Base pairing and miscoding properties of 1,N(6)-ethenoadenine- and 3,N(4)-ethenocytosine-containing RNA oligonucleotides

Two RNA phosphoramidites containing the bases 1,N(6)-ethenoadenine (εA) and 3,N(4)-ethenocytosine (εC) were synthesized. These building blocks were incorporated into two 12-mer oligoribonucleotides for evaluation of the base pairing properties of these base lesions by UV melting curve (Tm) and circular dichroism measurements. The Tm data of the resulting duplexes with the etheno modifications opposing all natural bases showed a substantial destabilization compared to the corresponding natural duplexes, confirming their inability to form base pairs. The coding properties of these lesions were further investigated by introducing them into 31-mer oligonucleotides and assessing their ability to serve as templates in primer extension reactions with HIV, AMV, and MMLV reverse transcriptases (RT). Primer extension reactions showed complete arrest of the incorporation process using MMLV RT and AMV RT, while HIV RT preferentially incorporates dAMP opposite εA and dAMP as well as dTMP opposite εC. The properties of these RNA lesions are discussed in the context of its putative biological role.

North Pacific Carbon Cycle Response to Climate Variability on Seasonal to Decadal Timescales

Climate variability drives significant changes in the physical state of the North Pacific, and there may be important impacts of this variability on the upper ocean carbon balance across the basin. We address this issue by considering the response of seven biogeochemical ocean models to climate variability in the North Pacific. The models' upper ocean pCO(2) and air-sea CO(2) flux respond similarly to climate variability on seasonal to decadal timescales. Modeled seasonal cycles of pCO(2) and its temperature- and non-temperature-driven components at three contrasting oceanographic sites capture the basic features found in observations (Takahashi et al., 2002, 2006; Keeling et al., 2004; Brix et al., 2004). However, particularly in the Western Subarctic Gyre, the models have difficulty representing the temporal structure of the total pCO(2) seasonal cycle because it results from the difference of these two large and opposing components. In all but one model, the air-sea CO(2) flux interannual variability (1 sigma) in the North Pacific is smaller ( ranges across models from 0.03 to 0.11 PgC/yr) than in the Tropical Pacific ( ranges across models from 0.08 to 0.19 PgC/yr), and the time series of the first or second EOF of the air-sea CO(2) flux has a significant correlation with the Pacific Decadal Oscillation (PDO). Though air-sea CO(2) flux anomalies are correlated with the PDO, their magnitudes are small ( up to +/- 0.025 PgC/yr ( 1 sigma)). Flux anomalies are damped because anomalies in the key drivers of pCO(2) ( temperature, dissolved inorganic carbon (DIC), and alkalinity) are all of similar magnitude and have strongly opposing effects that damp total pCO(2) anomalies.

Mineralogy of ODP Leg 104 holes

The mineralogical and geochemical study of samples from Sites 642, 643, and 644 enabled us to reconstruct several aspects of the Cenozoic paleoenvironmental evolution (namely volcanism, climate, hydrology) south of the Norwegian Sea and correlate it with evolution trends in the northeast Atlantic. Weathering products of early Paleogene volcanic material at Rockall Plateau, over the Faeroe-Iceland Ridge and the Voring Plateau indicate a hot and moist climate (lateritic environment) existed then. From Eocene to Oligocene, mineralogical assemblages of terrigenous sediments suggest the existence of a warm but somewhat less moist climate at that time than during the early Paleogene. At the beginning of early Miocene, climatic conditions were warm and damp. The large amounts of amorphous silica in Miocene sediment could indicate an important flux of silica from the continent then, or suggest the formation of upwelling. Uppermost lower Miocene and middle to upper Miocene clay assemblages suggest progressive cooling of the climate from warm to temperate at that time. At the end of early Miocene, hydrological exchanges between the North Atlantic and the Norwegian Sea became intense and gave rise to an important change in the mineralogy of deposits. From Pliocene to Pleistocene, the variable mineralogy of deposits reflects alternating glacial/interglacial climatic episodes, a phenomenon observed throughout the North Atlantic.

Automatic granularity-aware parallelization of programs with predicates, functions, and constraints

Abstract is not available

Pre-Feasibility Study of Hybrid Wind Power-H-2 System Connected to Electrical Grid

The growth of wind power as an electric energy source is profitable from an environmental point of view and improves the energetic independence of countries with little fossil fuel resources. However, the wind resource randomness poses a great challenge in the management of electric grids. This study raises the possibility of using hydrogen as a mean to damp the variability of the wind resource. Thus, it is proposed the use of all the energy produced by a typical wind farm for hydrogen generation, that will in turn be used after for suitable generation of electric energy according to the operation rules in a liberalized electric market.

A novel scanning lens instrument for evaluating Fresnel lens performance: equipment development and initial results

A system dedicated to the optical transmittance characterization of Fresnel lenses has been developed at NREL, in collaboration with the UPM. The system quantifies the optical efficiency of the lens by generating a performance map. The shape of the focused spot may also be analyzed to understand change in the lens performance. The primary instrument components (lasers and CCD detector) have been characterized to confirm their capability for performing optical transmittance measurements. Measurements performed on SoG and PMMA lenses subject to a variety of indoor conditions (e.g., UV and damp heat) identified differences in the optical efficiency of the evaluated lenses, demonstrating the ability of the Scanning Lens Instrument (SLI) to distinguish between the aged lenses.

Aportación de la monitorización mediante redes de sensores y técnicas no invasivas para la conservación preventiva del Patrimonio

La presente tesis doctoral presenta una serie de estudios en el campo del patrimonio basados en metodologías de monitorización mediante redes de sensores y técnicas no invasivas con el objetivo de realizar nuevas aportaciones a la conservación preventiva mediante el seguimiento de los daños de deterioro o la prevención de los mismos. Las metodologías de monitorización mediante el despliegue de redes tridimensionales basadas en data loggers abordan estudios microclimáticos, de confort y energéticos a corto plazo, donde se establecen conclusiones relativas a la eficiencia energética de tres sistemas de calefacción muy utilizados en iglesias de la región centro de la Península Ibérica, abordando aspectos de afección de los mismos en el confort de los ocupantes o en el deterioro de los elementos patrimoniales o constructivos. Se desplegaron además distintas plataformas de redes de sensores inalámbricas procediendo a analizar en esta tesis cuál es la que presenta mejores resultados en el ámbito del patrimonio con el objetivo de una monitorización a largo plazo y considerando aspectos de comunicaciones, consumo y configuración de las redes. Una vez conocida la plataforma que presenta mejores resultados comparativos se muestra una metodología de estudio de la calidad de las comunicaciones en múltiples escenarios de patrimonio cultural y natural con la misma, que servirá para establecer una serie de aspectos a considerar en el despliegue de redes de sensores inalámbricas en futuros escenarios a monitorizar. Al igual que ocurre con las redes de sensores basadas en data loggers, las tareas de monitorización desarrolladas en esta tesis mediante el despliegue de las distintas plataformas inalámbricas ha permitido la detección de numerosos fenómenos de deterioro que son descritos a lo largo de la investigación y cuyo seguimiento supone una aportación a la prevención de daños en los distintos escenarios. Asimismo en el desarrollo de la tesis se realiza una aportación para la conservación preventiva mediante la monitorización con distintas técnicas no invasivas como la termografía infrarroja, las medidas de humedad superficial mediante protimeter, las técnicas de prospección de resistividad eléctrica de alta resolución o la prospección georradar. De este modo se desarrollan distintas aportaciones y conclusiones acerca de las ventajas y/o limitaciones de uso de las mismas analizando la idoneidad de aplicar cada una de ellas en distintas fases de análisis o con distintas capacidades de detección o caracterización de los daños. El estudio de imbricación de dichas técnicas ha sido desarrollado en un escenario real que presenta graves daños por humedad, habiendo sido posible la caracterización del origen de los mismos. ABSTRACT This doctoral dissertation discusses field research conducted to monitor heritage assets with sensor networks and other non-invasive techniques. The aim pursued was to contribute to conservation by tracking or preventing decay-induced damage. Monitoring methodologies based on three-dimensional data logger networks were used in short-term micro-climatic, comfort and energy studies to draw conclusions about the energy efficiency of three heating systems widely used in central Iberian churches. The impact of these systems on occupant comfort and decay of heritage or built elements was also explored. Different wireless sensor platforms were deployed and analysed to determine which delivered the best results in the context of long-term heritage monitoring from the standpoints of communications, energy demand and network architecture. A methodology was subsequently designed to study communication quality in a number of cultural and natural heritage scenarios and help establish the considerations to be borne in mind when deploying wireless sensor networks for heritage monitoring in future. As in data logger-based sensor networks, the monitoring conducted in this research with wireless platforms identified many instances of decay, described hereunder. Tracking those situations will help prevent damage in the respective scenarios. The research also contributes to preventive conservation based on non-invasive monitoring using techniques such as infrared thermography, protimeter-based surface damp measurements, high resolution electrical resistivity surveys and georadar analysis. The conclusions drawn address the advantages and drawbacks of each technique and its suitability for the various phases of analysis and capacity to detect or characterise damage. This dissertation also describes the intermeshed usage of these techniques that led to the identification of the origin of severe damp-induced damage in a real scenario.

Biomarkers and inorganic proxies in the paleoenvironmental reconstruction of mires: The importance of landscape in Las Conchas (Asturias, Northern Spain)

We determined the lipid distributions (n-alkanes, n-alkan-2-ones, n-alkanoic acids), total organic carbon (TOC), total nitrogen (TN), Ca/Mg and ash content in Las Conchas mire, a 3.2 m deep bryophyte-dominated mire in Northern Spain covering 8000 cal yr BP. Bog conditions developed in the bottom 20 cm of the profile, and good preservation of organic matter (OM) was inferred from n-alkanoic acid distribution, with the exception of the uppermost 20 cm (last ca. 200 yr). Microbial synthesis of long chain saturated fatty acids from primary OM likely produced a dominance of short chain n-alkanoic acids with a bimodal distribution, as well as the lack of correspondence between the n-alkane and n-alkanoic acid profiles in the upper 20 cm. This was accompanied by an increase in ash content, a decrease in TOC and variation in n-alkane ratios, thereby suggesting significant changes in the mire, namely drainage and transformation to a meadow, in the last ca. 200 yr. The distribution of n-alkan-2-ones indicated an increase in bacterial source from the bottom of the record to 94 cm, whereas their distribution in the upper part could be attributed mainly to plant input and/or the microbial oxidation of n-alkanes. The different n-alkane proxies showed variations, which we interpreted in terms of changes in vegetation (Sphagnum vs. non-Sphagnum dominated phases) during the last 8000 cal yr BP. C23 was the most abundant homolog throughout most of the record, thereby suggesting dominant humid conditions alternating with short drier phases. However, such humid conditions were not linked to paleoclimatic variation but rather to geomorphological characteristics: Las Conchas mire, at the base of the Cuera Range, receives continuous runoff—even during drier periods—which is not necessarily accompanied by additional mineral input to peat, producing the development of Sphagnum moss typical of waterlogged ecotopes and damp habitats. Thus, although geochemical proxies indicated an ombrotrophic regime in the mire, geomorphological characteristics may make a considerable contribution to environmental conditions.

Soldier caste-specific gene expression in the mandibular glands of Hodotermopsis japonica (Isoptera: Termopsidae)

Although “polymorphic castes” in social insects are well known as one of the most important phenomena of polyphenism, few studies of caste-specific gene expressions have been performed in social insects. To identify genes specifically expressed in the soldier caste of the Japanese damp-wood termite Hodotermopsis japonica, we employed the differential-display method using oligo(dT) and arbitrary primers, compared mRNA from the heads of mature soldiers and pseudergates (worker caste), and identified a clone (PCR product) 329 bp in length termed SOL1. Northern blot analysis showed that the SOL1 mRNA is about 1.0 kb in length and is expressed specifically in mature soldiers, but not in pseudergates, even in the presoldier induction by juvenile hormone analogue, suggesting that the product is specific for terminally differentiated soldiers. By using the method of 5′- and 3′-rapid amplification of cDNA ends, we isolated the full length of SOL1 cDNA, which contained an ORF with a putative signal peptide at the N terminus. The sequence showed no significant homology with any other known protein sequences. In situ hybridization analysis showed that SOL1 is expressed specifically in the mandibular glands. These results strongly suggest that the SOL1 gene encodes a secretory protein specifically synthesized in the mandibular glands of the soldiers. Histological observations revealed that the gland actually develops during the differentiation into the soldier caste.

Retrograde Transport from the Pre-Golgi Intermediate Compartment and the Golgi Complex Is Affected by the Vacuolar H+-ATPase Inhibitor Bafilomycin A1

The effect of the vacuolar H+-ATPase inhibitor bafilomycin A1 (Baf A1) on the localization of pre-Golgi intermediate compartment (IC) and Golgi marker proteins was used to study the role of acidification in the function of early secretory compartments. Baf A1 inhibited both brefeldin A- and nocodazole-induced retrograde transport of Golgi proteins to the endoplasmic reticulum (ER), whereas anterograde ER-to-Golgi transport remained largely unaffected. Furthermore, p58/ERGIC-53, which normally cycles between the ER, IC, and cis-Golgi, was arrested in pre-Golgi tubules and vacuoles, and the number of p58-positive ∼80-nm Golgi (coatomer protein I) vesicles was reduced, suggesting that the drug inhibits the retrieval of the protein from post-ER compartments. In parallel, redistribution of β-coatomer protein from the Golgi to peripheral pre-Golgi structures took place. The small GTPase rab1p was detected in short pre-Golgi tubules in control cells and was efficiently recruited to the tubules accumulating in the presence of Baf A1. In contrast, these tubules showed no enrichment of newly synthesized, anterogradely transported proteins, indicating that they participate in retrograde transport. These results suggest that the pre-Golgi structures contain an active H+-ATPase that regulates retrograde transport at the ER–Golgi boundary. Interestingly, although Baf A1 had distinct effects on peripheral pre-Golgi structures, only more central, p58-containing elements accumulated detectable amounts of 3-(2,4-dinitroanilino)-3′-amino-N-methyldipropylamine (DAMP), a marker for acidic compartments, raising the possibility that the lumenal pH of the pre-Golgi structures gradually changes in parallel with their translocation to the Golgi region.