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ECOLOGICAL STUDIES OF EPIKARST COMMUNITIES IN ALPINE AND PRE-ALPINE CAVES
Federica Papi, 2016, doktorska disertacija

Opis: The karst ecosystem shows heterogeneity and variability of geology, hydrology, morphology and ecology in space and time. Chemical composition of water in karst plays a crucial role not only in dissolution of karst rocks and deposition but also in ecological processes. The heterogeneous nature of karst aquifers leads to difficulties in predicting groundwater flow and contaminant transport direction and travel times. For its position at the top of karst, epikarst represents the interface between surface and underground. Epikarst ecology, biodiversity and fauna have rarely been systematically studied. The typical absence of enterable passages makes necessary an indirect approach. In this research, epikarst biodiversity in relation to environmental conditions was studied in seven Alpine and Pre-Alpine caves, located at different altitudes, in Slovenia and in Italy: Snežna jama na planini Arto (1556 m a.s.l.), Jama pod Babjim zobom (860 m a.s.l.), Zadlaška jama (300 m a.s.l.) and Pološka jama (500 m a.s.l.), in Slovenian Alps and Pre-alps, and Grotta A del Ponte di Veja (600 m a.s.l.), Covolo della Croce (875 m a.s.l.) and Grotta di Roverè Mille (1005 m a.s.l.) in Lessinian Massif. In these caves, percolating water was monthly monitored for fauna in the period of one year. Temperature, discharge, conductivity and pH were measured at the same time, and water samples for the laboratory analyses of total hardness, concentrations of various ions (calcium, chlorine, nitrate, sulphate and phosphate) and dissolved organic carbon were taken. 66 aquatic and terrestrial, mostly hypogean, species were found. Aquatic fauna was dominant in all caves, with the exception of Covolo della Croce. Caves located at higher elevations harbour less diverse communities. No animals were found when discharge was very low and in correspondence of moonmilk formations. The most abundant and diverse group was Copepoda, with thirteen different species and 776 individuals at different maturity stadia, totally representing 61% of the community (between two and three copepod species per cave in Slovenia and between one and six per cave in Italy). The 62% of copepod species were stygobionts. Some copepod species (e.g. Speocyclops infernus) have wide ecological tolerance to environmental variables, other have more restricted tolerances (e.g. Lessinocamptus insoletus). With regard of copepods, there was a good agreement between the number of observed species and the total number of predicted species, confirming that the sampling method was appropriate and sampling complete. Correlations between the copepod community structure and measured parameters, obtained with Pearson correlation coefficient and principal component analysis (PCA) show different patterns. Presence of copepods was positively correlated with conductivity and dissolved organic carbon in Grotta di Roverè Mille, and with carbonate and nitrate in Pološka jama. In other caves not so high correlations were found between copepod species and measured parameters and between pairs of species. Investigations of the Alpine and Pre-alpine epikarst fauna can help to understand better the ecology of the epikarst fauna and its roles within the large range of different shallow subterranean habitats.
Najdeno v: osebi
Ključne besede: Epikarst, Alpine and Pre-Alpine caves, percolating water, speleobiology, fauna.
Objavljeno: 31.08.2016; Ogledov: 2352; Prenosov: 176
.pdf Polno besedilo (2,00 MB)

25.
Hexagonal lattice model of the patterns formed by hydrogen-bonded molecules on the surface
Sara Fortuna, David L. Cheung, Alessandro Troisi, 2010, izvirni znanstveni članek

Opis: We model the two-dimensional self-assembly of planar molecules capable of complementary interactions (like hydrogen bonding) as a set of hexagonal tiles on a hexagonal lattice. We use Monte Carlo simulations to study the phase diagrams of three model systems. The phases are characterized using a variety of order parameters, and they are studied as a function of the strength of the complementary interaction energy. This simplified model is proven to be capable of reproducing the phases encountered in real systems, unifying within the same framework most of the structures encountered experimentally.
Najdeno v: osebi
Ključne besede: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice
Objavljeno: 10.10.2016; Ogledov: 1576; Prenosov: 0
.pdf Polno besedilo (3,44 MB)

26.
Polymer Vesicles with a Colloidal Armor of Nanoparticles
Rong Chen, Daniel J. G. Pearce, Sara Fortuna, David L. Cheung, Stefan A. F. Bon, 2011, izvirni znanstveni članek

Opis: The fabrication of polymer vesicles with a colloidal armor made from a variety of nanoparticles is demonstrated. In addition, it is shown that the armored supracolloidal structure can be postmodified through film-formation of soft polymer latex particles on the surface of the polymersome, hereby effectively wrapping the polymersome in a plastic bag, as well as through formation of a hydrogel by disintegrating an assembled polymer latex made from poly(ethyl acrylate-co-methacrylic acid) upon increasing the pH. Furthermore, ordering and packing patterns are briefly addressed with the aid of Monte Carlo simulations, including patterns observed when polymersomes are exposed to a binary mixture of colloids of different size.
Najdeno v: osebi
Ključne besede: Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids
Objavljeno: 11.10.2016; Ogledov: 1415; Prenosov: 0
.pdf Polno besedilo (1,43 MB)

27.
Phase behaviour of self-assembled monolayers controlled by tuning physisorbed and chemisorbed states: a lattice-model view
Sara Fortuna, David L. Cheung, Karen Johnston, 2016, izvirni znanstveni članek

Opis: The self-assembly of molecules on surfaces into 2D structures is important for the bottom-up fabrication of functional nanomaterials, and the self-assembledstructure depends on the interplay between molecule-molecule interactions and molecule-surface interactions. Halogenated benzene derivatives on platinum have been shown to have two distinct adsorption states: a physisorbed state and a chemisorbed state, and the interplay between the two can be expected to have a profound effect on the self-assembly and phase behaviour of these systems. We developed a lattice model that explicitly includes both adsorption states, with representative interactions parameterised using density functional theory calculations. This model was used in Monte Carlo simulations to investigate pattern formation of hexahalogenated benzene molecules on the platinumsurface. Molecules that prefer the physisorbed state were found to self-assemble with ease, depending on the interactions between physisorbed molecules. In contrast, molecules that preferentially chemisorb tend to get arrested in disordered phases. However, changing the interactions between chemisorbed and physisorbed molecules affects the phase behaviour. We propose functionalising molecules in order to tune their adsorption states, as an innovative way to control monolayer structure, leading to a promising avenue for directed assembly of novel 2D structures.
Najdeno v: osebi
Ključne besede: lattice model, hexagonal lattice, Monte Carlo, DFT, density functional theory, benzene, physisorption, chemisorption, halogenated
Objavljeno: 11.10.2016; Ogledov: 1526; Prenosov: 0
.pdf Polno besedilo (5,75 MB)

28.
Nanobodies against surface biomarkers enable the analysis of tumor genetic heterogeneity in uveal melanoma Patient Derived Xenografts
Ronan Crepin, David Gentien, Angeline Duche, Audrey Rapinat, Cecile Reyes, Fariba Nemati, Gerald Massonnet, Didier Deacaudin, Selma Djander, Sandrine Moutel, Klervi Even Desrumeaux, Nathalie Cassoux, Sophie Piperno-Neumann, Sebastian Amigorena, Franck Perez, Sergio Roman-Roman, Ario de Marco, 2017, izvirni znanstveni članek

Opis: Monoclonal antibodies specific for biomarkers expressed on the surface of uveal melanoma (UM) cells would simplify the immune-capture and genomic characterization of heterogeneous tumor cells originated from patient derived xenografts (PDXs). Antibodies against four independent tumor antigens were isolated by panning a nanobody synthetic library. Such antibodies enabled flow-cytometry-based sorting of distinct cell sub-populations from UM PDXs and to analyze their genomic features. The complexity and specificity of the biochemical and genomic biomarker combinations mirrored the UM tumor polyclonality. The data showed that MUC18 is highly and universally displayed at the surface of UM cells with different genetic background and consequently represents a reliable pan-biomarker for their identification and purification. In contrast, the other three biomarkers were detected in very variable combinations in UM PDX cells. The availability of the identified nanobodies will be instrumental in developing clone-specific drug evaluation and rational clinical strategies based on accurate genomic profiling
Najdeno v: osebi
Ključne besede: nanobodies, uveal melanoma, patient derived xenografts, MUC18, membrane surface biomarkers, panning, tumor polyclonality
Objavljeno: 19.04.2017; Ogledov: 1403; Prenosov: 0
.pdf Polno besedilo (1,11 MB)

29.
The VPS4 component of the ESCRT machinery plays an essential role in HPV infectious entry and capsid disassembly
Lawrence Banks, Colin Crump, Anna Gozdzicka-Jozefiak, Martina Bergant, David Pim, Paola Massimi, Justyna Broniarczyk, 2017, izvirni znanstveni članek

Opis: Human Papillomavirus (HPV) infection involves multiple steps, from cell attachment, through endocytic trafficking towards the trans-Golgi network, and, ultimately, the entry into the nucleus during mitosis. An essential viral protein in infectious entry is the minor capsid protein L2, which engages different components of the endocytic sorting machinery during this process. The ESCRT machinery is one such component that seems to play an important role in the early stages of infection. Here we have analysed the role of specific ESCRT components in HPV infection, and we find an essential role for VPS4. Loss of VPS4 blocks infection with multiple PV types, suggesting an evolutionarily conserved critical step in infectious entry. Intriguingly, both L1 and L2 can interact with VPS4, and appear to be in complex with VPS4 during the early stages of virus infection. By using cell lines stably expressing a dominant-negative mutant form of VPS4, we also show that loss of VPS4 ATPase activity results in a marked delay in capsid uncoating, resulting in a defect in the endocytic transport of incoming PsVs. These results demonstrate that the ESCRT machinery, and in particular VPS4, plays a critical role in the early stages of PV infection.
Najdeno v: osebi
Ključne besede: HPV, ESCRT machinery, infection
Objavljeno: 08.05.2017; Ogledov: 1349; Prenosov: 100
.pdf Polno besedilo (1,10 MB)

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