Urban wind energy: empirical optimization of high-rise building roof shape for the wind energy exploitation

El programa Europeo HORIZON2020 en Futuras Ciudades Inteligentes establece como objetivo que el 20% de la energía eléctrica sea generada a partir de fuentes renovables. Este objetivo implica la necesidad de potenciar la generación de energía eólica en todos los ámbitos. La energía eólica reduce drásticamente las emisiones de gases de efecto invernadero y evita los riesgos geo-políticos asociados al suministro e infraestructuras energéticas, así como la dependencia energética de otras regiones. Además, la generación de energía distribuida (generación en el punto de consumo) presenta significativas ventajas en términos de elevada eficiencia energética y estimulación de la economía. El sector de la edificación representa el 40% del consumo energético total de la Unión Europea. La reducción del consumo energético en este área es, por tanto, una prioridad de acuerdo con los objetivos "20-20-20" en eficiencia energética. La Directiva 2010/31/EU del Parlamento Europeo y del Consejo de 19 de mayo de 2010 sobre el comportamiento energético de edificaciones contempla la instalación de sistemas de suministro energético a partir de fuentes renovables en las edificaciones de nuevo diseño. Actualmente existe una escasez de conocimiento científico y tecnológico acerca de la geometría óptima de las edificaciones para la explotación de la energía eólica en entornos urbanos. El campo tecnológico de estudio de la presente Tesis Doctoral es la generación de energía eólica en entornos urbanos. Específicamente, la optimization de la geometría de las cubiertas de edificaciones desde el punto de vista de la explotación del recurso energético eólico. Debido a que el flujo del viento alrededor de las edificaciones es exhaustivamente investigado en esta Tesis empleando herramientas de simulación numérica, la mecánica de fluidos computacional (CFD en inglés) y la aerodinámica de edificaciones son los campos científicos de estudio. El objetivo central de esta Tesis Doctoral es obtener una geometría de altas prestaciones (u óptima) para la explotación de la energía eólica en cubiertas de edificaciones de gran altura. Este objetivo es alcanzado mediante un análisis exhaustivo de la influencia de la forma de la cubierta del edificio en el flujo del viento desde el punto de vista de la explotación energética del recurso eólico empleando herramientas de simulación numérica (CFD). Adicionalmente, la geometría de la edificación convencional (edificio prismático) es estudiada, y el posicionamiento adecuado para los diferentes tipos de aerogeneradores es propuesto. La compatibilidad entre el aprovechamiento de las energías solar fotovoltaica y eólica también es analizado en este tipo de edificaciones. La investigación prosigue con la optimización de la geometría de la cubierta. La metodología con la que se obtiene la geometría óptima consta de las siguientes etapas: - Verificación de los resultados de las geometrías previamente estudiadas en la literatura. Las geometrías básicas que se someten a examen son: cubierta plana, a dos aguas, inclinada, abovedada y esférica. - Análisis de la influencia de la forma de las aristas de la cubierta sobre el flujo del viento. Esta tarea se lleva a cabo mediante la comparación de los resultados obtenidos para la arista convencional (esquina sencilla) con un parapeto, un voladizo y una esquina curva. - Análisis del acoplamiento entre la cubierta y los cerramientos verticales (paredes) mediante la comparación entre diferentes variaciones de una cubierta esférica en una edificación de gran altura: cubierta esférica estudiada en la literatura, cubierta esférica integrada geométricamente con las paredes (planta cuadrada en el suelo) y una cubierta esférica acoplada a una pared cilindrica. El comportamiento del flujo sobre la cubierta es estudiado también considerando la posibilidad de la variación en la dirección del viento incidente. - Análisis del efecto de las proporciones geométricas del edificio sobre el flujo en la cubierta. - Análisis del efecto de la presencia de edificaciones circundantes sobre el flujo del viento en la cubierta del edificio objetivo. Las contribuciones de la presente Tesis Doctoral pueden resumirse en: - Se demuestra que los modelos de turbulencia RANS obtienen mejores resultados para la simulación del viento alrededor de edificaciones empleando los coeficientes propuestos por Crespo y los propuestos por Bechmann y Sórensen que empleando los coeficientes estándar. - Se demuestra que la estimación de la energía cinética turbulenta del flujo empleando modelos de turbulencia RANS puede ser validada manteniendo el enfoque en la cubierta de la edificación. - Se presenta una nueva modificación del modelo de turbulencia Durbin k — e que reproduce mejor la distancia de recirculación del flujo de acuerdo con los resultados experimentales. - Se demuestra una relación lineal entre la distancia de recirculación en una cubierta plana y el factor constante involucrado en el cálculo de la escala de tiempo de la velocidad turbulenta. Este resultado puede ser empleado por la comunidad científica para la mejora del modelado de la turbulencia en diversas herramientas computacionales (OpenFOAM, Fluent, CFX, etc.). - La compatibilidad entre las energías solar fotovoltaica y eólica en cubiertas de edificaciones es analizada. Se demuestra que la presencia de los módulos solares provoca un descenso en la intensidad de turbulencia. - Se demuestran conflictos en el cambio de escala entre simulaciones de edificaciones a escala real y simulaciones de modelos a escala reducida (túnel de viento). Se demuestra que para respetar las limitaciones de similitud (número de Reynolds) son necesarias mediciones en edificaciones a escala real o experimentos en túneles de viento empleando agua como fluido, especialmente cuando se trata con geometrías complejas, como es el caso de los módulos solares. - Se determina el posicionamiento más adecuado para los diferentes tipos de aerogeneradores tomando en consideración la velocidad e intensidad de turbulencia del flujo. El posicionamiento de aerogeneradores es investigado en las geometrías de cubierta más habituales (plana, a dos aguas, inclinada, abovedada y esférica). - Las formas de aristas más habituales (esquina, parapeto, voladizo y curva) son analizadas, así como su efecto sobre el flujo del viento en la cubierta de un edificio de gran altura desde el punto de vista del aprovechamiento eólico. - Se propone una geometría óptima (o de altas prestaciones) para el aprovechamiento de la energía eólica urbana. Esta optimización incluye: verificación de las geometrías estudiadas en el estado del arte, análisis de la influencia de las aristas de la cubierta en el flujo del viento, estudio del acoplamiento entre la cubierta y las paredes, análisis de sensibilidad del grosor de la cubierta, exploración de la influencia de las proporciones geométricas de la cubierta y el edificio, e investigación del efecto de las edificaciones circundantes (considerando diferentes alturas de los alrededores) sobre el flujo del viento en la cubierta del edificio objetivo. Las investigaciones comprenden el análisis de la velocidad, la energía cinética turbulenta y la intensidad de turbulencia en todos los casos. ABSTRACT The HORIZON2020 European program in Future Smart Cities aims to have 20% of electricity produced by renewable sources. This goal implies the necessity to enhance the wind energy generation, both with large and small wind turbines. Wind energy drastically reduces carbon emissions and avoids geo-political risks associated with supply and infrastructure constraints, as well as energy dependence from other regions. Additionally, distributed energy generation (generation at the consumption site) offers significant benefits in terms of high energy efficiency and stimulation of the economy. The buildings sector represents 40% of the European Union total energy consumption. Reducing energy consumption in this area is therefore a priority under the "20-20-20" objectives on energy efficiency. The Directive 2010/31/EU of the European Parliament and of the Council of 19 May 2010 on the energy performance of buildings aims to consider the installation of renewable energy supply systems in new designed buildings. Nowadays, there is a lack of knowledge about the optimum building shape for urban wind energy exploitation. The technological field of study of the present Thesis is the wind energy generation in urban environments. Specifically, the improvement of the building-roof shape with a focus on the wind energy resource exploitation. Since the wind flow around buildings is exhaustively investigated in this Thesis using numerical simulation tools, both computational fluid dynamics (CFD) and building aerodynamics are the scientific fields of study. The main objective of this Thesis is to obtain an improved (or optimum) shape of a high-rise building for the wind energy exploitation on the roof. To achieve this objective, an analysis of the influence of the building shape on the behaviour of the wind flow on the roof from the point of view of the wind energy exploitation is carried out using numerical simulation tools (CFD). Additionally, the conventional building shape (prismatic) is analysed, and the adequate positions for different kinds of wind turbines are proposed. The compatibility of both photovoltaic-solar and wind energies is also analysed for this kind of buildings. The investigation continues with the buildingroof optimization. The methodology for obtaining the optimum high-rise building roof shape involves the following stages: - Verification of the results of previous building-roof shapes studied in the literature. The basic shapes that are compared are: flat, pitched, shed, vaulted and spheric. - Analysis of the influence of the roof-edge shape on the wind flow. This task is carried out by comparing the results obtained for the conventional edge shape (simple corner) with a railing, a cantilever and a curved edge. - Analysis of the roof-wall coupling by testing different variations of a spherical roof on a high-rise building: spherical roof studied in the litera ture, spherical roof geometrically integrated with the walls (squared-plant) and spherical roof with a cylindrical wall. The flow behaviour on the roof according to the variation of the incident wind direction is commented. - Analysis of the effect of the building aspect ratio on the flow. - Analysis of the surrounding buildings effect on the wind flow on the target building roof. The contributions of the present Thesis can be summarized as follows: - It is demonstrated that RANS turbulence models obtain better results for the wind flow around buildings using the coefficients proposed by Crespo and those proposed by Bechmann and S0rensen than by using the standard ones. - It is demonstrated that RANS turbulence models can be validated for turbulent kinetic energy focusing on building roofs. - A new modification of the Durbin k — e turbulence model is proposed in order to obtain a better agreement of the recirculation distance between CFD simulations and experimental results. - A linear relationship between the recirculation distance on a flat roof and the constant factor involved in the calculation of the turbulence velocity time scale is demonstrated. This discovery can be used by the research community in order to improve the turbulence modeling in different solvers (OpenFOAM, Fluent, CFX, etc.). - The compatibility of both photovoltaic-solar and wind energies on building roofs is demonstrated. A decrease of turbulence intensity due to the presence of the solar panels is demonstrated. - Scaling issues are demonstrated between full-scale buildings and windtunnel reduced-scale models. The necessity of respecting the similitude constraints is demonstrated. Either full-scale measurements or wind-tunnel experiments using water as a medium are needed in order to accurately reproduce the wind flow around buildings, specially when dealing with complex shapes (as solar panels, etc.). - The most adequate position (most adequate roof region) for the different kinds of wind turbines is highlighted attending to both velocity and turbulence intensity. The wind turbine positioning was investigated for the most habitual kind of building-roof shapes (flat, pitched, shed, vaulted and spherical). - The most habitual roof-edge shapes (simple edge, railing, cantilever and curved) were investigated, and their effect on the wind flow on a highrise building roof were analysed from the point of view of the wind energy exploitation. - An optimum building-roof shape is proposed for the urban wind energy exploitation. Such optimization includes: state-of-the-art roof shapes test, analysis of the influence of the roof-edge shape on the wind flow, study of the roof-wall coupling, sensitivity analysis of the roof width, exploration of the aspect ratio of the building-roof shape and investigation of the effect of the neighbouring buildings (considering different surrounding heights) on the wind now on the target building roof. The investigations comprise analysis of velocity, turbulent kinetic energy and turbulence intensity for all the cases.

Diseño de un modelo para la identificación y análisis de tramos de carreteras sin accidentes : una nueva visión de la seguridad vial

El planteamiento tradicional de análisis de la accidentalidad en carretera pasa por la consideración de herramientas paliativas, como son la identificación y gestión de los puntos negros o tramos de concentración de accidentes, o preventivas, como las auditorías e inspecciones de seguridad vial. En esta tesis doctoral se presenta un planteamiento complementario a estas herramientas, desde una perspectiva novedosa: la consideración de los tramos donde no se producen accidentes; son los denominados Tramos Blancos. La tesis persigue demostrar que existen determinados parámetros del diseño de las carreteras y del tráfico que, bajo características generales similares de las vías, tienen influencia en el hecho de que se produzcan o no accidentes, adicionalmente a la exposición al riesgo, como factor principal, y a otros factores. La propia definición de los Tramos Blancos, entendidos como tramos de carreteras de longitud representativa donde no se han producido accidentes con víctimas mortales o heridos graves durante un periodo largo de tiempo, garantiza que esta situación no se produzca como consecuencia de la aleatoriedad de los accidentes, sino que pudiera deberse a una confluencia específica de determinados parámetros de la geometría de la vía y del tráfico total y de vehículos pesados. Para el desarrollo de esta investigación se han considerado la red de autopistas de peaje y las carreteras convencionales de la Red del Estado de España, que supone un total de 17.000 kilómetros, y los datos de accidentes con víctimas mortales y heridos graves en el periodo 2006-2010, ambos incluidos, en estas redes (un total de 10.000 accidentes). La red viaria objeto de análisis supone el 65% de la longitud de la Red de Carreteras del Estado, por la que circula el 33% de su tráfico; en ella se produjeron en el año 2013 el 47% de los accidentes con víctimas y el 60% de las víctimas mortales de la Red de Carreteras del Estado. Durante la investigación se ha desarrollado una base de datos de 250.130 registros y más de 3.5 millones de datos en el caso de las autopistas de peaje de la Red de Carreteras del Estado y de 935.402 registros y más de 14 millones de datos en el caso de la red convencional del Estado analizada. Tanto las autopistas de peaje como las carreteras convencionales han sido clasificadas según sus características de tráfico, de manera que se valoren vías con nivel de exposición al riesgo similar. Para cada tipología de vía, se ha definido como longitud de referencia para que un tramo se considere Tramo Blanco la longitud igual al percentil 95 de las longitudes de tramos sin accidentes con heridos graves o víctimas mortales durante el periodo 2006-2010. En el caso de las autopistas de peaje, en la tipología que ha sido considerada para la definición del modelo, esta longitud de referencia se estableció en 14.5 kilómetros, mientras que en el caso de las carreteras convencionales, se estableció en 7.75 kilómetros. Para cada uno de los tipos de vía considerados se han construido una base de datos en la que se han incluido las variables de existencia o no de Tramo Blanco, así como las variables de tráfico (intensidad media diaria total, intensidad de vehículos pesados y porcentaje de vehículos pesados ), la velocidad media y las variables de geometría (número de carriles, ancho de carril, ancho de arcén derecho e izquierdo, ancho de calzada y plataforma, radio, peralte, pendiente y visibilidad directa e inversa en los casos disponibles); como variables adicionales, se han incluido el número de accidentes con víctimas, los fallecidos y heridos graves, índices de peligrosidad, índices de mortalidad y exposición al riesgo. Los trabajos desarrollados para explicar la presencia de Tramos Blancos en la red de autopistas de peaje han permitido establecer las diferencias entre los valores medios de las variables de tráfico y diseño geométrico en Tramos Blancos respecto a tramos no blancos y comprobar que estas diferencias son significativas. Así mismo, se ha podido calibrar un modelo de regresión logística que explica parcialmente la existencia de Tramos Blancos, para rangos de tráfico inferiores a 10.000 vehículos diarios y para tráficos entre 10.000 y 15.000 vehículos diarios. Para el primer grupo (menos de 10.000 vehículos al día), las variables que han demostrado tener una mayor influencia en la existencia de Tramo Blanco son la velocidad media de circulación, el ancho de carril, el ancho de arcén izquierdo y el porcentaje de vehículos pesados. Para el segundo grupo (entre 10.000 y 15.000 vehículos al día), las variables independientes más influyentes en la existencia de Tramo Blanco han sido la velocidad de circulación, el ancho de calzada y el porcentaje de vehículos pesados. En el caso de las carreteras convencionales, los diferentes análisis realizados no han permitido identificar un modelo que consiga una buena clasificación de los Tramos Blancos. Aun así, se puede afirmar que los valores medios de las variables de intensidad de tráfico, radio, visibilidad, peralte y pendiente presentan diferencias significativas en los Tramos Blancos respecto a los no blancos, que varían en función de la intensidad de tráfico. Los resultados obtenidos deben considerarse como la conclusión de un análisis preliminar, dado que existen otros parámetros, tanto de diseño de la vía como de la circulación, el entorno, el factor humano o el vehículo que podrían tener una influencia en el hecho que se analiza, y no se han considerado por no disponer de esta información. En esta misma línea, el análisis de las circunstancias que rodean al viaje que el usuario de la vía realiza, su tipología y motivación es una fuente de información de interés de la que no se tienen datos y que permitiría mejorar el análisis de accidentalidad en general, y en particular el de esta investigación. Adicionalmente, se reconocen limitaciones en el desarrollo de esta investigación, en las que sería preciso profundizar en el futuro, reconociendo así nuevas líneas de investigación de interés. The traditional approach to road accidents analysis has been based in the use of palliative tools, such as black spot (or road sections) identification and management, or preventive tools, such as road safety audits and inspections. This thesis shows a complementary approach to the existing tools, from a new perspective: the consideration of road sections where no accidents have occurred; these are the so-called White Road Sections. The aim of this thesis is to show that there are certain design parameters and traffic characteristics which, under similar circumstances for roads, have influence in the fact that accidents occur, in addition to the main factor, which is the risk exposure, and others. White Road Sections, defined as road sections of a representative length, where no fatal accidents or accidents involving serious injured have happened during a long period of time, should not be a product of randomness of accidents; on the contrary, they might be the consequence of a confluence of specific parameters of road geometry, traffic volumes and heavy vehicles traffic volumes. For this research, the toll motorway network and single-carriageway network of the Spanish National Road Network have been considered, which is a total of 17.000 kilometers; fatal accidents and those involving serious injured from the period 2006-2010 have been considered (a total number of 10.000 accidents). The road network covered means 65% of the total length of the National Road Network, which allocates 33% of traffic volume; 47% of accidents with victims and 60% of fatalities happened in these road networks during 2013. During the research, a database of 250.130 registers and more than 3.5 million data for toll motorways and 935.042 registers and more than 14 million data for single carriageways of the National Road Network was developed. Both toll motorways and single-carriageways have been classified according to their traffic characteristics, so that the analysis is performed over roads with similar risk exposure. For each road type, a reference length for White Road Section has been defined, as the 95 percentile of all road sections lengths without accidents (with fatalities or serious injured) for 2006-2010. For toll motorways, this reference length concluded to be 14.5 kilometers, while for single-carriageways, it was defined as 7.75 kilometers. A detailed database was developed for each type of road, including the variable “existence of White Road Section”, as well as variables of traffic (average daily traffic volume, heavy vehicles average daily traffic and percentage of heavy vehicles from the total traffic volume), average speed and geometry variables (number of lanes, width of lane, width of shoulders, carriageway width, platform width, radius, superelevation, slope and visibility); additional variables, such as number of accidents with victims, number of fatalities or serious injured, risk and fatality rates and risk exposure, have also been included. Research conducted for the explanation of the presence of White Road Sections in the toll motorway network have shown statistically significant differences in the average values of variables of traffic and geometric design in White Road Sections compared with other road sections. In addition, a binary logistic model for the partial explanation of the presence of White Road Sections was developed, for traffic volumes lower than 10.000 daily vehicles and for those running from 10.000 to 15.000 daily vehicles. For the first group, the most influent variables for the presence of White Road Sections were the average speed, width of lane, width of left shoulder and percentage of heavy vehicles. For the second group, the most influent variables were found to be average speed, carriageway width and percentage of heavy vehicles. For single-carriageways, the different analysis developed did not reach a proper model for the explanation of White Road Sections. However, it can be assumed that the average values of the variables of traffic volume, radius, visibility, superelevation and slope show significant differences in White Road Sections if compared with others, which also vary with traffic volumes. Results obtained should be considered as a conclusion of a preliminary analysis, as there are other parameters, not only design-related, but also regarding traffic, environment, human factor and vehicle which could have an influence in the fact under research, but this information has not been considered in the analysis, as it was not available. In parallel, the analysis of the circumstances around the trip, including its typology and motivation is an interesting source of information, from which data are not available; the availability of this information would be useful for the improvement of accident analysis, in general, and for this research work, in particular. In addition, there are some limitations in the development of the research work; it would be necessary to develop an in-depth analysis in the future, thus assuming new research lines of interest.

Metagenomic Anlaysis of microsymbiont selection by the legume plant host

Rhizobium leguminosarum bv.viciae is able to establish nitrogen-fixing symbioses with legumes of the genera Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants (Laguerre et al., Young et al.) provided evidence that different plant hosts are able to select different rhizobial genotypes among those available in a given soil. However, these studies were necessarily limited by the paucity of relevant biodiversity markers. We have now reappraised this problem with the help of genomic tools. A well-characterized agricultural soil (INRA Bretennieres) was used as source of rhizobia. Plants of Pisum sativum, Lens culinaris, Vicia sativa and V. faba were used as traps. Isolates from 100 nodules were pooled, and DNA from each pool was sequenced (BGI-Hong Kong; Illumina Hiseq 2000, 500 bp PE libraries, 100 bp reads, 12 Mreads). Reads were quality filtered (FastQC, Trimmomatic), mapped against reference R. leguminosarum genomes (Bowtie2, Samtools), and visualized (IGV). An important fraction of the filtered reads were not recruited by reference genomes, suggesting that plant isolates contain genes that are not present in the reference genomes. For this study, we focused on three conserved genomic regions: 16S-23S rDNA, atpD and nodDABC, and a Single Nucleotide Polymorphism (SNP) analysis was carried out with meta / multigenomes from each plant. Although the level of polymorphism varied (lowest in the rRNA region), polymorphic sites could be identified that define the specific soil population vs. reference genomes. More importantly, a plant-specific SNP distribution was observed. This could be confirmed with many other regions extracted from the reference genomes (data not shown). Our results confirm at the genomic level previous observations regarding plant selection of specific genotypes. We expect that further, ongoing comparative studies on differential meta / multigenomic sequences will identify specific gene components of the plant-selected genotypes

Topoisomerase II drives DNA transport by hydrolyzing one ATP

DNA topoisomerase II is a homodimeric molecular machine that couples ATP usage to the transport of one DNA segment through a transient break in another segment. In the presence of a nonhydrolyzable ATP analog, the enzyme is known to promote a single turnover of DNA transport. Current models for the enzyme’s mechanism based on this result have hydrolysis of two ATPs as the last step, used only to reset the enzyme for another round of reaction. Using rapid-quench techniques, topoisomerase II recently was shown to hydrolyze its two bound ATPs in a strictly sequential manner. This result is incongruous with the models based on the nonhydrolyzable ATP analog data. Here we present evidence that hydrolysis of one ATP by topoisomerase II precedes, and accelerates, DNA transport. These results indicate that important features of this enzyme’s mechanism previously have been overlooked because of the reliance on nonhydrolyzable analogs for studying a single reaction turnover. A model for the mechanism of topoisomerase II is presented to show how hydrolysis of one ATP could drive DNA transport.

Sequence variation in the Fanconi anemia gene FAA

Fanconi anemia (FA) is a genetically heterogeneous autosomal recessive syndrome associated with chromosomal instability, hypersensitivity to DNA crosslinking agents, and predisposition to malignancy. The gene for FA complementation group A (FAA) recently has been cloned. The cDNA is predicted to encode a polypeptide of 1,455 amino acids, with no homologies to any known protein that might suggest a function for FAA. We have used single-strand conformational polymorphism analysis to screen genomic DNA from a panel of 97 racially and ethnically diverse FA patients from the International Fanconi Anemia Registry for mutations in the FAA gene. A total of 85 variant bands were detected. Forty-five of the variants are probably benign polymorphisms, of which nine are common and can be used for various applications, including mapping studies for other genes in this region of chromosome 16q. Amplification refractory mutation system assays were developed to simplify their detection. Forty variants are likely to be pathogenic mutations. Seventeen of these are microdeletions/microinsertions associated with short direct repeats or homonucleotide tracts, a type of mutation thought to be generated by a mechanism of slipped-strand mispairing during DNA replication. A screening of 350 FA probands from the International Fanconi Anemia Registry for two of these deletions (1115–1118del and 3788–3790del) revealed that they are carried on about 2% and 5% of the FA alleles, respectively. 3788–3790del appears in a variety of ethnic groups and is found on at least two different haplotypes. We suggest that FAA is hypermutable, and that slipped-strand mispairing, a mutational mechanism recognized as important for the generation of germ-line and somatic mutations in a variety of cancer-related genes, including p53, APC, RB1, WT1, and BRCA1, may be a major mechanism for FAA mutagenesis.

How does a β-hairpin fold/unfold? Competition between topology and heterogeneity in a solvable model

We study the competition between topological effects and sequence inhomogeneities in determining the thermodynamics and the un/folding kinetics of a β-hairpin. Our work utilizes a new exactly solvable model that allows for arbitrary configurations of native contacts. In general, the competition between heterogeneity and topology results in a crossover of the dominant transition state. Interestingly, near this crossover, the single reaction coordinate picture can be seriously misleading. Our results also suggest that inferring the folding pathway from unfolding simulations is not always justified.

Effect Of DNA-dependent protein kinase on the molecular fate of the rAAV2 genome in skeletal muscle

We report here that the DNA-dependent protein kinase (DNA-PK) affects the molecular fate of the recombinant adeno-associated virus (rAAV) genome in skeletal muscle. rAAV-human α1-antitrypsin (rAAV-hAAT) vectors were delivered by intramuscular injection to either C57BL/6 (DNA-PKcs+) or C57BL/6-SCID [severe combined immunodeficient (SCID), DNA-PKcs−] mice. In both strains, high levels of transgene expression were sustained for up to 1 year after a single injection. Southern blot analysis showed that rAAV genomes persisted as linear episomes for more than 1 year in SCID mice, whereas only circular episomal forms were observed in the C57BL/6 strain. These results indicate that DNA-PK is involved in the formation of circular rAAV episomes.

Carbohydrates in Individual Cells of Epidermis, Mesophyll, and Bundle Sheath in Barley Leaves with Changed Export or Photosynthetic Rate1

Carbohydrate metabolism of barley (Hordeum vulgare) leaves induced to accumulate sucrose (Suc) and fructans was investigated at the single-cell level using single-cell sampling and analysis. Cooling of the root and shoot apical meristem of barley plants led to the accumulation of Suc and fructan in leaf tissue. Suc and fructan accumulated in both mesophyll and parenchymatous bundle-sheath (PBS) cells because of the reduced export of sugars from leaves under cooling and to increased photosynthesis under high photon fluence rates. The general trends of Suc and fructan accumulation were similar for mesophyll and PBS cells. The fructan-to-Suc ratio was higher for PBS cells than for mesophyll cells, suggesting that the threshold Suc concentration needed for the initiation of fructan synthesis was lower for PBS cells. Epidermal cells contained very low concentrations of sugar throughout the cooling experiment. The difference in Suc concentration between control and treated plants was much less if compared at the single-cell level rather than the whole-tissue level, suggesting that the vascular tissue contains a significant proportion of total leaf Suc. We discuss the importance of analyzing complex tissues at the resolution of individual cells to assign molecular mechanisms to phenomena observed at the whole-plant level.

Suppression of trkB expression by antisense oligonucleotides alters a neuronal phenotype in the rod pathway of the developing rat retina.

trkB is the high-affinity receptor for brain-derived neurotrophic factor (BDNF), a trophic molecule with demonstrated effects on the survival and differentiation of a wide variety of neuronal populations. In the mammalian retina, trkB is localized to both ganglion cells and numerous cells in the inner nuclear layer. Much information on the role of BDNF in neuronal development has been derived from the study of trkB- and BDNF-deficient mutant mice. This includes an attenuation of the numbers of cortical neurons immunopositive for the calcium-binding proteins, parvalbumin, and calbindin. Unfortunately, these mutant animals typically fail to survive for > 24-48 hr after birth. Since most retinal neuronal differentiation occurs postnatally, we have devised an alternative scheme to suppress the expression of trkB in the retina to examine the role of BDNF on the postnatal development of neurons of the inner retina. Neonatal rats were treated with intraocular injection of an antisense oligonucleotide (1-2 microliters of 10-100 microM solution) targeted to the trkB mRNA. Immunohistochemistry with a polyclonal antibody to trkB showed that the expression of trkB in retinal neurons was suppressed 48-72 hr following a single injection. Northern blot analysis demonstrated that antisense treatment had no effect on the level of trkB mRNA, even after multiple injections. This suggests an effect of trkB antisense treatment on protein translation, but not on RNA transcription. No alterations were observed in the thickness of retinal cellular or plexiform layers, suggesting that BDNF is not the sole survival factor for these neurons. There were, however, alterations in the patterns of immunostaining for parvalbumin, a marker for the narrow-field, bistratified AII amacrine cell-a central element of the rod (scotopic) pathway. This was evidenced by a decrease in both the number of immunostained somata (> 50%) and in the intensity of immunolabeling. However, the immunostaining pattern of calbindin was not affected. These studies suggest that the ligands for trkB have specific effects on the neurochemical phenotypic expression of inner retinal neurons and in the development of a well-defined retinal circuit.

Abordagem tecnológica da síntese de carbonato de glicerila: ensaios físico-químicos, espectroscópicos e viabilidade econômica

Este trabalho trata da proposta para a produção carbonato de glicerila como continuação de trabalho de Mestrado. Propõe-se estabelecer uma sequência para a obtenção e a purificação do produto, que envolve remoção e o aproveitamento de amônia e a remoção de eletrólitos, bem como a utilização de novos catalisadores. De maneira geral, análises espectrofotométricas demonstraram que o produto purificado apresentou características semelhantes às da especificação constante de produto já existente no mercado cedido para comparação (JEFFSOL®, Huntsman). Além disso, foi calculado o custo de produção tanto em escala laboratorial como em escala industrial. Análises de Ressonância Magnética Nuclear e Cromatografia a Gás, aliadas à Espectrofotometria no Infravermelho permitiram avaliar tanto a evolução das reações, bem como os rendimentos reacionais. Foi demonstrada a aplicabilidade das técnicas de RMN 1H e 13C para o cálculo dos rendimentos reacionais, bem como para a elucidação dos mecanismos reacionais. A partir de análises em escala laboratorial, foi possível verificar que, para as condições reacionais estudadas foram obtidas baixas conversões da glicerina e baixas seletividades para o carbonato de glicerila. E ainda, o sulfato de zinco apresentou o melhor desempenho. É importante salientar que, mesmo para baixas conversões, sua produção ainda é economicamente viável devido ao seu elevado valor de mercado. O estudo da produção em escala industrial contemplou a síntese de fluxograma de processo e posterior simulação, incluindo o dimensionamento dos principais equipamentos de processo para fins de análise econômica, via calculo de custos de capital (CAPEX) e operacionais (OPEX). Os resultados indicaram viabilidade econômica do projeto, sendo demonstrado que a implantação de uma nova unidade de produção de carbonato de glicerila pode ser bastante rentável mesmo para baixos rendimentos. O produto obtido possui diversas e interessantes aplicações cosméticas e farmacêuticas, principalmente por ser um tensoativo não iônico, de baixa toxicidade, biodegradável e produzido a partir de fontes renováveis. Assim, o carbonato de glicerila produzido é uma interessante forma de aproveitamento da glicerina proveniente da fabricação de biodiesel.