt E.

    2001-09-01

    Progress in sequencing the human genome and the DNA of other organisms is providing many opportunities for creating powerful systems for numerous and diverse applications in DNA testing. These systems and the chemical processes, such as PCR, which they are designed to carry out, have recently made great strides in miniaturization through advances in micro-fluidics and micro-optics. In addition, new techniques in biological processing, such as controlled ultrasonic lysis, are being applied to small, automated, integrated instruments designed to provide important DNA results in a timely and routine manner. These systems are bringing DNA identification out of the laboratory and into our daily lives. Instead of waiting for days or weeks for a result, we will have them in minutes. Instead of relying on the skills of molecular biologists, the average person will be able to run a DNA test. These new advances will widely impact many aspects of our medical practices, food processing, and public safety.

  12. DNA typing by capillary electrophoresis

    SciTech Connect

    Zhang, N.

    1997-10-08

    Capillary electrophoresis is becoming more and more important in nucleic acid analysis including DNA sequencing, typing and disease gene measurements. This work summarized the background of DNA typing. The recent development of capillary electrophoresis was also discussed. The second part of the thesis showed the principle of DNA typing based on using the allelic ladder as the absolute standard ladder in capillary electrophoresis system. Future work will be focused on demonstrating DNA typing on multiplex loci and examples of disease diagnosis in the on-line format of PCR-CE. Also capillary array electrophoresis system should allow high throughput, fast speed DNA typing. Only the introduction and conclusions for this report are available here. A reprint was removed for separate processing.

  13. DNA signals at isoform promoters.

    PubMed

    Dai, Zhiming; Xiong, Yuanyan; Dai, Xianhua

    2016-01-01

    Transcriptional heterogeneity is extensive in the genome, and most genes express variable transcript isoforms. However, whether variable transcript isoforms of one gene are regulated by common promoter elements remain to be elucidated. Here, we investigated whether isoform promoters of one gene have separated DNA signals for transcription and translation initiation. We found that TATA box and nucleosome-disfavored DNA sequences are prevalent in distinct transcript isoform promoters of one gene. These DNA signals are conserved among species. Transcript isoform has a RNA-determined unstructured region around its start site. We found that these DNA/RNA features facilitate isoform transcription and translation. These results suggest a DNA-encoded mechanism by which transcript isoform is generated. PMID:27353836

  14. BSSDATA - um programa otimizado para filtragem de dados em radioastronomia solar

    NASA Astrophysics Data System (ADS)

    Martinon, A. R. F.; Sawant, H. S.; Fernandes, F. C. R.; Stephany, S.; Preto, A. J.; Dobrowolski, K. M.

    2003-08-01

    A partir de 1998, entrou em operação regular no INPE, em São José dos Campos, o Brazilian Solar Spectroscope (BSS). O BSS é dedicado às observações de explosões solares decimétricas com alta resolução temporal e espectral, com a principal finalidade de investigar fenômenos associados com a liberação de energia dos "flares" solares. Entre os anos de 1999 e 2002, foram catalogadas, aproximadamente 340 explosões solares classificadas em 8 tipos distintos, de acordo com suas características morfológicas. Na análise detalhada de cada tipo, ou grupo, de explosões solares deve-se considerar a variação do fluxo do sol calmo ("background"), em função da freqüência e a variação temporal, além da complexidade das explosões e estruturas finas registradas superpostas ao fundo variável. Com o intuito de realizar tal análise foi desenvolvido o programa BSSData. Este programa, desenvolvido em linguagem C++, é constituído de várias ferramentas que auxiliam no tratamento e análise dos dados registrados pelo BSS. Neste trabalho iremos abordar as ferramentas referentes à filtragem do ruído de fundo. As rotinas do BSSData para filtragem de ruído foram testadas nos diversos grupos de explosões solares ("dots", "fibra", "lace", "patch", "spikes", "tipo III" e "zebra") alcançando um bom resultado na diminuição do ruído de fundo e obtendo, em conseqüência, dados onde o sinal torna-se mais homogêneo ressaltando as áreas onde existem explosões solares e tornando mais precisas as determinações dos parâmetros observacionais de cada explosão. Estes resultados serão apresentados e discutidos.

  15. Photoaddition of chlorpromazine to DNA.

    PubMed

    Kochevar, I E; Chung, F L; Jeffrey, A M

    1984-10-01

    Chlorpromazine, 2-chloro-N-(3-dimethylaminopropyl)phenothiazine (CPZ), is a frequently prescribed antipsychotic drug that causes cutaneous photosensitivity in man. CPZ is also phototoxic and photomutagenic in vitro. We have investigated the photoaddition of CPZ to DNA as a possible mechanism for these photobiologic effects. Prior to irradiation, CPZ binds non-covalently to double-stranded calf thymus DNA. At high nucleotide to CPZ ratios, the CPZ absorption maximum shifts from 305 nm to 340 nm with an isosbestic point at 323 nm and 90% of the CPZ fluorescence at 455 nm is quenched. The excitation and emission spectra for the unquenchable fluorescence are the same as those for unbound CPZ. The absorption and fluorescence spectra of unbound CPZ are restored at 0.1 mM magnesium acetate or 100 mM sodium acetate. Non-covalent binding of CPZ to heat-denatured DNA does not shift the CPZ absorption spectrum but quenches 65% of the CPZ fluorescence. Photolytic decomposition of CPZ was inhibited by binding to DNA. In the presence of high concentrations of double-stranded DNA or denatured DNA the photolysis rates were reduced by greater than 98% and 65%, respectively, compared to free CPZ. Formation of covalent photoadducts between CPZ and denatured DNA was 10-fold more efficient than photoadduct formation with double-stranded DNA. Approximately 10% of the CPZ which photodecomposed upon irradiation at 323 nm photoadded to denatured DNA. These results indicate that formation of a complex between CPZ and double-stranded DNA absorbing at 340 nm protects CPZ from photodecomposition and inhibits covalent photoadduct formation. PMID:6488389

  16. DNA Topology and the Initiation of Virus DNA Packaging

    PubMed Central

    Oh, Choon Seok; Sippy, Jean; Charbonneau, Bridget; Crow Hutchinson, Jennifer; Mejia-Romero, Olga Esther; Barton, Michael; Patel, Priyal; Sippy, Rachel; Feiss, Michael

    2016-01-01

    During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase’s small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in cosB, the recognition site. TerS binding to cosB positions TerL to cut the concatemeric DNA at the adjacent nicking site, cosN. TerL introduces staggered nicks in cosN, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the cosB-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead’s portal vertex and translocation ensues. DNA topology plays a role in the TerSλ-cosBλ interaction. Here we show that a site, I2, located between cosN and cosB, is critically important for an early DNA packaging step. I2 contains a complex static bend. I2 mutations block DNA packaging. I2 mutant DNA is cut by terminase at cosN in vitro, but in vivo, no cos cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by I2 mutations are presented. PMID:27144448

  17. DNA Topology and the Initiation of Virus DNA Packaging.

    PubMed

    Oh, Choon Seok; Sippy, Jean; Charbonneau, Bridget; Crow Hutchinson, Jennifer; Mejia-Romero, Olga Esther; Barton, Michael; Patel, Priyal; Sippy, Rachel; Feiss, Michael

    2016-01-01

    During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase's small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in cosB, the recognition site. TerS binding to cosB positions TerL to cut the concatemeric DNA at the adjacent nicking site, cosN. TerL introduces staggered nicks in cosN, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the cosB-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead's portal vertex and translocation ensues. DNA topology plays a role in the TerSλ-cosBλ interaction. Here we show that a site, I2, located between cosN and cosB, is critically important for an early DNA packaging step. I2 contains a complex static bend. I2 mutations block DNA packaging. I2 mutant DNA is cut by terminase at cosN in vitro, but in vivo, no cos cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by I2 mutations are presented. PMID:27144448

  18. School Budget Hold'em Facilitator's Guide

    ERIC Educational Resources Information Center

    Education Resource Strategies, 2012

    2012-01-01

    "School Budget Hold'em" is a game designed to help school districts rethink their budgeting process. It evolved out of Education Resource Strategies' (ERS) experience working with large urban districts around the country. "School Budget Hold'em" offers a completely new approach--one that can turn the budgeting process into a long-term visioning…

  19. View of Spacelab engineering Model (EM)

    NASA Technical Reports Server (NTRS)

    1981-01-01

    View of Spacelab engineering Model (EM) as it is being brought in the O and C bldg at Kenndey Space Center (27464); view of the EM as it is being offloaded from the C-54 aircraft. Kennedy Space Center alternative photo number is 108-KSC-80-OC-666 (27465); model taken out to launch pad (27466).

  20. EM international activities. February 1997 highlights

    SciTech Connect

    1997-02-01

    EM International Highlights is a brief summary of on-going international projects within the Department of Energy`s Office of Environmental Management (EM). This document contains sections on: Global Issues, activities in Western Europe, activities in central and Eastern Europe, activities in Russia, activities in Asia and the Pacific Rim, activities in South America, activities in North America, and International Organizations.