Factors driving the carbon mineralization priming effect in a sandy loam soil amended with different types of biochar

The effect of biochar on the soil carbon mineral- ization priming effect depends on the characteristics of the raw materials, production method and pyrolysis conditions. The goal of the present study is to evaluate the impact of three different types of biochar on physicochemical properties and CO2 emissions of a sandy loam soil. For this purpose, soil was amended with three different biochars (BI, BII and BIII) at a rate of 8 wt % and soil CO2 emissions were measured for 45 days. BI is produced from a mixed wood sieving from wood chip production, BII from a mixture of paper sludge and wheat husks and BIII from sewage sludge. Cumulative CO2 emissions of biochars, soil and amended soil were well fit to a simple first-order kinetic model with correlation coef- ficients (r 2 ) greater than 0.97. Results show a negative prim- ing effect in the soil after addition of BI and a positive prim- ing effect in the case of soil amended with BII and BIII. These results can be related to different biochar properties such as carbon content, carbon aromaticity, volatile matter, fixed carbon, easily oxidized organic carbon or metal and phenolic substance content in addition to surface biochar properties. Three biochars increased the values of soil field capacity and wilting point, while effects over pH and cation exchange capacity were not observed.

Relationship among slurry characteristics and gaseous emissions at different types of commercial Spanish pig farms

This study aimed to analyse several factors of variation of slurry composition and to establish prediction equations for potential methane (CH4) and ammonia (NH3) emissions. Seventy-nine feed and slurry samples were collected at two seasons (summer and winter) from commercial pig farms sited at two Spanish regions (Centre and Mediterranean). Nursery, growing-fattening, gestating and lactating facilities were sampled. Feed and slurry composition were determined, and potential CH4 and NH3 emissions measured at laboratory. Feed nutrient contents were used as covariates in the analysis. Near infrared reflectance spectroscopy (NIRS) was evaluated as a predicting tool for slurry composition and potential gaseous emissions. A wide variability was found both in feed and slurry composition. Mediterranean farms had a higher pH (p<0.001) and ash (p=0.02) concentration than those located at the Centre of Spain. Also, type of farm affected ether extract content of the slurry (p=0.02), with highest values obtained for the youngest animal facilities. Results suggested a buffer effect of dietary fibre on slurry pH and a direct relationship (p<0.05) with fibre constituents of manure. Dietary protein content did not affect slurry nitrogen content but decreased (p=0.003) total and volatile solids concentration. Prediction models of potential NH3 emissions (R2=0.89) and CH4 yield (R2=0.61) were obtained from slurry composition. Predictions from NIRS showed a high accuracy for most slurry constituents (R2>0.90) and similar accuracy of prediction of potential NH3 and CH4 emissions (R2=0.84 and 0.68, respectively) to models using slurry characteristics, which can be of interest to estimate emissions from commercial farms and establish mitigation strategies or optimize biogas production.

Development and fabrication of optical biosensors based on biophotonic sensing cells (BICELLs)

El objetivo de esta tesis es el desarrollo y caracterización de biosensores ópticos sin marcado basados en celdas sensoras biofotónicas (BICELLs). Éstas son un nuevo concepto de biosensor desarrollado por el grupo de investigación y consiste en la combinación de técnicas de interrogación vertical, junto a estructuras fotónicas producidas usando métodos de micro- y nanofabricación. Varias conclusiones son extraídas de este trabajo. La primera, que se ha definido una BICELL estándar basada en interferómetros Fabry-Perot (FP). Se ha demostrado su capacidad para la comparación de rendimiento entre BICELLs estructuradas y para la realización de inmunoensayos de bajo coste. Se han estudiado diferentes técnicas de fabricación disponibles para la producción de BICELLs. Se determinó que la litografía de contacto a nivel de oblea produce estructuras de bajo coste, reproducibles y de alta calidad. La resolución alcanzada ha sido de 700 nm. El estudio de la respuesta a inmunoensayos de las BICELLs producidas se ha desarrollado en este trabajo. Se estudió la influencia de BICELLs basadas en diferentes geometrías y tamaños. De aquí resulta un nuevo enfoque para predecir el comportamiento de respuesta para la detección biológica de cualquier biosensor óptico estructurado, relacionando su superficie efectiva y su sensibilidad óptica. También se demostró una técnica novedosa y de bajo coste para la caracterización experimental de la sensibilidad óptica, basada en el depósito de películas ultradelgadas. Finalmente, se ha demostrado el uso de BICELLs desarrolladas en esta tesis, en la detección de aplicaciones reales, tales como hormonas, virus y proteínas. ABSTRACT The objective of this thesis is the development and characterization of optical label-free biosensors based on Bio-Photonic sensing Cells (BICELLs). BICELL is a novel biosensor concept developed by the research group, and it consists of a combination of vertical interrogation optical techniques and photonic structures produced by using micro- and nano-fabrication methods. Several main conclusions are extracted from this work. Firstly, a standard BICELL is defined based on FP interferometers, which demonstrated its capacity for accomplishing performance comparisons among different structured BICELLs, as well as to achieve low-cost immunoassays. Different available fabrication techniques were studied for BICELL manufacturing. It is found that contact lithography at wafer scale produce cost-effective, reproducible and high quality structures. The resolution achieved was 700 nm. Study on the response of developed BICELLs to immunoassays is performed within this work. It is therefore studied the influence of BICELLs based on different geometries and sizes in the immunoassay, which resulted in a new approach to predict the biosensing behaviour of any structured optical biosensor relating to its effective surface and optical sensitivity. Also, it is demonstrated a novel and low-cost characterization technique of the experimental optical sensitivity, based on ultrathin-film deposition. Finally, it is also demonstrated the capability of using the developed BICELLs in this thesis for real applications detection of hormones, virus and proteins.

The Nucleoporin Nup153 Plays a Critical Role in Multiple Types of Nuclear Export

The fundamental process of nucleocytoplasmic transport takes place through the nuclear pore. Peripheral pore structures are presumably poised to interact with transport receptors and their cargo as these receptor complexes first encounter the pore. One such peripheral structure likely to play an important role in nuclear export is the basket structure located on the nuclear side of the pore. At present, Nup153 is the only nucleoporin known to localize to the surface of this basket, suggesting that Nup153 is potentially one of the first pore components an RNA or protein encounters during export. In this study, anti-Nup153 antibodies were used to probe the role of Nup153 in nuclear export in Xenopus oocytes. We found that Nup153 antibodies block three major classes of RNA export, that of snRNA, mRNA, and 5S rRNA. Nup153 antibodies also block the NES protein export pathway, specifically the export of the HIV Rev protein, as well as Rev-dependent RNA export. Not all export was blocked; Nup153 antibodies did not impede the export of tRNA or the recycling of importin β to the cytoplasm. The specific antibodies used here also did not affect nuclear import, whether mediated by importin α/β or by transportin. Overall, the results indicate that Nup153 is crucial to multiple classes of RNA and protein export, being involved at a vital juncture point in their export pathways. This juncture point appears to be one that is bypassed by tRNA during its export. We asked whether a physical interaction between RNA and Nup153 could be observed, using homoribopolymers as sequence-independent probes for interaction. Nup153, unlike four other nucleoporins including Nup98, associated strongly with poly(G) and significantly with poly(U). Thus, Nup153 is unique among the nucleoporins tested in its ability to interact with RNA and must do so either directly or indirectly through an adaptor protein. These results suggest a unique mechanistic role for Nup153 in the export of multiple cargos.

A human protein containing multiple types of protease-inhibitory modules

By using sensitive homology-search and gene-finding programs, we have found that a genomic region from the tip of the short arm of human chromosome 16 (16p13.3) encodes a putative secreted protein consisting of a domain related to the whey acidic protein (WAP) domain, a domain homologous with follistatin modules of the Kazal-domain family (FS module), an immunoglobulin-related domain (Ig domain), two tandem domains related to Kunitz-type protease inhibitor modules (KU domains), and a domain belonging to the recently defined NTR-module family (NTR domain). The gene encoding these WAP, FS, Ig, KU, and NTR modules (hereafter referred to as the WFIKKN gene) is intron-depleted—its single 1,157-bp intron splits the WAP module. The validity of our gene prediction was confirmed by sequencing a WFIKKN cDNA cloned from a lung cDNA library. Studies on the tissue-expression pattern of the WFIKKN gene have shown that the gene is expressed primarily in pancreas, kidney, liver, placenta, and lung. As to the function of the WFIKKN protein, it is noteworthy that it contains FS, WAP, and KU modules, i.e., three different module types homologous with domains frequently involved in inhibition of serine proteases. The protein also contains an NTR module, a domain type implicated in inhibition of zinc metalloproteinases of the metzincin family. On the basis of its intriguing homologies, we suggest that the WFIKKN protein is a multivalent protease inhibitor that may control the action of multiple types of serine proteases as well as metalloproteinase(s).

Quantitative Intercellular Localization of NADH-Dependent Glutamate Synthase Protein in Different Types of Root Cells in Rice Plants1

The quantitative analysis with immunogold-electron microscopy using a single-affinity-purified anti-NADH-glutamate synthase (GOGAT) immunoglobulin G (IgG) as the primary antibody showed that the NADH-GOGAT protein was present in various forms of plastids in the cells of the epidermis and exodermis, in the cortex parenchyma, and in the vascular parenchyma of root tips (<10 mm) of rice (Oryza sativa) seedlings supplied with 1 mm NH4+ for 24 h. The values of the mean immunolabeling density of plastids were almost equal among these different cell types in the roots. However, the number of plastids per individual cell type was not identical, and some parts of the cells in the epidermis and exodermis contained large numbers of plastids that were heavily immunolabeled. Although there was an indication of labeling in the mitochondria using the single-affinity-purified anti-NADH-GOGAT IgG, this was not confirmed when a twice-affinity-purified IgG was used, indicating an exclusively plastidial location of the NADH-GOGAT protein in rice roots. These results, together with previous work from our laboratory (K. Ishiyama, T. Hayakawa, and T. Yamaya [1998] Planta 204: 288–294), suggest that the assimilation of exogeneously supplied NH4+ ions is primarily via the cytosolic glutamine synthetase/plastidial NADH-GOGAT cycle in specific regions of the epidermis and exodermis in rice roots. We also discuss the role of the NADH-GOGAT protein in vascular parenchyma cells.

The Two Major Types of Plant Plasma Membrane H+-ATPases Show Different Enzymatic Properties and Confer Differential pH Sensitivity of Yeast Growth1

The proton-pumping ATPase (H+-ATPase) of the plant plasma membrane is encoded by two major gene subfamilies. To characterize individual H+-ATPases, PMA2, an H+-ATPase isoform of tobacco (Nicotiana plumbaginifolia), was expressed in Saccharomyces cerevisiae and found to functionally replace the yeast H+-ATPase if the external pH was kept above 5.0 (A. de Kerchove d'Exaerde, P. Supply, J.P. Dufour, P. Bogaerts, D. Thinès, A. Goffeau, M. Boutry [1995] J Biol Chem 270: 23828–23837). In the present study we replaced the yeast H+-ATPase with PMA4, an H+-ATPase isoform from the second subfamily. Yeast expressing PMA4 grew at a pH as low as 4.0. This was correlated with a higher acidification of the external medium and an approximately 50% increase of ATPase activity compared with PMA2. Although both PMA2 and PMA4 had a similar pH optimum (6.6–6.8), the profile was different on the alkaline side. At pH 7.2 PMA2 kept more than 80% of the maximal activity, whereas that of PMA4 decreased to less than 40%. Both enzymes were stimulated up to 3-fold by 100 μg/mL lysophosphatidylcholine, but this stimulation vanished at a higher concentration in PMA4. These data demonstrate functional differences between two plant H+-ATPases expressed in the same heterologous host. Characterization of two PMA4 mutants selected to allow yeast growth at pH 3.0 revealed that mutations within the carboxy-terminal region of PMA4 could still improve the enzyme, resulting in better growth of yeast cells.

Two types of calcium response limited to single spines in cerebellar Purkinje cells.

Of fundamental importance in understanding neuronal function is the unambiguous determination of the smallest unit of neuronal integration. It was recently suggested that a whole dendritic branchlet, including tens of spines, acts as the fundamental unit in terms of dendritic calcium dynamics in Purkinje cells. By contrast, we demonstrate that the smallest such unit is the single spine. The results show, by two-photon excited fluorescence laser scanning microscopy, that individual spines are capable of independent calcium activation. Moreover, two distinct spine populations were distinguished by their opposite response to membrane hyperpolarization. Indeed, in a subpopulation of spines calcium entry can also occur through a pathway other than voltage-gated channels. These findings challenge the assumption of a unique parallel fiber activation mode and prompt a reevaluation of the level of functional complexity ascribed to single neurons.

Interferon gamma signals via a high-affinity multisubunit receptor complex that contains two types of polypeptide chain.

Signaling by interferon gamma (IFN-gamma) requires two structurally related cell surface proteins: a ligand-binding polypeptide, known as the IFN-gamma receptor (IFN-gamma R), and an accessory factor. However, it is not known whether IFN-gamma forms a ternary complex with the IFN-gamma R and accessory factor to initiate signaling. Here we demonstrate complex formation between IFN-gamma and the two proteins, both in solution and at the cell surface. We observe complexes containing ligand, two molecules of IFN-gamma R (designated the IFN-gamma R alpha chain), and one or two molecules of accessory factor (designated the IFN-gamma R beta chain). Transfected cells expressing both IFN-gamma R chains bind IFN-gamma with higher affinity than do cells expressing alpha chain alone. Anti-beta-chain antibodies prevent the beta chain from participating in the ligand-receptor complex, reduce the affinity for IFN-gamma, and block signaling. Soluble alpha- or beta-chain extracellular domains also inhibit function. These results demonstrate that IFN-gamma signals via a high-affinity multisubunit complex that contains two types of receptor chain and suggest a potential approach to inhibiting specific actions of IFN-gamma by blocking the association of receptor subunits.

Types of Listeria monocytogenes predicted by the positions of EcoRI cleavage sites relative to ribosomal RNA sequences.

By using taxonomic characters derived from EcoRI restriction endonuclease digestion of genomic DNA and hybridization with a labeled rRNA operon from Escherichia coli, a polymorphic structure of Listeria monocytogenes, characterized by fragments with different frequencies of occurrence, was observed. This structure was expanded by creating predicted patterns through a recursive process of observation, expectation, prediction, and assessment of completeness. This process was applied, in turn, to normalized strain patterns, fragment bands, and positions of EcoRI recognition sites relative to rRNA regions. Analysis of 1346 strains provided observed patterns, fragment sizes, and their frequencies of occurrence in the patterns. Fragment size statistics led to the creation of unobserved combinations of bands, predicted pattern types. The observed fragment bands revealed positions of EcoRI sites relative to rRNA sequences. Each EcoRI site had a frequency of occurrence, and unobserved fragment sizes were postulated on the basis of knowing the restriction site locations. The result of the recursion process applied to the components of the strain data was an extended classification with observed and predicted members.

Types of evolutionary stability and the problem of cooperation.

The evolutionary stability of cooperation is a problem of fundamental importance for the biological and social sciences. Different claims have been made about this issue: whereas Axelrod and Hamilton's [Axelrod, R. & Hamilton, W. (1981) Science 211, 1390-1398] widely recognized conclusion is that cooperative rules such as "tit for tat" are evolutionarily stable strategies in the iterated prisoner's dilemma (IPD), Boyd and Lorberbaum [Boyd, R. & Lorberbaum, J. (1987) Nature (London) 327, 58-59] have claimed that no pure strategy is evolutionarily stable in this game. Here we explain why these claims are not contradictory by showing in what sense strategies in the IPD can and cannot be stable and by creating a conceptual framework that yields the type of evolutionary stability attainable in the IPD and in repeated games in general. Having established the relevant concept of stability, we report theorems on some basic properties of strategies that are stable in this sense. We first show that the IPD has "too many" such strategies, so that being stable does not discriminate among behavioral rules. Stable strategies differ, however, on a property that is crucial for their evolutionary survival--the size of the invasion they can resist. This property can be interpreted as a strategy's evolutionary robustness. Conditionally cooperative strategies such as tit for tat are the most robust. Cooperative behavior supported by these strategies is the most robust evolutionary equilibrium: the easiest to attain, and the hardest to disrupt.

A historical account of types of fuzzy sets and their relationships

In this paper, we review the definition and basic properties of the different types of fuzzy sets that have appeared up to now in the literature. We also analyze the relationships between them and enumerate some of the applications in which they have been used.

Effect of carbon fibres on the mechanical properties and corrosion levels of reinforced portland cement mortars

The changes in mechanical properties of portland cement mortars due to the addition of carbon fibres (CF) to the mix have been studied. Compression and flexural strengths have been determined in relation to the amount of fibres added to the mix, water/binder ratio, curing time and porosity. Additionally, the corrosion level of reinforcing steel bars embedded in portland cement mortars containing CF and silica fume (SF) have also been investigated and reinforcing steel corrosion rates have been determined. As a consequence of the large concentration of oxygen groups in CF surface, a good interaction between the CF and the water of the mortar paste is to be expected. A CF content of 0.5% of cement weight implies an optimum increase in flexural strength and an increase in embedded steel corrosion.