Wet tundra polygon centers and distance between polygon centroids on Samoylov Island, Lena Delta, Siberia, Russia, with links to shape files

Subgrid processes occur in various ecosystems and landscapes but, because of their small scale, they are not represented or poorly parameterized in climate models. These local heterogeneities are often important or even fundamental for energy and carbon balances. This is especially true for northern peatlands and in particular for the polygonal tundra, where methane emissions are strongly influenced by spatial soil heterogeneities. We present a stochastic model for the surface topography of polygonal tundra using Poisson-Voronoi diagrams and we compare the results with available recent field studies. We analyze seasonal dynamics of water table variations and the landscape response under different scenarios of precipitation income. We upscale methane fluxes by using a simple idealized model for methane emission. Hydraulic interconnectivities and large-scale drainage may also be investigated through percolation properties and thresholds in the Voronoi graph. The model captures the main statistical characteristics of the landscape topography, such as polygon area and surface properties as well as the water balance. This approach enables us to statistically relate large-scale properties of the system to the main small-scale processes within the single polygons.

Desarrollo de estructuras nanofotonicas de campo cercano para intensificacion localizada de luz en celulas solares de banda intermedia - Near-field nanophotonic structures for localized light enhancement in intermediate band solar cells

This doctoral thesis explores some of the possibilities that near-field optics can bring to photovoltaics, and in particular to quantum-dot intermediate band solar cells (QD-IBSCs). Our main focus is the analytical optimization of the electric field distribution produced in the vicinity of single scattering particles, in order to produce the highest possible absorption enhancement in the photovoltaic medium in their surroundings. Near-field scattering structures have also been fabricated in laboratory, allowing the application of the previously studied theoretical concepts to real devices. We start by looking into the electrostatic scattering regime, which is only applicable to sub-wavelength sized particles. In this regime it was found that metallic nano-spheroids can produce absorption enhancements of about two orders of magnitude on the material in their vicinity, due to their strong plasmonic resonance. The frequency of such resonance can be tuned with the shape of the particles, allowing us to match it with the optimal transition energies of the intermediate band material. Since these metallic nanoparticles (MNPs) are to be inserted inside the cell photovoltaic medium, they should be coated by a thin insulating layer to prevent electron-hole recombination at their surface. This analysis is then generalized, using an analytical separation-of-variables method implemented in Mathematica7.0, to compute scattering by spheroids of any size and material. This code allowed the study of the scattering properties of wavelengthsized particles (mesoscopic regime), and it was verified that in this regime dielectric spheroids perform better than metallic. The light intensity scattered from such dielectric spheroids can have more than two orders of magnitude than the incident intensity, and the focal region in front of the particle can be shaped in several ways by changing the particle geometry and/or material. Experimental work was also performed in this PhD to implement in practice the concepts studied in the analysis of sub-wavelength MNPs. A wet-coating method was developed to self-assemble regular arrays of colloidal MNPs on the surface of several materials, such as silicon wafers, amorphous silicon films, gallium arsenide and glass. A series of thermal and chemical tests have been performed showing what treatments the nanoparticles can withstand for their embedment in a photovoltaic medium. MNPs arrays are then inserted in an amorphous silicon medium to study the effect of their plasmonic near-field enhancement on the absorption spectrum of the material. The self-assembled arrays of MNPs constructed in these experiments inspired a new strategy for fabricating IBSCs using colloidal quantum dots (CQDs). Such CQDs can be deposited in self-assembled monolayers, using procedures similar to those developed for the patterning of colloidal MNPs. The use of CQDs to form the intermediate band presents several important practical and physical advantages relative to the conventional dots epitaxially grown by the Stranski-Krastanov method. Besides, this provides a fast and inexpensive method for patterning binary arrays of QDs and MNPs, envisioned in the theoretical part of this thesis, in which the MNPs act as antennas focusing the light in the QDs and therefore boosting their absorption

High optical sensitivity to ambient conditions of uncapped InGaAs surface quantum dots

The influence of the environment on the optical properties of self-assembled In0.5Ga0.5As surface quantum dots is studied as a function of different ambient conditions for sensing applications. Their room temperature photoluminescence (PL) quenches under vacuum and decreases strongly under dry O2 or N2 environments. Nevertheless, they have a strong signal at 1.55 lm in air or in a wet atmosphere. The presence of water molecules in the environment improves the PL intensity likely due to its polar character and therefore its easier adsorption by the surface dangling bonds, leading to a suppression of the non-radiative recombination centers.

Prominin, a novel microvilli-specific polytopic membrane protein of the apical surface of epithelial cells, is targeted to plasmalemmal protrusions of non-epithelial cells

Using a new mAb raised against the mouse neuroepithelium, we have identified and cDNA-cloned prominin, an 858-amino acid-containing, 115-kDa glycoprotein. Prominin is a novel plasma membrane protein with an N-terminal extracellular domain, five transmembrane segments flanking two short cytoplasmic loops and two large glycosylated extracellular domains, and a cytoplasmic C-terminal domain. DNA sequences from Caenorhabditis elegans predict the existence of a protein with the same features, suggesting that prominin is conserved between vertebrates and invertebrates. Prominin is found not only in the neuroepithelium but also in various other epithelia of the mouse embryo. In the adult mouse, prominin has been detected in the brain ependymal layer, and in kidney tubules. In these epithelia, prominin is specific to the apical surface, where it is selectively associated with microvilli and microvilli-related structures. Remarkably, upon expression in CHO cells, prominin is preferentially localized to plasma membrane protrusions such as filopodia, lamellipodia, and microspikes. These observations imply that prominin contains information to be targeted to, and/or retained in, plasma membrane protrusions rather than the planar cell surface. Moreover, our results show that the mechanisms underlying targeting of membrane proteins to microvilli of epithelial cells and to plasma membrane protrusions of non-epithelial cells are highly related.

Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers

The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, QB, within the RC. The binding of Cd2+ or Zn2+ has been previously shown to inhibit the rate of reduction and protonation of QB. We report here on the metal binding site, determined by x-ray diffraction at 2.5-Å resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd2+ and Zn2+ complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from QA− to QB was measured in the Cd2+-soaked crystal and found to be the same as in solution in the presence of Cd2+. In addition to the changes in the kinetics, a structural effect of Cd2+ on Glu-H173 was observed. This residue was well resolved in the x-ray structure—i.e., ordered—with Cd2+ bound to the RC, in contrast to its disordered state in the absence of Cd2+, which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of QB. The position of the Cd2+ and Zn2+ localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to QB⨪ are proposed.

E-cadherin induces mesenchymal-to-epithelial transition in human ovarian surface epithelium

Ovarian carcinomas are thought to arise in the ovarian surface epithelium (OSE). Although this tissue forms a simple epithelial covering on the ovarian surface, OSE cells exhibit some mesenchymal characteristics and contain little or no E-cadherin. However, E-cadherin is present in metaplastic OSE cells that resemble the more complex epithelia of the oviduct, endometrium and endocervix, and in primary epithelial ovarian carcinomas. To determine whether E-cadherin was a cause or consequence of OSE metaplasia, we expressed this cell-adhesion molecule in simian virus 40-immortalized OSE cells. In these cells the exogenous E-cadherin, all three catenins, and F-actin localized at sites of cell–cell contact, indicating the formation of functional adherens junctions. Unlike the parent OSE cell line, which had undergone a typical mesenchymal transformation in culture, E-cadherin-expressing cells contained cytokeratins and the tight-junction protein occludin. They also formed cobblestone monolayers in two-dimensional culture and simple epithelia in three-dimensional culture that produced CA125 and shed it into the culture medium. CA125 is a normal epithelial-differentiation product of the oviduct, endometrium, and endocervix, but not of normal OSE. It is also a tumor antigen that is produced by ovarian neoplasms and by metaplastic OSE. Thus, E-cadherin restored some normal characteristics of OSE, such as keratin, and it also induced epithelial-differentiation markers associated with weakly preneoplastic, metaplastic OSE and OSE-derived primary carcinomas. The results suggest an unexpected role for E-cadherin in ovarian neoplastic progression.

Plasmodium falciparum subtilisin-like protease 2, a merozoite candidate for the merozoite surface protein 1–42 maturase

The process of human erythrocyte invasion by Plasmodium falciparum parasites involves a calcium-dependent serine protease with properties consistent with a subtilisin-like activity. This enzyme achieves the last crucial maturation step of merozoite surface protein 1 (MSP1) necessary for parasite entry into the host erythrocyte. In eukaryotic cells, such processing steps are performed by subtilisin-like maturases, known as proprotein convertases. In an attempt to characterize the MSP1 maturase, we have identified a gene that encodes a P. falciparum subtilisin-like protease (PfSUB2) whose deduced active site sequence resembles more bacterial subtilisins. Therefore, we propose that PfSUB2 belongs to a subclass of eukaryotic subtilisins different from proprotein convertases. Pfsub2 is expressed during merozoite differentiation and encodes an integral membrane protein localized in the merozoite dense granules, a secretory organelle whose contents are believed to participate in a late step of the erythrocyte invasion. PfSUB2’s subcellular localization, together with its predicted enzymatic properties, leads us to propose that PfSUB2 could be responsible for the late MSP1 maturation step and thus is an attractive target for the development of new antimalarial drugs.

The importance of being discrete: Life always wins on the surface

Many systems in chemistry, biology, finance, and social sciences present emerging features that are not easy to guess from the elementary interactions of their microscopic individual components. In the past, the macroscopic behavior of such systems was modeled by assuming that the collective dynamics of microscopic components can be effectively described collectively by equations acting on spatially continuous density distributions. It turns out that, to the contrary, taking into account the actual individual/discrete character of the microscopic components of these systems is crucial for explaining their macroscopic behavior. In fact, we find that in conditions in which the continuum approach would predict the extinction of all of the population (respectively the vanishing of the invested capital or the concentration of a chemical substance, etc.), the microscopic granularity insures the emergence of macroscopic localized subpopulations with collective adaptive properties that allow their survival and development. In particular it is found that in two dimensions “life” (the localized proliferating phase) always prevails.

Insulin promotes rapid delivery of N-methyl-d- aspartate receptors to the cell surface by exocytosis

Insulin potentiates N-methyl-d-aspartate receptors (NMDARs) in neurons and Xenopus oocytes expressing recombinant NMDARs. The present study shows that insulin induced (i) an increase in channel number times open probability (nPo) in outside-out patches excised from Xenopus oocytes, with no change in mean open time, unitary conductance, or reversal potential, indicating an increase in n and/or Po; (ii) an increase in charge transfer during block of NMDA-elicited currents by the open channel blocker MK-801, indicating increased number of functional NMDARs in the cell membrane with no change in Po; and (iii) increased NR1 surface expression, as indicated by Western blot analysis of surface proteins. Botulinum neurotoxin A greatly reduced insulin potentiation, indicating that insertion of new receptors occurs via SNARE-dependent exocytosis. Thus, insulin potentiation occurs via delivery of new channels to the plasma membrane. NMDARs assembled from mutant subunits lacking all known sites of tyrosine and serine/threonine phosphorylation in their carboxyl-terminal tails exhibited robust insulin potentiation, suggesting that insulin potentiation does not require direct phosphorylation of NMDAR subunits. Because insulin and insulin receptors are localized to glutamatergic synapses in the hippocampus, insulin-regulated trafficking of NMDARs may play a role in synaptic transmission and plasticity, including long-term potentiation.

ADP-Glucose Pyrophosphorylase Is Localized to Both the Cytoplasm and Plastids in Developing Pericarp of Tomato Fruit1

The intracellular location of ADP-glucose pyrophosphorylase (AGP) in developing pericarp of tomato (Lycopersicon esculentum Mill) has been investigated by immunolocalization. With the use of a highly specific anti-tomato fruit AGP antibody, the enzyme was localized in cytoplasm as well as plastids at both the light and electron microscope levels. The immunogold particles in plastids were localized in the stroma and at the surface of the starch granule, whereas those in the cytoplasm occurred in cluster-like patterns. Contrary to the fruit, the labeling in tomato leaf cells occurred exclusively in the chloroplasts. These data demonstrate that AGP is localized to both the cytoplasm and plastids in developing pericarp cells of tomato.

Rapid appearance and asymmetric distribution of glucose transporter SGTP4 at the apical surface of intramammalian-stage Schistosoma mansoni.

Adult Schistosoma mansoni blood flukes reside in the mesenteric veins of their vertebrate hosts, where they absorb immense quantities of glucose through their tegument by facilitated diffusion. Previously, we obtained S. mansoni cDNAs encoding facilitated-diffusion schistosome glucose transporter proteins 1 and 4 (SGTP1 and SGTP4) and localized SGTP1 to the basal membranes of the tegument and the underlying muscle. In this study, we characterize the expression and localization of SGTP4 during the schistosome life cycle. Antibodies specific to SGTP4 appear to stain only the double-bilayer, apical membranes of the adult parasite tegument, revealing an asymmetric distribution relative to the basal transporter SGTP1. On living worms, SGTP4 is available to surface biotinylation, suggesting that it is exposed at the hose-parasite interface. SGTP4 is detected shortly after the transformation of free-living, infectious cercariae into schistosomula and coincides with the appearance of the double membrane. Within 15 min after transformation, anti-SGTP4 staining produces a bright, patchy distribution at the surface of schistosomula, which becomes contiguous over the entire surface of the schistosomula by 24 hr after transformation. SGTP4 is not detected in earlier developmental stages (eggs, sporocysts, and cercariae) that do not possess the specialized double membrane. Thus, SGTP4 appears to be expressed only in the mammalian stages of the parasite's life cycle and specifically localized within the host-interactive, apical membranes of the tegument.

Mouse Col18a1 is expressed in a tissue-specific manner as three alternative variants and is localized in basement membrane zones.

We have isolated overlapping cDNAs encoding the N-terminal non-triple-helical region of mouse alpha 1(XVIII) collagen and shown that three different variants of alpha 1(XVIII) collagen exist. Each of the three variants shows characteristic tissue-specific expression patterns. Immunohistochemical studies show positive staining for alpha 1(XVIII) collagen along the basement membrane zones of vessels in the intestinal villi, the choroid plexus, skin, liver, and kidney. Thus, we conclude that alpha 1(XVIII) collagen may interact (directly or indirectly) with components in basement membrane zones or on the basal surface of endothelial/epithelial cells.

Cell-surface-expressed T-cell antigen-receptor zeta chain is associated with the cytoskeleton.

The T-cell antigen receptor zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. zeta chain can associate with certain protein tyrosine kinases and retains the capacity to transduce signals independently of the other receptor subunits. Thus, zeta chain could couple cell-surface-expressed T-cell antigen receptors to the intracellular signal-transduction apparatus by its association with various intracellular molecules in addition to tyrosine kinases. In the process of searching for zeta chain-associated molecules we observed that after lysis of resting T cells with Triton X-100, zeta chain is localized in the detergent-insoluble fraction, in addition to its presence in the detergent-soluble fraction. Treatment of T cells with cytochalasin B, an actin-depolymerizing agent, leads to the complete dissociation of zeta chain from the Triton-insoluble fraction, suggesting a linkage between zeta chain and the cytoskeletal matrix. We have also determined that cytoskeletal-associated zeta chain is expressed on the cell surface. Furthermore, a tyrosine-phosphorylated 16-kDa zeta chain was detected only in the Triton-insoluble cytoskeletal fraction of resting T cells. zeta chain also maintains its association with the cytoskeleton when expressed in COS cells, inferring that the cytoskeletal elements involved in this linkage may be ubiquitous. Finally, we have localized a 42-amino acid region in the intracytoplasmic domain of zeta chain, which is crucial for maximal interaction between zeta chain and the cytoskeleton. Anchorage of cell-surface-expressed zeta chain to the cytoskeleton in resting T cells may facilitate recycling of receptor complexes and/or allow the transduction of external stimuli into the cell.

Ammonia removal using activated carbons: effect of the surface chemistry in dry and moist conditions

The effect of surface chemistry (nature and amount of oxygen groups) in the removal of ammonia was studied using a modified resin-based activated carbon. NH3 breakthrough column experiments show that the modification of the original activated carbon with nitric acid, that is, the incorporation of oxygen surface groups, highly improves the adsorption behavior at room temperature. Apparently, there is a linear relationship between the total adsorption capacity and the amount of the more acidic and less stable oxygen surface groups. Similar experiments using moist air clearly show that the effect of humidity highly depends on the surface chemistry of the carbon used. Moisture highly improves the adsorption behavior for samples with a low concentration of oxygen functionalities, probably due to the preferential adsorption of ammonia via dissolution into water. On the contrary, moisture exhibits a small effect on samples with a rich surface chemistry due to the preferential adsorption pathway via Brønsted and Lewis acid centers from the carbon surface. FTIR analyses of the exhausted oxidized samples confirm both the formation of NH4+ species interacting with the Brønsted acid sites, together with the presence of NH3 species coordinated, through the lone pair electron, to Lewis acid sites on the graphene layers.

Dyakonov surface waves in lossy metamaterials

We analyze the existence of localized waves in the vicinities of the interface between two dielectrics, provided one of them is uniaxial and lossy. We found two families of surface waves, one of them approaching the well-known Dyakonov surface waves (DSWs). In addition, a new family of wave fields exists which are tightly bound to the interface. Although its appearance is clearly associated with the dissipative character of the anisotropic material, the characteristic propagation length of such surface waves might surpass the working wavelength by nearly two orders of magnitude.