Using Clouds to Scale Grid Resources: An Economic Model

Infrastructure as a Service clouds are a flexible and fast way to obtain (virtual) resources as demand varies. Grids, on the other hand, are middleware platforms able to combine resources from different administrative domains for task execution. Clouds can be used by grids as providers of devices such as virtual machines, so they only use the resources they need. But this requires grids to be able to decide when to allocate and release those resources. Here we introduce and analyze by simulations an economic mechanism (a) to set resource prices and (b) resolve when to scale resources depending on the users’ demand. This system has a strong emphasis on fairness, so no user hinders the execution of other users’ tasks by getting too many resources. Our simulator is based on the well-known GridSim software for grid simulation, which we expand to simulate infrastructure clouds. The results show how the proposed system can successfully adapt the amount of allocated resources to the demand, while at the same time ensuring that resources are fairly shared among users.

Identificación y evaluación de los recursos pesqueros de la República de Guinea Bissau para su explotación sostenible

A través del conocimiento de los recursos pesqueros, es decir especies, cantidad extraíble, métodos de pesca, etc., se ofrece a la comunidad un medio para mejorar su nivel de vida. En el presente trabajo se han catalogado 171. especies cuya captura es rentable económicamente. Están agrupadas en tres Phyllum y 73 familias. Una vez realizada la identificación de especies, se ha elaborado un modelo matemático, que basado en la dinámica de poblaciones, nos permite estimar la cantidad de biomasa existente en el caladero para una determinada especie. En función de la biomasa estimada de esta forma, pueden planificarse las capturas, de tal forma que la explotación del recurso sea sostenible, para evitar que éste se agote. En función de la estimación, las autoridades económicas podrán planificar la política pesquera adecuada para conseguir la sostenibilidad ambiental y económica a medio y largo plazo. Se puede aplicar este modelo a cualquier especie, pero lo hemos particularizado a la gamba blanca por su especial interés económico para el país. Se observa cómo evolucionarán las capturas hasta el año 2027, en el que tanto la producción como el beneficio es máximo. A continuación obtenemos una estabilización de las capturas y por tanto de los ingresos, lo que nos permite mantener la extracción y la sostenibilidad de la especie. ABSTRACT The knowledge of fishery resources, i.e., species, the quantity of fish that can be caught, fishing methods, etc, provides the community with a means to improve their standard of living. In this work, we have listed some species the yield of which is economically profitable. They have been grouped into three categories… The mathematical model, based on population dynamics, allows us to plan the harvesting and to estimate resources. In turn, this will translate into an ability to plan the budget by the economic authorities, since the middle and long turn incomes are known. This model can be applied to any species, but we have chosen the white shrimp because of its special economic value for the country. It shows how the yields will develop up to a maximum in 2027. Then we will obtain a stable catch and therefore a stable income. This will allow us to maintain the harvesting and also the sustainability of the species.

Aplicación de la energía solar térmica en una incubadora comercial de perdiz roja y supervisión de la actividad biológica mediante sensores inteligentes

La perdiz roja es la especie cinegética por excelencia en la península ibérica, cuya cría en cautividad y suelta controlada comenzó a regularse en los años 70 con la aparición del ICONA. La incubación controlada de huevos de perdiz es imprescindible, con fines cinegéticos y de preservación de la especie, y se desarrolla con incubadoras comerciales de pequeña y mediana escala, distribuidas en zonas rurales con acceso limitado y/o deficiente al suministro eléctrico. En nuestras latitudes el aporte de energía solar térmica se perfila como una posibilidad de mejorar la eficiencia energética de éstas y otras instalaciones y de reducir la dependencia energética exterior. Hay diversos factores físico-químicos que influyen en la calidad de la incubación: temperatura, humedad relativa, y concentración de gases, de los cuales sólo los dos primeros son habitualmente supervisados y controlados en este tipo de incubadoras. Esta Tesis surge en el marco de dos proyectos de cooperación con la AECID, y tiene como objetivos: la caracterización espacial de variables relevantes (temperatura (T), humedad relativa (HR)) en la incubadora comercial durante el proceso de incubación, la determinación de la relación existente entre la evolución de variables ambientales durante el proceso de incubación y la tasa de nacimientos (35-77%), así como el diseño y evaluación del sistema de apoyo solar térmico para determinar su potencial de utilización durante las incubaciones comerciales. La instalación de un número limitado de sensores permite la monitorización precisa del proceso de incubación de los huevos. Los resultados más relevantes indican que en incubaciones comerciales los gradientes de T y HR han sido despreciables (1ºC de diferencia entre las posiciones con mayor y menor T media y un 4,5% de diferencia entre las posiciones con mayor y menor HR), mientras que el seguimiento y ajuste (mediante modelos de crecimiento) de la concentración de CO2 (r2 entre 0,948 y 0,987 en las 5 incubaciones, para un total de 43315 huevos) permite valorar la actividad fisiológica de los huevos e incluso predecir la tasa de éxito (nacimientos), basándose en la concentración de CO2 estimada mediante modelos de crecimiento en el día 20 de incubación (r2 entre 0,997 y 0,994 según el modelo de estimación empleado). El sistema ha sido valorado muy positivamente por los productores (Finca Cinegética Dehesa Vieja de Galapagar). El aporte térmico se ha diseñado (con mínima intrusión en el sistema comercial) sobre la base de un sistema de enfriamiento de emergencia original de la incubadora, al que se han incorporado un colector solar, un depósito, un sistema de electroválvulas, una bomba de circulación y sensores de T en distintos puntos del sistema, y cuyo control ha sido automatizado. En esta Tesis se muestra que la contribución solar puede aportar hasta un 42% de las demandas de energía en nuestras condiciones geográficas para una temperatura de consigna dentro de la incubadora de 36.8ºC, sin afectar a la estabilidad de la temperatura. Además, el rendimiento del colector solar se ha acotado entre un 44% y un 85%, de acuerdo con los cálculos termodinámicos; valores que se mantienen dentro del rango aportado por el fabricante (61%). En el futuro se plantea evaluar el efecto de distintas estrategias de control, tales como controladores difusos, que incorporan el conocimiento experto al control automático. ABSTRACT The partridge is the quintessential game species in the Iberian Peninsula, which controlled breeding and release, began to be regulated in the 70s with the emergence of ICONA. The controlled incubation of eggs is essential, and takes place in commercial incubators of small and medium scale, distributed in rural areas with limited and/or inadequate access to power. In our latitudes the contribution of solar thermal energy is emerging as a possibility to improve the energy efficiency of the facilities and to reduce external energy dependence. There are various physicochemical factors influencing the quality of incubation: temperature, relative humidity and concentration of gases, of which only the first two are typically monitored and controlled in such incubators. This PhD comes within the framework of two cooperation projects with AECID and aims: the spatial characterization of relevant variables in a commercial incubator (temperature (T), and relative humidity (HR)), determining the relationships in the changes in environmental variables during incubation and birth rates (35-77%) as well as the design and evaluation of solar thermal support system to determine its potential use during commercial incubations; the installation of a limited number of sensors has allowed accurate monitoring of incubation of eggs. The most relevant results indicate that in commercial incubations, the gradients in T and HR have been negligible (1°C difference between the highest and lowest positions T and average 4.5% difference between the highest and lowest positions HR), while monitoring and fit using growth models of the concentration of CO2 (r2 between 0.948 and 0.987 in 5 incubations, for a total amount of 43,315 eggs) allows assessing the physiological activity of the eggs and even predict the success rate (hatchability), based on the estimated concentration of CO2 by using growth models on day 20 of incubation (r2 between 0.997 and 0.994 depending on the fit model).The system has been highly valued by producers (Finca Cinegética Dehesa Vieja de Galapagar). The hybrid heat system is designed (with minimal intrusion into the commercial system) based on an emergency cooling device, original in the incubator. New elements have been incorporated: a solar collector, a tank, a system of solenoid valves, a circulating pump and T sensors at various points of the system, whose control has been automated. This PhD shows that the solar contribution is responsible for up to 42% of energy demands in our geographical conditions for a setpoint temperature inside the incubator of 36.8ºC, without questioning the stability of the temperature. Furthermore, the efficiency of the solar collector has been bounded between 44% and 85%, according to thermodynamic calculations; values remain within the range provided by the manufacturer (61%). In the future it is proposed to evaluate the effect of different control strategies, such as fuzzy controllers, which incorporate the expertise to automated control.

RELIGIÃO E COTIDIANO NA CIDADE DE ALTO PARAÍSO (RONDÔNIA)

O objetivo da presente pesquisa é explicitar a relação entre a religião e a vida cotidiana na cid ade de Alto Paraíso (RO). Pretende discutir o papel do imaginário religioso no processo de ocupação de um novo espaço geográfico e na luta pela sobrevivência neste contexto. Sistematiza, assim, a história de uma cidade a partir de depoimentos de seus primeiros habitantes, perguntando pelo lugar da religião nesta memória. A metodologia privilegia o depoimento oral, colhido através da técnica de entrevistas, transcritas, sistematizadas e problematizadas como fonte plausível de investigação. Tenta captar e visibilizar os sentidos que sujeitos anônimos atribuem a suas experiências de vida num processo de transformação de um espaço inóspito em um lugar habitável e promissor em termos econômicos e sociais. A pesquisa está dividida em três capítulos. O primeiro sistematiza a história de Alto Paraíso, privilegiando a memória dos primeiros moradores da região. O segundo debate a religião como agente na formação do imaginário e das transformações sociais. O terceiro capítulo discute o embricamento entre o trânsito religioso, as magias populares e os milagres institucionalizados.(AU)

RELIGIÃO E COTIDIANO NA CIDADE DE ALTO PARAÍSO (RONDÔNIA)

O objetivo da presente pesquisa é explicitar a relação entre a religião e a vida cotidiana na cid ade de Alto Paraíso (RO). Pretende discutir o papel do imaginário religioso no processo de ocupação de um novo espaço geográfico e na luta pela sobrevivência neste contexto. Sistematiza, assim, a história de uma cidade a partir de depoimentos de seus primeiros habitantes, perguntando pelo lugar da religião nesta memória. A metodologia privilegia o depoimento oral, colhido através da técnica de entrevistas, transcritas, sistematizadas e problematizadas como fonte plausível de investigação. Tenta captar e visibilizar os sentidos que sujeitos anônimos atribuem a suas experiências de vida num processo de transformação de um espaço inóspito em um lugar habitável e promissor em termos econômicos e sociais. A pesquisa está dividida em três capítulos. O primeiro sistematiza a história de Alto Paraíso, privilegiando a memória dos primeiros moradores da região. O segundo debate a religião como agente na formação do imaginário e das transformações sociais. O terceiro capítulo discute o embricamento entre o trânsito religioso, as magias populares e os milagres institucionalizados.(AU)

Domain-specific gene disruption reveals critical regulation of neuregulin signaling by its cytoplasmic tail

Neuregulins are a multi-isoform family of growth factors that activate members of the erbB family of receptor tyrosine kinases. The membrane-anchored isoforms contain the receptor-activating ligand in their extracellular domain, a single membrane-spanning region, and a long cytoplasmic tail. To evaluate the potential biological role of the intracellular domain of the membrane-anchored neuregulin isoforms, we used a domain-specific gene disruption approach to produce a mouse line in which only the region of the neuregulin gene encoding almost the entire intracellular domain was disrupted. Consistent with previous reports in which all neuregulin isoforms were disrupted, the resulting homozygous neuregulin mutants died at E10.5 of circulatory failure and displayed defects in neural and cardiac development. To further understand these in vivo observations, we evaluated a similarly truncated neuregulin construct after transient expression in COS-7 cells. This cytoplasmic tail-deleted mutant, unlike wild-type neuregulin isoforms, was resistant to proteolytic release of its extracellular-domain ligand, a process required for erbB receptor activation. Thus, proteolytic processing of the membrane-bound neuregulin isoforms involved in cranial ganglia and heart embryogenesis is likely developmentally regulated and is critically controlled by their intracellular domain. This observation indicates that erbB receptor activation by membrane-bound neuregulins most likely involves a unique temporally and spatially regulated “inside-out” signaling process that is critical for processing and release of the extracellular-domain ligand.

Kinetic characterization of brush border myosin-I ATPase

Brush border myosin-I (BBM-I) is a single-headed unconventional myosin found in the microvilli of intestinal epithelial cells. We used stopped-flow kinetic analysis to measure the rate and equilibrium constants for several steps in the BBM-I ATPase cycle. We determined the rates for ATP binding to BBM-I and brush border actomyosin-I (actoBBM-I), the rate of actoBBM-I dissociation by ATP, and the rates for the steps in ADP dissociation from actoBBM-I. The rate and equilibrium constants for several of the steps in the actoBBM-I ATPase are significantly different from those of other members of the myosin superfamily. Most notably, dissociation of the actoBBM-I complex by ATP and release of ADP from actoBBM-I are both very slow. The slow rates of these steps may play a role in lengthening the time spent in force-generating states and in limiting the maximal rate of BBM-I motility. In addition, release of ADP from the actoBBM-I complex occurs in at least two steps. This study provides evidence for a member of the myosin superfamily with markedly divergent kinetic behavior.

Cholecystokinin-8 protects central cholinergic neurons against fimbria–fornix lesion through the up-regulation of nerve growth factor synthesis

In this study, we demonstrate that cholecystokinin-8 (CCK-8) induces an increase in both nerve growth factor (NGF) protein and NGF mRNA in mouse cortex and hippocampus when i.p. injected at physiological doses. By using fimbria–fornix-lesioned mice, we have also demonstrated that repeated CCK-8 i.p. injections result in recovery of lesion-induced NGF deficit in septum and restore the baseline NGF levels in hippocampus and cortex. Parallel to the effects on NGF, CCK-8 increases choline acetyltransferase (Chat) activity in forebrain when injected in unlesioned mice and counteract the septo-hippocampal Chat alterations in fimbria–fornix-lesioned mice. To assess the NGF involvement in the mechanism by which CCK-8 induces brain Chat, NGF antibody was administrated intracerebrally to saline- and CCK-8-injected mice. We observe that pretreatment with NGF antibody causes a marked reduction of NGF and Chat activity in septum and hippocampus of both saline- and CCK-8-injected mice. This evidence indicates that the CCK-8 effects on cholinergic cells are mediated through the synthesis and release of NGF. Taken together, our results suggest that peripheral administration of CCK-8 may represent a potential experimental model for investigating the effects of endogenous NGF up-regulation on diseases associated with altered brain cholinergic functions.

Memory landscapes of single-enzyme molecules

Immobilized single horseradish peroxidase enzymes were observed by confocal fluorescence spectroscopy during catalysis of the oxidation reaction of the nonfluorescent dihydrorhodamine 6G substrate into the highly fluorescent product rhodamine 6G. By extracting only the non-Markovian behavior of the spectroscopic two-state process of enzyme-product complex formation and release, memory landscapes were generated for single-enzyme molecules. The memory landscapes can be used to discriminate between different origins of stretched exponential kinetics that are found in the first-order correlation analysis. Memory landscapes of single-enzyme data shows oscillations that are expected in a single-enzyme system that possesses a set of transient states. Alternative origins of the oscillations may not, however, be ruled out. The data and analysis indicate that substrate interaction with the enzyme selects a set of conformational substates for which the enzyme is active.

Mutations in the DnaK chaperone affecting interaction with the DnaJ cochaperone

Hsp70 chaperones assist protein folding by ATP-controlled cycles of substrate binding and release. ATP hydrolysis is the rate-limiting step of the ATPase cycle that causes locking in of substrates into the substrate-binding cavity of Hsp70. This key step is strongly stimulated by DnaJ cochaperones. We show for the Escherichia coli Hsp70 homolog, DnaK, that stimulation by DnaJ requires the linked ATPase and substrate-binding domains of DnaK. Functional interaction with DnaJ is affected by mutations in an exposed channel located in the ATPase domain of DnaK. It is proposed that binding to this channel, possibly involving the J-domain, allows DnaJ to couple substrate binding with ATP hydrolysis by DnaK. Evolutionary conservation of the channel and the J-domain suggests conservation of the mechanism of action of DnaJ proteins.

Intracellular Localization of Phospholipase D1 in Mammalian Cells

Phospholipase D (PLD) hydrolyzes phosphatidylcholine to generate phosphatidic acid. In mammalian cells this reaction has been implicated in the recruitment of coatomer to Golgi membranes and release of nascent secretory vesicles from the trans-Golgi network. These observations suggest that PLD is associated with the Golgi complex; however, to date, because of its low abundance, the intracellular localization of PLD has been characterized only indirectly through overexpression of chimeric proteins. We have used highly sensitive antibodies to PLD1 together with immunofluorescence and immunogold electron microscopy as well as cell fractionation to identify the intracellular localization of endogenous PLD1 in several cell types. Although PLD1 had a diffuse staining pattern, it was enriched significantly in the Golgi apparatus and was also present in cell nuclei. On fragmentation of the Golgi apparatus by treatment with nocodazole, PLD1 closely associated with membrane fragments, whereas after inhibition of PA synthesis, PLD1 dissociated from the membranes. Overexpression of an hemagglutinin-tagged form of PLD1 resulted in displacement of the endogenous enzyme from its perinuclear localization to large vesicular structures. Surprisingly, when the Golgi apparatus collapsed in response to brefeldin A, the nuclear localization of PLD1 was enhanced significantly. Our data show that the intracellular localization of PLD1 is consistent with a role in vesicle trafficking from the Golgi apparatus and suggest that it also functions in the cell nucleus.

Potential responses of soil organic carbon to global environmental change

Recent improvements in our understanding of the dynamics of soil carbon have shown that 20–40% of the approximately 1,500 Pg of C stored as organic matter in the upper meter of soils has turnover times of centuries or less. This fast-cycling organic matter is largely comprised of undecomposed plant material and hydrolyzable components associated with mineral surfaces. Turnover times of fast-cycling carbon vary with climate and vegetation, and range from <20 years at low latitudes to >60 years at high latitudes. The amount and turnover time of C in passive soil carbon pools (organic matter strongly stabilized on mineral surfaces with turnover times of millennia and longer) depend on factors like soil maturity and mineralogy, which, in turn, reflect long-term climate conditions. Transient sources or sinks in terrestrial carbon pools result from the time lag between photosynthetic uptake of CO2 by plants and the subsequent return of C to the atmosphere through plant, heterotrophic, and microbial respiration. Differential responses of primary production and respiration to climate change or ecosystem fertilization have the potential to cause significant interrannual to decadal imbalances in terrestrial C storage and release. Rates of carbon storage and release in recently disturbed ecosystems can be much larger than rates in more mature ecosystems. Changes in disturbance frequency and regime resulting from future climate change may be more important than equilibrium responses in determining the carbon balance of terrestrial ecosystems.

Mutations in the C-terminal fragment of DnaK affecting peptide binding.

Escherichia coli DnaK acts as a molecular chaperone through its ATP-regulated binding and release of polypeptide substrates. Overexpressing a C-terminal fragment (CTF) of DnaK (Gly-384 to Lys-638) containing the polypeptide substrate binding domain is lethal in wild-type E. coli. This dominant-negative phenotype may result from the nonproductive binding of CTF to cellular polypeptide targets of DnaK. Mutations affecting DnaK substrate binding were identified by selecting noncytotoxic CTF mutants followed by in vitro screening. The clustering of such mutations in the three-dimensional structure of CTF suggests the model that loops L1,2 and L4,5 form a rigid core structure critical for interactions with substrate.

ATPase activity of Escherichia coli Rep helicase crosslinked to single-stranded DNA: implications for ATP driven helicase translocation.

To examine the coupling of ATP hydrolysis to helicase translocation along DNA, we have purified and characterized complexes of the Escherichia coli Rep protein, a dimeric DNA helicase, covalently crosslinked to a single-stranded hexadecameric oligodeoxynucleotide (S). Crosslinked Rep monomers (PS) as well as singly ligated (P2S) and doubly ligated (P2S2) Rep dimers were characterized. The equilibrium and kinetic constants for Rep dimerization as well as the steady-state ATPase activities of both PS and P2S crosslinked complexes were identical to the values determined for un-crosslinked Rep complexes formed with dT16. Therefore, ATP hydrolysis by both PS and P2S complexes are not coupled to DNA dissociation. This also rules out a strictly unidirectional sliding mechanism for ATP-driven translocation along single-stranded DNA by either PS or the P2S dimer. However, ATP hydrolysis by the doubly ligated P2S2 Rep dimer is coupled to single-stranded DNA dissociation from one subunit of the dimer, although loosely (low efficiency). These results suggest that ATP hydrolysis can drive translocation of the dimeric Rep helicase along DNA by a "rolling" mechanism where the two DNA binding sites of the dimer alternately bind and release DNA. Such a mechanism is biologically important when one subunit binds duplex DNA, followed by subsequent unwinding.

Secretory granule targeting of atrial natriuretic peptide correlates with its calcium-mediated aggregation.

Atrial natriuretic peptide (ANP) is a 28-aa peptide hormone secreted predominantly from atrial cardiocytes. ANP is first synthesized in the form of a 126-aa precursor (proANP) which is targeted to dense core granules of the regulated secretory pathway. ProANP is stored until the cell receives a signal that triggers the processing and release of the mature peptide (regulated secretion). Various models have been proposed to explain the targeting of selected proteins to the regulated secretory pathway, including specific "sorting receptors" and calcium-mediated aggregation. As potential calcium binding regions had previously been reported in the profragment of ANP, the current study was undertaken in an effort to determine the relationship between the ability of ANP to enter the regulated secretory pathway and its calcium-mediated aggregation. Deletion and site-directed mutagenesis of selected regions of the prosegment demonstrates that acidic amino acids at positions 23 and 24 are critical for both regulated secretion of proANP from transfected AtT-20 cells and calcium-mediated aggregation of purified recombinant proANP in vitro. These results demonstrate that the ability of certain proteins to enter secretory granules is directly linked to their calcium-mediated aggregation.