WorldWideScience

Sample records for biological systems mecanismos

  1. INDEPENDÊNCIA OU MORTE: A APOPTOSE COMO MECANISMO DE DEFESA

    OpenAIRE

    Gasques, Luciano Seraphim; Galvanini, Paulo Alexandre; Favaretto, Fernando; Santana, Tamara Francislaine; Pamphile, João Alencar

    2015-01-01

    Nas relações desarmônicas, os hospedeiros tendem a selecionar mutações que conferem resistência aos patógenos, enquanto estes selecionam as que neutralizam a resistência. Dessa forma, o processo evolutivo desencadeia nos mais diversificados mecanismos de defesa, entre eles, um mecanismo pouco explorado, à apoptose. Esta revisão teve como objetivo verificar os principais sistemas biológicos que apresentam a apoptose como mecanismo de defesa. Entre os principais sistemas estudados neste trabalh...

  2. Estudios de mecanismos de seguridad en redes inalámbricas de sensores

    OpenAIRE

    Chivite Fernández, Patricia

    2010-01-01

    Este proyecto fin de carrera va a consistir en el estudio de los mecanismos para proveer seguridad en redes de sensores inalámbricas. En concreto, sobre redes de sensores Crossbow imote2®. Los principales sistemas de seguridad manejan diferentes mecanismos de cifrado y autentificación, así como mecanismos de detección de intrusión. En este marco de trabajo, la gestión de claves de cifrado y firma digital, así como los algoritmos criptográficos, los protocolos de autenticación y los mecanismos...

  3. Mecanismos implicados en la escritura de palabras del castellano

    Directory of Open Access Journals (Sweden)

    Jesús ALEGRÍA IZCOA

    2015-03-01

    Full Text Available El artículo examina los mecanismos cognitivos implicados en la escritura de palabras en lengua castellana. Este tema ha sido ampliamente estudiado en sistemas ortográficos inconsistentes/profundos como el inglés y el francés, pero mucho menos en sistemas consistentes/superficiales como el del castellano. Los datos analizados sugieren que los dos mecanismos de escritura que constituyen la base modelo de la doble ruta: el fonológico y el ortográfico-lexical, intervienen en la escritura de palabras. En comparación con otras ortografías menos consistentes, la adquisición de estos dos mecanismos es más rápida en castellano. Este resultado es conforme a las predicciones del modelo de autoenseñanza. Complementariamente estudiamos otros dos mecanismos implicados en la escritura de palabras: uno ortográfico de carácter subléxico, basado en la frecuencia de regularidades ortográficas, y el otro basado en el conocimiento morfológico. Los datos a este respecto son escasos en castellano. No obstante, los resultados muestran que los aprendices adquieren rápidamente rutinas ortográficas basadas en regularidades ortográficas subléxicas, y que utilizan conocimientos morfológicos para escribir palabras. Esto muestra que ambos factores intervienen en la escritura en todos los sistemas ortográficos alfabéticos, sea cual fuere su grado de consistencia-profundidad. Las diferencias entre sistemas no parecen ser cualitativas sino cuantitativas. Además, todos los mecanismos examinados en castellano se adquieren más rápidamente que en los sistemas menos consistentes.

  4. SIMULACIÓN DE MECANISMOS COMPLEJOS DE REACCIÓN.

    Directory of Open Access Journals (Sweden)

    Daniel A Barragán R.

    2010-10-01

    Full Text Available Se propone un método para la interpretación de mecanismos complejos de reacción, el cual es aplicado a la simulación del mecanismo de Gyórgyi-Field, (GF desarrollado para la reacción química oscilante de Belousov-Zhabotinsky (BZ. El método basado en la ley de acción de masas y en el principio de independencia y coexistencia de los pasos elementales, reproduce el comportamiento oscilatorio en la concentración de los intermediarios de reacción.

  5. Streptococcus pneumoniae, mecanismos de resistencia antimicrobiana

    Directory of Open Access Journals (Sweden)

    Amauri Noda Albelo

    2011-09-01

    Full Text Available El Streptococcus pneumoniae, principal agente causal de la neumonía comunitaria, líder en la etiología de la otitis media y la meningitis, en las últimas 3 décadas ha incrementado, de manera importante, su resistencia a los agentes terapéuticos más utilizados, como los betalactámicos, macrólidos, azálidos y fluroquinolonas. La versatilidad adaptativa del microorganismo le ha permitido crear mecanismos capaces de sobreponerse a cualquiera de estas agresiones terapéuticas con un grado variable de eficacia. Se realiza una revisión de los mecanismos más importantes implicados en la adquisición de resistencia antimicrobiana por S. pneumoniae, y se precisan algunos de los factores de riesgo implicados en infección por S. pneumoniae resistente.

  6. El ombudsman, como mecanismo de autorregulación

    OpenAIRE

    Dr. Hugo Aznar

    1999-01-01

    Políticos, empresarios, periodistas y la sociedad en general, todos apelan a la autorregulación cuando se habla de la ética de los medios. Pero ¿qué es la autorregulación y qué mecanismos existen para ponerla en práctica? En 'Comunicación responsable. Deontología y autorregulación de los medios' (Barcelona, 1999) he estudiado todos los mecanismos de autorregulación que pueden aplicarse en los medios (códigos, estatutos de redacción, libros de estilo, consejos, etc.). De cada uno de ellos se a...

  7. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  8. Aspectos celulares novedosos en los mecanismos de embriogénesis

    Directory of Open Access Journals (Sweden)

    Sara Elena Panizo Bruzón

    2014-08-01

    Full Text Available La decodificación del genoma humano inició una nueva era en la investigación científica, sobre todo en aquellos campos que involucran eventos celulares y, por consiguiente, a los mecanismos morfogenéticos básicos. Por su importancia, se realiza una revisión bibliográfica, con el objetivo de actualizar en aspectos relacionados con los fundamentos de los mecanismos morfogenéticos básicos. Para la revisión se emplearon los recursos disponibles en la red Infomed, se consultaron las bases de datos Medline y PubMed. En el estudio se indica que los mecanismos morfogenéticos son eventos celulares o fenómenos biológicos, cuya investigación actual intenta explicar, desde un nivel celular, subcelular o molecular, por qué se desencadenan las transformaciones expuestas por la embriología. Se describen los mecanismos morfogenéticos, teniendo en cuenta los últimos conocimientos generados al respecto, evidenciándose que cuando existen deficiencias en ellos, aparecen los defectos en el desarrollo. Se hace referencia a investigaciones que utilizan estos conocimientos a nivel celular, para comprender la génesis de enfermedades y desarrollar novedosos tratamientos

  9. Mecanismos adaptativos do sistema imunológico em resposta ao treinamento físico Adaptative mechanisms of the immune system in response to physical training

    Directory of Open Access Journals (Sweden)

    Carol Góis Leandro

    2007-10-01

    Full Text Available O treinamento físico, de intensidade moderada, melhora os sistemas de defesa, enquanto que o treinamento intenso causa imunossupressão. Os mecanismos subjacentes estão associados à comunicação entre os sistemas nervoso, endócrino e imunológico, sugerindo vias autonômicas e modulação da resposta imune. Células do sistema imune, quando expostas a pequenas cargas de estresse, desenvolvem mecanismo de tolerância. Em muitos tecidos tem-se demonstrado que a resposta a situações agressivas parece ser atenuada pelo treinamento físico aplicado previamente, isto é, o treinamento induz tolerância para situações agressivas/estressantes. Nesta revisão são relatados estudos sugerindo os mecanismos adaptativos do sistema imunológico em resposta ao treinamento físico.Moderate physical training enhances the defense mechanisms, while intense physical training induces to immune suppression. The underlying mechanisms are associated with the link between nervous, endocrine, and immune systems. It suggests autonomic patterns and modulation of immune response. Immune cells, when exposed to regular bouts of stress, develop a mechanism of tolerance. In many tissues, it has been demonstrated that the response to aggressive conditions is attenuated by moderate physical training. Thus, training can induce tolerance to aggressive/stressful situations. In this review, studies suggesting the adaptation mechanisms of the immune system in response to physical training will be reported.

  10. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  11. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  12. Diseño del mecanismo actuador de un dedo robot antropomórfico

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    Edgar Portilla Flores

    2011-01-01

    Full Text Available Los mecanismos pueden ser utilizados en el diseño de dedos robóticos para obtener sistemas de accionamiento adecuado para el posterior agarre o manipulación de objetos. En este trabajo se implementa una metodología de diseño para el mecanismo actuador de un "dedo antropomórfi co" desarrollado previamente mediante herramientas computacionales (CAD en la Universidad Militar Nueva Granada, UMNG de Colombia. La metodología propuesta parte de la obtención de las relaciones matemáticas de los elementos que conforman el sistema actuador y su posterior síntesis dimensional, lo anterior llevando en consideración que el mecanismo cumpla con características antropométricas basadas en la mano humana, para esto son tomadas diez posiciones (suministradas del trabajo realizado en la UMNG obtenidas en simulación computacional. Se presentan los resultados obtenidos mediante simulación numérica para el mecanismo actuador así como el modelado en CAD de los mecanismos, para fi nalmente realizar una discusión de los resultados.

  13. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  14. Ação de herbicidas sobre mecanismos de defesa das plantas aos patógenos

    OpenAIRE

    Rizzardi Mauro Antônio; Fleck Nilson Gilberto; Agostinetto Dirceu; Balbinot Jr. Alvadi Antônio

    2003-01-01

    As plantas necessitam defender-se continuamente do ataque de agentes biológicos e de estresses do ambiente. A imobilidade e a falta de sistema imunológico, como ocorre em animais, fizeram com que as plantas desenvolvessem mecanismos de defesa, em que cada célula possui tanto capacidade de defesa induzida quanto pré-formada. No entanto, esses mecanismos podem ser influenciados pelo uso de herbicidas. A presente revisão objetivou apresentar os efeitos de herbicidas em mecanismos de defesa das p...

  15. Impacto de mecanismos de seguridad en sensores IEEE 802.15.4

    OpenAIRE

    Tripp Barba, Carolina; Casademont Serra, Jordi

    2009-01-01

    En la actualidad son muchos los mecanismos de seguridad que el estándar IEEE 802.15.4 permite a las redes inalámbricas de sensores [1] Dicho estándar define las especificaciones de la Capa de Acceso al Medio y la Capa Física de los dispositivos inalámbricos de área personal. La última revisión corresponde al 2006. Dichas revisiones y actualizaciones son hechas por el grupo de trabajo 802.15. Sin embargo estos mecanismos consumen recursos como memoria y batería, que son...

  16. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  17. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  18. El ombudsman, como mecanismo de autorregulación

    Directory of Open Access Journals (Sweden)

    Dr. Hugo Aznar

    1999-01-01

    Full Text Available Políticos, empresarios, periodistas y la sociedad en general, todos apelan a la autorregulación cuando se habla de la ética de los medios. Pero ¿qué es la autorregulación y qué mecanismos existen para ponerla en práctica? En 'Comunicación responsable. Deontología y autorregulación de los medios' (Barcelona, 1999 he estudiado todos los mecanismos de autorregulación que pueden aplicarse en los medios (códigos, estatutos de redacción, libros de estilo, consejos, etc.. De cada uno de ellos se aborda su historia, sus funciones, su alcance, etc. El texto que sigue recoge -con algunas modificaciones para acortar su extensión- el apartado del libro dedicado al ombudsman, en el que se discute su papel a la hora de promover la ética y la deontología periodística.

  19. From systems biology to systems biomedicine.

    Science.gov (United States)

    Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

    2012-08-01

    Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  1. Síntesis Genética de Mecanismos para Aplicaciones en Prótesis de Miembro Inferior

    OpenAIRE

    Merchán-Cruz, E.A.; Lugo-González, E.; Ramírez-Gordillo, J.; Rodríguez-Cañizo, R.G.; Sandoval-Pineda, J.; Hernández-Gómez, L.H.

    2011-01-01

    Resumen: La síntesis de mecanismos planos representa un problema atractivo para ser resuelto mediante técnicas de computación evolutiva, ya que plantea un sistema indeterminado de ecuaciones no lineales cuyo tamaño es directamente dependiente del número de puntos de precisión definidos para describir la trayectoria deseada del acoplador. Este artículo presenta la optimización en el proceso de síntesis de mecanismos basado en algoritmos genéticos (AG) para el caso de un mecanismo plano de seis...

  2. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  3. Racionalización y optimización de mecanismos del Grupo Roca

    OpenAIRE

    Fernández Pérez, Alberto

    2015-01-01

    Este proyecto pretende replantear la elección de proveedores de los mecanismos de alimentación y descarga instalados en las tazas de los inodoros en las empresas que forman parte del Grupo Roca. Actualmente cada empresa dentro del Grupo elige de manera autónoma el proveedor que cree más conveniente para estos productos, y esto ha llevado a la utilización de más de 15 proveedores diferentes de estos mecanismos. El objetivo es por tanto, reducir el número de proveedores y escoger...

  4. Síntesis Genética de Mecanismos para Aplicaciones en Prótesis de Miembro Inferior

    Directory of Open Access Journals (Sweden)

    E.A. Merchán-Cruz

    2011-04-01

    Full Text Available Resumen: La síntesis de mecanismos planos representa un problema atractivo para ser resuelto mediante técnicas de computación evolutiva, ya que plantea un sistema indeterminado de ecuaciones no lineales cuyo tamaño es directamente dependiente del número de puntos de precisión definidos para describir la trayectoria deseada del acoplador. Este artículo presenta la optimización en el proceso de síntesis de mecanismos basado en algoritmos genéticos (AG para el caso de un mecanismo plano de seis barras tipo Watt utilizado como base para el diseño de una prótesis policéntrica de rodilla. La trayectoria deseada a ser descrita por el acoplador corresponde a la descrita por la rodilla durante un ciclo normal de marcha. La metodología propuesta ilustra claramente como, por la aplicación de AG's, la trayectoria generada evoluciona de manera natural desde una solución errática hasta una curva que se ajusta suavemente a la trayectoria deseada. Palabras clave: Síntesis de Mecanismos, Algoritmos Genéticos, Computación Evolutiva, Mecanismos Planos, Prótesis, Miembro Inferior

  5. MECANISMOS DE INTERTEXTUALIDADE NA TEXTUALIZAÇÃO DO GÊNERO NOTÍCIA

    OpenAIRE

    Silva Soares, Valéria Crístian

    2015-01-01

    Este texto faz uma abordagem sobre o fenômeno da intertextualidade na textualização do gênero notícia, como ocorre o referido fenômeno e quais os mecanismos utilizados para um texto relacionar-se com outros textos, o que numa visão global define intertextualidade. Analisamos como as notícias utilizam-se do recurso da intertextualidade para sua textualização através de mecanismos como a citação, a alusão, a ironia, a paródia, dentre outros, essa estratégia parece-nos apresentar-se com objetivo...

  6. UN NUEVO MECANISMO DE DEFENSA DEL APARATO URINARIO.

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    Pablo Gómez Martinez

    1984-07-01

    Full Text Available

    Son muchos los trabajos publicados que explican la resistencia natural del aparato urinario a la infección y las maneras como se defiende. Basta citar unos cuantos para demostrar que ninguno de ellos es plenamente satisfactorio: la naturaleza del epitelio, la evacuación completa del sistema excretor, el factor intrínseco vesical, el lavado hacia el exterior (wash
    out de Hinman, los mucoproteídos, la resistencia del paciente, la virulencia del germen infectante, son mecanismos comúnmente citados como factores en contra del proceso infeccioso.

    Sin embargo, hay que tener en cuenta que la infección no se produce si el organismo es inmune a agentes microbianos, y que si se desarrolla, es porque este mecanismo humoral está disminuido o ausente o alterado, o porque otros, posiblemente existentes, no han sido capaces de vencer el ataque infeccioso al individuo.

    Una vez establecida la infección, los mismos agentes bacterianos obran como antígenos capaces de producir anticuerpos, es decir, de desencadenar el proceso inmunológico que permitirá al paciente salir airoso de la lucha, o modificar la evolución clínica de la
    enfermedad.

    Ya sea natural o adquirida, generala local, la inmunidad es la que en esencia y básicamente, juega un papel de primera magnitud en la defensa del aparato urinario.

    Mecanismo inmunológico local. Hasta hace poco tiempo, la inmunología se ocupaba principalmente de la respuesta serológica a la infección, tanto en el hombre como en los animales y trataba de producir su inmunidad administrando una gran variedad de antígenos
    cuya respuesta se mide por el título de los anticuerpos producidos en el suero, como prueba de la eficacia del proceso. Nadie puede negar que la vacunación ha sido uno de los grandes triunfos de la humanidad en su lucha contra las epidemias.

    Sin embargo, estudios más recientes han demostrado que, aunque puede existir una relaci

  7. Mecanismos articulados: Geometría Dinámica y Cinemática en un entorno educativo STEM

    Directory of Open Access Journals (Sweden)

    Fco. Javier Manzano Mozo

    2017-05-01

    Presentamos dos repositorios digitales de mecanismos articulados, la Kinematics Models For Design Digital Library y el Laboratorio delle Macchine Matematiche así como una revisión de propuestas didácticas del uso educativo de este tipo de mecanismos.

  8. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  9. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

  10. El maltrato infantil: mecanismos subyacentes

    Directory of Open Access Journals (Sweden)

    Gladys S. Martínez

    2009-10-01

    Full Text Available La exposición durante la infancia a estrés traumático, en la forma de abuso o negligencia, está asociada con una mayor vulnerabilidad, la cual resulta en el desarrollo de diversas psicopatologías, relación que ha sido confirmada una y otra vez en estudios epidemiológicos; sin embargo, aún se desconocen los mecanismos neurales que subyacen dichas alteracionesy solo recientemente se han empezado a estudiar los cambios neurobiológicos subyacentes en padres y madres maltratadores. En esta revisión se resumen investigaciones en que se ha abordado esta temática y se presentan algunos de los modelos animales usados para su estudio.

  11. As múltiplas sintaxes dos mecanismos de busca no ciberespaço Las múltiples sintaxis de los mecanismos de búsqueda en el ciberespacio

    Directory of Open Access Journals (Sweden)

    Silvana Drumond Monteiro

    2009-12-01

    Full Text Available No período pós-moderno as máquinas estão organizando o conhecimento por meio dos mecanismos de busca. Para discutir e conhecer melhor essa realidade, o artigo propõe uma tipologia para os mecanismos de busca, visando a ilustrar as múltiplas sintaxes de organização e busca do conhecimento e informação no ciberespaço. Dessa forma, apresenta as categorias de classificação: anatomia, que são os processos básicos de funcionamento desses buscadores, ou seja, crawling, indexing e searching; a forma geral de indexação ou organização, que são os diretórios, programas, metabuscadores e híbridos; a ordenação e apresentação dos resultados, que refletem as múltiplas sintaxes; e o paradigma semiótico, que ilustra a multiplicidade semiótica dos mecanismos de busca. A partir dessa tipologia, os buscadores são exemplificados e discutidos, abarcando esse cenário de múltiplas sintaxes de indexação e busca da informação e conhecimento no ciberespaço e ao mesmo tempo construindo uma ontologia desse objeto. O ciberespaço sempre terá e trará o problema da taxonomia do conhecimento e da multiplicidade dos signos, seja em sua representação ou organização.

  12. Systems biology: the reincarnation of systems theory applied in biology?

    Science.gov (United States)

    Wolkenhauer, O

    2001-09-01

    With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

  13. OS MECANISMOS DE DEFESA PRESENTES NA NEUROSE OBSESSIVA: UM OLHAR SOBRE A FORMAÇÃO SINTOMÁTICA.

    Directory of Open Access Journals (Sweden)

    Henrique Guilherme Scatolin

    2014-02-01

    Full Text Available Este artigo pretende enfocar os principais mecanismos de defesa presentes na neurose obsessiva, tais como o deslocamento, a formação reativa, o isolamento e a anulação. Para desenvolver tal discussão, parte de uma releitura das obras pré-psicanalíticas até Inibições, Sintomas e Ansiedade de 1926, enfocando nesta a compreensão freudiana da formação do sintoma obsessivo e dos seus principais mecanismos de defesa. Conclui que, para uma melhor compreensão da etiologia sintomática nesta neurose, é necessário analisar cada mecanismo em sua particularidade; já que este expressa a singularidade de cada sintoma em sua essência. Estes mecanismos de defesa podem ser considerados como uma máscara que encobrem o sintoma, mas ao encobrir, revelam todos os desejos recalcados, denotando a história singular de cada paciente.

  14. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  15. El problema de la especificidad del mecanismo de la psicosis

    OpenAIRE

    Moreno, María Luján; Kopelovich, Mercedes

    2015-01-01

    El objetivo del presente trabajo es seguir el derrotero freudiano relativo a la construcción conceptual acerca del mecanismo de las psicosis, ubicando sus hitos centrales y los obstáculos encontrados por el maestro a la hora de delimitar su especificidad.

  16. Mecanismos efectores del interferón gamma contra la infección por Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Jorge Enrique Gómez

    1999-12-01

    Full Text Available Toxoplasma gondiies un protozoario parásito de desarrollo intracelular. La enfermedad humana producida por T: gondii es una causa importante de morbilidad y mortalidad neonatal y en pacientes inmunodeprimidos. En esta reseña, se revisan los conocimientos actuales sobre los mecanismos efectores del interferón gamma (IFN y, la principal citocina protectora contra Igondii, incluyendo los resultados que hemos obtenido en un modelo de infección in vifro de células humanas monocitarias (THPI. El IFN y protege las células humanas contra T gondii por mecanismos diferentes a aquéllos con los que protege las células de ratón. En el modelo de infección de célulasTHP1, el IFN y protege por dos mecanismos independientes. Un primer efecto es la reducción del porcentaje de células parasitadas, el cual está ligado a una disminución de la actividad PLA, parasitaria y celular. Se trata de un nuevo mecanismo efector del IFN y contra la infección toxoplásmica, diferente a los mecanismos parasiticidas y parasitostáticos previamente descritos. Un segundo efecto ocurre por interrupción del crecimiento parasitario intracelular a través de la activación de la enzima indoleamina-oxigenasa que degrada el triptófano, lo que constituye un efecto parasitostático. Contrariamente a lo que ocurre en el modelo de infección de células monocitarias de ratón, la producción de óxido nítrico (NO no juega un papel determinante en los monocitos humanos.

  17. Los mecanismos de lo político en las redes sociales de Internet

    Directory of Open Access Journals (Sweden)

    Luis César Torres Nabel

    2013-07-01

    Full Text Available El artículo propone una serie de mecanismos sociales que operan en acontecimientos políticos en las redes sociales de Internet. Dichos mecanismos son: el contagio social, las cascadas de información y la información desregulada. Con estos elementos y valiéndose de un buen número de hechos contemporáneos que le han dando interés al fenómeno político de las redes sociales, se analiza el impacto de las mismas bajo parámetros claros que sirvan para dar explicaciones desde las ciencias sociales.

  18. Prevalencia de los mecanismos de adaptación del paciente con enfermedad renal bajo tratamiento de hemodiálisis

    Directory of Open Access Journals (Sweden)

    David Jahel García Avendaño

    2016-01-01

    Full Text Available Introducción: La enfermedad renal crónica es resultante de diversas enfermedades crónico degenerativas. El paciente con dicha enfermedad y sometido a hemodiálisis sufre muchos cambios en su estilo de vida. Es por ello que es importante evaluar la prevalencia de los mecanismos de adaptación en el paciente en los aspectos psicológico, afectivo y social. Objetivo: Identificar la prevalencia de los mecanismos adaptativos en el área de lo psicológico, afectivo y social que utiliza el paciente con insuficiencia renal crónica bajo tratamiento de hemodiálisis. Materiales y Métodos: Es un estudio descriptivo de tipo cuantitativo, se utilizó el cuestionario “Mecanismos de adaptación de los pacientes con enfermedad renal crónica en terapia de hemodiálisis”. Se realizó en el año 2010; y presentó un coeficiente del Alfa de Cronbach de 7.0, los datos se analizaron mediante estadística descriptiva. Resultados y Discusión: El estudio arrojó una prevalencia en los mecanismos afectivos, con un 71.4% en la adaptación comprometida; los mecanismos  sociales sobresalen con un 61.9% en la adaptación compensatoria; no evidenciando porcentajes favorables en los mecanismos psicológicos. Conclusiones: La mayoría de las personas con enfermedad renal bajo tratamiento de hemodiálisis, utilizan diferentes mecanismos de adaptación a su proceso lo cual depende completamente del ambiente en el que se desarrollan y el acompañamiento familiar que reciben. Cómo citar este artículo: García DJ, Ochoa MC, Martínez NE, Gonzáles B, Sánchez M, Martínez M. Prevalencia de los mecanismos de adaptación del paciente con enfermedad renal bajo tratamiento de hemodiálisis. Rev Cuid. 2016; 7(1: 1144-51. http://dx.doi.org/10.15649/cuidarte.v7i1.167

  19. La supervisión indirecta como mecanismo de control en las franquicias

    Directory of Open Access Journals (Sweden)

    Alberto Mirabal Martínez

    2010-10-01

    Full Text Available El propósito del presente trabajo es explicar la utilización de la supervisión indirecta como mecanismo de control usado por los franquiciadores para el aseguramiento de los estándares y la calidad de servicio en el formato de franquicias, y examinar su presencia bajo la teoría de agencia y costos de transacción. Se realizó una investigación de naturaleza cualitativa conformada por 10 estudios de casos de unidades franquiciadas de origen nacional y foráneo con presencia en Venezuela. Los resultados arrojados demostraron (a la preeminencia del contrato como base general de la existencia de los distintos mecanismos de control, (b la aplicación a partir del mismo, del uso de formas de control no necesariamente especificadas en el contrato, (c la similar percepción de efectividad por parte de los franquiciados en concordancia a los controles aplicados por la vía de la supervisión indirecta y (d la variabilidad percibida en relación con el agrado por parte de los franquiciados respecto al uso de uno u otro mecanismo presente por la vía de la supervisión indirecta.

  20. Diseño de mecanismos de palancas asistido por computadora. // Computer Aided Design of lever mechanisms.

    Directory of Open Access Journals (Sweden)

    J. L. Betancourt Herrera

    2001-07-01

    Full Text Available En la práctica del diseño industrial hay múltiples problemas que requieren de la creación de un mecanismo concaracterísticas de movimiento peculiares. La elección de un método que permita la síntesis estructural, el planteamiento ysolución de las ecuaciones correspondientes, requeridas para el análisis cinemático de los mecanismos de palancas, en unaforma clara y simple, es un problema muy complejo de resolver en sentido general.Tomando como referencia la teoría para la formación de los grupos de Assur, el autor desarrolló el método de los gruposestructurales y sobre esta base el software DSM (Diseño y Simulación de Mecanismos, que es la herramienta de cómputopropuesta para apoyar al diseñador en el proceso de Diseño Cualitativo de Mecanismos de Palancas Asistido porComputadora, que consiste en un proceso iterativo entre síntesis y análisis con el que se pueden obtener los resultados de lavariación de la estructura de un mecanismo y de sus parámetros fundamentales, prácticamente en tiempo real.En el presente trabajo se definen y ejemplifican los conceptos y elementos principales relacionados con el diseñocualitativo de mecanismos de palancas asistido por computadora.Palabras claves: CAD, mecanismos de palancas, diseño industrial, análisis cinemático, síntesis estructural.___________________________________________________________________________AbstractThere are series of problems in industrial design practice that require a mechanism with specific characteristic movement.Selecting a method for achieving a clear and simple structural synthesis and cinematic analysis of lever mechanisms isgenerally understood as a hard-solving problem. Based on Assur´s Group Forming Theory, the author developed theStructural Groups Method and the DSM software (Design and Simulation of Mechanisms. This software is a tool intendedto help designers in the process of Computer Assisted Qualitative Design of Lever Mechanisms. It consists

  1. Micro-separation toward systems biology.

    Science.gov (United States)

    Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

    2006-02-17

    Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

  2. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  3. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. El mecanismo COLLECTING para la comprensión del concepto de serie numérica

    OpenAIRE

    Delgado, Laura; González, María Teresa; Monterrubio, María Consuelo; Codes, Myriam

    2013-01-01

    En esta comunicación se utiliza el modelo de Pirie y Kieren para analizar el trabajo de una pareja de alumnos universitarios mientras resuelven una tarea en la que han de estudiar el carácter de dos series numéricas. Durante el proceso de solución, los alumnos recurren al mecanismo “collecting” como una forma de folding back para incorporar un conocimiento previo necesario. Este mecanismo se manifiesta en dos momentos a lo largo de la resolución de la tarea.

  5. Excited states in biological systems

    International Nuclear Information System (INIS)

    Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

    1979-01-01

    Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

  6. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  7. Solar tracking mechanism in two axes; Mecanismo de seguimiento solar en dos ejes

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez Benitez, Juan Rafael; Ramos Berumen, Carlos; Beltran Adan, Jose; Lagunas Mendoza, Javier [Instituto de Investigaciones Electricas, Cuernavaca, Morelos (Mexico)]. E-mail: jlagunas@iie.org.mx; rramirez@iie.org.mx; cramos@iie.org.mx

    2010-11-15

    The Instituto de Investigaciones Electricas (IIE) has been interested in the Parabolic Dish technology for electricity generation in Mexico, then through its Non Conventional Energy Department has dedicated special tasks concerning to the knowledge and development of such technology. The structural component, reflective surface support and the tracking system which allows concentrate the solar energy into the receiver have been designed and manufactured. For the mechanical device and control of the solar tracking have been projected a set with servomotors, an electronic control as well as an interface for the equipment configuration and follow-up. In order for getting the following of the apparent movement of the sun, information on the sun paths through the year was analyzed and in consequence elevation and azimuth angles were determined. Using that approaches, for fixing the sun position sensors are not used and then only the control algorithm and the electronic device developed at the IIE were implemented. In this paper the sun tracking system and the electronic control device are presented. [Spanish] La tecnologia de plato parabolico para la generacion de electricidad en Mexico, ha sido de gran interes para el Instituto de Investigaciones Electricas, por lo que a traves de la Gerencia de Energias No Convencionales se ha avocado a la tarea de conocer y desarrollar esta tecnologia. Se ha disenado y fabricado la parte estructural, la base de la superficie reflejante y el sistema de seguimiento que permite concentrar la energia solar en el receptor. Para el mecanismo y control del seguidor solar se ha propuesto un mecanismo que utiliza servomotores, un control electronico asi como una interfaz para configurar el equipo y monitorear sus variables. Para lograr el seguimiento del movimiento aparente del sol se analizo la informacion en literatura de las trayectorias del sol a lo largo del ano, logrando asi determinar los angulos de altitud y azimut para acotar el

  8. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  9. CONTABILIDADE APLICADA AO SETOR PÚBLICO COMO MECANISMO INSTITUCIONAL ESTATAL DE MELHORIA DA ACCOUNTABILITY

    Directory of Open Access Journals (Sweden)

    Antonio Firmino da Silva Neto

    2015-12-01

    Full Text Available A informação contábil é um instrumento que proporciona a accountability, que pode ser considerada a razão de ser da Contabilidade. Este ensaio objetiva discutir a Contabilidade Aplicada ao Setor Público como um mecanismo institucional estatal e não-institucional de melhoria de accountability. A metodologia utilizada nesta pesquisa foi a dedutiva com embasamento nos artigos 84 e 110 da Lei Federal no 4.320/1964, Lei de Direito Financeiro, e nas discussões sobre mecanismos de accountability apresentadas por Oakerson (1989, Paul (1992, O’Donnell (1998, 1999, Schedler (1999, Dunn (1999, Elster (1999, Keohane (2002, Mainwaring (2003, Abrucio e Loureiro (2004. As considerações deste estudo são no sentido de que a Contabilidade Aplicada ao Setor Público pode ser caracterizada, preferencialmente, como um mecanismo institucional estatal de accountability, cujo papel é monitorar, fiscalizar, controlar, e com prerrogativas de exigir responsabilização por partes dos agentes públicos, contudo, sem “poderes” de punição ou sanção, mas que pode de uma forma indireta exercer essa prerrogativa como pré-condição para a melhoria da accountability

  10. Deteriorating mechanisms of electric generators; Mecanismos de deterioro de generadores electricos

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Tevillo, Arturo; Reyes Martinez, Oscar Alfonso; Robles Pimentel, Edgar Guillermo; Esparza Saucedo, Marcos; Lopez Azamar, Jose Ernesto; Medina Flores, Alfredo; Uribe Martinez, Manuel O [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1999-12-31

    It is of the greatest importance to know the deteriorating mechanisms that an electric generator undergoes, in order to take corrective measures to stop the process in order to avoid catastrophic damages that imply non scheduled interruptions for maintenance, or inclusively, to carry on the overhaul. In this paper are discussed the deteriorating mechanisms that have been found in the stator (winding and core) and the rotor of thermoelectric and hydroelectric power stations by the natural aging process and abnormal operation. [Espanol] Es de suma importancia conocer los mecanismos de deterioro que sufre un generador, para tomar medidas correctivas que detengan el proceso, con el fin de evitar danos catastroficos que impliquen salidas no programadas para dar mantenimiento, o incluso, para efectuar la rehabilitacion. En este articulo se discuten los mecanismos de deterioro que se han encontrado en el estator (devanado y nucleo) y el rotor de generadores termicos e hidroelectricos por el proceso natural de envejecimiento y por operacion anormal.

  11. Deteriorating mechanisms of electric generators; Mecanismos de deterioro de generadores electricos

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Tevillo, Arturo; Reyes Martinez, Oscar Alfonso; Robles Pimentel, Edgar Guillermo; Esparza Saucedo, Marcos; Lopez Azamar, Jose Ernesto; Medina Flores, Alfredo; Uribe Martinez, Manuel O. [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1998-12-31

    It is of the greatest importance to know the deteriorating mechanisms that an electric generator undergoes, in order to take corrective measures to stop the process in order to avoid catastrophic damages that imply non scheduled interruptions for maintenance, or inclusively, to carry on the overhaul. In this paper are discussed the deteriorating mechanisms that have been found in the stator (winding and core) and the rotor of thermoelectric and hydroelectric power stations by the natural aging process and abnormal operation. [Espanol] Es de suma importancia conocer los mecanismos de deterioro que sufre un generador, para tomar medidas correctivas que detengan el proceso, con el fin de evitar danos catastroficos que impliquen salidas no programadas para dar mantenimiento, o incluso, para efectuar la rehabilitacion. En este articulo se discuten los mecanismos de deterioro que se han encontrado en el estator (devanado y nucleo) y el rotor de generadores termicos e hidroelectricos por el proceso natural de envejecimiento y por operacion anormal.

  12. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  13. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  14. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  15. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  16. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  17. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  18. Mecanismo antidiurético en Rhodnius Prolixus (Stal, 1859 (Hemiptera, Reduviidae

    Directory of Open Access Journals (Sweden)

    Ivonne Gómez

    1986-12-01

    Full Text Available Se propone para R. prolixus un mecanismo antidiurético, cuya actividad se pone de manifiesto una vez transcurrido el periodo diurético y se mantiene hasta que el insecto es alimentado nuevamente. Presumiblemente este mecanismo actua a nivel del esfinter rectal proximal y es inhibido por la ingesta, distención mecanica del buche y desinhibición central por decapitación. Se sugiere que la actividad antidiurética es mantenida por vía nerviosa y se modifica cuando hay distensión del buche o canudo es interrumpida la senãl nerviosa por decapitación. Se pone de manifiesto que la excreción de orina en R. prolixus no es controlada exclusivamente por la hormona diurética, sino que factores no ligados a la hemolinfa mantienen en estado diurético y no diurético a los insectos.An antidiuretic mechanism is proposed for Rhodnius prolixus, whose activity is manifested when the diuretic phase has terminated and is maintained until the insect has fed again. Presumably this mechanism acts at the level of the proximal rectal sphincter and is inhibited by ingestion, mechanical distension of the gut and central desinhibition by decapitation. It is suggested that the antidiuretic activity is maintained by the nervous system and is modified when there is distention of the gut or when the nervous signal is interrupted by decapitacion. It is demonstrated that the excretion of urine in R. prolixus is not controlled exclusively by the diuretic hormone, but rather that factors not linked to the haemolvmph maintain the insects in a diuretic or nondiuretic state.

  19. Associated mechanisms of aluminum tolerance in plants/ Mecanismos associados à tolerância ao alumínio em plantas

    Directory of Open Access Journals (Sweden)

    Cecília Estima Sacramento dos Reis

    2007-10-01

    Full Text Available Aluminum toxicity is one of the major limiting factor regarding plant development in acid soils. The use of liming for correcting soil pH is not viable for some of acid soil areas (technique or economic reasons, making the development of Al tolerant genotypes the best alternative. Thus, the tolerance mechanisms as well as the genetic basis of Al tolerance has deserved special attention in the scientific community. In the last years, a significant progress has been achieved towards these goals, as well as in developing cultivars adapted to acid soils. The Al tolerance mechanisms are divided basically in two classes: the exclusion mechanisms that act after absorption or blocking its entry in the root system and those involved in detoxification, complexing the Al in specific organelles, mainly in the vacuoles. In many species, physiological mechanisms have been reported as responsible for the activation of organic acids (mainly citrate and malate that act as Al quelating agents, however many process are not yet understood and cleared. Currently, the basis for the internal detoxification is becoming clear through organic acid complexes and there sequestering by the vacuoles. Other potential mechanisms are the target for discussions.A toxicidade do alumínio é um dos principais fatores limitantes do desenvolvimento das plantas em solos ácidos. Pelo fato da utilização de corretivos da acidez do solo não ser a estratégia mais viável em muitas situações com solos ácidos (por razões técnicas e econômicas, o desenvolvimento de genótipos tolerantes ao Al tem sido o caminho mais focado, assim a investigação dos mecanismos de tolerância bem como as bases genéticas da tolerância ao Al têm merecido atenção especial pela pesquisa científica. Nos últimos anos, foi gerado um significativo progresso no entendimento das bases dos mecanismos de tolerância ao Al, assim como no desenvolvimento de cultivares mais adaptados as condições de

  20. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  1. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  2. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  3. Heuristic Strategies in Systems Biology

    Directory of Open Access Journals (Sweden)

    Fridolin Gross

    2016-06-01

    Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

  4. Mecanismos de abertura do sulco e da adubação nitrogenada em arroz de terras altas

    Directory of Open Access Journals (Sweden)

    Vagner do Nascimento

    2013-12-01

    Full Text Available A cultura do arroz adapta-se pouco ao sistema plantio direto (SPD em razão da maior compactação da camada superficial do solo, devido ao intenso tráfego de máquinas e não mobilização do solo. Nesse caso, o mecanismo utilizado na semeadora para a abertura dos sulcos com a finalidade de deposição do adubo pode ter grande importância para facilitar a penetração das raízes e aumentar a porosidade do solo. Diante disso, propôs-se este estudo com o objetivo de avaliar o desenvolvimento e a produtividade do arroz de terras altas em sistema plantio direto, em razão de mecanismos de distribuição do adubo na semeadura e de doses de N em cobertura, em Selvíria, Mato Grosso do Sul. O delineamento experimental utilizado foi em blocos casualizados, utilizando-se um esquema fatorial 2 x 6, constituído por mecanismos de distribuição do adubo (haste escarificadora e disco duplo e de doses de N em cobertura (0, 25, 50, 75, 100 e 125 kg ha-1, com quatro repetições. Concluiu-se que os mecanismos de distribuição do fertilizante não interferiram na produtividade de grãos do arroz de terras altas; o mecanismo do tipo haste escarificadora promoveu maior altura de plantas e maior número de grãos cheios nos dois anos de cultivo; a aplicação de nitrogênio em cobertura interferiu em algumas características agronômicas, produtivas e em componentes de rendimento de engenho; a produtividade do arroz aumentou até a dose de 69 kg ha-1 de N, no primeiro ano de cultivo.

  5. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  6. Globalización capitalista: mecanismos de regulación económica y política

    Directory of Open Access Journals (Sweden)

    William Ortiz Jiménez

    2012-06-01

    Full Text Available En el artículo se hace un análisis teórico sobre los mecanismos que inciden en las elecciones de gobierno así como la acción colectiva en redes descentralizadas como vías a partir de las cuales los ciudadanos pueden regular las decisiones políticas y, por medio de estas, las decisiones económicas, en el marco de la globalización capitalista. Los mecanismos en torno a la primera vía son analizados con base en la teoría principal-agente, y los referidos a la segunda, a partir de la teoría de redes sociales. En ambos casos, la dificultad radica en la efectiva aplicación de los dispositivos para el logro de los fines propuestos. Sobre estos mecanismos es posible identificar algunas condiciones necesarias para que la acción política ciudadana adquiera efectividad y poder, las cuales están relacionadas con las nuevas dinámicas sociopolíticas

  7. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

  8. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  9. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  10. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  11. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  12. Evolução dos conceitos e mecanismos da percepção de esforço: uma revisão de literatura

    Directory of Open Access Journals (Sweden)

    Gleber Pereira

    2014-08-01

    Full Text Available http://dx.doi.org/10.5007/1980-0037.2014v16n5p579 Os mecanismos e conceitos da percepção de esforço têm mudado ao longo do tempo. Assim, este artigo de revisão de literatura tem por objetivos: i investigar as revisões de literatura publicadas a partir de 1982, descrevendo os mecanismos causais de geração da percepção de esforço relatados e; ii verificar se os conceitos da percepção de esforço acompanharam as mudanças que ocorreram acerca dos seus mecanismos causais. Foram realizadas buscas nas bases de dados PubMed, Science Direct e Scielo com os termos “rate perceivedexertionandreview” e “perceivedexertionandreview”. No total, foram incluídos 18 artigos, que tiveram como objetivo principal a percepção geral de esforço em exercício físico. Apesar da antiga existência da teoria do Disparo corolário para explicar os mecanismos causais da percepção de esforço, verifica-se que, após as proposições de Borg, a maior parte da literatura descreve a percepção de esforço através do mecanismo de Feedback aferente, baseada em estudos correlacionais. Apenas em 2009, a teoria original do Disparo corolário reaparece. Quanto aos conceitos, a maioria deles remete ao mecanismo de feedback aferente, utilizando-se de constructos como respostas fisiológicas, estresse, desconforto e dor, que são incongruentes com a teoria do Disparo corolário e apresentam mecanismos distintos aos da percepção de esforço. Portanto, verificou-se que os estudos de Borg influenciaram nos mecanismos e conceitos contemporâneos da percepção de esforço. Com o passar do tempo, houve incorporação de constructos no conceito original de Borg, porém, sempre embasado na teoria do Feedback aferente.

  13. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  14. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  15. OS MECANISMOS DE DEFESA PRESENTES NA NEUROSE OBSESSIVA: UM OLHAR SOBRE A FORMAÇÃO SINTOMÁTICA.

    OpenAIRE

    Henrique Guilherme Scatolin

    2014-01-01

    Este artigo pretende enfocar os principais mecanismos de defesa presentes na neurose obsessiva, tais como o deslocamento, a formação reativa, o isolamento e a anulação. Para desenvolver tal discussão, parte de uma releitura das obras pré-psicanalíticas até Inibições, Sintomas e Ansiedade de 1926, enfocando nesta a compreensão freudiana da formação do sintoma obsessivo e dos seus principais mecanismos de defesa. Conclui que, para uma melhor compreensão da etiologia sintomática nesta neu...

  16. UN MODELO DEL MECANISMO DE ENTRADA DE LOS ROTAVIRUS A LA CÉLULA HOSPEDERA

    Directory of Open Access Journals (Sweden)

    Orlando Acosta Losada

    2009-04-01

    Full Text Available Antecedentes. La infección rotaviral es causa principal de gastroenteritis aguda severa en niños menores de cinco años. La capa protéica externa de la partícula viral está implicada en las interacciones iniciales virus-superficie celular. El mecanismo rotaviral de unión y entrada a la célula parece ser un proceso de múltiples pasos donde las proteínas rotavirales VP4 y VP7 interaccionan con diferentes moléculas de la superficie celular. Objetivo. Proponer un mecanismo de entrada de rotavirus a la célula que incorpore la actividad de la proteína disulfuro isomerasa (PDI. Material y métodos. Utilizando bases de datos electrónicas, se realizó una búsqueda de literatura original y de revisión publicada entre 1990 y 2009 sobre moléculas de la superficie rotaviral o celular participantes en el proceso de entrada del virus. El análisis de los resultados enfatizó las bases moleculares y celulares de las interacciones temporo-espaciales de las proteínas virales y las moléculas de unión/receptoras de la célula. Resultados. Se encontró fundamentos moleculares y celulares para incorporar la actividad de PDI a un mecanismo coherente de vías secuenciales o alternativas previas a la penetración viral. Se propone un mecanismo en que interaccionan las proteínas virales VP4, VP6 y VP7 con las moléculas de la superficie celular ácido siálico, integrinas, Hsc70 y PDI en un proceso endocítico caveola/“raft”-dependiente, caveolina/clatrina-independiente, dinamina-dependiente y sensible a depleción de colesterol. Conclusión. Se amplía el concepto de múltiples pasos en el proceso de entrada de rotavirus, donde la participación de PDI podría ser un blanco potencial de la acción de inhibidores de grupos tiol/disulfuro.

  17. Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

    Science.gov (United States)

    Degrazio, Dominick

    Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

  18. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    Science.gov (United States)

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  19. Mapas de ruido: mecanismo de control del ruido ambiental

    OpenAIRE

    Chávez García, Kelvin

    2012-01-01

    Los primeros mecanismos de control del ruido ambiental fueron los mapas acústicos. La Directiva Europea 2002149/CE del Parlamento Europeo y del Consejo de Evatuacián y Gestión del Ruido Ambiental, exige, a los estados miembros,  se midan los niveles de ruido, en su entorno local, con  el fin de contar con indicadores de ruido comunes. elaborar mapas de ruido y planes de acción destinados a reducir los efectos nocivos de ruido ambiental.  Las directrices para la elaboración de l...

  20. La proyección como proceso y como mecanismo

    OpenAIRE

    Brusset, Bernard

    2001-01-01

    La proyección es a la vez un mecanismo elemental testimonio de la fragilidad de la organización defensiva y un proceso cuyo rol es fundamental en el funcionamiento psíquico. En este doble aspecto, la proyección guarda especificidades diferentes en la neurosis y en la psicosis al punto que se las deba considerar como fundamentalmente diferentes? O bien las diferencias de contexto, del nivel del funcionamiento psíquico, de lugar, de función pueden explicar las diferencias clínicas justificando ...

  1. Propiedades espaciales del mecanismo atencional inhibitorio

    Directory of Open Access Journals (Sweden)

    Alejandro Castillo

    2003-01-01

    Full Text Available En una serie de tres experimentos se estudia una posible especificidad espacial del mecanismo atencional inhibitorio. A través del paradigma de priming negativo se examina en concreto si existen diferencias entre estímulos distractores situados dentro del foco atencional del sujeto y otros situados en la periferia. Mediante la utilización de una letter-matching task similar a la que emplearon Nelly, Lissner y Beck (1990, se obtiene efecto de priming negativo sólo en aquellas letras distractores que se sitúan fuera del foco de atención del sujeto. Los resultados sugieren que el sistema inhibitorio que actúa a nivel de características físicas y espaciales no puede inhibir los estímulos situados dentro del foco, por lo cual todos ellos son forzosa-mente procesados a nivel semántico.

  2. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  3. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  4. LA EXCEPCIÓN PRELIMINAR: FALTA DE COMPETENCIA DE LA CORTE INTERAMERICANA ¿UN MECANISMO EFECTIVO DE DEFENSA ESTATAL?

    OpenAIRE

    Andrés González Serrano

    2011-01-01

    El presente artículo demostrará que la excepción preliminar "falta de competencia en razón a la materia", sí es un mecanismo de defensa estatal efectivo. Sin embargo, también se podrá evidenciar que este mecanismo se ha tornado ineficaz debido que los agentes estatales de los diferentes Estados Parte de la Convención, son quienes han restado importancia a la excepción, al interponerla de forma no adecuada ante la Corte Interamericana de Derechos Humanos.

  5. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  6. Agressividade na condução e mecanismos de defesa em condutores infractores : perspectiva psicodinâmica

    OpenAIRE

    Rosário, Luís Miguel Agulheiro Santos Bonsucesso do

    2009-01-01

    Tese de mestrado, Psicologia (Psicologia Clínica e da Saúde - Núcleo de Psicologia Clínica Dinâmica), Universidade de Lisboa, Faculdade de Psicologia e de Ciências da Educação, 2009 Esta investigação teve como objectivo estudar a comparação entre a agressividade na condução e os mecanismos de defesa em condutores infractores. Para tal, recorreu-se a uma medida de auto-relato da agressividade na condução (DDDI) e a um inventário de mecanismos de defesa com uma componente semi-projectiva (DM...

  7. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  8. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  9. Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

    Science.gov (United States)

    Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

    2018-05-09

    Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

  10. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  11. Mudança dos mecanismos de defesa e das características de personalidade no processo terapêutico

    OpenAIRE

    Loureiro, Diana de Paiva Silvano Calado

    2012-01-01

    Dissertação de Mestrado apresentada ao ISPA - Instituto Universitário, na especialidade de Psicologia Clínica Os mecanismos de defesa são um dos conceitos mais originais e uma das mais duráveis contribuições teóricas da psicanálise. O objetivo desta revisão de literatura consiste em aprofundar questões relacionadas com o desenvolvimento e evolução de conceções acerca do conceito, compreender funções relevantes dos mecanismos de defesa, e sobretudo fazer uma pesquisa acerca da i...

  12. LA EXCEPCIÓN PRELIMINAR: FALTA DE COMPETENCIA DE LA CORTE INTERAMERICANA ¿UN MECANISMO EFECTIVO DE DEFENSA ESTATAL?

    Directory of Open Access Journals (Sweden)

    Andrés González Serrano

    2011-01-01

    Full Text Available El presente artículo demostrará que la excepción preliminar "falta de competencia en razón a la materia", sí es un mecanismo de defensa estatal efectivo. Sin embargo, también se podrá evidenciar que este mecanismo se ha tornado ineficaz debido que los agentes estatales de los diferentes Estados Parte de la Convención, son quienes han restado importancia a la excepción, al interponerla de forma no adecuada ante la Corte Interamericana de Derechos Humanos.

  13. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  14. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  15. O funcionamento de mecanismos coesivos na argumentação

    Directory of Open Access Journals (Sweden)

    Barbisan, Leci Borges

    2001-01-01

    Full Text Available Estuda-se neste trabalho o funcionamento de dois mecanismos coesivos no texto argumentativo: a elipse e a anáfora conceitual. Parte-se da hipótese de que ambos desempenham papel no processo argumentativo. Para as análises, utilizam-se conceitos da teoria da argumentação na língua, propostos por Jean-Claude Anscombre e Oswald Ducrot, em sua primeira versão, e Marion Carel e Oswald Ducrot, em seu segundo momento

  16. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

    of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

  17. A system for success: BMC Systems Biology, a new open access journal.

    Science.gov (United States)

    Hodgkinson, Matt J; Webb, Penelope A

    2007-09-04

    BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  18. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  19. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  20. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  1. Answering biological questions: Querying a systems biology database for nutrigenomics

    NARCIS (Netherlands)

    Evelo, C.T.; Bochove, K. van; Saito, J.T.

    2011-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

  2. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    Science.gov (United States)

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  3. Mecanismos de corrosión e inhibición electroquímica del acero galvanorrecocido

    Directory of Open Access Journals (Sweden)

    Arenas, M. A.

    2006-06-01

    Full Text Available The corrosion mechanism of galvannealed in 0,6 M NaCl has been evaluated by means of electrochemical impedance spectroscopy (EIS. After 48 hours and for longer immersion time, up to 1 month, in sodium chloride, the system is controlled by a diffusion process at finite layer. Moreover, the effectiveness of cerium salts as inhibitor added in the electrolyte has been studied. Inhibition percentages of about 85% for 500 and 1000 ppm at 24 hours have been found. On the hand, changes in the corrosion mechanism due to the cerium presence were shown.

    Se ha estudiado el mecanismo de corrosión de un acero galvanorrecocido, en 0,6 M de cloruro sódico, mediante espectroscopia de impedancia electroquímica. Los resultados revelan que el sistema, para tiempos mayores de 48 h de inmersión y hasta 1 mes en NaCl, está controlado por un proceso de difusión en capa finita. A su vez, se ha estudiado la efectividad de sales de cerio como inhibidor añadido en el medio agresivo, obteniéndose porcentajes de inhibición del 85% para concentraciones de 500 y 1.000 ppm a las 24 h de exposición. Además, los espectros de impedancia electroquímica revelan un cambio en el mecanismo de corrosión del galvanorrecocido por la adición del cerio en el medio.

  4. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  5. Creación de marca mediante la utilización de mecanismos estratégicos comunitarios y marketing

    OpenAIRE

    Melo Lopez, Paula Daniela; Fajardo Carrillo, María Alejandra

    2016-01-01

    El presente documento pretende mostrar la manera como se debe ejecutar la creación de marca mediante la utilización de mecanismos estratégicos comunitarios y marketing. El objetivo del estudio se basa en encontrar los mecanismos adecuados para el desarrollo y creación de una marca enfocándose en el análisis de las principales prácticas y modelos desarrollados en el área del marketing, examinando el impacto que la marca pueda generar en la comunidad en la cual la organización está incluida, es...

  6. Mecanismos de busca acadêmica: uma análise quantitativa

    Directory of Open Access Journals (Sweden)

    Diego Buchinger

    2014-04-01

    Full Text Available Os mecanismos de busca consolidaram a pesquisa por informação na internet,sendo os mecanismos de busca acadêmicos (MBAs, hoje, os principais meios para alcançar fontes científicas, como artigos de eventos ou periódicos. Ao invés de gastar horas em uma biblioteca, os MBAs ganham em popularidade pela facilidade de automatizar uma busca e acessar inúmeras bases de dados simultaneamente. Contudo, o caráter incremental das bases de materiais científicos e dos diversos MBAs existentes impõe um desafio aos pesquisadores, que é determinar um MBA que melhor atenda aos seus anseios de pesquisa. Nesse contexto, uma análise quantitativa dos recursos providos pelos MBAs foi realizada com objetivo de determinar quais são os melhores para facilitar as buscas por conteúdo científico, considerando recursos de busca, de refinamento e auxiliares. Dentre um grupo de 40 MBAs iniciais, sete apresentaram-se com σ = 0,5 acima da média nos critérios utilizados, na seguinte ordem: 1o Web of Knowledge; 2o Engineering Village; 3o Scopus SciVerse; 4o IEEE Xplore; 5o ACM Digital Library; 6o Science Direct; e 7o Springer Link. Esses MBAs deveriam ser melhor explorados pelos pesquisadores pois tem inúmeros recursos capazes de facilitar sobremaneira e elevar a qualidade do trabalho de pesquisa.

  7. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  8. Ação de herbicidas sobre mecanismos de defesa das plantas aos patógenos

    Directory of Open Access Journals (Sweden)

    Rizzardi Mauro Antônio

    2003-01-01

    Full Text Available As plantas necessitam defender-se continuamente do ataque de agentes biológicos e de estresses do ambiente. A imobilidade e a falta de sistema imunológico, como ocorre em animais, fizeram com que as plantas desenvolvessem mecanismos de defesa, em que cada célula possui tanto capacidade de defesa induzida quanto pré-formada. No entanto, esses mecanismos podem ser influenciados pelo uso de herbicidas. A presente revisão objetivou apresentar os efeitos de herbicidas em mecanismos de defesa das plantas contra patógenos, bem como analisar as possíveis conseqüências desse conhecimento no manejo de plantas daninhas e de culturas. Alguns herbicidas influenciam a severidade de doenças, induzindo ou inibindo a síntese de fitoalexinas. Herbicidas do grupo químico difeniléteres geram espécies reativas de oxigênio, as quais mediam a ativação de genes de defesa responsáveis pela síntese de fitoalexinas e também por reação de hipersensibilidade. O uso de subdoses de glyphosate ocasiona efeito contrário, diminuindo a produção de fitoalexinas e aumentando a severidade de doenças. A constatação desses efeitos requer a adoção de estratégias de manejo que minimizem seus impactos negativos ou que se beneficiem desses efeitos, como pode ocorrer quando do uso de bioherbicidas.

  9. El cerebro y las drogas, sus mecanismos neurobiológicos

    OpenAIRE

    Méndez Díaz, Mónica; Ruiz Contreras, Alejandra E.; Prieto Gómez, Berta; Romano, Antonio; Caynas, Seraid; Prospéro García, Oscar

    2010-01-01

    La definición de adicción propuesta por la Organización Mundial de la Salud, dicha de manera sucinta, indica que es una enfermedad cerebral que provoca una búsqueda compulsiva de la droga y su uso, a pesar de las consecuencias adversas que ésta provoque. La fisiopatología de la enfermedad sugiere una interacción entre mecanismos cerebrales, cambios genéticos y medio ambiente. El objetivo de este artículo es discutir la evidencia que existe sobre los sistemas cerebrales que son afectados por l...

  10. Taller: mecanismos de reuso en OO : Arquitectura, patrones y frameworks

    OpenAIRE

    Urciuolo, Adriana Beatriz; Sandoval, Sandra

    2002-01-01

    En el presente trabajo se describe la experiencia de dictado de un taller sobre mecanismos orientados a objetos para diseño de software reusable, dirigido a alumnos de la carrera Licenciatura en Informática (U.N.P.S.J.B. – Sede Ushuaia); el mismo ha sido implementado en forma preliminar, durante el presente ciclo lectivo, dada la necesidad de incorporar conceptos avanzados de diseño orientado a objetos, que permitan una mejor comprensión de las ventajas del paradigma. No siendo posible alcanz...

  11. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  12. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  13. Los mecanismos de la democracia directa: Argumentos a favor y en contra desde la teoría de la democracia

    Directory of Open Access Journals (Sweden)

    Patricia Marenghi

    2007-07-01

    Full Text Available La ponencia presenta una diversidad de afirmaciones que definen diferentes concepciones de la democracia y que, según se interpreten, respaldan afirmativa o negativamente la implementación de mecanismos de democracia directa o participativa. Se acentúan algunos de los argumentos teóricos que subyacen a la utilización de estos mecanismos y que llevan a sus detractores a afirmar que –y a sus partidarios a contradecir que- : a los representantes tienen más conocimientos sobre las consecuencias de las decisiones políticas; b el ciudadano común no puede tomar decisiones informadas (incluso racionales sobre problemas extremadamente complejos; c el participante del mecanismo de democracia directa actúa aisladamente, sin discusión, lo que niega la posibilidad de hacer concesiones o de cambiar de postura en el debate, y por lo tanto, la deliberación de los representantes lleva siempre a resultados mejores basados en el intercambio y la revisión de los argumentos.

  14. Los mecanismos autónomos de resolución extrajudicial de conflictos colectivos laborales: el caso español y apuntes sobre la legislación colombiana

    Directory of Open Access Journals (Sweden)

    Pierre-Henri Cialti

    2016-01-01

    Full Text Available El ámbito laboral es, sin lugar a dudas, un foco de conflictos, ya que las relaciones empleadores - trabajadores presentan genéticamente un antagonismo de intereses y un conflicto latente. Esta singularidad obliga a contemplar e inventar mecanismos capaces de regular de forma adecuada este conflicto inherente y consustancial al mundo laboral. Pues bien, el ordenamiento jurídico español no ha dejado de fomentar la utilización de mecanismos extrajudiciales de resolución de conflictos, especialmente en materia laboral. Ciertamente, dichos mecanismos favorecen la paz laboral y, de forma indirecta, refuerzan la productividad de las empresas y el aparato productivo nacional. La singularidad en la materia reside en el hecho de que la ley remite a la negociación colectiva el fomento de estos mecanismos extrajudiciales y los apoya materialmente. Estos mecanismos denominados “autónomos”, que se utilizan esencialmente en la resolución de conflictos colectivos, centrarán nuestro propósito. Así, abordaremos en primer lugar los fundamentos constitucional, legal y convencional de estos mecanismos. En segundo lugar analizaremos su funcionamiento y su puesta en marcha mediante los procesos de mediación, conciliación y arbitraje. Destacaremos una tendencia preocupante según la cual las últimas reformas legales intervenidas en España tratan de menoscabar estos mecanismos en beneficio del aumento de los poderes del empresario. Finalmente, se hacen algunos apuntes respecto al derecho colombiano, que presenta sustanciales diferencias, especialmente el amplio marco de actuación del arbitraje obligatorio, que se explican por un contexto histórico y social muy distintos.

  15. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  16. Mecanismo de ação dos anestésicos inalatórios

    Directory of Open Access Journals (Sweden)

    Renato Ângelo Saraiva

    2002-02-01

    Full Text Available JUSTIFICATIVA E OBJETIVOS: Estudos clínicos e experimentais têm sido desenvolvidos para identificar os locais onde os anestésicos (inalatórios atuam e para determinar quais as alterações funcionais que esses fármacos produzem nas estruturas do sistema nervoso central determinantes do estado de anestesia que é observado clinicamente. O objetivo deste trabalho é descrever os resultados obtidos por vários autores em estudos clínicos e experimentais realizados recentemente na tentativa de esclarecer os mecanismos de ação dos anestésicos inalatórios no sistema nervoso central. CONTEÚDO: Para facilitar a compreensão dos complexos mecanismos de ação dos anestésicos inalatórios no sistema nervoso central, eles foram divididos em três níveis: o macroscópico, o microscópico e o molecular. Recentemente um grupo de autores descreveram estes mecanismos de ação em: orgânicos, celulares, e inibidores da entropia. Estes mecanismos tentariam explicar o estado de anestesia que teria como característica a capacidade de prover ao paciente duas ações principais: 1 imobilidade, inibição da resposta a estímulos nociceptivos; e 2 amnésia. Outros efeitos (desejáveis também são obtidos pela administração de anestésicos: analgesia e hipnose. Entretanto, tais efeitos seja isoladamente ou juntos, não definem o estado de anestesia. Embasados nestes conceitos, este grupo adota e divulga a classificação dos anestésicos em: 1 anestésicos completos, os que produzem imobilidade e amnésia; e 2 incompletos ou não imobilizantes, os que não produzem imobilidade mas produzem amnésia. CONCLUSÕES: De acordo com os resultados de vários estudos realizados recentemente, provavelmente a amnésia e a inconsciência ocorrem pela ação do anestésico predominantemente no cérebro, enquanto a imobilidade, ou seja, a inibição da resposta ao estímulo nociceptivo por movimento, seria pela ação do anestésico preferencialmente e inicialmente

  17. Mecanismos de control en la ciudad de Osorno en el contexto de dictadura militar 1973 - 1990

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Sepúlveda Chávez

    2014-12-01

    Full Text Available El siguiente trabajo tiene como objetivo describir los mecanismos de poder y control utilizados en la ciudad de Osorno bajo en el período de Dictadura Militar.  El Golpe Militar del 11 de septiembre de 1973 y la instauración de una dictadura de diecisiete años en Chile, fue un hecho que marcó a la sociedad chilena en general.  Durante el tiempo que duró, se intentó omitir los violentos actos ejecutados contra todos los contrarios al régimen militar.  Sistemáticas violaciones a los Derechos Humanos, segregación, desigualdad social, instauración del sistema neoliberal, entre otras, son solo algunas de sus principales secuelas, que fueron respaldadas por los variados mecanismos de control utilizados por el Estado chileno.

  18. POSIBLES MECANISMOS DE ACCIÓN BIOLÓGICA DE LA ACTIVIDAD FÍSICA EN EL CÁNCER DE MAMA

    OpenAIRE

    Jairo Alejandro Fernández Ortega; José Antonio de Paz Fernández

    2014-01-01

    La evidencia científica ha demostrado la importancia de la actividad física como una estrategia efectiva para disminuir el riesgo y la recidiva del cáncer de mama. Sin embargo, hasta el momento no se conocen con precisión los mecanismos de acción biológicos del ejercicio sobre el cáncer de mama. El propósito de este artículo es realizar una revisión sistemática exhaustiva de la literatura e identificar las posibles hipótesis que se plantean de los mecanismos de acción biológicos del ejercicio...

  19. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

    With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

  20. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  1. MECANISMOS UTILIZADOS PARA MONITOREAR EL PODER DE MERCADO EN MERCADOS ELÉCTRICOS: REFLEXIONES PARA COLOMBIA

    Directory of Open Access Journals (Sweden)

    Jesús Alonso Botero

    2013-12-01

    Full Text Available El propósito de este trabajo es analizar la viabilidad de la utilización del índice de oferta residual (IOR en el mercado eléctrico mayorista en Colombia, con el fin de promover la competencia. Esto se hace a partir de la revisión de la literatura relacionada con las experiencias internacionales respecto a los mecanismos para monitorear el poder de mercado y del análisis del Documento 118 de la Comisión de Regulación de Energía y Gas (CREG, 2010. La principal conclusión es que el IOR no es un buen mecanismo de control en mercados hidráulicos, mientras que el desarrollo de los mercados de largo plazo ha sido utilizado con gran éxito para mitigar el riesgo de abuso de poder de mercado, seg°n lo muestra la experiencia internacional.

  2. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  3. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

  4. Mecanismos moleculares por los cuales los ácidos grasos podrían influir en la captación de glucosa

    Directory of Open Access Journals (Sweden)

    Clara Eugenia Pérez

    2005-04-01

    Full Text Available Esta revisión tiene el propósito de actualizar el probable mecanismo molecular que ejercen los ácidos grasos en las células que captan glucosa, bajo el estimulo de la insulina y su posible implicación en la diabetes mellitus tipo 2 en la que suelen asociarse resistencia a la insulina, obesidad y síndrome metabólico. Entre los mecanismos moleculares por los cuales un aumento de los ácidos grasos libres podría producir resistencia a la insulina, se encuentra la disminución de los niveles de xilulosa 5-fosfato que bloquea la glucólisis por inhibición de la fosfofructocinasa, ello conduce a un aumento de los productos finales en la vía de las hexosaminas y a la activación de la proteincinasa C, un conocido activador de inhibidor de la cinasa Kappa Beta que inhibe la fosforilación del receptor del sustrato de insulina en tirosina, bloqueando los transportadores de glucosa. Existen investigaciones que sugieren que los ácidos grasos libres están implicados en la insulino-resistencia pero el mecanismo bioquímico no esta dilucidado del todo, pues no hay un mecanismo integral que los relacione o interconecte para concluir determinantemente cómo los altos niveles de ácidos grasos libres inducen la resistencia a la insulina.

  5. Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

    Science.gov (United States)

    Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

    2017-07-05

    Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  7. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. On the interplay between mathematics and biology: hallmarks toward a new systems biology.

    Science.gov (United States)

    Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

    2015-03-01

    This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  10. Systems Biology — the Broader Perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Bard

    2013-06-01

    Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

  11. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

  12. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  13. Mecanismos de transmisión de la política monetaria.

    OpenAIRE

    Chuecos, Alicia E.

    2006-01-01

    SUMARIO Editorial Peña, Aura Elena Artículos La calidad en la microempresa merideña y su impacto en el ambiente. Bustos F, Carlos E. Mecanismos de transmisión de la política monetaria. Chuecos, Alicia Contabilidad de Costos: una evaluación a la cátedra. Molina, Olga Rosa Las normas internacionales de contabilidad. Monge, Pedro Análisis de la cadena de valor industrial y de la cadena de valor agregado para las pequeñas y medianas indust...

  14. Optoelectronic system and apparatus for connection to biological systems

    Science.gov (United States)

    Okandan, Murat; Nielson, Gregory N.

    2018-03-06

    The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

  15. A review of imaging techniques for systems biology

    Directory of Open Access Journals (Sweden)

    Po Ming J

    2008-08-01

    Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

  16. Electron and Proton Transfer by the Grotthuss Mechanism in Aqueous Solution and in Biological Systems; Transfert d'Electrons et de Protons par le Mecanisme de Grotthuss en Solution Aqueuse et dans les Systemes Biologiques; Perenos ehlektronov i protonov mekhanizmom grotkhusa v vodnom rastvore i v biologicheskikh sistemakh; Transferencia Electronica y Protonica por el Mecanismo de Grotthuss en Soluciones Acuosas y en Sistemas Biologicos

    Energy Technology Data Exchange (ETDEWEB)

    Horne, R. A.; Courant, R. A.; Johnson, D. S. [Arthur D. Little, Inc. Cambridge, MA (United States)

    1965-10-15

    TheFe{sup ll}-Fe{sup III} electron-exchange reaction and certain long-range biological redox reactions involve the transfer of electrons by a Grotthuss-type mechanism over water bridges. The Grotthuss mechanism is also responsible for the anomalously great electrical conductivity of acidic aqueous solutions. At ordinary pressures the rate-determining step of the Grotthuss mechanism is the rotation of H{sub 2}O, or possibly H{sub 3}O+, and not the actual proton flip itself. The Grotthuss mechanism is confined to the ''free'' rotatable monomeric water between the Frank-Wen clusters in liquid water and avoids areas of relative order. The concentration dependence of protonic conduction can be represented by an equation based upon a cube root of concentration extrapolation and containing Arrhenius terms in which the activation energies are those for the rotation of and the formation of ''holes'' in the solvent water. Thus chemical energy and/or electrical energy can be transmitted rapidly over relatively great distances by the Grotthuss mechanism. Such processes are involved in a variety of phenomena of biological significance, examples being muscular contraction and the chemistry of the respiratory pigments. (author) [French] L'echange d'electrons dans Fe{sup II}-Fe{sup III} et certaines reactions biologiques d'oxydo-reduction a long terme font intervenir le transfert d'electrons par un mecanisme du type de Grotthuss sur des ponts d'eau. Le mecanisme de Grotthuss explique egalement la conductivite anormalement grande des solutions aqueuses d'acides. Sous les pressions ordinaires, l'etape du mecanisme de Grotthuss qui determine la vitesse est la rotation de H{sub 2}O ou peut-etre de H{sub 3}O+, et non pas le changement d'orientation du proton meme. Le mecanisme de Grotthuss est limite a l'eau monomerique ' libre ' , susceptible de rotation, entre les amas de Frank-Wen dans l'eau liquide et il evite les zones d'ordre relatif. On peut representer les variations de la

  17. A system for success: BMC Systems Biology, a new open access journal

    OpenAIRE

    Webb Penelope A; Hodgkinson Matt J

    2007-01-01

    Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  18. Systems biology of neutrophil differentiation and immune response

    DEFF Research Database (Denmark)

    Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

    2005-01-01

    Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

  19. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  20. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    Science.gov (United States)

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  2. BetaWB - A language for modular representation of biological systems

    DEFF Research Database (Denmark)

    Ihekwaba, Adoha; Larcher, Roberto; Mardare, Radu Iulian

    2007-01-01

    A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007......A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007...

  3. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

  4. 3S - Systematic, systemic, and systems biology and toxicology.

    Science.gov (United States)

    Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

    2018-01-01

    A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

  5. A dedicated database system for handling multi-level data in systems biology.

    Science.gov (United States)

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

  6. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

  7. Mecanismos de resistencia a Metales tóxicos (CD bajo variaciones abióticas en Microalgas

    Directory of Open Access Journals (Sweden)

    Alondra A. Cortés Téllez

    2018-01-01

    Full Text Available En los ecosistemas acuáticos, la presencia de ciertos metales (Cu, Zn, Fe a concentraciones traza son esencialespara distintas actividades biológicas. Sin embargo, otros metales como el Cd y Pb son considerados tóxicos aconcentraciones muy bajas y no participan como micronutrientes. Estos metales interactúan con componentesesenciales a través de enlaces iónicos y covalentes induciendoestrés oxidativo, reemplazo de cationes esenciales,etc. Asimismo, presentan la capacidad de acumularse y biomagnificarse a lo largo de la cadena trófica, promoviendoalta sensibilidad en la mayoría de los organismos acuáticos, mientras que otros como las microalgas, han desarrolladouna gran variedad de estrategias de detoxificación para minimizar los efectos tóxicos de losmetales a través de lainducción de mecanismos de adaptación y resistencia que les permiten la supervivencia a esos ambientes extremos.Por ende, es indispensable conocer la gama de mecanismos de resistencia que estos organismos presentan a laexposición de metales tóxicos presentes en el ecosistema acuático. Así, los objetivos de esta revisión son: identificary describir los principales mecanismos moleculares actualmente descritos en microalgas verdes implicados en laresistencia a metales tóxicos en relación específica con el cadmio; dar a conocer la influencia de distintos factoresambientales sobre esta respuesta y los episodios de corresistencia hacia otros metales de carácter tóxico.

  8. A globalização vista do norte e do sul: quais os seus mecanismos sociais?

    Directory of Open Access Journals (Sweden)

    Olivier Giraud

    Full Text Available Procura-se, neste artigo, definir a globalização a partir da identificação de uma série de mecanismos sociais por meio dos quais essa age diretamente sobre os comportamentos individuais e coletivos ou ainda sobre a maneira de pensar, as crenças, as identidades, as formas de institu-cionalização, etc. O que constitui a especificidade da globalização é justamente o fato de ser um fenômeno social que se manifesta em todo o planeta. Será que os mecanismos específicos que caracterizam o funcionamento da globalização são aplicáveis nas mesmas condições nas sociedades que apresentam fortes diferenças como é o caso das sociedades do Norte e do Sul? Diferentes mecanismos ligados ao reforço da competição econômica internacional e às suas conseqüências sobre o sistema de proteção social, ou ainda ligados à difusão de normas e de práticas políticas no contexto da globalização, serão abordados em seguida. De forma mais sistemática, quatro cenários convergência, divergência, hibridação e recomposição das hierarquias internacionais serão apresentados no contexto de uma análise comparativa dos efeitos da globalização nas sociedades do Sul e do Norte.

  9. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  10. Prototype of a control board solar tracking mechanism on a shaft; Prototipo de una tarjeta de control del mecanismo de seguimiento solar en un eje

    Energy Technology Data Exchange (ETDEWEB)

    Ramos Berumen, Carlos; Ramirez Benitez, Juan Rafael; Lopez Perez, Manuel de Jesus; Beltran Adan, Jose; Lagunas Mendoza, Javier [Instituto de Investigaciones Electricas, Cuernavaca, Morelos (Mexico)

    2010-11-15

    A solar concentrator prototype of Parabolic Trough (PT) for solar process heat generation has been designed, manufactured and put into operation by the Instituto de Investigaciones Electricas. By means of a sun tracking mechanism controlled by an automatic device, the PT is moving from East to West during the day then this way the solar energy is focused continually over the lineal receiver. Such movement is reached thanks to the electronic module fitted with special software. In this paper, the design of an electronic module based on calculation algorithm of the sun position along the day and over the year which controls the PT sun tracking is presented. The main purpose of the development is to integrate a control system which is using the algorithm of low cost (it was tested in a commercial system with success). [Spanish] El Instituto de Investigaciones Electricas (IIE) ha disenado, fabricado y puesto en operacion un prototipo de concentrador solar de canal parabolico para la generacion de calor de proceso. La tecnologia termosolar a concentracion de canal parabolica mantiene el concentrador moviendose de este a oeste durante el dia, enfocando continuamente el sol en el receptor lineal, mediante un mecanismo y un control automatico que permite el seguimiento aparente del sol. Se ha desarrollado el software para el control del mecanismo de seguimiento solar. En este articulo se presenta el diseno de un modulo electronico que controla el mecanismo de seguimiento solar de un canal parabolico, el cual tiene sus bases en un algoritmo que calcula la posicion del sol durante todo el dia y a lo largo del ano. El proposito principal es integrar un sistema de control de bajo costo, que utilice el algoritmo desarrollado por el IIE, el cual fue probado con exito en un sistema comercial para el seguimiento solar de un canal parabolico.

  11. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  12. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  13. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  14. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

  15. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. The aims of systems biology: between molecules and organisms.

    Science.gov (United States)

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  17. EDUCACION SUPERIOR, MECANISMOS DE ASEGURAMIENTO DE LA CALIDAD Y FORMACION DOCENTE

    OpenAIRE

    Miranda J,Christian

    2007-01-01

    El ensayo presenta impresiones académicas sobre los mecanismos de aseguramiento de la calidad de la Educación Superior, mediante el análisis histórico de la regulación universitaria y la conceptualización de los enfoques evaluativos vigentes en la materia. Además, relata las experiencias vividas por el autor, en su rol de Coordinador del proceso de Autoevaluación del Programa de Magíster en Educación, mención Política y Gestión Educativas de la Universidad Austral de Chile ante la Comisión Na...

  18. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  19. Variação espacial da fotossíntese e de mecanismos de fotoproteção no cafeeiro (Coffea arabica L.)

    OpenAIRE

    Dias, Paulo Cesar

    2006-01-01

    O comportamento das trocas gasosas, dos parâmetros de fluorescência da clorofila a e do sistema antioxidativo foi estudado em plantas adultas de café arábica cultivadas em campo e orientadas no sentido norte-sul, em Viçosa-MG, objetivando-se identificar potenciais mecanismos de fotoproteção e avaliar como tais mecanismos se ajustariam espacial e diurnamente. Para isso, procederam-se às avaliações em diferentes posições da copa, em agosto de 2005, época relativamente fria, seca e com alta inso...

  20. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  1. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  2. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  3. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  4. Modeling of Biological Intelligence for SCM System Optimization

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

  5. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  6. Advances in Structural Biology and the Application to Biological Filament Systems.

    Science.gov (United States)

    Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

    2018-04-01

    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  7. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  8. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  9. Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    De Domenico, Manlio

    2018-03-01

    Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

  10. Systems biology solutions for biochemical production challenges.

    Science.gov (United States)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

    2017-06-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  12. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  13. ANÁLISIS CINEMÁTICO Y DISEÑO DE UN MECANISMO DE CUATRO BARRAS PARA FALANGE PROXIMAL DE DEDO ANTROPOMÓRFICO

    Directory of Open Access Journals (Sweden)

    Édgar Alfredo Portilla Flores

    2010-01-01

    Full Text Available En este artículo, se presenta el análisis cinemático y una metodología de diseño paramétrico de la falange proximal para un dedo antropomórfico1 de un grado de libertad. El diseño del mecanismo se lleva a cabo, tomando diez posiciones de la barra de salida del mismo. Se presenta la simulación dinámica, utilizando un modelo de CAD para comprobar la factibilidad de los resultados obtenidos por el mecanismo. Por último, se muestra el análisis comparativo entre los resultados de la cinemática obtenidos numéricamente y los experimentales.

  14. Dietary antioxidant synergy in chemical and biological systems.

    Science.gov (United States)

    Wang, Sunan; Zhu, Fan

    2017-07-24

    Antioxidant (AOX) synergies have been much reported in chemical ("test-tube" based assays focusing on pure chemicals), biological (tissue culture, animal and clinical models), and food systems during the past decade. Tentative synergies differ from each other due to the composition of AOX and the quantification methods. Regeneration mechanism responsible for synergy in chemical systems has been discussed. Solvent effects could contribute to the artifacts of synergy observed in the chemical models. Synergy in chemical models may hardly be relevant to biological systems that have been much less studied. Apparent discrepancies exist in understanding the molecular mechanisms in both chemical and biological systems. This review discusses diverse variables associated with AOX synergy and molecular scenarios for explanation. Future research to better utilize the synergy is suggested.

  15. It's the System, Stupid: How Systems Biology Is Transforming.

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

  16. Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

    NARCIS (Netherlands)

    Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

    2015-01-01

    There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

  17. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  18. Tracing organizing principles: Learning from the history of systems biology

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

  19. An online model composition tool for system biology models.

    Science.gov (United States)

    Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

    2013-09-05

    There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

  20. SEEK: a systems biology data and model management platform.

    Science.gov (United States)

    Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

    2015-07-11

    Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and

  1. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  3. Déficit bilateral: origem, mecanismos e implicações para o treino de força.

    Directory of Open Access Journals (Sweden)

    Cíntia Ehlers Botton

    2012-10-01

    Full Text Available http://dx.doi.org/10.5007/1980-0037.2012v14n6p749 Vários estudos têm demonstrado uma menor capacidade de gerar força quando os exercícios de um programa de treinamento são executados bilateralmente em relação à soma da força executada pelos membros separadamente. Esse fenômeno, que tem sido bem descrito na literatura científica, é chamado de déficit bilateral. Os mecanismos causadores do déficit não são totalmente claros, mas parecem estar relacionados a mecanismos neu­rais, como um bloqueio dos hemisférios cerebrais ocorrido durante a contração bilateral que reduz a ativação de unidades motoras e a força produzida. Em relação a cada forma de execução (unilateral e bilateral a longo prazo, as adaptações parecem ser específicas ao tipo de contração utilizada durante o treinamento. Portanto, em consideração à rele­vância da realização de exercícios executados unilateralmente e bilateralmente dentro de um programa de treino de força, assim como o efeito de cada forma de execução a longo prazo nas adaptações morfológicas e neurológicas do treinamento, esse artigo teve como objetivos caracterizar o fenômeno déficit bilateral, explorar seus principais mecanismos causadores, bem como discutir a influência de cada tipo de treinamento (unilateral e bilateral nas adaptações do treinamento de força.

  4. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  5. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    Science.gov (United States)

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  6. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    Science.gov (United States)

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  7. Guías para el uso racional de antibióticos beta-lactámicos: mecanismos de resistencia y su interpretación clínica.

    Directory of Open Access Journals (Sweden)

    César A. Arias

    2003-06-01

    Full Text Available Los antibióticos ß-lactámicos son los compuestos más ampliamente usados para tratar infecciones adquiridas en el hospital o en la comunidad. Sin embargo, la resistencia a estos antibióticos en bacterias Gram negativas y Gram positivas se ha incrementado, lo cual limita su eficacia terapéutica. Se debe estar alerta a este fenómeno y seleccionar la terapia de acuerdo con el mecanismo de resistencia probable del germen aislado. La lectura interpretativa de los patrones de susceptibilidad permite un enfoque más racional del problema de resistencia y se convierte en una guía fundamental para el manejo de situaciones específicas. Dada la complejidad de los mecanismos de resistencia, es indispensable que el laboratorio identifique los microorganismos según especie y determine la susceptibilidad de un número razonable de antimicrobianos. La resistencia a ß-lactámicos en Enterobacteriaceae se debe principalmente a la producción de ß-lactamasas codificadas cromosómicamente o en plásmidos. Los mecanismos de impermeabilidad y la producción de bombas de exclusión molecular son los más comunes en microorganismos 'no fermentadores', por lo cual la terapia debe responder a estos fenómenos. En bacterias Gram positivas existen varios mecanismos involucrados: producción de proteínas de unión a penicilina (PBP alteradas, síntesis de nuevas PBP o producción de ß-lactamasas. Se discuten aquí las opciones terapéuticas basadas en el conocimiento de los mecanismos de resistencia.

  8. Noninvasive biological sensor system for detection of drunk driving.

    Science.gov (United States)

    Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

    2011-01-01

    Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

  9. POSIBLES MECANISMOS DE ACCIÓN BIOLÓGICA DE LA ACTIVIDAD FÍSICA EN EL CÁNCER DE MAMA

    Directory of Open Access Journals (Sweden)

    Jairo Alejandro Fernández Ortega

    2014-11-01

    Full Text Available La evidencia científica ha demostrado la importancia de la actividad física como una estrategia efectiva para disminuir el riesgo y la recidiva del cáncer de mama. Sin embargo, hasta el momento no se conocen con precisión los mecanismos de acción biológicos del ejercicio sobre el cáncer de mama. El propósito de este artículo es realizar una revisión sistemática exhaustiva de la literatura e identificar las posibles hipótesis que se plantean de los mecanismos de acción biológicos del ejercicio sobre el cáncer de mama. Se realizó una revisión sistemática de la literatura publicada desde 1990 hasta 2011 sobre los efectos del ejercicio en el cáncer de mama.

  10. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  11. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. SEEK: a systems biology data and model management platform.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

    2015-01-01

    Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

  13. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  14. The role of mechanics in biological and bio-inspired systems.

    Science.gov (United States)

    Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

    2015-07-06

    Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

  15. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  16. Heavy-ion microbeam system at JAEA-Takasaki for microbeam biology

    International Nuclear Information System (INIS)

    Funayama, Tomoo; Wada, Seiichi; Yokota, Yuichiro

    2008-01-01

    Research concerning cellular responses to low dose irradiation, radiation-induced bystander effects, and the biological track structure of charged particles has recently received particular attention in the field of radiation biology. Target irradiation employing a microbeam represents a useful means of advancing this research by obviating some of the disadvantages associated with the conventional irradiation strategies. The heavy-ion microbeam system at Japan Atomic Energy Agency (JAEA)-Takasaki, which was planned in 1987 and started in the early 1990's, can provide target irradiation of heavy charged particles to biological material at atmospheric pressure using a minimum beam size 5 μm in diameter. A variety of biological material has been irradiated using this microbeam system including cultured mammalian and higher plant cells, isolated fibers of mouse skeletal muscle, silkworm (Bombyx mori) embryos and larvae, Arabidopsis thaliana roots, and the nematode Caenorhabditis elegans. The system can be applied to the investigation of mechanisms within biological organisms not only in the context of radiation biology, but also in the fields of general biology such as physiology, developmental biology and neurobiology, and should help to establish and contribute to the field of 'microbeam biology'. (author)

  17. Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

    Science.gov (United States)

    Ippolito, Corey; Plice, Laura; Pisanich, Greg

    2003-01-01

    The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

  18. Collaborative Systems Biology Projects for the Military Medical Community.

    Science.gov (United States)

    Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

    2017-09-01

    This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

  19. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

    Directory of Open Access Journals (Sweden)

    Sorokin Anatoly

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  20. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  1. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  2. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

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

  3. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

  4. Predictive modelling of complex agronomic and biological systems.

    Science.gov (United States)

    Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

    2013-09-01

    Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

  5. Una red neuronal binaria para la identificación de mecanismos isomorfos. // A binary Neural network for identifying isomorphic mechanisms.

    Directory of Open Access Journals (Sweden)

    G. Galán Marín

    2002-05-01

    Full Text Available Un problema de importancia primordial en el diseño mecánico es identificar los mecanismos isomorfos, puesto que los isomorfismos nodetectados generan soluciones duplicadas y por tanto suponen un esfuerzo innecesario en el proceso de diseño. Desde 1960, una grancantidad de métodos han sido propuestos para la detección de mecanismos isomorfos. Sin embargo, diversos trabajos han mostrado queaunque pueden existir algoritmos eficaces para casos particulares, en el caso general los métodos tradicionales para la detección deisomorfismos en cadenas cinemáticas no proporcionan usualmente soluciones eficientes para este problema, que ha sido clasificado comoNP-duro. Un eficaz método alternativo para la resolución de problemas NP-duros ha surgido recientemente con las redes neuronales. Eneste trabajo proponemos un nuevo modelo de red neuronal binaria diseñado para la resolución del problema de detección de mecanismosisomorfos. El modelo propuesto se halla basado en unas dinámicas discretas que garantizan una rápida y correcta convergencia de la redhacia soluciones aceptables. Las simulaciones numéricas muestran en los mecanismos analizados que la red neuronal propuestaproporciona excelentes resultados, mostrándose además muy superior a la red de Hopfield continua tradicional en lo que respecta al tiempode computación y en la facilidad de su implementación.Palabras claves: Mecanismos isomorfos, síntesis de mecanismos, isomorfismo de grafos, red neuronal binaria,redes de Hopfield.____________________________________________________________________________AbstractAn important step in the kinematic mechanism synthesis process is to identify graph isomorphism whilegenerating new mechanisms. Undetected isomorphisms result in duplicate solutions and unnecessary effort.Since 1960, a lot of methods have been proposed for the graph isomorphism identification. Some authors haveconcluded that, in the general case, the traditional methods of

  6. Mecanismos de defensa y respuestas de las plantas en la interacción micorrícica: una revisión

    Directory of Open Access Journals (Sweden)

    Margarita Ramírez Gómez

    2012-01-01

    planta. Este documento está orientado a hacer una revisión de las respuestas de defensa que presentan las plantas bajo condiciones de simbiosis con HFMA, con el fin tener un acercamiento sobre los posibles mecanismos de atenuación de las mismas, de forma tal que permite el establecimiento de la simbiosis. Además, se desea tener una aproximación al tema de la capacidad de defensa que presenta la planta micorrizada  frente a un amplio grupo de organismos patógenos. Palabras clave: hongos formadores de micorriza arbuscular (HFMA; mecanismos de defensa de planta;   simbiosis; priming; protección de planta Summary: Harmonic processes between plant and arbuscular mycorrhyzal fungi (AMF are required for the symbiosis formation between the two organisms. These processes depend on specific signalling for the plant-fungus recognition, colonisation and bidirectional nutrient exchange. Plants show defence responses against invasive organisms, however they react weakly and localised when challenged by AMF. The benefits derived from the mycorrization are described for the nutritional aspect; however, it is known that mycorrhized plants are more tolerant to biotic stresses. Mycorrhizal induced resistance (MIR is especially important for the control of foliar pathogens, leaf cutters and necrotrophs.  There has also been found that mycorrhizal plants are protected both locally and systemically and their protection is related with jasmonic acid levels at their tissues. One of the most important mechanisms for MIR is the so called “priming” that allows plants to exert a fast and efficient defence response. Possible mechanisms to unravel mycorrhizal plants lower defence systems include: defence suppressor activation, differential plants response towards AMF from inexistent to low, and plant defence response suppression during the AMF symbiosis. The symbiosis control  is known to be regulated by the plant, however, no role has been assigned to the AMF for the weakening of the

  7. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

    2007-09-19

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  8. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  9. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  10. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  11. Vibrational resonances in biological systems at microwave frequencies.

    Science.gov (United States)

    Adair, Robert K

    2002-03-01

    Many biological systems can be expected to exhibit resonance behavior involving the mechanical vibration of system elements. The natural frequencies of such resonances will, generally, be in the microwave frequency range. Some of these systems will be coupled to the electromagnetic field by the charge distributions they carry, thus admitting the possibility that microwave exposures may generate physiological effects in man and other species. However, such microwave excitable resonances are expected to be strongly damped by interaction with their aqueous biological environment. Although those dissipation mechanisms have been studied, the limitations on energy transfers that follow from the limited coupling of these resonances to the electromagnetic field have not generally been considered. We show that this coupling must generally be very small and thus the absorbed energy is so strongly limited that such resonances cannot affect biology significantly even if the systems are much less strongly damped than expected from basic dissipation models.

  12. Inverse Problems in Systems Biology: A Critical Review.

    Science.gov (United States)

    Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

    2018-01-01

    Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

  13. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  14. Systems-biology dissection of eukaryotic cell growth

    Directory of Open Access Journals (Sweden)

    Andrews Justen

    2010-05-01

    Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

  15. It’s the System, Stupid: How Systems Biology Is Transforming

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient. PMID:22478806

  16. A dedicated database system for handling multi-level data in systems biology

    OpenAIRE

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Background Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging...

  17. Mapas de ruido: mecanismo de control del ruido ambiental

    Directory of Open Access Journals (Sweden)

    Kelvin Chávez García

    2012-12-01

    Full Text Available Los primeros mecanismos de control del ruido ambiental fueron los mapas acústicos. La Directiva Europea 2002149/CE del Parlamento Europeo y del Consejo de Evatuacián y Gestión del Ruido Ambiental, exige, a los estados miembros,  se midan los niveles de ruido, en su entorno local, con  el fin de contar con indicadores de ruido comunes. elaborar mapas de ruido y planes de acción destinados a reducir los efectos nocivos de ruido ambiental.  Las directrices para la elaboración de los  mapas  acústicos son en base a la normativa  Española sobre ruido. Los requerimientos  en base a la normativa, garantizan los resultados, lo cual permitirá elaborar los planes de acción. El estudio busca comunicar la necesidad de utilizar herramientas como  los  mapas  acústicos y ejercer un control de los  impactos por ruido ambiental.

  18. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

    Science.gov (United States)

    Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  19. Deterioro de la percepción visual en el envejecimiento: Mecanismos cerebrales compensadores

    Directory of Open Access Journals (Sweden)

    José Manuel Rodríguez-Ferrer

    2015-08-01

    Full Text Available Se han estudiado los efectos del envejecimiento normal en la percepción visual y la existencia de posibles mecanismos cerebrales compensadores. En tres grupos de 30 personas con edad media de 19,6, 42,6 y 65,7 años, se midieron los tiempos de respuesta a la presentación de estímulos (un círculo gris de 0.5 grados de diámetro de forma secuencial en 24 posiciones del campo visual, distribuidas en 8 coordenadas polares y 3 excentricidades (2.15, 3.83 y 5.53 grados de campo visual. El estímulo se presentó durante 100 milisegundos, con bajo y alto contraste (6% y 78%, respectivamente. Los experimentos se realizaron con y sin atención encubierta a los estímulos. Se observó un incremento progresivo de los tiempos de respuesta con la edad para los estímulos del 6% de contrate y de los presentados en la excentricidad de 5.53º. La atención redujo los tiempos de respuesta en los tres grupos de edad, especialmente en jóvenes y mayores. Los resultados muestran que durante el envejecimiento se produce un deterioro selectivo y progresivo en la percepción de estímulos de bajo contraste y que este deterioro es mayor en las zonas periféricas maculares. A partir de los sesenta años se potencia el desarrollo de mecanismos compensadores que implican una mayor eficacia de la atención visual.

  20. Systems Biology of Saccharomyces cerevisiae Physiology and its DNA Damage Response

    DEFF Research Database (Denmark)

    Fazio, Alessandro

    The yeast Saccharomyces cerevisiae is a model organism in biology, being widely used in fundamental research, the first eukaryotic organism to be fully sequenced and the platform for the development of many genomics techniques. Therefore, it is not surprising that S. cerevisiae has also been widely...... used in the field of systems biology during the last decade. This thesis investigates S. cerevisiae growth physiology and DNA damage response by using a systems biology approach. Elucidation of the relationship between growth rate and gene expression is important to understand the mechanisms regulating...... set of growth dependent genes by using a multi-factorial experimental design. Moreover, new insights into the metabolic response and transcriptional regulation of these genes have been provided by using systems biology tools (Chapter 3). One of the prerequisite of systems biology should...

  1. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  2. Echinococcus as a model system: biology and epidemiology.

    Science.gov (United States)

    Thompson, R C A; Jenkins, D J

    2014-10-15

    The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  3. Thermostability of biological systems: fundamentals, challenges, and quantification.

    Science.gov (United States)

    He, Xiaoming

    2011-01-01

    This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

  4. Mecanismos neurocognitivos de la terapia basada en mindfulness / Neurocognitive mechanisms of the mindfulness based therapy

    Directory of Open Access Journals (Sweden)

    Manolete S. Moscoso

    2015-12-01

    Full Text Available RESUMEN Presentamos un resumen y una breve historia del creciente campo de Intervenciones Basadas en mindfulness o conciencia plena. En los últimos tiempos, existe un gran interés en este modelo terapéutico para reducir la vulnerabilidad al estrés crónico y distrés emocional. Mindfulness requiere intencionalmente enfocar nuestra atención a las experiencias que ocurren en el momento presente. A medida que la investigación avanza en esta temática, es vital definir cuidadosamente la estructura de mindfulness y comprender mejor sus mecanismos de acción neurocognitiva. Este informe presenta un marco conceptual que enfatiza el papel central de control atencional y mecanismos de sostenibilidad para desarrollar las habilidades de conciencia plena. También, repasamos la estructura de mindfulness y la autorregulación de las emociones; luego describimos brevemente nuestra investigación relacionada con nuestro programa de Reducción del Estrés en Cáncer de Mama basado en Mindfulness (MBSR-AC en la University of South Florida. Se presenta, a partir de esta premisa, un modelo propuesto que explica nuestros mecanismos cognitivos basados en la lógica del modelo de biocomportamental. ABSTRACT We are presenting an overview and a brief history of the growing field of Mindfulness Based Interventions. There has been a significant interest in this therapeutic model to reduce vulnerability to chronic stress and emotional distress in recent times. Mindfulness requires intentionally bringing our attention to the experiences that occur in the present moment. As the research advances in this line of inquiry, it is vital to carefully define the construct of Mindfulness and better understand its neurocognitive mechanisms of action. This review presents conceptual framework that emphasizes the central role of attentional control and sustainability mechanisms to build mindfulness skills. We also review the construct of Mindfulness and self-regulation of

  5. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  6. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases.

    Science.gov (United States)

    Oh, Soo Jin; Choi, Young Ki; Shin, Ok Sarah

    2018-03-01

    Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. © Copyright: Yonsei University College of Medicine 2018.

  7. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  8. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  9. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  10. ANÁLISIS DE SENSIBILIDAD DE LAS CONSTANTES CINÉTICAS COMO HERRAMIENTA PARA LA ELUCIDACIÓN DEL MECANISMO DE POLIMERIZACIÓN DE COMPUESTOS ACRILFURÁNICOS

    Directory of Open Access Journals (Sweden)

    Jurgen Lange

    2013-01-01

    Full Text Available A partir del análisis de sensibilidad de las constantes cinéticas de un mecanismo propuesto para la polimerización radicálica de los compuestos acrilfuránicos [Acrilato (AF y Metacrilato de Furfurilo (MF] se investiga cuáles son los pasos elementales relevantes en la fenomenología. En este trabajo, se analiza la aplicación de la metodología de Come, la cual permite clasificar los pasos elementales de un mecanismo propuesto en 3 categorías: No sensible, No determinante y Sensible. Los resultados obtenidos con esta herramienta en la simulación de los datos experimentales de la polimerización radicálica de AF y MF revelan que el mecanismo cinético consta esencialmente de cinco pasos elementales: 1 Iniciación primaria, 2 propagación, 3 transferencias degradativas intermolecular y primaria, 4 reiniciación y 5 terminación cruzada. Así, considerando estos pasos elementales en modelos matemáticos, se pudo simular exitosamente la polimerización del AF y MF en diferentes condiciones experimentales.

  11. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

    Directory of Open Access Journals (Sweden)

    Mi Huaiyu

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  12. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  13. Mecanismos de control en la ciudad de Osorno: contexto de dictadura militar, 1973-1990

    OpenAIRE

    Sepúlveda Chávez, Miguel Ángel

    2015-01-01

    El siguiente trabajo tiene como objetivo describir los mecanismos de poder y de control utilizados en la ciudad de Osorno bajo el periodo de dictadura militar, el cual implícitamente es un primer acercamiento a una investigación que busca comprender el proceso de resistencia vivido en la ciudad durante el periodo dictatorial. El golpe militar del 11 de septiembre de 1973 y la instauración de una dictadura durante 17 años en Chile, fue un hecho que marcó a la sociedad chilena en general. Duran...

  14. MECANISMOS CELULARES IMPLICADOS EN EL DESARROLLO DE HIPERTROFIA DEL MUSCULO ESQUELETICO INDUCIDA POR TESTOSTERONA

    OpenAIRE

    BASUALTO ALARCON, CARLA EDITH

    2012-01-01

    El músculo esquelético es un tejido blanco para la acción de los esteroides anabólicos, siendo la testosterona la principal hormona fisiológica. Esta hormona actúa diferencialmente durante el desarrollo de un individuo cumpliendo roles diversos en el período embrionario, en la pubertad y en la vida adulta. Se ha demostrado que la testosterona es capaz de inducir un incremento en la masa muscular de individuos adultos tratados con dosis supra-fisiológicas, sin embargo los mecanismos c...

  15. Mecanismos de cardiotoxicidad: antineoplásicos, anti-inflamatorios no esteroideos, antipsicóticos, cocaetileno y simpaticomiméticos

    Directory of Open Access Journals (Sweden)

    Lukas Salazar, MD

    2011-03-01

    Full Text Available La interacción constante del organismo humano con diferentes sustancias, que incluso en muchas ocasiones se consideran inofensivas, tiene un alto impacto sobre todos los sistemas, siendo el cardiovascular uno de los más afectados. Por lo tanto, es vital reconocer los mecanismos por los cuales estas sustancias ejercen su efecto tóxico sobre este sistema, bien sea afectando la estabilidad de membrana y la función contráctil o generando disfunción de organelos intracelulares y estrés oxidativo. Numerosos estudios han descubierto efectos lesivos de sustancias, como la clozapina y las catecolaminas, que han tenido amplio uso durante largos años. En la actualidad aún se realizan investigaciones que buscan esclarecer los mecanismos cardiotóxicos de medicamentos de formulación común, entre ellos antineoplásicos y anti-inflamatorios no esteroideos (AINE, así como de sustancias de uso habitual que causan adicción, tales como alcohol, cocaína y cocaetileno, su metabolito activo.

  16. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  17. Detergencia. Sus principales mecanismos

    Directory of Open Access Journals (Sweden)

    Gómez Herrera, Carlos

    1996-12-01

    Full Text Available Advances on research, technology and applications for detergent processes increase rapidly. They keep provoking, as during last decades, repercussions on several fields (domestic, industrial, sanitary, energetic, environmental, legislative. To control as much as possible these repercussions, it is necessary to assess the actual knowledge about detergency mechanisms. This informative article starts by reviewing the essential elements for detergent processes (substrate, soil, cleaning bath. Subsequently several physico-chemical key factors for effectiveness of the textile washing are discussed. These factors are: a removal of liquid oily soils (by rolling-up, or by spontaneous microemulsification; b separation of solid particles (by interfacial or electrostatic interactions; c antiredeposition effects (by solubilization, emulsification or suspension; d water hardness influence; e washing physical conditions (temperature, agitation, time. The article ends by establishing the necessity for maintaining close collaboration among experts on different fields to optimize both detergent processes and their repercussions.

    Los avances en investigación, tecnología y aplicaciones de las operaciones detersivas aumentan rápidamente. Estos siguen provocando, como durante las últimas décadas, repercusiones en muy diversos campos (domésticos, industriales, sanitarios, energéticos, medioambientales, legislativos. Para controlar en lo posible estas repercusiones, resulta necesario valorar los conocimientos actuales sobre los mecanismos de la detergencia. Este artículo de información comienza revisando los elementos esenciales de las operaciones detersivas (sustrato, suciedad, baño. A continuación discute varios factores químicofísicos clave para la eficacia en el lavado de artículos textiles. Estos factores son: a eliminación de suciedades oleosas líquidas (por «rolling-up», o por microemulsificación; b separación de partículas s

  18. Reforço à flexão em vigas de concreto armado com manta de fibra de carbono: mecanismos de incremento de ancoragem

    Directory of Open Access Journals (Sweden)

    Vladimir José Ferrari

    2002-04-01

    Full Text Available O desprendimento dos laminados de plásticos reforçados com fibras da face inferior tracionada das vigas reforçadas à flexão é um problema complexo e indesejável, pois ocorre sem aviso, antecipando a ruína da viga reforçada e impossibilitando o total aproveitamento das propriedades resistentes à tração do reforço. Neste trabalho estudou-se o comportamento de vigas de concreto armado, reforçadas à flexão com manta de fibra de carbono, e avaliou-se a incorporação de mecanismos de incremento de ancoragem para evitar o desprendimento prematuro da manta com conseqüente aumento da capacidade resistente à flexão da viga. Nove vigas foram divididas em cinco grupos em conformidade com mecanismo de incremento de ancoragem adotado. Um dos mecanismos, além de evitar o desprendimento prematuro do reforço, também proporcionou incremento na resistência à flexão mais de 95%, em relação à viga sem reforço, e incrementos em torno de 20%, em relação às vigas sem incremento de ancoragem.

  19. Mecanismos específicos de patogenicidade de protozoários de mucosa: Entamoeba histolytica, Giardia lamblia e Trichomonas vaginalis

    Directory of Open Access Journals (Sweden)

    Patrícia de Brum Vieira

    2012-04-01

    Full Text Available Entamoeba histolytica e Giardia lamblia são protozoários que podem parasitar a mucosa intestinal, causando principalmente diarreia. Trichomonas vaginalis coloniza a mucosa vaginal causando tricomonose, a doença sexualmente transmissível não viral mais comum no mundo. Embora coletivamente estes parasitos infectem mais de um bilhão de pessoas a cada ano, seus mecanismos de patogenicidade ainda não estão totalmente esclarecidos. Assim, esta revisão reúne os principais mecanismos envolvidos na patogenicidade destes protozoários, bem como os fatores do microambiente que podem interferir no sucesso da colonização. A patogênese da E. histolytica envolve adesão, lise, fagocitose de células epiteliais e bactérias, invasão tecidual por ação de enzimas e evasão da resposta imune do hospedeiro. A lectina Gal/GalNAc, os amebaporos e as cisteína proteases são as principais moléculas envolvidas nesses processos. O estabelecimento da giardiose depende de diversos mecanismos patogênicos e de virulência desenvolvidos pela G. lamblia, tais como as moléculas envolvidas na adesão, encistamento e variação antigênica. Para o sucesso da colonização da mucosa vaginal, o T. vaginalis expressa moléculas como as adesinas de superfície, lipofosfoglicanos e galectina, envolvidas na adesão às células epiteliais vaginais e alteração da expressão gênica, tanto do parasito como do hospedeiro.

  20. El mimetismo como mecanismo psicótico de autoconservación en el niño

    Directory of Open Access Journals (Sweden)

    María Teresa Padilla Velázquez

    Full Text Available Este trabajo describe la solución ante un conflicto identificatorio por medio de la mimetización como mecanismo psicótico de sobrevivencia. El niño psicótico presenta alteraciones continuas, y una de las formas de alteración que se ha observado es el fenómeno del mimetismo, término procedente de la zoología. En lo psicológico el término mimetismo se emplea para indicar como el niño psicótico puede recurrir a éste, tanto en conducta como en actitudes identificatorias con sus objetos cercanos. Se presenta el caso de una paciente psicótica de 10 años en la que se observa como utiliza el mimetismo como un mecanismo psicótico de autoconservación. En el caso se observan que la paciente obtiene protección mimetizándose a través de actuaciones identificatorias con sus objetos cercanos. El mimetismo puede considerarse como un aspecto dificil de predecir dadas las constantes fluctuaciones de las identificaciones, sin embargo, paradójicamente es un aspecto predecible en el análisis de niños, ya que ante el miedo a la aniquilación se mimetizan.

  1. El mecanismo de Desarrollo Limpio : oportunidades de Desarrollo Sostenible para Países en Desarrollo en el Protocolo de Kioto. Caso Colombia como posible potencia continental ambiental

    OpenAIRE

    Betancourt Mesa, Juan Manuel

    2009-01-01

    El Cambio Climático y los Mecanismos de Desarrollo Limpio (MDL) en Colombia: Con el protocolo de Kyoto nacen los Mecanismos de Desarrollo Limpio, los cuales posibilitan a los países en desarrollo el generar cambios en los modelos de producción de las industrias altamente contaminantes por producciones limpias, obteniendo beneficios adicionales por la comercialización de los títulos de Reducciones Certificadas de las Emisiones (RCE). Nuestro país, tiene un potencial importante para fomentar el...

  2. Mecanismos moleculares de la síntesis de celulosa en bacterias

    Directory of Open Access Journals (Sweden)

    Micaela Marcela Méndez Ortiz

    2004-01-01

    Full Text Available La celulosa (C6H10O5n es un biopolímero de gran interés biotecnológico. El presente trabajo ofrece una revisión breve de los aspectos más relevantes que conciernen a los determinantes genéticos y moleculares involucrados en la síntesis de celulosa en bacterias. El análisis de los genes de Acetobacter xylinum involucrados en la síntesis de celulosa ha permitido la identificación de varias especies bacterianas capaces de producir celulosa, así como la elucidación de mecanismos biosintéticos que involucran a la molécula reguladora c-di-GMP, sintetizada por proteínas que poseen dominios GGDEF, las cuales están ampliamente distribuidas entre las bacterias.

  3. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  4. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Directory of Open Access Journals (Sweden)

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  5. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-04-27

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  6. Hemostasia del desarrollo : nuevos mecanismos de regulación de la reactividad plaquetaria en neonatos

    OpenAIRE

    Caparrós Pérez, Eva

    2017-01-01

    Las alteraciones en la reactividad plaquetaria se han asociado con el desarrollo de procesos trombóticos y hemorrágicos. Los neonatos, especialmente los pretérmino, tienen mayor incidencia de hemorragia intracraneal (HIC) que cualquier otro grupo de edad y, aunque su patogenia es multifactorial, la hiporreactividad de sus plaquetas podría ser un factor contribuyente. Los mecanismos genéticos y moleculares que subyacen a la hiporreactividad de las plaquetas neonatales están pobremente caracter...

  7. Specifications of Standards in Systems and Synthetic Biology.

    Science.gov (United States)

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-09-04

    Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

  8. Network science of biological systems at different scales: A review

    Science.gov (United States)

    Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

    2018-03-01

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

  9. Quantitative, high-resolution proteomics for data-driven systems biology

    DEFF Research Database (Denmark)

    Cox, J.; Mann, M.

    2011-01-01

    Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem...... primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics...... data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far....

  10. Mecanismos de hidratação do óxido de magnésio Mechanisms of magnesium oxide hydration

    Directory of Open Access Journals (Sweden)

    L. F. Amaral

    2007-12-01

    Full Text Available O óxido de magnésio, MgO, é uma importante matéria-prima para a indústria de refratários por ser um material de elevada refratariedade (ponto de fusão próximo a 2800 °C, resistente a escórias básicas, e de custo competitivo. No entanto, em presença de água, o MgO rapidamente se hidrata formando hidróxido de magnésio, Mg(OH2. Essa reação leva a uma expansão volumétrica de até três vezes, limitando sua aplicação em concretos refratários. Para desenvolver soluções que minimizem este problema, torna-se necessário um melhor entendimento do mecanismo pelo qual o MgO se hidrata e quais as principais variáveis envolvidas. Dois mecanismos distintos para esta reação foram propostos: a dissolução seguida de precipitação e b reação em uma única etapa ocorrendo diretamente na superfície das partículas. Este trabalho apresenta uma revisão crítica com relação aos mecanismos propostos e sua potencial aplicação em concretos refratários contendo MgO. Suspensões aquosas de MgO e diferentes técnicas de caracterização (ensaios reológicos oscilatórios, medidas de expansão volumétrica aparente e condutividade iônica permitiram correlacionar os mecanismos apresentados, principalmente com respeito à cinética da reação de hidratação.Magnesium oxide, MgO, is an important raw material for refractories industry due to its high refractoriness (melting point of approximately 2800 ºC, corrosion resistance in basic environment and competitive cost. Nevertheless, MgO presents a great tendency to react with water producing magnesium hydroxide, Mg(OH2. This reaction generates a threefold volumetric expansion and could lead to material breakdown inhibiting its application in refractory castables. In order to develop solutions to minimize this effect, a further understanding of the magnesia hydration mechanism and the main variables involved in this reaction is required. Two different mechanisms were proposed: a

  11. Tritium fractionation in biological systems and in analytical procedures

    International Nuclear Information System (INIS)

    Kim, M.A.; Baumgaertner, F.

    1991-01-01

    The organically bound tritium (OBT) is evaluated in biological systems by measuring the tritium distribution ratio (R-value), i.e. tritium concentrations in organic substance to tissue water. The determination of the R-value is found to involve always isotope fractionation in applied analytical procedures and hence the evaluation of the true OBT-value in a given biological system appears more complicated than hitherto known in the literature. The present work concentrates on the tritium isotope fraction in the tissue water separation and on the resulting effects on the R-value. The analytical procedures examined are vacuum freeze drying under equilibrium and non-equilibrium conditions and azeotropic distillation. The vaporization isotope effects are determined separately in the phase transition of solid or liquid to gas in pure water systems as well as in real biological systems, e.g. maize plant. The results are systematically analysed and the influence of isotope effects on the R-value is rigorously quantified. (orig.)

  12. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  13. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  14. EPR spectroscopy of complex biological iron-sulfur systems.

    Science.gov (United States)

    Hagen, Wilfred R

    2018-02-21

    From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

  15. Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

    KAUST Repository

    Gomez-Cabrero, David

    2017-08-23

    Summary Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.

  16. Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

    KAUST Repository

    Gomez-Cabrero, David; Marabita, Francesco; Tarazona, Sonia; Cano, Isaac; Roca, Josep; Conesa, Ana; Sabatier, Philippe; Tegner, Jesper

    2017-01-01

    Summary Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.

  17. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

    NARCIS (Netherlands)

    Cvijovic, Marija; Höfer, Thomas; Acimovic, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; Atauri, de Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, C.; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; Martins dos Santos, V.A.P.; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T.; Hohmann, Stefan

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological

  18. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  19. Parasitología (Biología)

    OpenAIRE

    Simón Martín, Fernando; Morchón García, Rodrigo

    2008-01-01

    1.Conceptos generales en parasitología: Concepto de organismo parásito y de parasitismo. Concepto de parasitología. Origen y evolución de los parásitos. Influencia de la vida parasitaria en los organismos correspondientes. Propagación parasitaria: ciclos biológicos, metamorfosis y reproducción parasitaria. Clases de parásitos y de hospedadores. Especificidad parasitaria. Epidemiología parasitaria. Mecanismos patogénicos de los parásitos. Respuesta del hospedador: inmunidad. Mecanismos de evas...

  20. Category of Metabolic-Replication Systems in Biology and Medicine

    OpenAIRE

    I. C. Baianu

    2012-01-01

    Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important questio...

  1. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  2. Los mecanismos de la democracia en el pensamiento político de Alexis de Tocqueville

    Directory of Open Access Journals (Sweden)

    Gil, Tomás

    2011-08-01

    Full Text Available The article intends to reconstruct the functionalist conception of Tocqueville’s democracy, a concept that focus on the beneficial effects of the democracy by describing some of the mechanisms of its practical way of operating.

    El artículo se propone reconstruir la concepción funcionalista de la democracia de Tocqueville, una concepción que se concentra en los efectos benéficos de la democracia, describiendo algunos de los mecanismos de su funcionamiento práctico.

  3. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  4. Function of dynamic models in systems biology: linking structure to behaviour.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens

    2013-10-08

    Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

  5. Glycoengineering in CHO cells: Advances in systems biology

    DEFF Research Database (Denmark)

    Tejwani, Vijay; Andersen, Mikael Rørdam; Nam, Jong Hyun

    2018-01-01

    are not well understood. A systems biology approach combining different technologies is needed for complete understanding of the molecular processes accounting for this variability and to open up new venues in cell line development. In this review, we describe several advances in genetic manipulation, modeling......For several decades, glycoprotein biologics have been successfully produced from Chinese hamster ovary (CHO) cells. The therapeutic efficacy and potency of glycoprotein biologics are often dictated by their post translational modifications, particularly glycosylation, which unlike protein synthesis....... Recently, CHO cells have also been explored for production of therapeutic glycosaminoglycans (e.g. heparin), which presents similar challenges as producing glycoproteins biologics. Approaches to controlling heterogeneity in CHO cells and directing the biosynthetic process toward desired glycoforms...

  6. Design of fluidized-bed, biological denitrification systems

    International Nuclear Information System (INIS)

    Patton, B.D.; Hancher, C.W.; Pitt, W.W.; Walker, J.F.

    1982-01-01

    Many commercial processes yield nitrate-containing wastewaters that are being discharged to the environment because traditional recovery or disposal methods are economically unacceptable. The anticipated discharge limits (i.e., 10 to 20 g (NO 3 - )/m 3 ) being considered by many states will not allow continued release of these wastewaters. The new discharge standards can be met economically by use of the fluidizied-bed, biological denitrification process. Research and development studies were conducted with 0.05-, 0.10-, 0.20-, and 0.50-m-diam fluidized-bed bioreactor systems. Feed nitrate concentrations were in the 0 to 10,000 g (NO 3 - )/m 3 range. Using the data from these studies, rate expressions were developed for the destruction of nitrate as a function of nitrate concentration. Methods were also developed for sizing bioreactors and biomass control systems. The sizing methods for fluidized-bed denitrification systems are described, and support systems such as sampling and analysis, instrumentation and controls, utilities, and bacteria storage are discussed. Operation of the process is also briefly discussed to aid the designer. Using the methods presented in this report, fluidized-bed, biological denitrification systems can be designed to treat nitrate wastewater streams

  7. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter; Lente, Gabor

    2014-01-01

    This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.

  8. Learning (from) the errors of a systems biology model.

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-11

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a data driven mathematical method which automatically detects such model errors in ordinary differential equation (ODE) models. We demonstrate for real and simulated data, how the dynamic elastic-net approach can be used to automatically (i) reconstruct the error signal, (ii) identify the target variables of model error, and (iii) reconstruct the true system state even for incomplete or preliminary models. Our work provides a systematic computational method facilitating modelling of open biological systems under uncertain knowledge.

  9. Investigating cholesterol metabolism and ageing using a systems biology approach.

    Science.gov (United States)

    Morgan, A E; Mooney, K M; Wilkinson, S J; Pickles, N A; Mc Auley, M T

    2017-08-01

    CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins. Therefore, it is apparent research into additional therapies for hypercholesterolaemia and CVD prevention is a growing necessity. However, it is also imperative to recognise this complex biological system cannot be studied using a reductionist approach; rather its biological uniqueness necessitates a more integrated methodology, such as that offered by systems biology. In this review, we firstly discuss cholesterol metabolism and how it is affected by diet and the ageing process. Next, we describe therapeutic strategies for hypercholesterolaemia, and finally how the systems biology paradigm can be utilised to investigate how ageing interacts with complex systems such as cholesterol metabolism. We conclude by emphasising the need for nutritionists to work in parallel with the systems biology community, to develop novel approaches to studying cholesterol metabolism and its interaction with ageing.

  10. Systems Biology of Meridians, Acupoints, and Chinese Herbs in Disease

    Directory of Open Access Journals (Sweden)

    Li-Ling Lin

    2012-01-01

    Full Text Available Meridians, acupoints, and Chinese herbs are important components of traditional Chinese medicine (TCM. They have been used for disease treatment and prevention and as alternative and complementary therapies. Systems biology integrates omics data, such as transcriptional, proteomic, and metabolomics data, in order to obtain a more global and complete picture of biological activity. To further understand the existence and functions of the three components above, we reviewed relevant research in the systems biology literature and found many recent studies that indicate the value of acupuncture and Chinese herbs. Acupuncture is useful in pain moderation and relieves various symptoms arising from acute spinal cord injury and acute ischemic stroke. Moreover, Chinese herbal extracts have been linked to wound repair, the alleviation of postmenopausal osteoporosis severity, and anti-tumor effects, among others. Different acupoints, variations in treatment duration, and herbal extracts can be used to alleviate various symptoms and conditions and to regulate biological pathways by altering gene and protein expression. Our paper demonstrates how systems biology has helped to establish a platform for investigating the efficacy of TCM in treating different diseases and improving treatment strategies.

  11. Simultaneous biological nutrient removal: evaluation of autotrophic denitrification, heterotrophic nitrification, and biological phosphorus removal in full-scale systems.

    Science.gov (United States)

    Littleton, Helen X; Daigger, Glen T; Strom, Peter F; Cowan, Robert A

    2003-01-01

    Simultaneous biological nutrient removal (SBNR) is the biological removal of nitrogen and phosphorus in excess of that required for biomass synthesis in a biological wastewater treatment system without defined anaerobic or anoxic zones. Evidence is growing that significant SBNR can occur in many systems, including the aerobic zone of systems already configured for biological nutrient removal. Although SBNR systems offer several potential advantages, they cannot be fully realized until the mechanisms responsible for SBNR are better understood. Consequently, a research program was initiated with the basic hypothesis that three mechanisms might be responsible for SBNR: the reactor macroenvironment, the floc microenvironment, and novel microorganisms. Previously, the nutrient removal capabilities of seven full-scale, staged, closed-loop bioreactors known as Orbal oxidation ditches were evaluated. Chemical analysis and microbiological observations suggested that SBNR occurred in these systems. Three of these plants were further examined in this research to evaluate the importance of novel microorganisms, especially for nitrogen removal. A screening tool was developed to determine the relative significance of the activities of microorganisms capable of autotrophic denitrification and heterotrophic nitrification-aerobic denitrification in biological nutrient removal systems. The results indicated that novel microorganisms were not substantial contributors to SBNR in the plants studied. Phosphorus metabolism (anaerobic release, aerobic uptake) was also tested in one of the plants. Activity within the mixed liquor that was consistent with current theories for phosphorus-accumulating organisms (PAOs) was observed. Along with other observations, this suggests the presence of PAOs in the facilities studied.

  12. Mecanismos psicobiológicos y del desarrollo de la reactividad al estrés en roedores y humanos

    Directory of Open Access Journals (Sweden)

    Leonardo A. Ortega

    2011-03-01

    Full Text Available La investigación con modelos animales ha tenido un avance importante sobre elconocimiento de los mecanismos psicobiológicos que subyacen a las diferenciasindividuales que existen con referencia a la reactividad al estrés. La investigaciónanimal también ha ayudado en la comprensión de los correlatos psicobiológicosde la reactividad al estrés en humanos, al sugerir mecanismos neuroquímicosparticulares para la investigación y al producir modelos generales defuncionamiento psicológico aplicables en humanos. En este artículo se describenlos elementos neuroquímicos básicos de la reactividad al estrés. Adicionalmente,se utiliza el modelo de epigénesis probabilística para incluir los elementos deldesarrollo y genéticos que proveen el contexto necesario para la comprensión delas diferencias individuales en la reactividad al estrés. Finalmente, se describenalgunos resultados y potenciales avances en la investigación de la psicobiologíadel trastorno de estrés postraumático en términos de los conceptos que han surgidodesde la investigación animal.

  13. Separating intrinsic from extrinsic fluctuations in dynamic biological systems.

    Science.gov (United States)

    Hilfinger, Andreas; Paulsson, Johan

    2011-07-19

    From molecules in cells to organisms in ecosystems, biological populations fluctuate due to the intrinsic randomness of individual events and the extrinsic influence of changing environments. The combined effect is often too complex for effective analysis, and many studies therefore make simplifying assumptions, for example ignoring either intrinsic or extrinsic effects to reduce the number of model assumptions. Here we mathematically demonstrate how two identical and independent reporters embedded in a shared fluctuating environment can be used to identify intrinsic and extrinsic noise terms, but also how these contributions are qualitatively and quantitatively different from what has been previously reported. Furthermore, we show for which classes of biological systems the noise contributions identified by dual-reporter methods correspond to the noise contributions predicted by correct stochastic models of either intrinsic or extrinsic mechanisms. We find that for broad classes of systems, the extrinsic noise from the dual-reporter method can be rigorously analyzed using models that ignore intrinsic stochasticity. In contrast, the intrinsic noise can be rigorously analyzed using models that ignore extrinsic stochasticity only under very special conditions that rarely hold in biology. Testing whether the conditions are met is rarely possible and the dual-reporter method may thus produce flawed conclusions about the properties of the system, particularly about the intrinsic noise. Our results contribute toward establishing a rigorous framework to analyze dynamically fluctuating biological systems.

  14. Two faces of entropy and information in biological systems.

    Science.gov (United States)

    Mitrokhin, Yuriy

    2014-10-21

    The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  16. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

    Science.gov (United States)

    Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  17. Mecanismos de la acción neuroprotectora de los cannabinoides en la enfermedad de Alzheimer

    OpenAIRE

    Martín Moreno, Ana María

    2010-01-01

    El papel neuroprotector de los cannabinoides in vivo e in vitro es conocido, pero el mecanismo a través del cual llevan a cabo su acción neuroprotectora, en el contexto de la enfermedad de Alzheimer, no había sido abordado en su conjunto. Los objetivos del presente trabajo son 5: 1. Estudiar el efecto de distintos agonistas cannabinoides, en particular aquellos carentes de efectos psicoactivos, sobre funciones microgliales tales como la generación de nitritos o la migración, que puedan se...

  18. El debate Santos – Zuluaga, el uso de formas y secuencias recurrentes como mecanismos lingüístico-discursivos

    Directory of Open Access Journals (Sweden)

    Bayter Henry Hernández

    2015-11-01

    Full Text Available Nos proponemos analizar los mecanismos lingüístico-discursivos movilizados por los dos candidatos a las últimas elecciones colombianas de 2014. Nuestro objetivo es poner de manifiesto las diferentes estructuras discursivas utilizadas por los dos candidatos durante el debate entre la primera y la segunda vuelta del 9 de junio de 2014.

  19. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  20. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  1. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  2. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  3. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the…

  4. Implantación de IPv6 : red, mecanismos de transición IPv4-IPv6, servicios de aplicación y migración de aplicaciones

    OpenAIRE

    Rodríguez Hervella, Juan Francisco

    2003-01-01

    El presente proyecto fin de carrera trata los aspectos más importantes de la gestión y migración de las redes IP hacia el nuevo protocolo de red IPv6 y pone gran énfasis en experiencias de implantación de los mismos. A lo largo de este proyecto se profundiza sobre los distintos mecanismos de transición IPv4/IPv6 existentes, concretamente se describen y se prueban (en entornos Linux y FreeBSD) los siguientes: .Túneles 6t04, automáticos, configurados. .Mecanismo DSTM, TRT, ISATAP, NAT-PT. Tambi...

  5. Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-16-2-0032 TITLE: Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines PRINCIPAL INVESTIGATOR...CONTRACT NUMBER Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines 5b. GRANT NUMBER W81XWH-16-2-0032 5c. PROGRAM ELEMENT...cell) responses will be measured using molecular and cellular approaches and the data analyzed using a systems biology approach. During the first

  6. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    Science.gov (United States)

    Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

    2004-06-01

    Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

  7. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

    NARCIS (Netherlands)

    Swat, Maciej; Kiełbasa, Szymon M.; Polak, Sebastian; Olivier, Brett; Bruggeman, Frank J.; Tulloch, Mark Quinton; Snoep, Jacky L.; Verhoeven, Arthur J.; Westerhoff, Hans V.

    2011-01-01

    The utility of model repositories is discussed in the context of systems biology (SB). It is shown how such repositories, and in particular their live versions, can be used for computational SB: we calculate the robustness of the yeast glycolytic network with respect to perturbations of one of its

  8. Standards, Data Exchange and Intellectual Property Rights in Systems Biology

    DEFF Research Database (Denmark)

    van Zimmeren, Esther; Rutz, Berthold; Minssen, Timo

    2016-01-01

    ” of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on “Synthetic Biology & Intellectual Property Rights” organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which...... we provided a number of recommendations for a variety of stakeholders. The current article offers some deeper reflections about the interface between IPRs, standards and data exchange in Systems Biology resulting from an Expert Meeting funded by another ERA-Net, ERASysAPP. The meeting brought...... together experts and stakeholders (e.g. scientists, company representatives, officials from public funding organizations) in systems biology (SysBio) from different countries.  Despite the different profiles of the stakeholders at the meeting and the variety of interests, many concerns and opinions were...

  9. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    Science.gov (United States)

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  10. Boolean modeling in systems biology: an overview of methodology and applications

    International Nuclear Information System (INIS)

    Wang, Rui-Sheng; Albert, Réka; Saadatpour, Assieh

    2012-01-01

    Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology. (paper)

  11. Converting differential-equation models of biological systems to membrane computing.

    Science.gov (United States)

    Muniyandi, Ravie Chandren; Zin, Abdullah Mohd; Sanders, J W

    2013-12-01

    This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  12. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Bicout, D.; Field, M.

    1996-01-01

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  13. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  14. Mecanismos de abertura do sulco e adubação nitrogenada no cultivo do feijoeiro em sistema plantio direto Furrows opening mechanism for nitrogen fertilizer application in common bean crop under no-tillage

    Directory of Open Access Journals (Sweden)

    Orivaldo Arf

    2008-01-01

    Full Text Available Algumas culturas têm pouca adaptação ao sistema plantio direto, em vista da maior compactação da camada superficial do solo e, nesse caso, o mecanismo utilizado na semeadora para a abertura dos sulcos para deposição do fertilizante pode ter grande importância no sentido de facilitar a penetração das raízes. Este experimento foi desenvolvido em Selvíria (MS, com o objetivo de avaliar a produtividade do feijão de inverno cultivado em sistema plantio direto, em função da utilização de mecanismos de abertura para distribuição de fertilizantes na semeadura e da adubação nitrogenada em cobertura. O delineamento experimental utilizado foi em blocos casualizados, utilizando-se esquema fatorial 2 x 6, constituído por mecanismos de distribuição de fertilizante (haste escarificadora e disco duplo e doses de N em cobertura (0, 25, 50, 75, 100 e 125 kg ha-1, com quatro repetições. Recomenda-se o uso da haste escarificadora como mecanismo de distribuição do fertilizante, para o cultivo do feijoeiro de inverno. A adubação nitrogenada em cobertura proporciona incrementos à produtividade do feijoeiro de inverno.Some crops have shown no adaptation to no-tillage system as a function of compaction soil superficial layer. In way, the mechanism used in seeder to open furrows for deposition of fertilizer can have great importance to facilitate the penetration of roots. This experiment was carried in Selvíria (MS, with the objective to evaluate the winter common bean crop yield under no-tillage system, as function of fertilizer distribution opening mechanisms in sowing (chisel and coulter blade and sidedressing nitrogen application (0, 25, 50, 75, 100 and 125 kg ha-1. The experimental design was a randomized block, arranged in a 2 x 6 factorial scheme, constituted by fertilizer distribution opening mechanisms in sowing (chisel and coulter blade and sidedressing nitrogen doses (0, 25, 50, 75, 100 and 125 kg ha-1, with four replications

  15. Análisis de los Mecanismos de Transferencia Tecnológica entre los Sectores Científico-tecnológico y Productivo de Argentina

    Directory of Open Access Journals (Sweden)

    Ana Inés Malizia

    2013-12-01

    El objetivo de este artículo es analizar el comportamiento de las estructuras de gestión que, en la Argentina, actúan como interfaz en la relación entre los sectores científico-tecnológicos y los productivos. Estas estructuras son denominadas “Oficinas de Vinculación Tecnológica y Transferencia”. En ese sentido, se presentan los resultados obtenidos a partir del análisis cuantitativo de los distintos mecanismos de gestión de la interacción entre ambos sectores. A partir del procesamiento estadístico de información de base, se obtuvieron resultados que permitieron definir y categorizar distintas variables relacionadas con las características de estas oficinas y de los sectores de la demanda. El análisis de la relación entre estas variables, permitió obtener información de base a partir de la cual se realizan inferencias acerca del comportamiento general sobre la generación y gestión de los mecanismos que regulan su relación con los sectores científico-tecnológicos y los productivos en la República Argentina. Palabras clave: mecanismos de transferencia de conocimiento, sistema nacional de innovación, estructuras de interfaz, oficinas de vinculación tecnológica y transferencia

  16. Coping mechanisms used by non-burned out and burned out workers in the family health strategy Mecanismos utilizados para enfrentar el agotamiento por trabajadores que actúan en el programa estrategia de la salud de la familia Mecanismos de enfrentamento utilizados por trabalhadores esgotados e não esgotados da estratégia de saúde da família

    Directory of Open Access Journals (Sweden)

    Letícia de Lima Trindade

    2009-10-01

    Full Text Available This study aimed to investigate stress coping mechanisms used by workers of 16 Family Health Strategy (FHS teams in Santa Maria, RS, Brazil. Six workers with scores compatible with the Burnout Syndrome, identified through the Maslach Burnout Inventory, and six workers without the syndrome were interviewed in January and February 2007. In the reports' content analysis, we identified that burned out workers predominantly used individual mechanisms to cope with occupational problems, while non-burned out workers sought collective mechanisms. These findings indicate the importance of interpersonal relationships among FHS team members to cope with occupational stress and the need to develop collective strategies to prevent stress and maintain workers' health.La investigación objetivó investigar los mecanismos para enfrentar el estrés, utilizados por los trabajadores de los dieciséis equipos de la Estrategia de la Salud de la Familia (ESF de Santa Maria, RS, Brasil. Fueron entrevistados, en los meses de enero y febrero de 2007, seis trabajadores con puntajes compatibles con el síndrome de Burnout, identificados por el Maslach Burnout Inventory, y seis sin el síndrome. En el análisis de contenido de las declaraciones, se identificó que los trabajadores agotados utilizan, predominantemente, mecanismos individuales para enfrentamiento de los problemas laborales, en cuanto los no agotados recurren a mecanismos colectivos. Lo encontrado apunta para la importancia de las relaciones interpersonales entre los miembros del equipo de la ESF para el enfrentamiento del estrés laboral y para la necesidad de construir estrategias colectivas, con el objetivo de prevenir el estrés y mantener la salud del trabajador.A pesquisa objetivou investigar os mecanismos de enfrentamento do estresse utilizados pelos trabalhadores das dezesseis equipes da Estratégia de Saúde da Família (ESF de Santa Maria, RS, Brasil. Foram entrevistados, nos meses de janeiro e

  17. Breeding system and pollination biology of the semidomesticated ...

    African Journals Online (AJOL)

    Breeding system and pollination biology of the semidomesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae ): Implications for fruit production, selective breeding, and conservation of genetic resources.

  18. Multiway modeling and analysis in stem cell systems biology

    Directory of Open Access Journals (Sweden)

    Vandenberg Scott L

    2008-07-01

    Full Text Available Abstract Background Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of biological systems. Stem cells are an attractive target for this analysis, due to their broad therapeutic potential. A central theme of systems biology is the use of computational modeling to reconstruct complex systems from a wealth of reductionist, molecular data (e.g., gene/protein expression, signal transduction activity, metabolic activity, etc.. A number of deterministic, probabilistic, and statistical learning models are used to understand sophisticated cellular behaviors such as protein expression during cellular differentiation and the activity of signaling networks. However, many of these models are bimodal i.e., they only consider row-column relationships. In contrast, multiway modeling techniques (also known as tensor models can analyze multimodal data, which capture much more information about complex behaviors such as cell differentiation. In particular, tensors can be very powerful tools for modeling the dynamic activity of biological networks over time. Here, we review the application of systems biology to stem cells and illustrate application of tensor analysis to model collagen-induced osteogenic differentiation of human mesenchymal stem cells. Results We applied Tucker1, Tucker3, and Parallel Factor Analysis (PARAFAC models to identify protein/gene expression patterns during extracellular matrix-induced osteogenic differentiation of human mesenchymal stem cells. In one case, we organized our data into a tensor of type protein/gene locus link × gene ontology category × osteogenic stimulant, and found that our cells expressed two distinct, stimulus-dependent sets of functionally related genes as they underwent osteogenic differentiation. In a second case, we organized DNA microarray data in a three-way tensor of gene IDs × osteogenic stimulus × replicates, and found that application of tensile strain to a

  19. Tritium isotope fractionation in biological systems and in analytical procedures

    International Nuclear Information System (INIS)

    Kim, M.A.; Baumgaertner, Franz

    1989-01-01

    The organically bound tritium (OBT) is evaluated in biological systems by determining the tritium distribution ratio (R-value), i.e. tritium concentrations in organic substance to cell water. The determination of the R-value always involves isotope fractionation is applied analytical procedures and hence the evaluation of the true OBT -value in a given biological system appears more complicated than hitherto known in the literature. The present work concentrates on the tritium isotope fractionation in the cell water separation and on the resulting effects on the R-value. The analytical procedures examined are vacuum freeze drying under equilibrium and non-equilibrium conditions and azeotropic distillation. The vaporization isotope effects are determined separately in the phase transition of solid or liquid to gas in pure tritium water systems as well as in real biological systems, e.g. corn plant. The results are systematically analyzed and the influence of isotope effects on the R-value is rigorously quantified

  20. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  1. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  2. A Generic Language for Biological Systems based on Bigraphs

    DEFF Research Database (Denmark)

    Damgaard, Troels Christoffer; Krivine, Jean

    Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et...

  3. Metabolomics for functional genomics, systems biology, and biotechnology.

    Science.gov (United States)

    Saito, Kazuki; Matsuda, Fumio

    2010-01-01

    Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

  4. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

    Science.gov (United States)

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. © 2016 The Author(s).

  5. Mecanismos de resistencia natural al VIH en seres humanos: un resumen de 10 años de investigación en población colombiana

    Directory of Open Access Journals (Sweden)

    María Teresa Rugeles

    2011-03-01

    Aunque los estudios llevados a cabo por nuestro grupo de investigación han corroborado el papel protector de algunos de los mecanismos de protección previamente propuestos, la investigación actual en esta área, a nivel mundial, ha hecho evidente que el fenómeno de resistencia natural depende de múltiples factores con una gran influencia genética, y que sólo mediante estudios multicéntricos que involucren individuos con diferente componente genético, podrán establecerse los mecanismos universales de protección. Profundizar en el conocimiento en esta área permitirá el desarrollo de nuevas medidas preventivas y terapéuticas para la infección por el VIH-1.

  6. Data management and data enrichment for systems biology projects.

    Science.gov (United States)

    Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Müller, Wolfgang

    2017-11-10

    Collecting, curating, interlinking, and sharing high quality data are central to de.NBI-SysBio, the systems biology data management service center within the de.NBI network (German Network for Bioinformatics Infrastructure). The work of the center is guided by the FAIR principles for scientific data management and stewardship. FAIR stands for the four foundational principles Findability, Accessibility, Interoperability, and Reusability which were established to enhance the ability of machines to automatically find, access, exchange and use data. Within this overview paper we describe three tools (SABIO-RK, Excemplify, SEEK) that exemplify the contribution of de.NBI-SysBio services to FAIR data, models, and experimental methods storage and exchange. The interconnectivity of the tools and the data workflow within systems biology projects will be explained. For many years we are the German partner in the FAIRDOM initiative (http://fair-dom.org) to establish a European data and model management service facility for systems biology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  8. Polynomial algebra of discrete models in systems biology.

    Science.gov (United States)

    Veliz-Cuba, Alan; Jarrah, Abdul Salam; Laubenbacher, Reinhard

    2010-07-01

    An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation. This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis. alanavc@vt.edu Supplementary data are available at Bioinformatics online.

  9. Synthetic and systems biology for microbial production of commodity chemicals.

    Science.gov (United States)

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  10. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    Rice, MaryJoe K; Ruder, Warren C

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  11. Creating biological nanomaterials using synthetic biology.

    Science.gov (United States)

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  12. Mecanismo de acción de hormonas tiroideas sobre el páncreas endócrino

    OpenAIRE

    Cortizo, Ana María

    1987-01-01

    El rol de las hormonas tiroideas en la Diabetes Mellitus y la función endocrina del páncreas fue estudiado por primera vez en 1944 por B. A. Houssay (1 ). Trabajando con perros parcialmente panceatectomizados, sometidos a tratamiento con hormonas tiroideas, observó que adquirían una forma de diabetes irreversible, que persistía aún después de interrumpir el tratamiento tiroideo. Llamó a ésta Diabetes Meta.tiroidea ; su mecanismo parecía ser un agotamiento pancreático consecutivo a ...

  13. Fusiones y adquisiciones: mecanismos de internacionalización de bancos latinoamericanos

    Directory of Open Access Journals (Sweden)

    Julie Janeth Bertel Chadid

    2017-07-01

    Full Text Available Desde los años noventa, a nivel global, se han registrado un número elevado de fusiones y adquisiciones (en adelante M&As en el mundo financiero cuyo objetivo es apalancar el crecimiento internacional del sector. Como la banca latinoamericana no ha sido la excepción, hemos examinado si las M&As son mecanismos de internacionalización empleados por los bancos latinoamericanos; para ello, escogimos como casos de estudio el principal banco de Brasil, el de Colombia y el de Perú, observando el comportamiento del indicador y dimensionando el grado de internacionalización, durante el período 1990-2014. Aplicamos varias metodologías de medición a fin de no dejar por fuera aspectos importantes de la internacionalización. Los resultados del estudio presentan evidencia del uso de las M&As por los bancos latinoamericanos como estrategias de internacionalización para llegar a nuevos mercados.

  14. Optical sensors and their applications for probing biological systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina

    There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant and mammal......There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant...... of a trapped cell. The project could provide new insights into the desired biosensor for future membrane-protein cell studies....

  15. Estrategias gerenciales como mecanismo de responsabilidad social en el sector turístico de Santa Marta - Colombia

    OpenAIRE

    José de los Santos Zarate Díaz; Wilfrido Enrique Gutiérrez Ospino

    2014-01-01

    El propósito de este artículo es analizar las estrategias gerenciales como mecanismo de responsabilidad social en el sector turístico de Santa Marta, Colombia. Para tal efecto, se realizó revisión bibliográfica que permitió relacionar aspectos fundamentales de las estrategias gerenciales y la responsabilidad social como instrumento importante en cualquier corporación empresarial que persiga lograr objetivos para posicionarse en los mercados de servicios altamente competitivos. La revisión bib...

  16. Request for Travel Funds for Systems Radiation Biology Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Barcellos-Hoff, Mary Helen [NYU School of Medicine

    2014-03-22

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expenses of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.

  17. Priming previne a insuficiência renal aguda nefrotóxica através da estimulação do mecanismo de defesa antioxidante

    Directory of Open Access Journals (Sweden)

    Fernanda Duarte

    2016-06-01

    Full Text Available RESUMO Introdução: Priming é um mecanismo de proteção induzida pela exposição anterior de uma célula ou órgão a baixas ou mesmas concentrações de uma substância tóxica. Objetivo: analisar o mecanismo de priming induzido pela exposição a gentamicina em células tubulares proximais humanas e na insuficiência renal aguda (IRA. Métodos: Células tubulares foram expostos a 2 mM de gentamicina durante 24 horas, enquanto ratos Wistar foram expostas a 40 mg/kg durante 3 dias. Depois de uma semana, as células foram expostas à mesma concentração durante 24h e os ratos durante dez dias. Os animais condicionados foram comparados com ratos controle e tratados com gentamicina durante 10 dias. Foram analisados parâmetros bioquímicos, o estresse oxidativo foi analisado por hidroperóxidos e proteínas carboniladas urinárias, enquanto a defesa antioxidante foi estudada pela atividade antioxidante do plasma e imunomarcação e atividade da catalase, superóxido dismutase, heme oxigenase-1 (HO-1 nos rins. Necrose, apoptose, proliferação e expressão da endotelina-1 (ET-1 e HO-1 foram estudadas em células. Resultados: o condicionamento dos animais inibiu o aumento da creatinina, ureia, excreção urinária de sódio e de proteína induzida por gentamicina. Bosentana, antagonista do receptor ET-1, e hemin, indutor de HO-1, potencializaram a inibição. O mecanismo de proteção foi mediado pela indução de enzimas antioxidantes HO-1, catalase e SOD atividade e redução do estresse oxidativo. O condicionamento inibiu a morte celular e induziu a proliferação via produção de ET-1. Conclusão: o mecanismo de condicionamento é persistente e multifactorial, o estímulo da defesa antioxidante poderia mimetizar o processo de condicionamento e impedir a IRA.

  18. Continuum analysis of biological systems conserved quantities, fluxes and forces

    CERN Document Server

    Suraishkumar, G K

    2014-01-01

    This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

  19. STUDENTS’ CONCEPTIONS OF BIOLOGICAL IMAGES AS REPRESENTATIONAL DEVICES/ CONCEPCIONES DE LOS ESTUDIANTES SOBRE IMÁGENES DE BIOLOGÍA COMO MECANISMOS REPRESENTACIONALES/ CONCEPÇÕES DOS ESTUDANTES SOBRE IMAGENS DE BIOLOGIA COMO MECANISMOS REPRESENTACIONAIS

    Directory of Open Access Journals (Sweden)

    Asunción López-Manjón

    2012-12-01

    Full Text Available The study analyzes students’ conceptions of the representational nature attributed to images in biology. The conceptions regarding the relationship between representation and referent can be categorized into realism and constructivism. 171 students aged 12, 14, and 16 participated in the study. Some had had specific instruction in biology and some had not. Several instruments, such as Likert scale questionnaires, and multiple choice and open-ended questions were used to measure the conceptions. Students show realistic conception about the nature of a cell microphotography. The primacy of perceptive aspects in visual representations may explain these results, the difficulties students have in learning them, and the need of their explicit instruction.

  20. Next-generation mammalian genetics toward organism-level systems biology.

    Science.gov (United States)

    Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

    2017-01-01

    Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

  1. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  2. UPDATE ON THE MECHANISM OF ACTION OF ESTROGEN RECEPTORS. Actualización sobre el mecanismo de acción de los receptores estrogénicos

    Directory of Open Access Journals (Sweden)

    Ieda Millas

    2016-03-01

    Full Text Available Los mecanismos de acción de los receptores estrogénicos (ER han sido estudiados debido a sus importantes funciones en el crecimiento celular y la diferenciación de varios órganos y tejidos, relacionados o no con la reproducción. Como en otros procesos regulatorios, los mecanismos de ligados a receptor son cruciales para permitir la acción de los estrógenos que finalmente producirían efectos en el metabolismo celular. Aunque muy estudiados, los mecanismos de acción de los receptores estrogénicos no han sido completamente desentrañados. El presente estudio es una revisión de la literatura sobre el mecanismo de acción de ER ? y ER ? en el cuerpo humano. El conocimiento de la localización y concentraciones de ER en diferentes tejidos es esencial para determinar tratamientos específicos para diferentes patologías, tales como cáncer de mama. Más aún, en tejidos no reproductivos, tales como la mucosa de los cornetes nasales, la presencia de ER ? y ER ? podría explicar las variaciones en la actividad secretora acorde con la variación hormonal. También se consideran las acciones ER neuroproductivas y antinflamatorias en el sistema nervioso central al igual que su función de respuesta alérgica en el epitelio de la conjuntiva y podrían aplicarse a otros estudios referidos al diagnóstico, desarrollo de drogas y el tratamiento de diferentes enfermedades asociados a acciones hormonales. The action mechanisms of estrogen receptors (ER have been studied due to their important functions in cellular growth and differentiation in several organs and tissues, either or not directly related to reproduction. As in other regulatory processes, the mechanisms of receptor ligand binding are crucial to enable the action of the estrogen hormone that will ultimately produce effects in the cellular metabolism. Although extensively studied, the mechanisms of action of estrogen receptors are not completely unraveled. The present study is a literature

  3. A Checklist for Successful Quantitative Live Cell Imaging in Systems Biology

    Science.gov (United States)

    Sung, Myong-Hee

    2013-01-01

    Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. However, due to the multidisciplinary techniques that are necessary for adaptation of such systems biology approaches, dissemination to a wide research community has been relatively slow. In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. The importance of these technical considerations will be elaborated with examples of successes and shortcomings. Future efforts will benefit by avoiding some pitfalls and by utilizing the lessons collectively learned from recent applications of imaging in systems biology. PMID:24709701

  4. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  5. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

    Science.gov (United States)

    Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  6. cellPACK: a virtual mesoscope to model and visualize structural systems biology.

    Science.gov (United States)

    Johnson, Graham T; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

    2015-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.

  7. System as metaphor in the psychology and biology of shame.

    Science.gov (United States)

    Maunder, R

    1996-01-01

    Biological theories of brain and psychological theories of mind are two systems of explanation that seem related to one another. The nature of the relationship is problematic and constitutes the age-old mind-body problem. The most prominent solutions currently are variations of materialism. While psychological theories can be consistent with materialism, there remains a difficulty in comprehending nonphysical (social, psychological) causes of physical effects. This difficulty is an obstacle to integration in psychiatry, where we routinely assume that illnesses that include or depend on biological dysfunction are caused multifactorially by causal agents such as perceived parental warmth, parental loss, stressful life events, genetics, and personality (Hammen et al. 1992; Kendler et al. 1993). Unity theory adopts the stance that neurobiological theories and psychological theories are essentially disparate explanations of the same psychobiological events; thus the relationship of mind to brain is one of shared reference (Goodman 1991; Maunder 1995). In Goodman's model the gap between biological and psychological systems is not bridgeable. Different conceptual categories refer to the same referents but cannot interact with each other. Stepping into the breach, systems theory has been presented as offering a language that can bridge the gap between psychological and biological theories of causation (Schwartz 1981; Weiner 1989). Thus, there is a controversy about the applicability of systems theory for integration in psychiatry.

  8. Segurança hemisférica: uma discussão sobre a validade e atualidade de seus mecanismos institucionais Hemispheric security: a discussion about the validity and the contemporary of its institutional mechanisms

    Directory of Open Access Journals (Sweden)

    Graciela De Conti Pagliai

    2006-06-01

    Full Text Available As profundas mudanças que ocorreram no sistema internacional com o término da Guerra Fria provocaram revisão de seus padrões, em especial, dos parâmetros de segurança coletiva hemisférica baseados em mecanismos que visavam garantir a segurança dos Estados-membro mediante a legítima defesa individual ou coletiva. Os Estados-membros indicaram a necessidade de repensar estes arranjos de maneira que os mecanismos estivessem apropriados para enfrentar as novas e difusas ameaças à segurança hemisférica.The deep changes that occurred in the international system with the end of the Cold War provoked the revision of theirs patterns, mainly the hemispheric collective security parameters based on mechanisms that aimed at assuring the security of the member states by means of inherent right of individual or collective self-defense. The member states pointed out the necessity of rethinking these arrangements so that the mechanisms could be suitable to face new and diffuse threatens to hemispheric security.

  9. Networks as a Privileged Way to Develop Mesoscopic Level Approaches in Systems Biology

    OpenAIRE

    Alessandro Giuliani

    2014-01-01

    The methodologies advocated in computational biology are in many cases proper system-level approaches. These methodologies are variously connected to the notion of “mesosystem” and thus on the focus on relational structures that are at the basis of biological regulation. Here, I describe how the formalization of biological systems by means of graph theory constitutes an extremely fruitful approach to biology. I suggest the epistemological relevance of the notion of graph resides in its multil...

  10. When one model is not enough: Combining epistemic tools in systems biology

    DEFF Research Database (Denmark)

    Green, Sara

    2013-01-01

    . The conceptual repertoire of Rheinberger’s historical epistemology offers important insights for an analysis of the modelling practice. I illustrate this with a case study on network modeling in systems biology where engineering approaches are applied to the study of biological systems. I shall argue...

  11. La violencia como mecanismo del debate público en Venezuela durante el siglo XX

    Directory of Open Access Journals (Sweden)

    Inés Guardia Rolando

    2008-01-01

    Full Text Available El objetivo del presente ensayo es describir los mecanismos por medio de los cuales la violencia política se presenta como uno de los elementos fundamentales del debate público en dos coyunturas históricas en Venezuela: en la Revolución de Octubre y en la Revolución Bolivariana. El trabajo se desarrolla en torno a dos ideas: primero se abordará el problema de la violencia y el miedo desde una perspectiva teórica, luego se describirá cada una de estas coyunturas históricas; finalmente se revisa comparativamente este fenómeno que se repite a lo largo del tiempo en Venezuela.

  12. Anita Fricek: la pintura contemporánea como mecanismo de crítica institucional

    Directory of Open Access Journals (Sweden)

    Stephen Zepke

    2009-04-01

    Full Text Available Este ensayo formula la pregunta acerca de las relaciones posibles entre el arte contemporáneo y la propuesta estética de Gilles Deleuze. Valiéndose de su propia disyunción, pone en contacto dos asuntos yuxtapuestos: lo “conceptual” y la “sensación”. A partir de esa conexión y a través de la obra pictórica de la artista suiza Anita Fricek, el autor critica la propuesta de estética inmanente de la sensación de Deleuze, y la vincula con el mecanismo de crítica institucional inmerso en la propuesta pictórica-crítica de Fricek.

  13. A distributed approach for parameters estimation in System Biology models

    International Nuclear Information System (INIS)

    Mosca, E.; Merelli, I.; Alfieri, R.; Milanesi, L.

    2009-01-01

    Due to the lack of experimental measurements, biological variability and experimental errors, the value of many parameters of the systems biology mathematical models is yet unknown or uncertain. A possible computational solution is the parameter estimation, that is the identification of the parameter values that determine the best model fitting respect to experimental data. We have developed an environment to distribute each run of the parameter estimation algorithm on a different computational resource. The key feature of the implementation is a relational database that allows the user to swap the candidate solutions among the working nodes during the computations. The comparison of the distributed implementation with the parallel one showed that the presented approach enables a faster and better parameter estimation of systems biology models.

  14. How do precision medicine and system biology response to human body's complex adaptability?

    Science.gov (United States)

    Yuan, Bing

    2016-12-01

    In the field of life sciences, although system biology and "precision medicine" introduce some complex scientifific methods and techniques, it is still based on the "analysis-reconstruction" of reductionist theory as a whole. Adaptability of complex system increase system behaviour uncertainty as well as the difficulties of precise identifification and control. It also put systems biology research into trouble. To grasp the behaviour and characteristics of organism fundamentally, systems biology has to abandon the "analysis-reconstruction" concept. In accordance with the guidelines of complexity science, systems biology should build organism model from holistic level, just like the Chinese medicine did in dealing with human body and disease. When we study the living body from the holistic level, we will fifind the adaptability of complex system is not the obstacle that increases the diffificulty of problem solving. It is the "exceptional", "right-hand man" that helping us to deal with the complexity of life more effectively.

  15. Ion beam induced fluorescence imaging in biological systems

    International Nuclear Information System (INIS)

    Bettiol, Andrew A.; Mi, Zhaohong; Vanga, Sudheer Kumar; Chen, Ce-belle; Tao, Ye; Watt, Frank

    2015-01-01

    Imaging fluorescence generated by MeV ions in biological systems such as cells and tissue sections requires a high resolution beam (<100 nm), a sensitive detection system and a fluorescent probe that has a high quantum efficiency and low bleaching rate. For cutting edge applications in bioimaging, the fluorescence imaging technique needs to break the optical diffraction limit allowing for sub-cellular structure to be visualized, leading to a better understanding of cellular function. In a nuclear microprobe this resolution requirement can be readily achieved utilizing low beam current techniques such as Scanning Transmission Ion Microscopy (STIM). In recent times, we have been able to extend this capability to fluorescence imaging through the development of a new high efficiency fluorescence detection system, and through the use of new novel fluorescent probes that are resistant to ion beam damage (bleaching). In this paper we demonstrate ion beam induced fluorescence imaging in several biological samples, highlighting the advantages and challenges associated with using this technique

  16. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  17. Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-16-2-0031 TITLE: Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines PRINCIPAL...SUBTITLE 5a. CONTRACT NUMBER Systems Biology of the Immune Response to Live and Inactivated Dengue Virus Vaccines 5b. GRANT NUMBER W81XWH-16-2-0031 5c...adaptive (T and B cell) responses will be measured using molecular and cellular approaches and the data analyzed using a systems biology approach

  18. Mecanismos celulares en respuesta al estrés: sirtuinas

    Directory of Open Access Journals (Sweden)

    Nancy Paola Echeverri Ruiz

    2010-07-01

    Full Text Available Desde hace algún tiempo se conoce el papel de la restricción calórica sobre la longevidad y la prevención de enfermedades crónicas, pero hasta hace poco los mecanismos celulares involucrados comienzan a ser elucidados. El estrés celular se podría definir como el estado en el que la célula no presenta las condiciones óptimas de supervivencia, siendo el oxidativo un tipo de estrés en el que se generan radicales libres nocivos para las estructuras celulares. La restricción calórica podría incrementar la resistencia celular a diferentes formas de estrés. Las sirtuinas, proteínas deacetilasas de histonas tipo III, están involucradas en la relación entre balance energético y transcripción génica, permitiendo que la célula responda a la restricción calórica y sobreviva a situaciones de estrés oxidativo. En esta relación las sirtuinas regulan genes de la familia FOXO, cMYC, hTERT, p53, entre otros. La activación o silenciamiento de estos genes es importante en los procesos de apoptosis, reparación y muerte celular.

  19. Modelos y mecanismos de interacción universidad-empresa-estado: retos para las universidades colombianas

    Directory of Open Access Journals (Sweden)

    Katherine Pineda Márquez

    2011-01-01

    Full Text Available Las interacciones entre las universidades y el entorno han sido objeto de estudio en las últimas décadas, sobre todo en el marco de la nueva economía, donde se toma el conocimiento como factor estratégico para la generación de riqueza, y a las universidades como las organizaciones que deben producirlo. El objeto de este artículo es presentar una revisión de literatura alrededor de los principales modelos y mecanismos de interacción Universidad-entorno, con el fin de identificar algunos retos para las universidades colombianas. Esta revisión se realizó en fuentes secundarias, principalmente en bases de datos científicas, y arrojó como resultado que estos modelos y mecanismos han tendido a homogeneizarse, aplicándose indistintamente en los contextos particulares de cada región, produciendo resultados positivos especialmente en Estados Unidos y otros países industrializados, y, por el contrario, fuertes diferencias ideológicas y limitaciones en las interacciones entre los diferentes actores, así como en las capacidades en términos de ciencia, tecnología e innovación de los países en desarrollo, como Colombia. Algunos de los retos que tienen las universidades colombianas están relacionados con el desafío de incrementar sus capacidades de investigación, su acumulación y transferencia de conocimiento, mejorar sus políticas de propiedad intelectual y construir su propio modelo de interacción a partir de sus capacidades internas y del contexto en el cual están inmersas.

  20. Interactions of nanomaterials and biological systems: implications to personalized nanomedicine☆

    Science.gov (United States)

    Zhang, Xue-Qing; Xu, Xiaoyang; Bertrand, Nicolas; Pridgen, Eric; Swami, Archana; Farokhzad, Omid C.

    2012-01-01

    The application of nanotechnology to personalized medicine provides an unprecedented opportunity to improve the treatment of many diseases. Nanomaterials offer several advantages as therapeutic and diagnostic tools due to design flexibility, small sizes, large surface-to-volume ratio, and ease of surface modification with multivalent ligands to increase avidity for target molecules. Nanomaterials can be engineered to interact with specific biological components, allowing them to benefit from the insights provided by personalized medicine techniques. To tailor these interactions, a comprehensive knowledge of how nanomaterials interact with biological systems is critical. Herein, we discuss how the interactions of nanomaterials with biological systems can guide their design for diagnostic, imaging and drug delivery purposes. A general overview of nanomaterials under investigation is provided with an emphasis on systems that have reached clinical trials. Finally, considerations for the development of personalized nanomedicines are summarized such as the potential toxicity, scientific and technical challenges in fabricating them, and regulatory and ethical issues raised by the utilization of nanomaterials. PMID:22917779

  1. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  2. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    International Nuclear Information System (INIS)

    Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  3. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, Daniel D. [Integrative Genetics and Genomics, University of California Davis, Davis, CA (United States); Department of Biomedical Engineering, University of California Davis, Davis, CA (United States); Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng, E-mail: cmtan@ucdavis.edu [Department of Biomedical Engineering, University of California Davis, Davis, CA (United States)

    2014-12-09

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  4. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  5. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  6. Distribution and Biological Effects of Nanoparticles in the Reproductive System.

    Science.gov (United States)

    Liu, Ying; Li, Hongxia; Xiao, Kai

    2016-01-01

    Nanoparticles have shown great potential in biomedical applications such as imaging probes and drug delivery. However, the increasing use of nanoparticles has raised concerns about their adverse effects on human health and environment. Reproductive tissues and gametes represent highly delicate biological systems with the essential function of transmitting genetic information to the offspring, which is highly sensitive to environmental toxicants. This review aims to summarzie the penetration of physiological barriers (blood-testis barrier and placental barrier), distribution and biological effects of nanoparticles in the reproductive system, which is essential to control the beneficial effects of nanoparticles applications and to avoid their adverse effects on the reproductive system. We referred to a large number of relevant peer-reviewed research articles about the reproductive toxicity of nanoparticles. The comprehensive information was summarized into two parts: physiological barrier penetration and biological effects of nanoparticles in male or female reproductive system; distribution and metabolism of nanoparticles in the reproductive system. The representative examples were also presented in four tables. The in vitro and in vivo studies imply that some nanoparticles are able to cross the blood-testis barrier or placental barrier, and their penetration depends on the physicochemical characteristics of nanoparticles (e.g., composition, shape, particle size and surface coating). The toxicity assays indicate that nanoparticles might induce adverse physiological effects and impede fertility or embryogenesis. The barrier penetration, adverse physiological effects, distribution and metabolism are closely related to physicochemical characteristics of nanoparticles. Further systematic and mechanistic studies using well-characterized nanoparticles, relevant administration routes, and doses relevant to the expected exposure level are required to improve our

  7. Mecanismos de selecci?n de pareja en funci?n del sexo: un estudio en poblaci?n colombiana

    OpenAIRE

    Verdugo Rios, Ang?lica Mar?a; ?lvarez Tob?as, Lina Mar?a

    2017-01-01

    La teor?a evolucionista expuesta por Buss 1996 plantea que existen mecanismos diferentes en el ofrecimiento y b?squeda de atributos a la hora de seleccionar una potencial pareja sexual. Partiendo de dicha teor?a y de investigaciones que la sustentan, el objetivo de esta investigaci?n es confirmar estas predicciones en poblaci?n colombiana y relaciones a largo plazo. Para esto se realiz? un an?lisis de categor?as como edad, atractivo f?sico y recursos encontradas en anuncios de la p?gina www.c...

  8. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  9. Mecanismos de explotación sexual de niñas y adolescentes en los alrededores del puerto fluvial de Pucallpa

    Directory of Open Access Journals (Sweden)

    Jaris Mujica

    2011-12-01

    Full Text Available La explotación sexual de niñas y adolescentes es un fenómeno que ha crecido con la expansión de las industrias extractivas (de madera, petróleo, minerales y gas en la Amazonía peruana. El artículo es parte de una larga investigación en la ciudad de Pucallpa y la ruta norte del río Ucayali, y tiene como objetivo central mostrar la dinámica económica de los mecanismos de explotación sexual comercial de niñas y adolescentes en los alrededores del principal puerto fluvial. Se estudia los mecanismos de explotación local de los bares y restaurantes del puerto, la demanda y las percepciones sobre la explotación sexual de las niñas, y las lógicas económicas que ello implica. Se trata de un negocio cuya rentabilidad está anexada al comercio de bebidas alcohólicas y alimentos; y que no obedece a una lógica criminal organizada sino a un conjunto de redes familiares.

  10. Biomimicry, Biofabrication, and Biohybrid Systems: The Emergence and Evolution of Biological Design.

    Science.gov (United States)

    Raman, Ritu; Bashir, Rashid

    2017-10-01

    The discipline of biological design has a relatively short history, but has undergone very rapid expansion and development over that time. This Progress Report outlines the evolution of this field from biomimicry to biofabrication to biohybrid systems' design, showcasing how each subfield incorporates bioinspired dynamic adaptation into engineered systems. Ethical implications of biological design are discussed, with an emphasis on establishing responsible practices for engineering non-natural or hypernatural functional behaviors in biohybrid systems. This report concludes with recommendations for implementing biological design into educational curricula, ensuring effective and responsible practices for the next generation of engineers and scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Creation of computer system for simulation nanoparticles interaction with biological objects concept

    International Nuclear Information System (INIS)

    Sarana, Yu.V.; Smol'nik, N.S.; Mel'nov, S.B.

    2014-01-01

    Main problem of nanotoxicology is that biological effects of most nanoparticles are unknown. So creation of system predictioning nanoparticles biological activity spectra is a great challenge. Here we give a concept of such system creation; it includes 6 stages realization of which help to implement nanotechnology most safely and effectively. (authors)

  12. Modelos informáticos para entender la evolución. (Mecanismos de evolución adaptativa facilitada

    Directory of Open Access Journals (Sweden)

    Cedano, Juan

    2002-05-01

    Full Text Available Not available

    «La generación espontánea de la vida en la tierra habría tenido tantas probabilidades de darse como el ensamblaje de un avión 747 por un tornado a su paso por un depósito de chatarra». Fred Hoyle

    El modelo darwinista es un modelo sencillo que pretende explicar la manera en la que los seres vivos han evolucionado. La simplicidad de sus planteamientos ha facilitado la difusión de estas ideas. Pero esa misma simplicidad hace que difícilmente pueda explicar la complejidad de los seres vivos. Tampoco explica la enorme velocidad de evolución de las especies, que se deduce de la aparente ausencia de intermediarios en el registro fósil. Para soslayar estos problemas, diversos autores han sugerido la presencia en la célula de mecanismos adaptativos y no preadaptativos, como sugiere el modelo darwinista. La arquitectura de los sistemas informáticos, así como los lenguajes de programación, han tendido, a medida que se han ido haciendo mas complejos, a adoptar la filosofía de los servicios prestados o programación orientada a objeto. Otras herramientas como el debugger han facilitado tremendamente la tarea de los programadores para depurar código y localizar y corregir errores de programación. La adopción de esta filosofía de trabajo ha posibilitado la aparición de sistemas informáticos complejos, robustos y de fácil actualización. Los principios que han posibilitado el aumento en complejidad, su robustez y han facilitado la evolución de lo sistemas informáticos, también podrían estar presentes en la célula. A estos mecanismos los podríamos llamar de «adaptación facilitada», y permitirían: a introducir azar «controladamente» en los genes, b acotar los conjuntos de genes sobre los que este mecanismo actúa, c «validar» si los cambios introducidos han sido o no adaptativos, d facilitar la fijación de dichos cambios en el genoma y e facilitar la propagación horizontal

  13. Reinvestigación de la formación de alquinilciclopropanocarbonitrilos a partir de complejos carbeno de Fischer: Diastereoselectividad y Mecanismo

    OpenAIRE

    Solis Moreno, Guillermo

    2015-01-01

    La reinvestigación de la síntesis de los alquinilciclopropanocarbonitrilos ha permitido corregir la configuración asignada al diastereoisómero mayoritario de la reacción, en la publicación original a través de experimentos de RMN de NOE y NOESY. Adicionalmente, aparece detallado el mecanismo de la reacción estudiado a través de calculos computacionales.

  14. Mecanismos de control en la ciudad de Osorno en el contexto de dictadura militar 1973 - 1990

    OpenAIRE

    Miguel Ángel Sepúlveda Chávez

    2014-01-01

    El siguiente trabajo tiene como objetivo describir los mecanismos de poder y control utilizados en la ciudad de Osorno bajo en el período de Dictadura Militar.  El Golpe Militar del 11 de septiembre de 1973 y la instauración de una dictadura de diecisiete años en Chile, fue un hecho que marcó a la sociedad chilena en general.  Durante el tiempo que duró, se intentó omitir los violentos actos ejecutados contra todos los contrarios al régimen militar.  Sistemáticas violaciones a los Derechos Hu...

  15. Dieta cetogênica: como o uso de uma dieta pode interferir em mecanismos neuropatológicos

    OpenAIRE

    Pereira, Érica Silva; Alves, Marion; Sacramento, Thaiana; Rocha, Vera Lúcia

    2010-01-01

    p. 78-82 A dieta cetogênica tem sido usada de forma ampla e com sucesso para o tratamento de crianças com epilepsia de difícil controle desde a década de 1920. Mas foi somente há uma década que a dieta cetogênica deixou de ser vista como um tratamento alternativo ou de última escolha para estes pacientes e seu uso tem sido considerado em todo o mundo. O objetivo deste trabalho foi revisar o conhecimento disponível acerca da dieta cetogênica: mecanismo de ação, eficácia, tolerabili...

  16. Estudio del ingreso de los bachilleres a la universidad: mecanismos y procesos de admisión

    OpenAIRE

    Analuiza Valdiviezo, Héctor Luciano

    2016-01-01

    El ingreso de los estudiantes a la universidad, significa abordar un tema que discute los procesos y mecanismos de admisión y que además presenta distintas posiciones que todavía no encuentran un punto de convergencia en el enfoque social e incluso ideológico de la universidad que queremos para cada país; resulta que las políticas que se ejecutan para democratizar el acceso a los centros de educación superior para unos pueden ser vanas y para otros muy significativas en el anhelo de iniciar u...

  17. Mecanismos de influencia sobre la comprobación corporal en las conductas de atracón

    OpenAIRE

    Antonios Dakanalis; Giuseppe Carrà; C. Alix Timko; Chiara Volpato; Joana Pla-Sanjuanelo; M. Assunta Zanetti; Massimo Clerici; Giuseppe Riva

    2015-01-01

    A pesar del papel teórico que desempeñan las conductas de comprobación corporal en el proceso de mantenimiento de la conducta de atracón, los mecanismos por los que pueden afectar a los atracones siguen sin estar claros. Tomando el modelo de la objetivación de la patología alimentaria como marco teórico, los autores examinaron las posibles funciones que desempeñan la vergüenza corporal, la ansiedad por la apariencia y la restricción alimentaria en la comprobación del cuerpo y los atracones. ...

  18. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  19. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...

  20. Degradation characteristics of 2,4-dichlorophenoxyacetic acid in electro-biological system

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, JingLi, E-mail: jinglizhangczp@126.com [Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Institute of Urban Construction, Tianjin 300384 (China); Cao, ZhanPing; Zhang, HongWei [School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, LianMei [Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Institute of Urban Construction, Tianjin 300384 (China); Sun, XuDong; Mei, Feng [School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387 (China)

    2013-11-15

    Highlights: • The 2,4-D reductive degradation was studied in an electro-biological system. • The electric auxiliary accelerates 2,4-D microbial degradation. • A electron transfer is achieved between the electrode, bacteria and the pollutants. • The paper provides a promising way for the degradation of persistent organics. -- Abstract: The reductive degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) was studied in an electro-biological system, a biological system and an electric catalytic system, respectively. Electrochemical characteristics were monitored by cyclic voltammetry and the intermediate products of 2,4-D degradation were determined by high speed liquid chromatography (HPLC). The results showed that all 2,4-D degradations in the three systems conformed to the kinetics characteristics of one-order reaction, and the degradation kinetics constants were 28.74 × 10{sup −2} h{sup −1}, 19.73 × 10{sup −2} h{sup −1} and 3.54 × 10{sup −2} h{sup −1}, respectively. The kinetics constant in the electro-biological system was higher than the sum in the other two systems by 19%. The electrochemical assistance provided the electrons and accelerated the electron transfer rate in the microbial degradation of 2,4-D. The degradation resulted from the microbial reduction strengthened by the electrochemical assistance. The electron transfer existed between the electrode, cytochrome, NAD and the pollutants. A long-range electron transfer process could be achieved on the multi-phase interfaces between the electrode, bacteria and the pollutants.

  1. Contribución a la Síntesis Dimensional de Mecanismos Planos para Generación de Trayectoria

    OpenAIRE

    Sánchez Marín, Francisco T.

    2000-01-01

    En este trabajo se han analizado por separado los elementos que definen el problema de sintesis dimensional óptima de mecanismos planos para generacion de trayectoria. Se ha contribuido a la normalización de proposición de funciones objetivo mediante el enunciado de requisitos que deben cumplir.Se ha propuesto la comparación geométrica de las curvas como función objetivo y se han elaborado métodos discretos. Asimismo se ha utilizado un método de optimización combinado exhaustivo-gradiante que...

  2. Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux

    International Nuclear Information System (INIS)

    Xu Li; Chu Xiakun; Yan Zhiqiang; Zheng Xiliang; Zhang Kun; Zhang Feng; Yan Han; Wu Wei; Wang Jin

    2016-01-01

    In this review, we explore the physical mechanisms of biological processes such as protein folding and recognition, ligand binding, and systems biology, including cell cycle, stem cell, cancer, evolution, ecology, and neural networks. Our approach is based on the landscape and flux theory for nonequilibrium dynamical systems. This theory provides a unifying principle and foundation for investigating the underlying mechanisms and physical quantification of biological systems. (topical review)

  3. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  4. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  5. Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

    Science.gov (United States)

    Vilas, Carlos; Balsa-Canto, Eva; García, Maria-Sonia G; Banga, Julio R; Alonso, Antonio A

    2012-07-02

    Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations.This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented methodology can be used for the efficient dynamic optimization of

  6. Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2010-10-01

    Introduction Duchenne muscular dystrophy (DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with...SUBJECT TERMS Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION...better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant proposal is led by Dr. Eric Hoffman, and it

  7. Ultra-Structure database design methodology for managing systems biology data and analyses

    Directory of Open Access Journals (Sweden)

    Hemminger Bradley M

    2009-08-01

    Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

  8. ADAM: analysis of discrete models of biological systems using computer algebra.

    Science.gov (United States)

    Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

    2011-07-20

    Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web

  9. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  10. Tradução intersemiótica dos mecanismos de busca no ciberespaço

    Directory of Open Access Journals (Sweden)

    Silvana Drumond Monteiro

    2013-08-01

    Full Text Available Introdução: O processo de busca faz parte da sociedade atual e os mecanismos de busca são os responsáveis pela indexação e elaboração dos índices contemporâneos no ciberespaço.Objetivo: Neste trabalho, a tradução intersemiótica verbo-visual do Google Images e oSKope, considerados híbridos por misturar linguagens, foi analisada visando avaliar o nível de equivalência dos signos nos resultados.Metodologia: A partir da categorização dos mecanismos, o paradigma semiótico vem sendo perscrutado, visando entender as matrizes da linguagem-pensamento, de Santaella, no funcionamento dos buscadores. Entende-se a intersemiose como a mistura das linguagens, sendo a hibridização sua característica principal. O conceito de tradução, apropriado de Jackobson, engloba a transmutação do signo dentro de uma língua (intralingual, de uma língua para outra (interlingual, ou a tradução propriamente dita, e entre uma linguagem e outra (intersemiótica. Outro conceito incorporado na pesquisa foi a tradução intrassemiótica, dentro da matriz visual, para colaborar com a análise da linguagem visual, que tem a forma como eixo de inteligibilidade e a figura como representação do visível.Resultados: O comportamento intersemiótico dos dois buscadores demonstrou-se, de maneira geral, satisfatório.Conclusões: O aprendizado da linguagem pela máquina faz diferença entre os níveis de tradução, entre o igual e o parecido, sobre o princípio de similaridade da forma, seja de uma língua, seja de uma imagem.

  11. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  12. Assessoria de Imprensa em Instituições Religiosas: mecanismos profissionais versus proselitismo

    Directory of Open Access Journals (Sweden)

    Eduardo Teixeira

    2012-12-01

    Full Text Available Ao agir por meio da assessoria de imprensa, as instituições religiosas constroem alicerces pela comunicação profissional, planejada e estratégica e, agregam valor aos públicos ao mostrar a sua imagem e suas ações e também ao discutir projetos. A incorporação das ferramentas comunicacionais disponíveis na assessoria de imprensa é um dos mecanismos que torna possível ampliar o vínculo e a participação social das instituições religiosas através da mídia, fortalecendo a identidade da instituição e fundamentando os relacionamentos com a comunidade na qual ela está inserida. Dessa maneira, as ações eclesiais não ficam atreladas apenas ao proselitismo, que em muitos casos atinge o patamar de “guerra santa” midiatizada nos veículos de comunicação brasileiros.

  13. The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

    Science.gov (United States)

    Ganguli, Suman; Hunt, C Anthony

    2004-01-01

    Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

  14. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.; Erban, R.; Giles, M.; Maini, P. K.

    2011-01-01

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new

  15. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  16. Complex fluids in biological systems experiment, theory, and computation

    CERN Document Server

    2015-01-01

    This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

  17. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  18. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  19. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

    2016-01-01

    Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches...... for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites....... The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production....

  20. Macroscopic Quantum-Type Potentials in Theoretical Systems Biology

    Directory of Open Access Journals (Sweden)

    Laurent Nottale

    2013-12-01

    Full Text Available We review in this paper the use of the theory of scale relativity and fractal space-time as a tool particularly well adapted to the possible development of a future genuine systems theoretical biology. We emphasize in particular the concept of quantum-type potentials, since, in many situations, the effect of the fractality of space—or of the underlying medium—can be reduced to the addition of such a potential energy to the classical equations of motion. Various equivalent representations—geodesic, quantum-like, fluid mechanical, stochastic—of these equations are given, as well as several forms of generalized quantum potentials. Examples of their possible intervention in high critical temperature superconductivity and in turbulence are also described, since some biological processes may be similar in some aspects to these physical phenomena. These potential extra energy contributions could have emerged in biology from the very fractal nature of the medium, or from an evolutive advantage, since they involve spontaneous properties of self-organization, morphogenesis, structuration and multi-scale integration. Finally, some examples of applications of the theory to actual biological-like processes and functions are also provided.

  1. Modular microfluidic system for biological sample preparation

    Science.gov (United States)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  2. Mecanismos implicados en la acción antioxidante de polifenoles naturales en productos de la pesca y acuicultura

    OpenAIRE

    Maestre, Rodrigo

    2012-01-01

    El objetivo de la presente tesis doctoral consistió en el estudio de los mecanismos que rigen la actividad de aquellos polifenoles de origen natural con mayor actividad antioxidante sobre el músculo de pescado. Asimismo, la investigación comprendió el efecto que dichos polifenoles pueden ejercer sobre la digestión y biodisponibilidad de los compuestos lipídicos del pescado, en particular los PUFAs ω-3. Para ello se eligió un extracto de uva rico en procianidinas que en estudios...

  3. Modelling, abstraction, and computation in systems biology: A view from computer science.

    Science.gov (United States)

    Melham, Tom

    2013-04-01

    Systems biology is centrally engaged with computational modelling across multiple scales and at many levels of abstraction. Formal modelling, precise and formalised abstraction relationships, and computation also lie at the heart of computer science--and over the past decade a growing number of computer scientists have been bringing their discipline's core intellectual and computational tools to bear on biology in fascinating new ways. This paper explores some of the apparent points of contact between the two fields, in the context of a multi-disciplinary discussion on conceptual foundations of systems biology. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Magnetic Actuation of Biological Systems

    Science.gov (United States)

    Lauback, Stephanie D.

    Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

  5. Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

    Science.gov (United States)

    Saks, Valdur; Monge, Claire; Guzun, Rita

    2009-01-01

    We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed. PMID:19399243

  6. Growing trend of CE at the omics level: the frontier of systems biology.

    Science.gov (United States)

    Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

    2010-01-01

    In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

  7. Fertilizer distribution mechanisms and side dress nitrogen fertilization in upland rice under no-tillage system Mecanismos de distribuição de fertilizante e adubação nitrogenada em cobertura no arroz de terras altas em sistema plantio direto

    Directory of Open Access Journals (Sweden)

    Carlos Alexandre Costa Crusciol

    2010-10-01

    Full Text Available Some crops have shown not to adapt to the no-tillage system (NTS as a consequence of the compaction of the superficial soil layer. In a certain way, the mechanism used in seeders to open furrows for the deposition of fertilizers can have great importance in facilitating root penetration. This study was carried out to evaluate the influence of two fertilizer distribution mechanisms and N fertilization in upland rice (Oryza sativa under NTS. The experiment was carried out in the growing seasons 2001/2002 and 2002/2003, in Botucatu, state of São Paulo, Brazil. A completely randomized block design was applied, with subdivided plots and four replications. Main plots consisted of two furrow opening mechanisms (furrow opener and double disk. Subplots consisted of four side dressing N levels (0, 40, 80 and 120 kg ha-1. The following parameters were evaluated: furrow and seed deposition depth, plant population, plant height, number of stems and panicles m-2, number of spikelets per panicle, spikelet fertility, weight of 1,000 grains, shoot dry matter, grain yield and N levels in the flag leaf. The success for upland rice establishment under the NTS in dry winter regions of Brazil is directly associated to the furrow opening mechanism of the seed-drill. The furrow opener mechanism resulted in deeper seed deposition, consequently decreasing seedling population, number of panicles per area and grain yield. Side dressing N fertilization in upland rice under NTS increases grain yield whenever the double disk mechanism is used to sow.Algumas culturas têm pouca adaptação ao sistema plantio direto (SPD, em vista da alta compactação da camada superficial do solo. Nesse caso, o mecanismo utilizado na semeadora para a abertura dos sulcos para deposição do fertilizante pode ter grande importância no sentido de facilitar a penetração das raízes. Avaliouse a influência do mecanismo de distribuição de fertilizante e da adubação nitrogenada na cultura

  8. Contextualización teórica de los mecanismos de protección en el mundo de la moda colombiana

    Directory of Open Access Journals (Sweden)

    Paola Andrea Zuluaga Ortiz

    2013-07-01

    Full Text Available Este artículo es el resultado de la primera parte de la investigación titulada “Mecanismos de protección en el mundo de la moda colombiana”. El documento presenta la importancia actual económica y social de la moda en Colombia, así como las dos posturas existentes frente a la protección de las creaciones de moda, mediante una norma redactada exclusivamente para estos casos. Así mismo, hace una breve explicación de cómo podrían protegerse estas creaciones con la normativa vigente de derechos de autor y propiedad industrial. Para lograr su objetivo, en la primera parte presenta una breve contextualización del mercado de la moda en Colombia; posteriormente hace una referencia de los diferentes argumentos presentados por quienes abogan por una normativa especial que regule estas creaciones, y por quienes rechazan esta postura, y creen en la libre circulación; en la tercera parte realiza una presentación de los posibles mecanismos legislativos vigentes que podrían tutelar este tipo de creaciones; y finalmente concluye que por medio de la normativa de derechos de autor y de propiedad industrial es posible proteger estas creaciones.

  9. Adoção de práticas de Green Supply Chain Management: mecanismos de indução e a importância das empresas focais

    Directory of Open Access Journals (Sweden)

    Ariana Fernandes Arantes

    2014-12-01

    Full Text Available Este artigo tem como objetivo analisar como práticas de Green Supply Chain Management (GSCM estão sendo induzidas, tanto interna quanto externamente, por empresas consideradas focais em suas cadeias de suprimentos localizadas no Brasil e atuantes no segmento de alta tecnologia. Foram realizados oito estudos de casos por meio da triangulação de fontes de dados: entrevistas, observações diretas e obtenção de dados secundários. Há mecanismos específicos para induzir práticas de GSCM internamente e externamente e destacam-se os mecanismos: treinamento ambiental, atividades logísticas, seleção e avaliação de fornecedores e marketing verde. Constatou-se também que a empresa focal é o vetor nesse processo.

  10. PANOPTISMO ORGANIZACIONAL – REFLEXÕES SOBRE A INSERÇÃO TECNOLÓGICA E AS ALTERAÇÕES NOS MECANISMOS DE CONTROLE NAS ORGANIZAÇÕES CONTEMPORÂNEAS

    Directory of Open Access Journals (Sweden)

    Monique Fonseca Cardoso

    2011-05-01

    Full Text Available O estudo tem como objetivo compreender a relação existente entre o emprego da tecnologia e os mecanismos de controle organizacional. São abordados os seguintes pontos: Tecnologia nas Organizações; Controle pela Tecnologia de Gestão; Vigilância Eletrônica: Controle pela Tecnologia Física; Panoptismo nas Organizações. As tecnologias aperfeiçoam os mecanismos de controle, tornando-os mais invisíveis e abrangentes. Tal refinamento vem sendo conseguido pela intensificação da utilização das tecnologias no processo de trabalho, em especial da vigilância eletrônica. A analogia ao panoptismo vem sendo associada aos sistemas de controle organizacional, e se tornando mais real, à medida que tais sistemas se sofisticam.

  11. Especiação e seus mecanismos: histórico conceitual e avanços recentes

    Directory of Open Access Journals (Sweden)

    Eduardo Colley

    2013-12-01

    Full Text Available Apresenta uma abordagem histórica sobre conceitos gerais de especiação e seus mecanismos, a partir das ideias primordiais até as teorias mais recentes que visam elucidar a origem da biodiversidade. Sabe-se que especiação é um tema polêmico e complexo que abrange praticamente todas as linhas de pesquisa dentro da biologia, além da geologia e da paleontologia. O objetivo principal do artigo é clarificar os conceitos teóricos sobre a origem das espécies animais, na ordem cronológica em que foram estabelecidos, ao longo do desenvolvimento da biologia evolutiva como ciência.

  12. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  13. Predicting biological system objectives de novo from internal state measurements

    Directory of Open Access Journals (Sweden)

    Maranas Costas D

    2008-01-01

    Full Text Available Abstract Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth and the subsequent application of linear programming (LP to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning. Results We present a novel method called Biological Objective Solution Search (BOSS for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae. Conclusion We illustrate how BOSS offers insight into the functional organization of biochemical networks

  14. Approaches to Quality Risk Management When Using Single-Use Systems in the Manufacture of Biologics.

    Science.gov (United States)

    Ishii-Watabe, Akiko; Hirose, Akihiko; Katori, Noriko; Hashii, Norikata; Arai, Susumu; Awatsu, Hirotoshi; Eiza, Akira; Hara, Yoshiaki; Hattori, Hideshi; Inoue, Tomomi; Isono, Tetsuya; Iwakura, Masahiro; Kajihara, Daisuke; Kasahara, Nobuo; Matsuda, Hiroyuki; Murakami, Sei; Nakagawa, Taishiro; Okumura, Takehiro; Omasa, Takeshi; Takuma, Shinya; Terashima, Iyo; Tsukahara, Masayoshi; Tsutsui, Maiko; Yano, Takahiro; Kawasaki, Nana

    2015-10-01

    Biologics manufacturing technology has made great progress in the last decade. One of the most promising new technologies is the single-use system, which has improved the efficiency of biologics manufacturing processes. To ensure safety of biologics when employing such single-use systems in the manufacturing process, various issues need to be considered including possible extractables/leachables and particles arising from the components used in single-use systems. Japanese pharmaceutical manufacturers, together with single-use suppliers, members of the academia and regulatory authorities have discussed the risks of using single-use systems and established control strategies for the quality assurance of biologics. In this study, we describe approaches for quality risk management when employing single-use systems in the manufacturing of biologics. We consider the potential impact of impurities related to single-use components on drug safety and the potential impact of the single-use system on other critical quality attributes as well as the stable supply of biologics. We also suggest a risk-mitigating strategy combining multiple control methods which includes the selection of appropriate single-use components, their inspections upon receipt and before releasing for use and qualification of single-use systems. Communication between suppliers of single-use systems and the users, as well as change controls in the facilities both of suppliers and users, are also important in risk-mitigating strategies. Implementing these control strategies can mitigate the risks attributed to the use of single-use systems. This study will be useful in promoting the development of biologics as well as in ensuring their safety, quality and stable supply.

  15. Iterative Systems Biology for Medicine – time for advancing from network signature to mechanistic equations

    KAUST Repository

    Gomez-Cabrero, David

    2017-05-09

    The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of systems biology arduous. However, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

  16. Growing trend of CE at the omics level: the frontier of systems biology--an update.

    Science.gov (United States)

    Ban, Eunmi; Park, Soo Hyun; Kang, Min-Jung; Lee, Hyun-Jung; Song, Eun Joo; Yoo, Young Sook

    2012-01-01

    Omics is the study of proteins, peptides, genes, and metabolites in living organisms. Systems biology aims to understand the system through the study of the relationship between elements such as genes and proteins in biological system. Recently, systems biology emerged as the result of the advanced development of high-throughput analysis technologies such as DNA sequencers, DNA arrays, and mass spectrometry for omics studies. Among a number of analytical tools and technologies, CE and CE coupled to MS are promising and relatively rapidly developing tools with the potential to provide qualitative and quantitative analyses of biological molecules. With an emphasis on CE for systems biology, this review summarizes the method developments and applications of CE for the genomic, transcriptomic, proteomic, and metabolomic studies focusing on the drug discovery and disease diagnosis and therapies since 2009. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Expresión diferencial de proteínas en Leishmania (Viannia panamensis asociadas con mecanismos de resistencia a antimoniato de meglumina

    Directory of Open Access Journals (Sweden)

    Ronald Guillermo Peláez

    2012-05-01

    Full Text Available Introducción. Los mecanismos de resistencia al antimonio pentavalente conocidos hasta el momento,se han descrito ampliamente en cepas del subgénero Leishmania, pero poco se sabe sobre lasproteínas involucradas en los mecanismos de resistencia presentes en cepas del subgénero Viannia,como Leishmania panamensis. Objetivo. Identificar proteínas diferencialmente expresadas entre las cepas de L. panamensis(UA140, sensible y resistente al antimonio pentavalente, y analizar el posible papel de estas proteínasen mecanismos de resistencia. Materiales y métodos. Las proteínas de las cepas, sensible y resistente al antimonio pentavalente, secompararon usando electroforesis bidimensional. Las proteínas con aumento de la expresión fueronaisladas e identificadas por espectrometría de masas mediante MALDI-TOF/TOF (Matrix AssistedLaser Desorption Ionization/Time of Flight. La expresión del ARNm de cinco de estas proteínas secuantificó mediante PCR en tiempo real. Resultados. Los geles bidimensionales de las cepas sensible y resistente detectaron 532±39 y 541±43manchas proteicas. Se encontraron 10 manchas con aumento de la expresión en la cepa resistente,identificadas como proteínas de choque térmico (Hsp60 mitocondrial, Hsp70 mitocondrial y citosólica,isomerasa de disulfuro, proteasa de cisteína, enolasa, factor de elongación 5-α, la subunidad 5-α delproteasoma y dos proteínas hipotéticas nombradas como Sp(2 y Sp(25. Conclusión. Este es el primer estudio llevado a cabo con una cepa resistente al antimonio pentavalenteen L. panamensis, en el cual se han identificado proteínas que están relacionadas con el mecanismode resistencia del parásito frente al medicamento, abriendo el camino para futuros estudios de estasproteínas como blancos terapéuticos.   doi: http://dx.doi.org/10.7705/biomedica.v32i3.392

  18. [Habitability and biological life support systems for man].

    Science.gov (United States)

    Gazenko, O G; Grigor'ev, A I; Meleshko, G I; Shepelev, E Ia

    1990-01-01

    This paper discusses general concepts and specific details of the habitability of space stations and planetary bases completely isolated from the Earth for long periods of time. It emphasizes inadequacy of the present-day knowledge about natural conditions that provide a biologically acceptable environment on the Earth as well as lack of information about life support systems as a source of consumables (oxygen, water, food) and a tool for waste management. The habitability of advanced space vehicles is closely related to closed bioregenerative systems used as life support systems.

  19. From globally coupled maps to complex-systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp [Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2015-09-15

    Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

  20. Newton, Laplace, and The Epistemology of Systems Biology

    Science.gov (United States)

    Bittner, Michael L.; Dougherty, Edward R.

    2012-01-01

    For science, theoretical or applied, to significantly advance, researchers must use the most appropriate mathematical methods. A century and a half elapsed between Newton’s development of the calculus and Laplace’s development of celestial mechanics. One cannot imagine the latter without the former. Today, more than three-quarters of a century has elapsed since the birth of stochastic systems theory. This article provides a perspective on the utilization of systems theory as the proper vehicle for the development of systems biology and its application to complex regulatory diseases such as cancer. PMID:23170064

  1. Avaliação dos mecanismos de aderência entre argamassa colante e substrato não poroso

    Directory of Open Access Journals (Sweden)

    Eduardo Pereira

    Full Text Available A resistência de aderência de um sistema de revestimento cerâmico é uma das mais importantes propriedades deste tipo de acabamento. O conhecimento das propriedades dos substratos e argamassas, e a capacidade de bem avaliar a interação entre os elementos são preceitos básicos para construírem-se revestimentos duráveis. Nesse sentido, o aperfeiçoamento dos modelos que descrevem os mecanismos de aderência, objetos de estudo deste trabalho, são essenciais, principalmente devido a diferenças nas características dos materiais relativas à porosidade, verificadas tanto em substratos como nas placas. O planejamento experimental consistiu no assentamento de um revestimento cerâmico externo utilizando-se a técnica de piso sobre piso, ensaios de resistência de aderência, aquisição de imagens em MEV dos pisos retirados do campo de testes e caracterização das argamassas colantes de estudo. Os resultados mostraram uma relação entre a resistência de aderência e a extensão de contato entre a argamassa e o substrato, indicando que o mecanismo de aderência para o assentamento de placas sobre substratos não porosos está diretamente relacionado com a extensão do contato entre os materiais, resultando em um modelo de aderência para o caso de revestimento cerâmico em substrato pouco poroso.

  2. Mecanismos de democracia directa en América Latina: Una revisión comparada

    Directory of Open Access Journals (Sweden)

    Steffan Gómez Campos

    2010-07-01

    Full Text Available Parte de la premisa que concibe a la democracia directa como una forma de reforzar la democracia representativa, en tanto exista una sólida cultura política y un marco institucional arraigado en los principios democráticos fundamentales. Realiza una perspectiva comparada basada fundamentalmente, en las previsiones constitucionales de los 18 países de América Latina. Tiene como objetivo primordial comparar los arreglos institucionales en materia de democracia directa, para establecer las características comunes y diferencias más significativas dentro de la región. Con base en ello se clasifican los mecanismos de democracia directa en las siguientes tres categorías: a el referéndum (y el plebiscito; b la iniciativa popular; y c la revocatoria de mandato.

  3. Roles of Nicotinamide Adenine Dinucleotide (NAD+ in Biological Systems

    Directory of Open Access Journals (Sweden)

    Palmiro Poltronieri

    2018-01-01

    Full Text Available NAD+ has emerged as a crucial element in both bioenergetic and signaling pathways since it acts as a key regulator of cellular and organism homeostasis. NAD+ is a coenzyme in redox reactions, a donor of adenosine diphosphate-ribose (ADPr moieties in ADP-ribosylation reactions, a substrate for sirtuins, a group of histone deacetylase enzymes that use NAD+ to remove acetyl groups from proteins; NAD+ is also a precursor of cyclic ADP-ribose, a second messenger in Ca++ release and signaling, and of diadenosine tetraphosphate (Ap4A and oligoadenylates (oligo2′-5′A, two immune response activating compounds. In the biological systems considered in this review, NAD+ is mostly consumed in ADP-ribose (ADPr transfer reactions. In this review the roles of these chemical products are discussed in biological systems, such as in animals, plants, fungi and bacteria. In the review, two types of ADP-ribosylating enzymes are introduced as well as the pathways to restore the NAD+ pools in these systems.

  4. Using systems and structure biology tools to dissect cellular phenotypes.

    Science.gov (United States)

    Floratos, Aris; Honig, Barry; Pe'er, Dana; Califano, Andrea

    2012-01-01

    The Center for the Multiscale Analysis of Genetic Networks (MAGNet, http://magnet.c2b2.columbia.edu) was established in 2005, with the mission of providing the biomedical research community with Structural and Systems Biology algorithms and software tools for the dissection of molecular interactions and for the interaction-based elucidation of cellular phenotypes. Over the last 7 years, MAGNet investigators have developed many novel analysis methodologies, which have led to important biological discoveries, including understanding the role of the DNA shape in protein-DNA binding specificity and the discovery of genes causally related to the presentation of malignant phenotypes, including lymphoma, glioma, and melanoma. Software tools implementing these methodologies have been broadly adopted by the research community and are made freely available through geWorkbench, the Center's integrated analysis platform. Additionally, MAGNet has been instrumental in organizing and developing key conferences and meetings focused on the emerging field of systems biology and regulatory genomics, with special focus on cancer-related research.

  5. Machismo a golpe de Whatsapp. El móvil: mecanismo de violencia sexista en los estudiantes universitarios

    OpenAIRE

    Villegas-Castrillo, Esther; Suriá Martínez, Raquel; Rosser Limiñana, Ana

    2014-01-01

    En nuestra sociedad, se muestra un contexto de violencia, que se visibiliza de manera cotidiana en todas las esferas. Generalmente, sus orígenes están vinculados con situaciones de violencia estructural y/o cultural que se va transmitiendo mediante los mecanismos de comunicación, aprendizaje social, imitación, asimilación o enseñanza. Las nuevas tecnologías, en concreto el uso del móvil, es un ejercicio cotidiano y creciente. Para los jóvenes, la tecnología forma parte de su vida desde la más...

  6. Dynamic analysis of piping with multiple damping mechanisms; Analisis dinamico de tuberias con multiples mecanismos de amortiguamiento

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz Lopez, Pablo [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1990-12-31

    This paper describes a damping criterion that allows realizing in a more convenient form the dynamic analysis of piping and structures in general, subjected to independent stimulations, fabricated in different materials and/or damping devices. This criterion, named composed damping, is applicable to the method of modal superimposition. [Espanol] En este trabajo se describe un criterio de amortiguamiento que permite realizar en una forma mas conveniente el analisis dinamico de tuberias y estructuras en general, sujetas a excitaciones independientes, compuestas de diferentes materiales y/o mecanismos de amortiguamiento. Este criterio, denominado amortiguamiento compuesto, es aplicable en el metodo de superposicion modal.

  7. Dynamic analysis of piping with multiple damping mechanisms; Analisis dinamico de tuberias con multiples mecanismos de amortiguamiento

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz Lopez, Pablo [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1989-12-31

    This paper describes a damping criterion that allows realizing in a more convenient form the dynamic analysis of piping and structures in general, subjected to independent stimulations, fabricated in different materials and/or damping devices. This criterion, named composed damping, is applicable to the method of modal superimposition. [Espanol] En este trabajo se describe un criterio de amortiguamiento que permite realizar en una forma mas conveniente el analisis dinamico de tuberias y estructuras en general, sujetas a excitaciones independientes, compuestas de diferentes materiales y/o mecanismos de amortiguamiento. Este criterio, denominado amortiguamiento compuesto, es aplicable en el metodo de superposicion modal.

  8. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  9. Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

    Directory of Open Access Journals (Sweden)

    Valdur Saks

    2009-03-01

    Full Text Available We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed.

  10. MECANISMOS DE MODULACION DE LA EXPRESION DEL FACTOR DE TRANSCRIPCION RUNX2 DURANTE EL CICLO CELULAR DE PREOSTEOBLASTOS

    OpenAIRE

    VARELA FIGUEROA, NELSON MIGUEL

    2010-01-01

    Runx2 regula el compromiso de linaje, la proliferación y la diferenciación de las células osteoprogenitoras. La regulación de los niveles de este factor de transcrpción, durante el ciclo celular de preosteoblastos, es considerada como uno de los aspectos críticos que modulan su función. Los antecedentes sugieren una estrecha relación entre el ciclo celular y la expresión del gen Runx2, pero existen varias interrogantes sobre los mecanismos y procesos que regulan las oscilacione...

  11. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  12. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  13. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  14. The Systems Biology Research Tool: evolvable open-source software

    OpenAIRE

    Wright, J; Wagner, A

    2008-01-01

    Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform calle...

  15. Mecanismos institucionales de control y transparencia en la rendición de cuentas en la gestión del programa de vaso de leche en el distrito de Carabayllo - Lima, año 2014

    OpenAIRE

    Ángeles Cueto, Víctor Alberto; Caller Loaiza, Alejandrina

    2017-01-01

    El presente trabajo de investigación tuvo como objetivo general, determinar si los mecanismos institucionales de control y transparencia en la rendición de cuentas inciden en la gestión del Programa del Vaso de Leche de la Municipalidad de Carabayllo - Lima, año 2014, contando con el apoyo de la Sub gerencia de dicha corporación edil, ubicada en el Distrito de Carabayllo, Provincia de Lima, Región Lima. Asimismo, se formuló como hipótesis general, los mecanismos institucionales de control...

  16. Biological indicators for monitoring water quality of MTF canals system

    Science.gov (United States)

    Sethi, S. L.

    1975-01-01

    Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

  17. Influencia del movimiento tridimensional sobre mecanismos planetarios en aerogeneradores (1ª Parte // Influence of Tridimensional movement in planetary gears used in wind generators. (First part

    Directory of Open Access Journals (Sweden)

    J. Wellesley-Bourke Funcasta

    2000-03-01

    Full Text Available En el trabajo se desarrolla el basamento matemático para establecer el análisis del efecto nocivo que se produce sobre losrodamientos de los mecanismos planetarios empleados en los aerogeneradores, dado esto por las condiciones variables delviento en cuanto a su velocidad y dirección.Palabras claves: Efecto giroscópico, engranajes planetarios, cargas dinámicas, energía eólica.________________________________________________________________________________AbstractIn this paper is presented the mathematical base that allow to establish the analysis that deals with the noxious effect that isproduced on the bearings of the planetary mechanisms in the wind energy corversor systems, given by the variable conditionsof the velocity and direction of the wind.Key words: Gyroscopic effect, planetary gears, dynamic loads, eolic energy.

  18. MECANISMOS DE PROTECCIÓN DE LOS TENEDORES DE BONOS EN EL MERCADO DE VALORES CHILENO

    Directory of Open Access Journals (Sweden)

    Jaime Ramiro Gallegos Zúñiga

    2013-01-01

    Full Text Available El presente informe busca exponer el régimen general que regula la emisión de bonos en Chile, presentando también algunas breves similitudes y diferencias con algunos aspectos del Derecho comparado. Una segunda parte de este estudio se centrará en los particulares mecanismos de defensa de los tenedores de bonos, frente a los demás inversionistas, que les posiciona como sujetos pri - vilegiados dentro del ordenamiento jurídico nacional, dada la relevancia que cobra el correc - to funcionamiento del mercado de capitales en el país, en atención a la adopción hace más de treinta años de un sistema de capitalización individual de las cotizaciones previsionales.

  19. Respuesta a la hipoxia: Un mecanismo sistémico basado en el control de la expresión génica Response to hypoxia: A systemic mechanism based on the control of gene expression

    Directory of Open Access Journals (Sweden)

    Carlos Caramelo

    2006-04-01

    Full Text Available La respuesta hipóxica, sobre la que se dispone de nuevos datos críticamente importantes, puede esquematizarse en tres sistemas, vg. de detección o sensor de oxígeno, de regulación, que controla la expresión génica y efector. El elemento principal de organización del sistema regulador es un factor de transcripción específico, el factor inducible por hipoxia 1 (HIF-1. En presencia de oxígeno, la subunidad a del HIF-1 (HIF-1a se modifica por las hidroxilasas, que constituyen el punto central del mecanismo sensor, induciendo su catabolismo por el proteosoma. Por el contrario, en hipoxia, o en presencia de algunos factores de crecimiento que incrementan su síntesis, el HIF-1a se transloca al núcleo, donde, unido al HIF-1b, actúa como factor transcripcional de genes con elementos de respuesta hipóxica (HRE en su promotor. Estos regulan la síntesis de una amplia serie de proteínas, que abarcan desde enzimas respiratorias y transportadores hasta hormonas involucradas en la regulación a escala del organismo de la circulación y la eritropoyesis. El papel del HIF-1 no se restringe a la mera inducción de una respuesta adaptativa a la falta de oxígeno, sino que participa significativamente en los mecanismos de reparación celular. Una simple lista de algunas alteraciones de importancia fisiopatológica, tanto estimulatorias como inhibitorias, que involucran al sistema de HIF-1, incluiría: enfermedad pulmonar crónica, adaptación al tabaco/humo, anemia/hemorragia, isquemia/reperfusión, crecimiento, vascularización y resistencia celular de los tumores, preeclampsia y crecimiento intrauterino retardado, hiper o hipovascularización retiniana, sobredosis de fármacos, enfermedad inflamatoria intestinal y curación de heridas. Esta sola enumeración ilustra la importancia de este mecanismo.New, critically important data have been recently generated about the response to hypoxia. This response can be schematized in three main systems or

  20. Macro to microfluidics system for biological environmental monitoring.

    Science.gov (United States)

    Delattre, Cyril; Allier, Cédric P; Fouillet, Yves; Jary, Dorothée; Bottausci, Frederic; Bouvier, Denis; Delapierre, Guillaume; Quinaud, Manuelle; Rival, Arnaud; Davoust, Laurent; Peponnet, Christine

    2012-01-01

    Biological environmental monitoring (BEM) is a growing field of research which challenges both microfluidics and system automation. The aim is to develop a transportable system with analysis throughput which satisfies the requirements: (i) fully autonomous, (ii) complete protocol integration from sample collection to final analysis, (iii) detection of diluted molecules or biological species in a large real life environmental sample volume, (iv) robustness and (v) flexibility and versatility. This paper discusses all these specifications in order to define an original fluidic architecture based on three connected modules, a sampling module, a sample preparation module and a detection module. The sample preparation module highly concentrates on the pathogens present in a few mL samples of complex and unknown solutions and purifies the pathogens' nucleic acids into a few μL of a controlled buffer. To do so, a two-step concentration protocol based on magnetic beads is automated in a reusable macro-to-micro fluidic system. The detection module is a PCR based miniaturized platform using digital microfluidics, where reactions are performed in 64 nL droplets handled by electrowetting on dielectric (EWOD) actuation. The design and manufacture of the two modules are reported as well as their respective performances. To demonstrate the integration of the complete protocol in the same system, first results of pathogen detection are shown. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Co-culture systems and technologies: taking synthetic biology to the next level.

    Science.gov (United States)

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M

    2014-07-06

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  2. EVALUACIÓN DE LOS PROYECTOS DE MECANISMO DE DESARROLLO LIMPIO PRESENTADOS A LA UNFCCC: LOS CRITERIOS DE SOSTENIBILIDAD ENTRE 2004 Y 2008

    Directory of Open Access Journals (Sweden)

    JAVIER SABOGAL AGUILAR

    2010-01-01

    Full Text Available El cambio climático es visto como uno de los problemas ambientales con mayores impactos sobre los sistemas humanos y naturales. La preocupación social sobre esta problemática es creciente como resultado del aumento de evidencia científi ca y fenómenos catastrófi cos, por lo que se ha buscado una respuesta antrópica (Sabogal, 2007. Los proyectos de Mecanismo de Desarrollo Limpio (MDL hacen parte de la propuesta de solución, generando una contribución a la mitigación de Gases Efecto Invernadero (GEI, sin embargo, contrario a la normatividad del Protocolo de Kioto, su impacto no es tan claro en términos de sostenibilidad. El presente artículo evalúa la presencia y el cumplimiento del objetivo de sostenibilidad en los proyectos de MDL presentados al Convención Marco de las Naciones Unidas sobre el Cambio Climático y el Protocolo de Kyoto (UNFCCC,para el periodo comprendido entre 2004 y 2008, identifi cando tendencias globales y planteando recomendaciones de mejoramiento en la aplicación del mecanismo.

  3. Organizing principles as tools for bridging the gap between system theory and biological experimentation.

    Science.gov (United States)

    Mekios, Constantinos

    2016-04-01

    Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems biology. In particular, examples reviewed in this paper suggest that rigorous mathematical expressions of design principles, imported primarily from engineering, could produce experimentally confirmable predictions of the regulatory properties of small biological networks. But this is not enough for contemporary systems biologists who adopt the holistic aspirations of early systemologists, seeking high-level organizing principles that could provide insights into problems of biological complexity at the whole-system level. While the presented evidence is not conclusive about whether this strategy could lead to the realization of the lofty goal of a comprehensive explanatory integration, it suggests that the ongoing quest for organizing principles is pragmatically advantageous for systems biologists. The formalisms postulated in the course of this process can serve as bridges between system-theoretic concepts and the results of molecular experimentation: they constitute theoretical tools for generalizing molecular data, thus producing increasingly accurate explanations of system-wide phenomena.

  4. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-25

    The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel new industrial processes have been developed over the last 10 years. Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy integrate with omics data and at the same time have been shown to have excellent predictive power. Despite our extensive knowledge of yeast metabolism and its regulation we are still facing challenges when we want to engineer complex traits, such as improved tolerance to toxic metabolites like butanol and elevated temperatures or when we want to engineer the highly complex protein secretory pathway. In this presentation it will be demonstrated how we can combine directed evolution with systems biology analysis to identify novel targets for rational design-build-test of yeast strains that have improved phenotypic properties. In this lecture an overview of systems biology of yeast will be presented together with examples of how genome-scale metabolic modeling can be used for prediction of cellular growth at different conditions. Examples will also be given on how adaptive laboratory evolution can be used for identifying targets for improving tolerance towards butanol, increased temperature and low pH and for improving secretion of heterologous proteins.

  5. The quest for a new modelling framework in mathematical biology. Comment on "On the interplay between mathematics and biology: Hallmarks towards a new systems biology" by N. Bellomo et al.

    Science.gov (United States)

    Eftimie, Raluca

    2015-03-01

    One of the main unsolved problems of modern physics is finding a "theory of everything" - a theory that can explain, with the help of mathematics, all physical aspects of the universe. While the laws of physics could explain some aspects of the biology of living systems (e.g., the phenomenological interpretation of movement of cells and animals), there are other aspects specific to biology that cannot be captured by physics models. For example, it is generally accepted that the evolution of a cell-based system is influenced by the activation state of cells (e.g., only activated and functional immune cells can fight diseases); on the other hand, the evolution of an animal-based system can be influenced by the psychological state (e.g., distress) of animals. Therefore, the last 10-20 years have seen also a quest for a "theory of everything"-approach extended to biology, with researchers trying to propose mathematical modelling frameworks that can explain various biological phenomena ranging from ecology to developmental biology and medicine [1,2,6]. The basic idea behind this approach can be found in a few reviews on ecology and cell biology [6,7,9-11], where researchers suggested that due to the parallel between the micro-scale dynamics and the emerging macro-scale phenomena in both cell biology and in ecology, many mathematical methods used for ecological processes could be adapted to cancer modelling [7,9] or to modelling in immunology [11]. However, this approach generally involved the use of different models to describe different biological aspects (e.g., models for cell and animal movement, models for competition between cells or animals, etc.).

  6. Metabolic, Replication and Genomic Category of Systems in Biology, Bioinformatics and Medicine

    OpenAIRE

    I. C. Baianu

    2012-01-01

    Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life’s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important quest...

  7. The SEEK: a platform for sharing data and models in systems biology.

    Science.gov (United States)

    Wolstencroft, Katy; Owen, Stuart; du Preez, Franco; Krebs, Olga; Mueller, Wolfgang; Goble, Carole; Snoep, Jacky L

    2011-01-01

    Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be heterogeneous and often involves high-throughput "omics" analyses. Models are developed iteratively from data generated in the projects and from the literature. Consequently, there is a growing requirement for exchanging experimental data, mathematical models, and scientific protocols between consortium members and a necessity to record and share the outcomes of experiments and the links between data and models. The overall output of a research consortium is also a valuable commodity in its own right. The research and associated data and models should eventually be available to the whole community for reuse and future analysis. The SEEK is an open-source, Web-based platform designed for the management and exchange of systems biology data and models. The SEEK was originally developed for the SysMO (systems biology of microorganisms) consortia, but the principles and objectives are applicable to any systems biology project. The SEEK provides an index of consortium resources and acts as gateway to other tools and services commonly used in the community. For example, the model simulation tool, JWS Online, has been integrated into the SEEK, and a plug-in to PubMed allows publications to be linked to supporting data and author profiles in the SEEK. The SEEK is a pragmatic solution to data management which encourages, but does not force, researchers to share and disseminate their data to community standard formats. It provides tools to assist with management and annotation as well as incentives and added value for following these recommendations. Data exchange and reuse rely on sufficient annotation, consistent metadata descriptions, and the use of standard exchange formats for models, data, and the experiments they are derived from. In this chapter, we present the SEEK platform

  8. Understanding genetic variation - the value of systems biology.

    Science.gov (United States)

    Hütt, Marc-Thorsten

    2014-04-01

    Pharmacology is currently transformed by the vast amounts of genome-associated information available for system-level interpretation. Here I review the potential of systems biology to facilitate this interpretation, thus paving the way for the emerging field of systems pharmacology. In particular, I will show how gene regulatory and metabolic networks can serve as a framework for interpreting high throughput data and as an interface to detailed dynamical models. In addition to the established connectivity analyses of effective networks, I suggest here to also analyze higher order architectural properties of effective networks. © 2013 The British Pharmacological Society.

  9. Cell illustrator 4.0: a computational platform for systems biology.

    Science.gov (United States)

    Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

    2011-01-01

    Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

  10. Evaluation of impedance on biological Tissues using automatic control measurement system

    Energy Technology Data Exchange (ETDEWEB)

    Kil, Sang Hyeong; Shin, Dong Hoon; Lee, Seong Mo [Pusan National University, Yangsan (Korea, Republic of); Lee, Moo Seok; Kim, Sang Sik [Pusan National University, Busan (Korea, Republic of); Kim, Gun FDo; Lee, Jong Kyu [Pukyung National University, Busan (Korea, Republic of)

    2015-08-15

    Each biological tissue has endemic electrical characteristics owing to various differences such as those in cellular arrangement or organization form. The endemic electrical characteristics change when any biological change occurs. This work is a preliminary study surveying the changes in the electrical characteristics of biological tissue caused by radiation exposure. For protection against radiation hazards, therefore the electrical characteristics of living tissue were evaluated after development of the automatic control measurement system using LabVIEW. No alteration of biological tissues was observed before and after measurement of the electrical characteristics, and the biological tissues exhibited similar patterns. Through repeated measurements using the impedance/gain-phase analyzer, the coefficient of variation was determined as within 10%. The reproducibility impedance phase difference in electrical characteristics of the biological tissue did not change, and the tissue had resistance. The absolute value of impedance decreased constantly in proportion to the frequency. It has become possible to understand the electrical characteristics of biological tissues through the measurements made possible by the use of the developed.

  11. Evaluation of impedance on biological Tissues using automatic control measurement system

    International Nuclear Information System (INIS)

    Kil, Sang Hyeong; Shin, Dong Hoon; Lee, Seong Mo; Lee, Moo Seok; Kim, Sang Sik; Kim, Gun FDo; Lee, Jong Kyu

    2015-01-01

    Each biological tissue has endemic electrical characteristics owing to various differences such as those in cellular arrangement or organization form. The endemic electrical characteristics change when any biological change occurs. This work is a preliminary study surveying the changes in the electrical characteristics of biological tissue caused by radiation exposure. For protection against radiation hazards, therefore the electrical characteristics of living tissue were evaluated after development of the automatic control measurement system using LabVIEW. No alteration of biological tissues was observed before and after measurement of the electrical characteristics, and the biological tissues exhibited similar patterns. Through repeated measurements using the impedance/gain-phase analyzer, the coefficient of variation was determined as within 10%. The reproducibility impedance phase difference in electrical characteristics of the biological tissue did not change, and the tissue had resistance. The absolute value of impedance decreased constantly in proportion to the frequency. It has become possible to understand the electrical characteristics of biological tissues through the measurements made possible by the use of the developed.

  12. Mechanisms of quinolone resistance in Salmonella spp. / Mecanismos de resistência às quinolonas em Salmonella spp.

    Directory of Open Access Journals (Sweden)

    Tereza Cristina Rocha Moreira de Oliveira

    2010-07-01

    Full Text Available Salmonellosis is a common and widespread zoonotic disease of humans and a frequent cause of foodborne disease. Treatment of severe and systemic salmonellosis is usually done with fluoroquinolones. In this review resistance mechanisms of Salmonella to quinolones are discussed. Single point mutations in the quinolone resistant determining region (QRDR of the gyrA gene may be sufficient to generate high levels of resistance to non-fluorated quinolones and also may decrease the fluoroquinolones susceptibility. Other resistance mechanisms that should be considered are mutations in parC gene, the possibility of acquiring resistance through plasmidial transference and hyper-expression of efflux pumps. Fluoroquinolones resistance is still relatively uncommon in Salmonella compared to other species belonging to the Enterobacteriaceae family. However, the more careful use of fluoroquinolones in veterinary and human medicine is essential to decrease the selective pressure which can avoid the emergence and spread of resistant clones and consequently maintain the clinical efficacy of this group of antibiotics.A salmonelose é uma zoonose de importância mundial e uma das mais freqüentes doenças de origem alimentar. As fluoroquinolonas são a principal opção para o tratamento de salmoneloses graves ou sistêmicas. Esta revisão de literatura teve como objetivo apresentar os principais mecanismos envolvidos na resistência de Salmonella spp a estes antimicrobianos. Mutações de ponto na Região Determinante de Resistência à Quinolona (QRDR do gene gyrA podem gerar altos níveis de resistência a quinolonas não-fluoradas, além de reduzir a suscetibilidade as fluoroquinolonas. Outros mecanismos de resistência que também precisam ser considerados são as mutações no gene parC, a possibilidade do envolvimento de plasmídios de resistência e o sistema de efluxo ativo. A resistência às fluoroquinolonas ainda é incomum em Salmonella spp., quando

  13. How causal analysis can reveal autonomy in models of biological systems

    Science.gov (United States)

    Marshall, William; Kim, Hyunju; Walker, Sara I.; Tononi, Giulio; Albantakis, Larissa

    2017-11-01

    Standard techniques for studying biological systems largely focus on their dynamical or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or the dynamics of the system as a whole disregards the organizational structure of the system-whether there are subsets of elements with joint causes or effects, and whether the system is strongly integrated or composed of several loosely interacting components. Integrated information theory offers a theoretical framework to (1) investigate the compositional cause-effect structure of a system and to (2) identify causal borders of highly integrated elements comprising local maxima of intrinsic cause-effect power. Here we apply this comprehensive causal analysis to a Boolean network model of the fission yeast (Schizosaccharomyces pombe) cell cycle. We demonstrate that this biological model features a non-trivial causal architecture, whose discovery may provide insights about the real cell cycle that could not be gained from holistic or reductionist approaches. We also show how some specific properties of this underlying causal architecture relate to the biological notion of autonomy. Ultimately, we suggest that analysing the causal organization of a system, including key features like intrinsic control and stable causal borders, should prove relevant for distinguishing life from non-life, and thus could also illuminate the origin of life problem. This article is part of the themed issue 'Reconceptualizing the origins of life'.

  14. Mecanismos de cardiotoxicidad: antineoplásicos, anti-inflamatorios no esteroideos, antipsicóticos, cocaetileno y simpaticomiméticos Mechanisms of cardiotoxicity: antineoplastics, nonsteroidal anti-inflammatory drugs, antipsychotics, cocaethylene and sympathomimetics

    Directory of Open Access Journals (Sweden)

    Lukas Salazar

    2011-04-01

    Full Text Available La interacción constante del organismo humano con diferentes sustancias, que incluso en muchas ocasiones se consideran inofensivas, tiene un alto impacto sobre todos los sistemas, siendo el cardiovascular uno de los más afectados. Por lo tanto, es vital reconocer los mecanismos por los cuales estas sustancias ejercen su efecto tóxico sobre este sistema, bien sea afectando la estabilidad de membrana y la función contráctil o generando disfunción de organelos intracelulares y estrés oxidativo. Numerosos estudios han descubierto efectos lesivos de sustancias, como la clozapina y las catecolaminas, que han tenido amplio uso durante largos años. En la actualidad aún se realizan investigaciones que buscan esclarecer los mecanismos cardiotóxicos de medicamentos de formulación común, entre ellos antineoplásicos y anti-inflamatorios no esteroideos (AINE, así como de sustancias de uso habitual que causan adicción, tales como alcohol, cocaína y cocaetileno, su metabolito activo.The constant interaction of the human body with different substances that are even in many cases considered harmless has a high impact on all systems, being the cardiovascular system one of the most affected. Therefore, it is vital to recognize the mechanisms by which these substances exert their toxic effect on this system, either affecting the membrane stability and the contractile function, or generating intracellular organelles dysfunction and oxidative stress. Numerous studies have found that drugs which have been widely used for many years such as clozapine and catecholamines, have harmful effects. Research is still being done seeking to clarify the cardiotoxic mechanisms of drugs commonly formulated, including anticancer and non steroidal anti-inflammatory drugs (NSAIDs, as well as commonly used substances that cause addiction, such as alcohol, cocaine and cocaethylene, its active metabolite.

  15. Systems biology approaches to the study of cardiovascular drugs

    NARCIS (Netherlands)

    Nikolsky, Y.; Kleemann, R.

    2010-01-01

    Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and comprehensive

  16. BIOZON: a system for unification, management and analysis of heterogeneous biological data

    Directory of Open Access Journals (Sweden)

    Yona Golan

    2006-02-01

    Full Text Available Abstract Background Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. Description Here we present a system (Biozon that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways. It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. Conclusion The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

  17. Systems of organic farming in spring vetch I: Biological response of sucking insect pests

    Directory of Open Access Journals (Sweden)

    Ivelina Nikolova

    2015-04-01

    Full Text Available Four systems of organic farming and a conventional farming system were studied over the period 2012-2014. The organic system trial variants included: I – an organic farming system without any biological products used (growth under natural soil fertility – Control; II – an organic farming system involving the use of a biological foliar fertilizer and a biological plant growth regulator (Polyversum+Biofa; III – an organic farming system in which a biological insecticide (NeemAzal T/S was used; IV – an organic farming system including a combination of three organic products: the foliar fertilizer, the plant growth regulator and the bioinsecticide (Polyversum+Biofa+NeemAzal T/S. Variant V represented a conventional farming system in which synthetic products were used in combination (foliar fertilizer, plant growth regulator and insecticide: Masterblend+Flordimex 420+Nurelle D. Treatment of vetch plants with the biological insecticide NeemAzal in combination with Biofa and Polyversum resulted in the lowest density of sucking pests, compared to all other organic farming methods tested (i.e. without NeemAzal, with NeemAzal alone, and its combination with Biofa and Polyversum. The greatest reduction in pest numbers during the vegetation period in that variant was observed in species of the order Thysanoptera (36.0-41.4%, followed by Hemiptera, and the families Aphididae (31.6-40.3% and Cicadellidae (27.3-28.6%. This combination showed an efficient synergistic interaction and an increase in biological efficacy as compared to individual application of NeemAzal. The highest toxic impact was found against Thrips tabaci, followed by Acyrthosiphon pisum. An analysis of variance regarding the efficacy against the species A. pisum, E. pteridis and T. tabaci showed that type of treatment had the most dominant influence and statistically significant impact.

  18. La escritura en el archivo: mecanismos de dominio y control en el Nuevo Reino de Granada

    Directory of Open Access Journals (Sweden)

    Alfonso Rubio Hernández

    2007-11-01

    Full Text Available Estudio que explora la manera en que se construye el archivo colonial a través de mecanismos jurídico-administrativos, dedicados a ejercer el control sobre las poblaciones subordinadas y el mantenimiento del poder colonial. El paso del testimonio oral, de los indígenas, al documento escrito, característico de la cultura letrada española, representó un desafío cultural. Paulatinamente, los indígenas aprendieron a usar el documento escrito y a emprender litigios judiciales. El control burocrático de la monarquía española dependió centralmente del uso y archivo de la documentación escrita y del papel que jugaron los letrados.

  19. A data integration approach for cell cycle analysis oriented to model simulation in systems biology

    Directory of Open Access Journals (Sweden)

    Mosca Ettore

    2007-08-01

    Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

  20. The mammary gland in domestic ruminants: a systems biology perspective.

    Science.gov (United States)

    Ferreira, Ana M; Bislev, Stine L; Bendixen, Emøke; Almeida, André M

    2013-12-06

    Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance. © 2013.

  1. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-01

    . Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy

  2. Evolving cell models for systems and synthetic biology.

    Science.gov (United States)

    Cao, Hongqing; Romero-Campero, Francisco J; Heeb, Stephan; Cámara, Miguel; Krasnogor, Natalio

    2010-03-01

    This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm's results as well as of the resulting evolved cell models.

  3. Improvements in algal lipid production: a systems biology and gene editing approach.

    Science.gov (United States)

    Banerjee, Avik; Banerjee, Chiranjib; Negi, Sangeeta; Chang, Jo-Shu; Shukla, Pratyoosh

    2018-05-01

    In the wake of rising energy demands, microalgae have emerged as potential sources of sustainable and renewable carbon-neutral fuels, such as bio-hydrogen and bio-oil. For rational metabolic engineering, the elucidation of metabolic pathways in fine detail and their manipulation according to requirements is the key to exploiting the use of microalgae. Emergence of site-specific nucleases have revolutionized applied research leading to biotechnological gains. Genome engineering as well as modulation of the endogenous genome with high precision using CRISPR systems is being gradually employed in microalgal research. Further, to optimize and produce better algal platforms, use of systems biology network analysis and integration of omics data is required. This review discusses two important approaches: systems biology and gene editing strategies used on microalgal systems with a focus on biofuel production and sustainable solutions. It also emphasizes that the integration of such systems would contribute and compliment applied research on microalgae. Recent advances in microalgae are discussed, including systems biology, gene editing approaches in lipid bio-synthesis, and antenna engineering. Lastly, it has been attempted here to showcase how CRISPR/Cas systems are a better editing tool than existing techniques that can be utilized for gene modulation and engineering during biofuel production.

  4. Recent developments in systems biology and metabolic engineering of plant microbe interactions

    Directory of Open Access Journals (Sweden)

    Vishal Kumar

    2016-09-01

    Full Text Available Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

  5. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

    Science.gov (United States)

    Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

    2011-04-15

    The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

  6. Casual Games and Casual Learning About Human Biological Systems

    Science.gov (United States)

    Price, C. Aaron; Gean, Katherine; Christensen, Claire G.; Beheshti, Elham; Pernot, Bryn; Segovia, Gloria; Person, Halcyon; Beasley, Steven; Ward, Patricia

    2016-02-01

    Casual games are everywhere. People play them throughout life to pass the time, to engage in social interactions, and to learn. However, their simplicity and use in distraction-heavy environments can attenuate their potential for learning. This experimental study explored the effects playing an online, casual game has on awareness of human biological systems. Two hundred and forty-two children were given pretests at a Museum and posttests at home after playing either a treatment or control game. Also, 41 children were interviewed to explore deeper meanings behind the test results. Results show modest improvement in scientific attitudes, ability to identify human biological systems and in the children's ability to describe how those systems work together in real-world scenarios. Interviews reveal that children drew upon their prior school learning as they played the game. Also, on the surface they perceived the game as mainly entertainment but were easily able to discern learning outcomes when prompted. Implications for the design of casual games and how they can be used to enhance transfer of knowledge from the classroom to everyday life are discussed.

  7. MECANISMO DE GELATINIZACIÓN DEL ALMIDÓN NATIVO DE BANANO EXPORTABLE DEL ECUADOR

    Directory of Open Access Journals (Sweden)

    Omar Martínez

    2015-05-01

    Full Text Available El presente trabajo tuvo como objetivo fundamental estudiar el mecanismo de gelatinización del almidón nativo de banano de la especie Musa sapientum L. exportable del Ecuador. Se estudiaron las variedades Cavendish, Filipino, Valery y Orito, y a su vez, se estudió su potencial para ser añadido en alimentos que demanden características tecnológicas funcionales deseables como agentes espesantes, gelificantes y estabilizantes. También se determinó el tamaño, la forma de gránulos de almidón, temperatura de gelatinización y viscosidad máxima; obteniéndose los siguientes valores: de 25 a 35 μm; 77,7 a 80 °C y de 259 a 270 UB, respectivamente. Según los resultados obtenidos, el almidón nativo de banano de las variedades estudiadas, puede ser incorporado en la elaboración de alimentos que demanden  las características mencionadas.

  8. Factor de crecimiento transformante beta-1: estructura, función y mecanismos de regulación en cáncer

    Directory of Open Access Journals (Sweden)

    Peralta-Zaragoza Oscar

    2001-01-01

    Full Text Available El factor de crecimiento transformante beta-1 (TGF-beta1 es sintetizado por muchas estirpes celulares como linfocitos, macrófagos y células dendríticas, y su expresión regula de manera autócrina o parácrina la diferenciación, proliferación y el estado de activación de éstas y muchas otras células. En general, el TGF-beta1 tiene propiedades pleiotrópicas en el contexto de la respuesta inmune durante el desarrollo de infecciones y procesos neoplásicos; sin embargo, los mecanismos de acción y regulación de la expresión de esta citocina aún no se comprenden del todo. En la presente revisión se describen las propiedades biológicas y los procesos moleculares que regulan la expresión del TGF-beta1, para entender los efectos de esta citocina durante la proliferación y la diferenciación celular. El conocimiento de los mecanismos moleculares de la regulación del TGF-beta1 puede representar una importante estrategia de tratamiento del cáncer. El texto completo en inglés de este artículo está disponible en: http://www.insp.mx/salud/index.html

  9. Mecanismos de aprendizagem em organizações: desenvolvimento e validação de uma escala de medida.

    Directory of Open Access Journals (Sweden)

    Antonio Isidro da Silva Filho

    2009-02-01

    Full Text Available O presente estudo objetivou desenvolver e validar a Escala de Mecanismos deAprendizagem em Organizações (Emao. A partir da Measurement Scale of OrganizationalLearning de López, Peón e Ordás (2005, composta dos fatores aquisiçãodo conhecimento, distribuição, interpretação e memória organizacional, foirealizada a tradução dos itens da língua inglesa para o português e adequação delinguagem para a cultura brasileira. Feito isso, realizou-se a análise de construtoe semântica dos itens; e dos 25 itens originais, 22 permaneceram para validaçãoempírica da escala. Quinhentos e vinte e dois funcionários de uma instituiçãofinanceira com sede em Brasília (DF responderam ao instrumento de pesquisa.Após as análises fatoriais, identificou-se a melhor solução (rotação Varimax comtrês fatores, de KMO igual a 0,92. Os fatores foram denominados: AquisiçãoInterna e Externa de Conhecimentos (7 itens, Q = 0,81, Compartilhamento deConhecimentos (11 itens, Q = 0,87 e Codificação e Controle de Conhecimentos (4itens, Q = 0,71. Concluindo o estudo, descrevem-se recomendações para futuraspesquisas visando ao melhoramento da escala validada, bem como à realização deestudos que verifiquem as relações entre mecanismos de aprendizagem em organizaçõescom outras variáveis da literatura de comportamento organizacional.

  10. Study of the effects of radon in three biological systems

    International Nuclear Information System (INIS)

    Tavera, L.; Balcazar, M.; Lopez, A.; Brena, M.; Rosa, M.E. De la; Villalobos P, R.

    2002-01-01

    The radon and its decay products are responsible of the 3/4 parts of the exposure of the persons to the environmental radiation. The discovery at the end of XIX Century of the illnesses, mainly of cancer, which appeared in the presence of radon, lead to an accelerated growing of the radon studies: monitoring, dosimetry, effects on the persons, etc. Several epidemiological studies of radon in miners and population in general have been realized; advancing in the knowledge about the concentration-lung cancer risk relationship, but with discrepancies in the results depending on the concentration levels. Therefor, studies which consuming time, efforts and money go on doing. The research of the radon effects in biological systems different to human, allows to realize studies in less time, in controlled conditions and generally at lower cost, generating information about the alpha radiation effects in the cellular field. Therefor it was decided to study the response of three biological systems exposed to radon: an unicellular bacteria Escherichia Coli which was exposed directly to alpha particles from an electrodeposited source for determining the sensitivity limit of the chose technique. A plant, Tradescantia, for studying the cytogenetic effect of the system exposed to controlled concentrations of radon. An insect, Drosophila Melanogaster, for studying the genetic effects and the accumulated effects in several generations exposed to radon. In this work the experimental settlements are presented for the expositions of the systems and the biological results commenting the importance of these. (Author)

  11. Governança corporativa: a formação de mecanismos por investidores institucionais, o caso PREVI

    OpenAIRE

    Jesus, Roberto Martins Ribeiro de

    2004-01-01

    O objetivo geral deste trabalho de dissertação de mestrado é identificar e analisar os principais fatores históricos e institucionais que contribuíram para a formação dos atuais mecanismos de govemança corporativa adotados pela Caixa de Previdência dos Funcionários do Banco do Brasil (PREVI) em relação às empresas em que detém participação acionária relevante. Tendo como foco da investigação o centenário e maior fundo de pensão da América Latina, com investimentos totais da ...

  12. Biological removal of algae in an integrated pond system

    CSIR Research Space (South Africa)

    Meiring, PGJ

    1995-01-01

    Full Text Available A system of oxidation ponds in series with a biological trickling filter is described. It was known that this arrangement was incapable of reducing effectively the levels of algae present in the pond liquid even though nitrification was effected...

  13. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. Small programs as building unit. Why PERL? Why not BioPerl? Why not PERL modules? Advantage of independent programs. Language independent; Can be run independently.

  14. The role of analytical sciences in medical systems biology

    NARCIS (Netherlands)

    Greef, J. van der; Stroobant, P.; Heijden, R. van der

    2004-01-01

    Medical systems biology has generated widespread interest because of its bold conception and exciting potential, but the field is still in its infancy. Although there has been tremendous progress achieved recently in generating, integrating and analysing data in the medical and pharmaceutical field,

  15. Animal protein production modules in biological life support systems: Novel combined aquaculture techniques based on the closed equilibrated biological aquatic system (C.E.B.A.S.)

    Science.gov (United States)

    Blüm, V.; Andriske, M.; Kreuzberg, K.; Schreibman, M. P.

    Based on the experiences made with the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) which was primarily deveoloped for long-term and multi-generation experiments with aquatic animals and plants in a space station highly effective fresh water recycling modules were elaborated utilizing a combination of ammonia oxidizing bacteria filters and higher plants. These exhibit a high effectivity to eliminate phosphate and anorganic nitrogen compounds and arc. in addidition. able to contribute to the oxygen supply of the aquatic animals. The C.E.B.A.S. filter system is able to keep a closed artificial aquatic ecosystem containing teleost fishes and water snails biologically stable for several month and to eliminate waste products deriving from degraded dead fishes without a decrease of the oxygen concentration down to less than 3.5 mg/l at 25 °C. More advanced C.E.B.A.S. filter systems, the BIOCURE filters, were also developed for utilization in semiintensive and intensive aquaculture systems for fishes. In fact such combined animal-plant aquaculture systems represent highly effective productions sites for human food if proper plant and fish species are selected The present papers elucidates ways to novel aquaculture systems in which herbivorous fishes are raised by feeding them with plant biomass produced in the BIOCURE filters and presents the scheme of a modification which utilizes a plant species suitable also for human nutrition. Special attention is paid to the benefits of closed aquaculture system modules which may be integrated into bioregenerative life support systems of a higher complexity for, e. g.. lunar or planetary bases including some psychologiccal aspects of the introduction of animal protein production into plant-based life support systems. Moreover, the basic reproductive biological problems of aquatic animal breeding under reduced gravity are explained leading to a disposition of essential research programs in this context.

  16. Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis.

    Science.gov (United States)

    O'Malley, Maureen A

    2012-01-01

    Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

  17. Metabolic adaptation of a human pathogen during chronic infections - a systems biology approach

    DEFF Research Database (Denmark)

    Thøgersen, Juliane Charlotte

    modeling to uncover how human pathogens adapt to the human host. Pseudomonas aeruginosa infections in cystic fibrosis patients are used as a model system for under-­‐ standing these adaptation processes. The exploratory systems biology approach facilitates identification of important phenotypes...... by classical molecular biology approaches where genes and reactions typically are investigated in a one to one relationship. This thesis is an example of how mathematical approaches and modeling can facilitate new biologi-­‐ cal understanding and provide new surprising ideas to important biological processes....... and metabolic pathways that are necessary or related to establishment of chronic infections. Archetypal analysis showed to be successful in extracting relevant phenotypes from global gene expression da-­‐ ta. Furthermore, genome-­‐scale metabolic modeling showed to be useful in connecting the genotype...

  18. Efficient Bayesian estimates for discrimination among topologically different systems biology models.

    Science.gov (United States)

    Hagen, David R; Tidor, Bruce

    2015-02-01

    A major effort in systems biology is the development of mathematical models that describe complex biological systems at multiple scales and levels of abstraction. Determining the topology-the set of interactions-of a biological system from observations of the system's behavior is an important and difficult problem. Here we present and demonstrate new methodology for efficiently computing the probability distribution over a set of topologies based on consistency with existing measurements. Key features of the new approach include derivation in a Bayesian framework, incorporation of prior probability distributions of topologies and parameters, and use of an analytically integrable linearization based on the Fisher information matrix that is responsible for large gains in efficiency. The new method was demonstrated on a collection of four biological topologies representing a kinase and phosphatase that operate in opposition to each other with either processive or distributive kinetics, giving 8-12 parameters for each topology. The linearization produced an approximate result very rapidly (CPU minutes) that was highly accurate on its own, as compared to a Monte Carlo method guaranteed to converge to the correct answer but at greater cost (CPU weeks). The Monte Carlo method developed and applied here used the linearization method as a starting point and importance sampling to approach the Bayesian answer in acceptable time. Other inexpensive methods to estimate probabilities produced poor approximations for this system, with likelihood estimation showing its well-known bias toward topologies with more parameters and the Akaike and Schwarz Information Criteria showing a strong bias toward topologies with fewer parameters. These results suggest that this linear approximation may be an effective compromise, providing an answer whose accuracy is near the true Bayesian answer, but at a cost near the common heuristics.

  19. Heavy water effects on the structure, functions and behavior of biological systems

    International Nuclear Information System (INIS)

    Buzgariu, Wanda; Caloianu, Maria; Moldovan, Lucia; Titescu, G.

    2003-01-01

    The H 2 O substitution for D 2 O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

  20. Autonomy and the Ambiguity of Biological Rationalities: Systems Theory, ADHD and Kant

    Science.gov (United States)

    Haye, Andrés; Matus, Claudia; Cottet, Pablo; Niño, Sebastián

    2018-01-01

    We present a theoretical review of notions of autonomy to show how they organize discourses within social sciences around the biological reality of ideal self-regulating individuals. First, we reconstruct key meanings of autonomy in biological theory, focusing on theories of autopoietic systems and their connections to constructivist…

  1. La participación ciudadana en la encrucijada. Los mecanismos de democracia directa en Ecuador, Perú y Argentina

    Directory of Open Access Journals (Sweden)

    Yanina Welp

    2008-05-01

    Full Text Available Mediante el estudio comparado de Argentina, Ecuador y Perú, el artículo analiza en qué medida las consultas populares, la iniciativa ciudadana y la revocatoria de mandato podrían contribuir a, por un lado, fortalecer la “democracia delegativa”, esto es, el protagonismo del Poder Ejecutivo basado en el apoyo popular y contra los otros poderes del estado o, por otro lado, incrementar la calidad de la democracia introduciendo mecanismos de control y de participación en la toma de decisiones por parte del ciudadano.

  2. Las redes de acción pública como sistemas asociativos complejos : problemas y mecanismos de integración

    OpenAIRE

    Luna, Matilde; Velasco, José Luis

    2009-01-01

    Este trabajo analiza las propiedades sistémicas de las interacciones en las redes de gobernanza. Se identifican cuatro propiedades básicas: la autonomía individual de los participantes, la autonomía política de la red, la interdependencia de sus componentes y el dinamismo. También se analizan cuatro mecanismos y procesos para la integración y toma de decisiones: la confianza, la traducción, la negociación y la deliberación. Se concluye que para funcionar adecuadamente, las redes deben lograr ...

  3. On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2011-01-01

    In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network’s evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective. PMID:22084563

  4. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

    DEFF Research Database (Denmark)

    Herrgard, Markus; Swainston, Neil; Dobson, Paul

    2008-01-01

    and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology...

  5. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. A journey from simple computer programs to drug/vaccine informatics. Limitations of existing web services. History repeats (Web to Standalone); Graphics vs command mode. General purpose ...

  6. Macrófagos e inducción de arginasa como mecanismo de evasión de parásitos Macrophages and arginase induction as a mechanism for parasite escape

    Directory of Open Access Journals (Sweden)

    Cinthia C Stempin

    2007-12-01

    make possible their survival and replication in the host. Some parasites modulate the production of several toxic molecules synthesized by the immune system. Several parasites are highly sensitive to nitric oxide (ON and their derivatives. ON is produced in macrophages (MΦ after stimulation with microbial products or cytokines. In the past, M Φ were defined as inflammatory cells (classically activated MΦ, able to produce inflammatory mediators, to act like antigens presenting cells and to kill intracellular pathogens. Nevertheless, activated MΦ involve a more heterogeneous group of cells with different biological markers that can carry out different immunological functions. Alternatively activated MΦ fail to produce ON due to the arginase induction and consequently they have diminished their capacity to kill intracellular pathogens. It has been reported the induction of arginase by different parasites; therefore this mechanism could favor their survival in the host. In our group, we studied the participation of arginase in a model of Trypanosoma cruzi infection and the intracellular signals involved in the replication of this parasite in MΦ. The data obtained from our works would allow the understanding of some mechanisms by which cells can be programmed to favor the establishment of chronic parasitic infections.

  7. Universally sloppy parameter sensitivities in systems biology models.

    Directory of Open Access Journals (Sweden)

    Ryan N Gutenkunst

    2007-10-01

    Full Text Available Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a "sloppy" spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our growth-factor-signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.

  8. Universally sloppy parameter sensitivities in systems biology models.

    Science.gov (United States)

    Gutenkunst, Ryan N; Waterfall, Joshua J; Casey, Fergal P; Brown, Kevin S; Myers, Christopher R; Sethna, James P

    2007-10-01

    Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a "sloppy" spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our growth-factor-signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.

  9. Um possível mecanismo de ação para o efeito anticonvulsivante do p-cimeno

    Directory of Open Access Journals (Sweden)

    Talita Mendes de Oliveira

    2014-01-01

    Full Text Available O presente estudo teve como objetivo investigar o efeito anticonvulsivante do p-cimeno (CIM, bem como verificar a concentração das monoaminas (dopamina (DA, noradrenalina (NA, serotonina (5-HT, e seus metabólitos (ácido dihidroxifenilacético (DOPAC, ácido homovanílico (HVA e ácido 5-hidroxi-indol-acético (5- HIAA no hipocampo de camundongos tratados com cloridrato de pilocarpina 400 mg/kg (P400; i.p. e nos grupos tratados com a associação de CIM (50, 100 ou 150 mg/kg e P400. Nesse estudo foi avaliada a latência para a primeira crise epiléptica e a taxa de mortalidade. Os resultados revelaram que o CIM produziu um aumento na latência para primeira crise epilética, bem como promoveu uma proteção significativa contra a mortalidade induzida pelo processo convulsivo. O monoterpeno nas doses testadas também foi capaz de produzir um aumento da latência para instalação do estado de mal epilético induzido por pilocarpina. Além disso, durante os estudos para identificar o mecanismo de ação nenhum dos efeitos do p-cimeno nesse modelo foram bloqueados pelo pré-tratamento com atropina. Complementando os estudos para identificar o provável mecanismo de ação do p-cimeno, foi verificado que os efeitos desse monorterpeno foram revertidos pelo flumazenil, um antagonista do sistema GABAérgico, sugerindo que esse monoterpeno pode atuar por meio desse sistema. Também, em nossos resultados também foi visto uma diminuição dos níveis de DA e um aumento do conteúdo de seus metabólitos (DOPAC e HVA durante as crises epilépticas. Por outro lado foi detectado um aumento na concentração de NA e 5-HT, e uma diminuição no metabólito da 5-HT (5- HIAA durante as crises epilépticas. Dessa forma, o CIM na presença do estímulo convulsivo, reverte os efeitos produzidos nos níveis das monoaminas e seus metabólitos observados durante as crises epilépticas, sugerindo que este monoterpeno produz efeito anticonvulsivante por meio da

  10. Improving integrative searching of systems chemical biology data using semantic annotation.

    Science.gov (United States)

    Chen, Bin; Ding, Ying; Wild, David J

    2012-03-08

    Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  11. CINRG: Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2013-10-01

    Contract W81XWH-09-1-0726 SYSTEMS BIOLOGY OF GLUCOCORTICOIDS IN MUSCLE DISEASE Introduction Duchenne muscular dystrophy (DMD) is the most... muscle and enable the development of better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant...common and incurable muscular dystrophy of childhood. Muscle regeneration fails with advancing age, leading to considerable fibrosis. Corticosteroid

  12. Systems biology technologies enable personalized traditional Chinese medicine: a systematic review.

    Science.gov (United States)

    Wang, Xijun; Zhang, Aihua; Sun, Hui; Wang, Ping

    2012-01-01

    Traditional Chinese medicine (TCM), an alternative medicine, focuses on the treatment of human disease via the integrity of the close relationship between body and syndrome analysis. It remains a form of primary care in most Asian countries and its characteristics showcase the great advantages of personalized medicine. Although this approach to disease diagnosis, prognosis and treatment has served the medical establishment well for thousands of years, it has serious shortcomings in the era of modern medicine that stem from its reliance on reductionist principles of experimentation and analysis. In this way, systems biology offers the potential to personalize medicine, facilitating the provision of the right care to the right patient at the right time. We expect that systems biology will have a major impact on future personalized therapeutic approaches which herald the future of medicine. Here we summarize current trends and critically review the potential limitations and future prospects of such treatments. Some characteristic examples are presented to highlight the application of this groundbreaking platform to personalized TCM as well as some of the necessary milestones for moving systems biology of a state-of-the-art nature into mainstream health care.

  13. A second inheritance system: the extension of biology through culture.

    Science.gov (United States)

    Whiten, Andrew

    2017-10-06

    By the mid-twentieth century (thus following the 'Modern Synthesis' in evolutionary biology), the behavioural sciences offered only the sketchy beginnings of a scientific literature documenting evidence for cultural inheritance in animals-the transmission of traditional behaviours via learning from others (social learning). By contrast, recent decades have seen a massive growth in the documentation of such cultural phenomena, driven by long-term field studies and complementary laboratory experiments. Here, I review the burgeoning scope of discoveries in this field, which increasingly suggest that this 'second inheritance system', built on the shoulders of the primary genetic inheritance system, occurs widely among vertebrates and possibly in invertebrates too. Its novel characteristics suggest significant implications for our understanding of evolutionary biology. I assess the extent to which this second system extends the scope of evolution, both by echoing principal properties of the primary, organic evolutionary system, and going beyond it in significant ways. This is well established in human cultural evolution; here, I address animal cultures more generally. The further major, and related, question concerns the extent to which the consequences of widespread animal cultural transmission interact with the primary, genetically based inheritance systems, shaping organic evolution.

  14. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  15. Advances in reproductive biology and seed production systems of ...

    African Journals Online (AJOL)

    Eucalyptus globulus is the main eucalypt species grown in Australian plantations. The focus on seedling deployment systems, coupled with exploitation of large, open-pollinated base populations for breeding purposes over the last two decades, has required a detailed understanding of the reproductive biology of this ...

  16. Aspectos relacionados à ocorrência e mecanismo de ação de fumonisinas

    Directory of Open Access Journals (Sweden)

    Pozzi Claudia Rodrigues

    2002-01-01

    Full Text Available As fumonisinas são micotoxinas produzidas por fungos do gênero Fusarium, um dos principais fitopatógenos de grãos de milho. Isoladas em 1988, a partir de amostras de milho mofado proveniente de região com alta incidência de câncer do esôfago na África, foram relacionadas à ocorrência de leucoencefalomalácia eqüina e hidrotórax e edema pulmonar suíno, e outras patologias animais. A presente revisão aborda aspectos da ocorrência natural das fumonisinas em grãos de milho, características físico-química das moléculas e efeitos toxicológicos em eqüinos, suínos, aves e bovinos, além do provável mecanismo de ação das micotoxinas.

  17. Stress-associated synchronization and desynchronization in geologic and biologic systems

    Science.gov (United States)

    Kluchevsky, A. V.; Kluchevskaya, A. A.

    2010-12-01

    Variations in the annual numbers of representative earthquakes in three areas and six districts of the Baikal rift zone in 1964-2002 were subjected to correlation analysis. Episodes of significant correlations of shock flow rates were found against the background of chaotic seismic activity. They followed the rearrangements (catastrophes) of stresses in the lithosphere, which are also stressing factors for the whole rift geodynamic system. The episode of the late 1970s-early 1980s was particularly long and showed the maximum correlation. Therefore, it can be considered the principal event in seismic process synchronization in the Baikal Rift Zone. The same approach to data analysis revealed similar synchronization and desynchronization phenomena in the behavior of Baikalian turbellaria when they deviated from homeostasis as a result of illumination, which is a stress for this biologic system. Possible reasons for the behavior of biologic and geodynamic systems are discussed in terms of the synergetic concept of phenomena in living and nonliving nature.

  18. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    Directory of Open Access Journals (Sweden)

    Daniel eLewis

    2014-12-01

    Full Text Available As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo systems, with only a few examples of prominent work done on predicting the dynamics of cell-free systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  19. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  20. Ionic interactions in biological and physical systems: a variational treatment.

    Science.gov (United States)

    Eisenberg, Bob

    2013-01-01

    Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when

  1. A geometric initial guess for localized electronic orbitals in modular biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Beckman, P. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States); Fattebert, J. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lau, E. Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Osei-Kuffuor, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-11

    Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N3) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol, facilitates first-principles simulations in biological systems of sizes which were previously impossible.

  2. MODELLING OF RADIONUCLIDE MIGRATION IN THE SYSTEM OF NUCLEAR POWER PLANT BIOLOGICAL PONDS

    Directory of Open Access Journals (Sweden)

    Ю. Кутлахмедов

    2011-04-01

    Full Text Available Migration of radionuclide coming from nuclear power plant into the system of biological pondsand then into the water reservoir-cooler is considered in the article. The theme of the work ismodeling of radionuclide migration process in the system of biological ponds on the example of thePivdennoukrainska nuclear power plant using chamber models method. Typical water ecosystemconsisting of three chambers (chamber-water, chamber-biota and chamber-bed silt was the basistaken by the authors. Application of chamber models method allowed authors to develop thedynamic chamber model of radionuclide migration in nuclear power plant biological ponds. Thismodel allows to forecast values and dynamics of radioactive water pollution based on limitedecosystem monitoring data. Thus, parameters of radioactive capacity of nuclear power plantbiological ponds system and water reservoir-cooler were modeled by authors, the estimation andprognosis of radionuclide distribution and accumulation in the system of nuclear power plantbiological ponds were done. Authors also explain the roles of basin water, biomass and bed silt inradionuclide deposition

  3. Systems biology-embedded target validation: improving efficacy in drug discovery.

    Science.gov (United States)

    Vandamme, Drieke; Minke, Benedikt A; Fitzmaurice, William; Kholodenko, Boris N; Kolch, Walter

    2014-01-01

    The pharmaceutical industry is faced with a range of challenges with the ever-escalating costs of drug development and a drying out of drug pipelines. By harnessing advances in -omics technologies and moving away from the standard, reductionist model of drug discovery, there is significant potential to reduce costs and improve efficacy. Embedding systems biology approaches in drug discovery, which seek to investigate underlying molecular mechanisms of potential drug targets in a network context, will reduce attrition rates by earlier target validation and the introduction of novel targets into the currently stagnant market. Systems biology approaches also have the potential to assist in the design of multidrug treatments and repositioning of existing drugs, while stratifying patients to give a greater personalization of medical treatment. © 2013 Wiley Periodicals, Inc.

  4. Data management strategies for multinational large-scale systems biology projects.

    Science.gov (United States)

    Wruck, Wasco; Peuker, Martin; Regenbrecht, Christian R A

    2014-01-01

    Good accessibility of publicly funded research data is essential to secure an open scientific system and eventually becomes mandatory [Wellcome Trust will Penalise Scientists Who Don't Embrace Open Access. The Guardian 2012]. By the use of high-throughput methods in many research areas from physics to systems biology, large data collections are increasingly important as raw material for research. Here, we present strategies worked out by international and national institutions targeting open access to publicly funded research data via incentives or obligations to share data. Funding organizations such as the British Wellcome Trust therefore have developed data sharing policies and request commitment to data management and sharing in grant applications. Increased citation rates are a profound argument for sharing publication data. Pre-publication sharing might be rewarded by a data citation credit system via digital object identifiers (DOIs) which have initially been in use for data objects. Besides policies and incentives, good practice in data management is indispensable. However, appropriate systems for data management of large-scale projects for example in systems biology are hard to find. Here, we give an overview of a selection of open-source data management systems proved to be employed successfully in large-scale projects.

  5. Developmental biology, the stem cell of biological disciplines

    OpenAIRE

    Gilbert, Scott F.

    2017-01-01

    Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines.” Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, ...

  6. Biological regeneration of phenol-loaded activated carbon (up flow system)

    International Nuclear Information System (INIS)

    Durrani, M.A.Q.J.; Mirajuddin; Martin, R.J.

    1995-01-01

    This paper represents the report on the biological regeneration of totally activated carbon following the experimental studies carried out at the University of Birmingham, U.K. Biological regeneration is one of several methods that may be used to restore the adsorptive capacity of exhausted granular activated carbon. This study deals with in situ biological regeneration on a pilot scale. The principal objective of this research was to ascertain whether biological regeneration of GAC could occur under conditions typical of water treatment. The important parameters which may have the greatest impact on bio regeneration for a given adsorbate were studied. The research investigated the extent of bio regeneration for phenol of concentration 50 mg/l. Bio regeneration in the total exhaustion system was evaluated in terms of regeneration efficiency and the substrate removal. A three mode procedure was followed for each bio regeneration run. The prepared carbon was initialing exhausted with an adsorbate; it was then bio regenerated with a mixed culture of bacteria, and lastly the carbon was saturated. In the totally exhausted GAC system, the bio regeneration was enhanced by increasing the duration of regeneration for a fixed initial biomass content of the bioreactor. The regenerated phenol loaded GAC bed had nearly gained its original adsorption after the 5-day period of regeneration. Bacterial counts in the effluents of regenerated GAC columns were significantly more than those of fresh carbon effluents. (author)

  7. Posiciones y debates en torno a los mecanismos de solución de controversias inversor – Estado

    Directory of Open Access Journals (Sweden)

    Magdalena Bas Vilizzio

    2017-05-01

    Full Text Available Los mecanismos de solución de controversias inversor - Estado previstos en más de 3000 tratados bilaterales de inversión y otros instrumentos jurídicos han sido centro de numerosas críticas en los últimos años. En esta línea, en primer lugar, se analizarán los riesgos que entraña el sistema arbitral del Centro de Arreglo de Diferencias relativas a Inversiones (CIADI o la Corte Permanente de Arbitraje (CPA, entre otros, y que han sido identificados desde el ámbito académico, social y gubernamental. Este trabajo analizará específicamente la conformación de los tribunales arbitrales, la ausencia de una instancia de apelación, la inclusión de una amplia diversidad de temas dentro del concepto de inversión protegida y el factor social en el arbitraje de inversiones, especialmente en relación al género y nacionalidad de los árbitros. Asimismo, se examinarán los diferentes caminos hacia la reforma o intentos de mejoramiento parcial del sistema en base a ejemplos concretos. Tal es el caso de la eliminación de ciertas áreas de la solución de controversias inversor - Estado, como las políticas de control del tabaco del Acuerdo de Asociación Transpacífico; la creación de un sistema de Cortes de Inversiones como propone la Unión Europea en los acuerdos que está negociando con terceros Estados; o la exclusión de los mecanismos de solución de controversias de los acuerdos de protección de inversiones, como en el nuevo modelo de Acuerdo de cooperación y facilitación de inversiones de Brasil.

  8. What does systems biology mean for drug development?

    Science.gov (United States)

    Schrattenholz, André; Soskić, Vukić

    2008-01-01

    The complexity and flexibility of cellular architectures is increasingly recognized by impressive progress on the side of molecular analytics, i.e. proteomics, genomics and metabolomics. One of the messages from systems biology is that the number of molecular species in cellular networks is orders of magnitude bigger than anticipated by genomic analysis, in particular by fast posttranslational modifications of proteins. The requirements to manage external signals, integrate spatiotemporal signal transduction inside an organism and at the same time optimizing networks of biochemical and chemical reactions result in chemically extremely fine tuned molecular entities. Chemical side reactions of enzymatic activity, like e.g. random oxidative damage of proteins by free radicals during aging constantly introduce epigenetic alterations of protein targets. These events gradually and on an individual stochastic scale, keep modifying activities of these targets, and their affinities and selectivities towards biological and pharmacological ligands. One further message is that many of the key reactions in living systems are essentially based on interactions of low affinities and even low selectivities. This principle is responsible for the enormous flexibility and redundancy of cellular circuitries. So, in complex disorders like cancer or neurodegenerative diseases, which are rooted in relatively subtle and multimodal dysfunction of important physiologic pathways, drug discovery programs based on the concept of high affinity/high specificity compounds ("one-target, one-disease"), which still dominate the pharmaceutical industry increasingly turn out to be unsuccessful. Despite improvements in rational drug design and high throughput screening methods, the number of novel, single-target drugs fell much behind expectations during the past decade and the treatment of "complex diseases" remains a most pressing medical need. Currently a change of paradigm can be observed with

  9. Fabrication, Characterization, and Biological Activity of Avermectin Nano-delivery Systems with Different Particle Sizes

    Science.gov (United States)

    Wang, Anqi; Wang, Yan; Sun, Changjiao; Wang, Chunxin; Cui, Bo; Zhao, Xiang; Zeng, Zhanghua; Yao, Junwei; Yang, Dongsheng; Liu, Guoqiang; Cui, Haixin

    2018-01-01

    Nano-delivery systems for the active ingredients of pesticides can improve the utilization rates of pesticides and prolong their control effects. This is due to the nanocarrier envelope and controlled release function. However, particles containing active ingredients in controlled release pesticide formulations are generally large and have wide size distributions. There have been limited studies about the effect of particle size on the controlled release properties and biological activities of pesticide delivery systems. In the current study, avermectin (Av) nano-delivery systems were constructed with different particle sizes and their performances were evaluated. The Av release rate in the nano-delivery system could be effectively controlled by changing the particle size. The biological activity increased with decreasing particle size. These results suggest that Av nano-delivery systems can significantly improve the controllable release, photostability, and biological activity, which will improve efficiency and reduce pesticide residues.

  10. Teleology and its constitutive role for biology as the science of organized systems in nature.

    Science.gov (United States)

    Toepfer, Georg

    2012-03-01

    'Nothing in biology makes sense, except in the light of teleology'. This could be the first sentence in a textbook about the methodology of biology. The fundamental concepts in biology, e.g. 'organism' and 'ecosystem', are only intelligible given a teleological framework. Since early modern times, teleology has often been considered methodologically unscientific. With the acceptance of evolutionary theory, one popular strategy for accommodating teleological reasoning was to explain it by reference to selection in the past: functions were reconstructed as 'selected effects'. But the theory of evolution obviously presupposes the existence of organisms as organized and regulated, i.e. functional systems. Therefore, evolutionary theory cannot provide the foundation for teleology. The underlying reason for the central methodological role of teleology in biology is not its potential to offer particular forms of (evolutionary) explanations for the presence of parts, but rather an ontological one: organisms and other basic biological entities do not exist as physical bodies do, as amounts of matter with a definite form. Rather, they are dynamic systems in stable equilibrium; despite changes of their matter and form (in metabolism and metamorphosis) they maintain their identity. What remains constant in these kinds of systems is their 'organization', i.e. the causal pattern of interdependence of parts with certain effects of each part being relevant for the working of the system. Teleological analysis consists in the identification of these system-relevant effects and at the same time of the system as a whole. Therefore, the identity of biological systems cannot be specified without teleological reasoning. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. ANALISIS DEL DELITO DE USURPACION DE MARCAS Y PATENTES EN LA CIUDAD DE CUCUTA, Y MECANISMOS JURIDICOS DE PROTECCION A LA DEFENSA DEL DERECHO DE PROPIEDAD INDUSTRIAL

    OpenAIRE

    Florez Caceres, Diego Armando; Leon Yañez, María Alejandra

    2010-01-01

    Situación actual del delito de usurpación de marcas en Cúcuta Impacto económico y social del delito en Cúcuta Mecanismos jurídicos de protección que establece la legislación frente al delito de usurpación y marcas

  12. Physics and biology

    International Nuclear Information System (INIS)

    Frauenfelder, H.

    1988-01-01

    The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

  13. Interaction of biological systems with static and ELF electric and magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, L.E.; Kelman, B.J.; Weigel, R.J. (eds.)

    1987-01-01

    Although background levels of atmospheric electric and geomagnetic field levels are extremely low, over the past several decades, human beings and other life forms on this planet have been subjected to a dramatically changing electromagnetic milieu. An exponential increase in exposure to electromagnetic fields has occurred, largely because of such technological advances as the growth of electrical power generation and transmission systems, the increased use of wireless communications, and the use of radar. In addition, electromagnetic field generating devices have proliferated in industrial plants, office buildings, homes, public transportation systems, and elsewhere. Although significant increases have occurred in electromagnetic field strenghths spanning all frequency ranges, this symposium addresses only the impact of these fields at static and extremely low frequencies (ELF), primarily 50 and 60 Hz. This volume contains the proceedings of the symposium entitled /open quotes/Interaction of biological systems with static and ELF electric and magnetic fields/close quotes/. The purpose of the symposium was to provide a forum for discussions of all aspects of research on the interaction of static and ELF electromagnetic fields with biological systems. These systems include simple biophysical models, cell and organ preparations, whole animals, and man. Dosimetry, exposure system design, and artifacts in ELF bioeffects research were also addressed, along with current investigations that examine fundamental mechanisms of interactions between the fields and biological processes. Papers are indexed separately.

  14. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  15. Distribuição de combustível no estado de São Paulo: estruturas de governança e mecanismos complementares de coordenação

    Directory of Open Access Journals (Sweden)

    Selene de Souza Siqueira Soares

    2015-06-01

    Full Text Available RESUMO Neste trabalho, o foco é o estudo das governanças das transações adotadas pelas distribuidoras de combustíveis com os postos varejistas, segundo abordagem teórica da nova economia institucional (NEI. Foi realizada pesquisa de campo, por meio de entrevistas presenciais com 25 empresas distribuidoras, as quais respondem por aproximadamente 80% das vendas nacionais de gasolina e etanol. Os resultados sugerem que as estruturas de governança diferenciam-se pela especificidade de ativos e que as governanças híbridas são as mais recorrentes. Nas conclusões, indica-se ainda que o porte dos distribuidores tem sido determinante na escolha dos mecanismos de coordenação utilizados e que a demora em fazer valer os contratos tem sido a principal causa da emergência dos mecanismos complementares, sendo sua utilização direcionada basicamente à proteção dos ativos específicos nas transações.

  16. Comparative systems biology between human and animal models based on next-generation sequencing methods.

    Science.gov (United States)

    Zhao, Yu-Qi; Li, Gong-Hua; Huang, Jing-Fei

    2013-04-01

    Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

  17. Novel approaches to the integration and analysis of systems biology data

    OpenAIRE

    Ramírez, Fidel

    2011-01-01

    The opportunity to investigate whole cellular systems using experimental and computational high-throughput methods leads to the generation of unprecedented amounts of data. Processing of these data often results in large lists of genes or proteins that need to be analyzed and interpreted in the context of all other biological information that is already available. To support such analyses, repositories aggregating and merging the biological information contained in different databases are req...

  18. Improving integrative searching of systems chemical biology data using semantic annotation

    Directory of Open Access Journals (Sweden)

    Chen Bin

    2012-03-01

    Full Text Available Abstract Background Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. Results We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i simplifies the process of building SPARQL queries, (ii enables useful new kinds of queries on the data and (iii makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Availability Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  19. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  20. Sistemas de recuperação de informações e mecanismos de busca na web: panorama atual e tendências

    Directory of Open Access Journals (Sweden)

    Renato Rocha Souza

    Full Text Available Busca-se traçar um panorama das características básicas dos sistemas de recuperação de informações, apresentando seus modelos de recuperação mais comuns. São apresentados com ênfase especial os mecanismos de busca na web, seu estado atual de desenvolvimento e algumas tendências para o futuro. Dentre estas tendências, destacam-se notadamente aquelas introduzidas pelo Google, como o algoritmo pagerank, dentre outras inovações.