Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Relatório de atividade profissional

Relatório de atividade profissional de mestrado em Ciências - Formação Contínua de Professores (área de especialização em Biologia e Geologia)

Desenvolvimento de um motor BMW para servir de Range Extender

Dissertação de mestrado integrado em Engenharia Mecânica

Optimização do processo de recolha de resíduos: desenvolvimento de ferramentas de investigação operacional para o problema de orientação de equipas com multi-restrições

Tese de Doutoramento em Engenharia Industrial e de Sistemas.

Exploitation of Ashbya gossypii for the production of high-value products from glycerol feedstocks

Dissertação de mestrado em Bioengenharia

Operation modes for the electric vehicle in smart grids and smart homes : present and proposed modes

This paper presents the main operation modes for an electric vehicle (EV) battery charger framed in smart grids and smart homes, i.e., are discussed the present-day and are proposed new operation modes that can represent an asset towards EV adoption. Besides the well-known grid to vehicle (G2V) and vehicle to grid (V2G), this paper proposes two new operation modes: Home-to-vehicle (H2V), where the EV battery charger current is controlled according to the current consumption of the electrical appliances of the home (this operation mode is combined with the G2V and V2G); Vehicle-for-grid (V4G), where the EV battery charger is used for compensating current harmonics or reactive power, simultaneously with the G2V and V2G operation modes. The vehicle-to-home (V2H) operation mode, where the EV can operate as a power source in isolated systems or as an off-line uninterruptible power supply to feed priority appliances of the home during power outages of the electrical grid is presented in this paper framed with the other operation modes. These five operation modes were validated through experimental results using a developed 3.6 kW bidirectional EV battery charger prototype, which was specially designed for these operation modes. The paper describes the developed EV battery charger prototype, detailing the power theory and the voltage and current control strategies used in the control system. The paper presents experimental results for the various operation modes, both in steady-state and during transients.

Characterization of the in vivo cardiac electrophysiologic effects of high-dose cocaine in closed-chest, anesthetized dogs with normal hearts

OBJECTIVE: To characterize the cardiac electrophysiologic effects of cocaine. METHODS: In 8 dogs (9-13 kg), electrophysiologic parameters and programmed stimulation were undertaken using transvenous catheters at baseline, and after cocaine intravenous infusion (12 mg/kg bolus followed by 0.22 mg/kg/min for 25 minutes). RESULTS: Cocaine plasma levels (n=5) rose to 6.73± 0.56 mg/mL. Cocaine did not affect sinus cycle length and arterial pressure. Cocaine prolonged P wave duration (54±6 vs 73±4 ms, P<0.001), PR interval (115±17 vs 164±15 ms, P<0.001), QRS duration (62±10 vs 88±14 ms, P<0.001), and QTc interval (344±28 vs 403±62 ms, P=0.03) but not JT interval (193±35 vs 226±53 ms, NS). Cocaine prolonged PA (9±6 vs 23±8 ms, P<0.001), AH (73±16 vs 92±15 ms; P=0.03), and HV (35±5 vs 45±3ms; P<0.001) intervals and Wenckebach point (247±26 vs 280±28 ms, P=0.04). An increase occurred in atrial (138±8 vs 184± 20 ms; P<0.001) and ventricular (160±15 vs 187±25 ms; P=0.03) refractoriness at a cycle length of 300 ms. Atrial arrhythmias were not induced in any dog. Ventricular fibrillation (VF) was induced in 2/8 dogs at baseline and 4/8 dogs after cocaine. CONCLUSION: High doses of cocaine exert significant class I effects and seem to enhance inducibility of VF but not of atrial arrhythmias.

Effects of high glucose concentrations on the endothelial function of the renal microcirculation of rabbits

OBJECTIVE: To assess the acute effects of high glucose concentrations on vascular reactivity in the isolated non diabetic rabbit kidney. METHODS: Rabbits were anaesthetized for isolation of the kidneys. Renal arteries and veins were cannulated for perfusion with Krebs-Henselleit solution and measurement of perfusion pressure. After 3 hours of perfusion with glucose 5,5 mM (control ) and 15 mM, the circulation was submitted to sub maximal precontraction (80% of maximal response) trough continuous infusion of noradrenaline 10 mM. Vascular reactivity was then assessed trough dose-responses curves with endothelium-dependent (acetylcholine) and independent (sodium nitroprusside) vasodilators. The influence of hyperosmolarity was analyzed with perfusion with mannitol 15mM. RESULTS: A significant reduction in the endothelium-dependent vasodilation in glucose 15mM group was observed compared to that in control, but there was no difference in endothelium-independent vasodilation. After perfusion with mannitol 15 mM, a less expressive reduction in endothelium-dependent vasodilation was observed, only reaching significance in regard to the greatest dose of acetylcholine. CONCLUSION: High levels of glucose similar to those found in diabetic patients in the postprandial period can cause significant acute changes in renal vascular reactivity rabbits. In diabetic patients these effects may also occur and contribute to diabetes vascular disease.

The influence of patient's consciousness regarding high blood pressure and patient's attitude in face of disease controlling medicine intake

OBJECTIVE: To assess the relation between blood pressure control and the following: the Morisky-Green test, the patient's consciousness regarding high blood pressure, the patient's attitude in face of medicine intake, the patient's attendance at medical consultations, and the subjective physician's judgment. METHODS: We studied 130 hypertensive patients with the following characteristics: 73% females, 60±11 years, 58% married, 70% white, 45% retired, 45% with incomplete elementary schooling, 64% had a familial income of 1 to 3 minimum wages, body mass index of 30±7 kg/m², consciousness regarding the disease for a mean period of 11±9.5 years, and mean treatment duration of 8 ±7 years. RESULTS: Only 35% of the hypertensive individuals had blood pressure under control and a longer duration of treatment (10±7 vs 7±6.5 years; P<0.05). The retiree predominated. The result of the Morisky-Green test did not relate to blood pressure control. In evaluating the attitude in face of medicine intake, the controlled patients achieved significantly higher scores than did the noncontrolled patients (8±1.9 vs 7 ±2, P<0.05). The hypertensive patients had higher levels of consciousness regarding their disease and its treatment, and most (70%) patients attended 3 or 4 medical consultations, which did not influence blood pressure control. The physicians attributed significantly higher scores regarding adherence to treatment to controlled patients (6±0.8 vs 5±1.2; P<0.05). CONCLUSION: Consciousness regarding the disease, the Morisky-Green test, and attendance to medical consultations did not influence blood pressure control.

Diseño de sistemas de comunicaciones de alta velocidad. Design of high-speed communication systems.

El crecimiento exponencial del tráfico de datos es uno de los mayores desafíos que enfrentan actualmente los sistemas de comunicaciones, debiendo los mismos ser capaces de soportar velocidades de procesamiento de datos cada vez mas altas. En particular, el consumo de potencia se ha transformado en uno de los parámetros de diseño más críticos, generando la necesidad de investigar el uso de nuevas arquitecturas y algoritmos para el procesamiento digital de la información. Por otro lado, el análisis y evaluación de nuevas técnicas de procesamiento presenta dificultades dadas las altas velocidades a las que deben operar, resultando frecuentemente ineficiente el uso de la simulación basada en software como método. En este contexto, el uso de electrónica programable ofrece una oportunidad a bajo costo donde no solo se evaluan nuevas técnicas de diseño de alta velocidad sino también se valida su implementación en desarrollos tecnológicos. El presente proyecto tiene como objetivo principal el estudio y desarrollo de nuevas arquitecturas y algoritmos en electrónica programable para el procesamiento de datos a alta velocidad. El método a utilizar será la programación en dispositivos FPGA (Field-Programmable Gate Array) que ofrecen una buena relación costo-beneficio y gran flexibilidad para integrarse con otros dispositivos de comunicaciones. Para la etapas de diseño, simulación y programación se utilizaran herramientas CAD (Computer-Aided Design) orientadas a sistemas electrónicos digitales. El proyecto beneficiara a estudiantes de grado y postgrado de carreras afines a la informática y las telecomunicaciones, contribuyendo al desarrollo de proyectos finales y tesis doctorales. Los resultados del proyecto serán publicados en conferencias y/o revistas nacionales e internacionales y divulgados a través de charlas de difusión y/o encuentros. El proyecto se enmarca dentro de un área de gran importancia para la Provincia de Córdoba, como lo es la informática y las telecomunicaciones, y promete generar conocimiento de gran valor agregado que pueda ser transferido a empresas tecnológicas de la Provincia de Córdoba a través de consultorias o desarrollos de productos.

Juventud vulnerable y escuela media: representaciones y experiencias sobre la autoridad escolar. Vulnerable youth and high school: representation and experiences on scholastic authority.

La investigación busca responder cómo experimentan, se representan y caracterizan grupos juveniles en situación de vulnerabilidad social de la ciudad de Córdoba, la autoridad en la escuela media considerada en tres actores institucionales claves: docentes, preceptores y directores. Se propone indagar acerca de la autoridad desde dos dimensiones: las representaciones juveniles de la autoridad pedagógica (ligada al desempeño de los profesores) y la autoridad en términos de límites que reconocen en los directivos y preceptores vinculándola con el espacio institucional de la escuela. Objetivos Explorar las relaciones con la autoridad escolar vivenciadas en su tránsito por la escuela secundaria por jóvenes en condiciones de vulnerabilidad social de la ciudad de Córdoba. Indagar como vivencian los jóvenes las leyes y normativas escolares atendiendo a la cercanía o distancia con las prácticas que ellos ponen en juego en el seno de sus grupos de referencia. Identificar desde las voces de adolescentes de sectores populares los problemas de convivencia escolar más frecuentes, apuntando a reconocer qué posiciones advierten ante tales situaciones en los adultos que se desempeñan en diferentes roles en la escuela. Explorar en las interacciones y conflictos que se plantean en sus relaciones con docentes, directivos y preceptores. Conocer las valoraciones que los jóvenes efectúan sobre las estrategias de autoridad puestas en juego por profesores (vinculándolas con el desempeño cotidiano en sus asignaturas), preceptores y directivos. Materiales y métodos: Se seguirán dos etapas: a) Realización de grupos focales con adolescentes de 15-17 en situación de vulnerabilidad social que asisten a la escuela media. Se prevé la utilización de muestras intencionales. b) Aplicación de un cuestionario estandarizado a jóvenes de escuelas secundarias en situación de vulnerabilidad. Las preguntas del cuestionario serán elaboradas en forma de escalas de tipo Likert construidas a partir de la información obtenida en la primera etapa Resultados: La investigación producirá conocimientos acerca de: - formas de legitimación de la autoridad escolar por parte de jóvenes socialmente vulnerables - características de la autoridad escolar en docentes, preceptores y directores - modelos institucionales de autoridad escolar Importancia: La significatividad de los resultados se vincula con el marco de las discusiones que se vienen desarrollando en torno a las transformaciones de la educación secundaria, dentro de las cuales la recreación del vínculo docente-alumno y la redefinición de los marcos de autoridad institucionales resultan sustantivos de cara a la mejora. Pertinencia: El trabajo ayudará a identificar núcleos críticos ligados con la gestión de convivencia y de la autoridad escolar, lo que servirá para identificar aspectos de los formatos institucionales que deberían ser revisados y aquellos que podrían ser objeto de afianzamiento y multiplicación.

Caracterización de moléculas de rizobacterias y de leguminosas con alto impacto productivo y tecnológico en la provincia de Córdoba. Characterization of rhizobacteria and legumes molecules with high production and technological impact in the province of Córdoba.

La provincia de Córdoba cuenta con alto desarrollo agrícola a base de cereales y leguminosas, como por ejemplo el maní. Pero este cultivo con los años ha trasladado su zona de siembra original y se ha extendido hacia otras áreas de mayor riesgo ambiental a raíz de la implantación de la soja. Diversas son las consecuencias de estas dos acciones y que se extienden desde lo agroecológico hasta lo científico-técnico. Este previo estado del arte y las referencias bibliográficas que apuntan a la necesitad de aumentar el valor agregado de los cultivos, nos ha llevado a formular una hipótesis de trabajo y es que las plantas de maní y soja así como las rizobacterias que se asocian con ellas, son productoras de diversas moléculas con potencial uso biológico en la productividad del cultivo y en aplicaciones tecnológicas, biológicas e industriales. Sumado a lo anterior y a las ideas gubernamentales de la necesidad de obtener conocimiento y capitalizarlo como riqueza, y la imperiosa urgencia de responder a demandas regionales, se presenta este proyecto cuyo objetivo general apunta a estudiar la producción de diversas moléculas de rizobacterias y leguminosas con el fin de mejorar la productividad de los cultivos y desarrollar nuevas aplicaciones tecnológicas en la provincia de Córdoba. Para cumplir dentro de los dos años de trabajo solicitados con lo expuesto anteriormente, la investigación será dividida en objetivos específicos y que consisten en investigar la producción de moléculas de raíces de maní y soja, analizar la respuesta microbiana a las rizodeposiciones de ambas leguminosas y evaluar el posible papel biológico y aplicación tecnológica de moléculas de ambos tipos de organismos. Nuestro grupo es de caracter multidisciplinar y ahondará en la diversidad molecular producida por raíces de maní y soja en direfentes días y la respuesta de las rizobacterias que se asocian ellas utilizando técnicas químicas (HPLC, GC, GC-masa) y herramientas microbiológicas y bioquímicas clásicas. Con fines de aplicación tecnológica se determinará la posible acción antioxidante de los extractos vegetales sobre sistemas modelos de ensayo así como la búsqueda de enzimas y hormonas microbianas aplicables en otros campos de la ciencia. De esta forma se pretende atender algunas demandas de diferentes sectores del centro sur de Córdoba y del país pero fundamentalmente posibilitar nuevas aplicaciones de las leguminosas y de las rizobacterias además de permitir la formación académicas de alumnos de grado y posgrado de la UNRC. The province of Cordoba has high agricultural development based on cereals and legumes such as peanuts. But the crop over the years has transferred his original planting area and has spread to other areas of greatest environmental risk following the introduction of soybeans. The previous state and regional art references that point to the necessity of increasing the value-added crops, has led us to formulate a working hypothesis is that the peanut and soybean plants and rhizobacteria associated with they are products of various biological molecules with potential use in crop productivity and biological technology and industrial applications. The general objective is aimed at studying the production of various molecules and legumes rhizobacteria to improve crop productivity and develop new technological applications in the Cordoba province. This form is intended to meet some demands of different sectors of the center south of Cordoba and the country but enabling new applications of legumes and rhizobacteria in addition to allowing the academic training of undergraduates and graduate of the UNRC.

The challenges of establishing the electric vehicle in Ireland

This thesis investigates the challenges of establishing the electric vehicle (EV) in Ireland and how the Irish government and industry are trying to meet them. It further seeks to provide information on Irish consumers’ attitudes towards the electric vehicle and their willingness to purchase it. The review of the literature showed that the Irish government is investing significant funds in trying to establish the market for the electric vehicle and position itself as a world leader in adopting the electric vehicle. The EV will also have an important role to play in how Ireland meets its targets for CO2 reductions towards 2020. Climate change and use of fossil fuels are driving the need for increased use of renewable energy and increased energy independence while reducing the greenhouse gas emissions that are the leading cause of climate change. The transport sector is almost completely dependent on the use of fossil fuel and resultantly is one of the largest sources of these GHG emissions. These issues are leading to the design and production of more energy efficient and environmentally friendly vehicles. The ultimate goal is to achieve a zero emissions vehicle. The electric vehicle is presently the only vehicle being mass produced that has the potential to be zero emissions. There are however issues that customers may not be willing to overlook such as the lower range of the vehicle and the length of time it takes to recharge. Vehicle cost is also an important issue that customers may not overlook. Knowing what the consumer’s attitudes are towards the EV and their willingness to purchase them is important as these new vehicles begin to appear in the showrooms. The consumers will be vital to how successful this market becomes. Using an online questionnaire methodology, in a sample of 118 consumers, the major conclusion to be drawn from the research is that the vehicle price, the convenience to recharge and vehicle range were the three most essential issues for the consumers if they were purchasing an EV. The success of the electric vehicle market may depend on what measures are taken to overcome them.