Sequence and Copy Number Analyses of HEXB Gene in Patients Affected by Sandhoff Disease: Functional Characterization of 9 Novel Sequence Variants

Sandhoff disease (SD) is a lysosomal disorder caused by mutations in the HEXB gene. To date, 43 mutations of HEXB have been described, including 3 large deletions. Here, we have characterized 14 unrelated SD patients and developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay to investigate the presence of large HEXB deletions. Overall, we identified 16 alleles, 9 of which were novel, including 4 sequence variation leading to aminoacid changes [c.626C>T (p.T209I), c.634C>A (p.H212N), c.926G>T (p.C309F), c.1451G>A (p.G484E)] 3 intronic mutations (c.1082+5G>A, c.1242+1G>A, c.1169+5G>A), 1 nonsense mutation c.146C>A (p.S49X) and 1 small in-frame deletion c.1260_1265delAGTTGA (p.V421_E422del). Using the new MLPA assay, 2 previously described deletions were identified. In vitro expression studies showed that proteins bearing aminoacid changes p.T209I and p.G484E presented a very low or absent activity, while proteins bearing the p.H212N and p.C309F changes retained a significant residual activity. The detrimental effect of the 3 novel intronic mutations on the HEXB mRNA processing was demonstrated using a minigene assay. Unprecedentedly, minigene studies revealed the presence of a novel alternative spliced HEXB mRNA variant also present in normal cells. In conclusion, we provided new insights into the molecular basis of SD and validated an MLPA assay for detecting large HEXB deletions.

COMPARISON MEASURES OF MAPS GENERATED BY GEOSTATISTICAL METHODS

This study uses several measures derived from the error matrix for comparing two thematic maps generated with the same sample set. The reference map was generated with all the sample elements and the map set as the model was generated without the two points detected as influential by the analysis of local influence diagnostics. The data analyzed refer to the wheat productivity in an agricultural area of 13.55 ha considering a sampling grid of 50 x 50 m comprising 50 georeferenced sample elements. The comparison measures derived from the error matrix indicated that despite some similarity on the maps, they are different. The difference between the estimated production by the reference map and the actual production was of 350 kilograms. The same difference calculated with the mode map was of 50 kilograms, indicating that the study of influential points is of fundamental importance to obtain a more reliable estimative and use of measures obtained from the error matrix is a good option to make comparisons between thematic maps.

Axioms for the coincidence index of maps between manifolds of the same dimension

We study the coincidence theory of maps between two manifolds of the same dimension from an axiomatic viewpoint. First we look at coincidences of maps between manifolds where one of the maps is orientation true, and give a set of axioms such that characterizes the local index (which is an integer valued function). Then we consider coincidence theory for arbitrary pairs of maps between two manifolds. Similarly we provide a set of axioms which characterize the local index, which in this case is a function with values in Z circle plus Z(2). We also show in each setting that the group of values for the index (either Z or Z circle plus Z(2)) is determined by the axioms. Finally, for the general case of coincidence theory for arbitrary pairs of maps between two manifolds we provide a set of axioms which characterize the local Reidemeister trace which is an element of an abelian group which depends on the pair of functions. These results extend known results for coincidences between orientable differentiable manifolds. (C) 2012 Elsevier B.V. All rights reserved.

Polar foliations and isoparametric maps

A singular Riemannian foliation F on a complete Riemannian manifold M is called a polar foliation if, for each regular point p, there is an immersed submanifold Sigma, called section, that passes through p and that meets all the leaves and always perpendicularly. A typical example of a polar foliation is the partition of M into the orbits of a polar action, i.e., an isometric action with sections. In this article we prove that the leaves of H : M -> Sigma, coincide with the level sets of a smooth map H: M -> Sigma, if M is simply connected. In particular, the orbits of a polar action on a simply connected space are level sets of an isoparametric map. This result extends previous results due to the author and Gorodski, Heintze, Liu and Olmos, Carter and West, and Terng.

Chains of Infinite Order, Chains with Memory of Variable Length, and Maps of the Interval

We show how to construct a topological Markov map of the interval whose invariant probability measure is the stationary law of a given stochastic chain of infinite order. In particular we characterize the maps corresponding to stochastic chains with memory of variable length. The problem treated here is the converse of the classical construction of the Gibbs formalism for Markov expanding maps of the interval.

Wecken type problems for self-maps of the Klein bottle

We consider various problems regarding roots and coincidence points for maps into the Klein bottle . The root problem where the target is and the domain is a compact surface with non-positive Euler characteristic is studied. Results similar to those when the target is the torus are obtained. The Wecken property for coincidences from to is established, and we also obtain the following 1-parameter result. Families which are coincidence free but any homotopy between and , , creates a coincidence with . This is done for any pair of maps such that the Nielsen coincidence number is zero. Finally, we exhibit one such family where is the constant map and if we allow for homotopies of , then we can find a coincidence free pair of homotopies.

Comparison measures of maps generated by geostatistical methods

This study uses several measures derived from the error matrix for comparing two thematic maps generated with the same sample set. The reference map was generated with all the sample elements and the map set as the model was generated without the two points detected as influential by the analysis of local influence diagnostics. The data analyzed refer to the wheat productivity in an agricultural area of 13.55 ha considering a sampling grid of 50 x 50 m comprising 50 georeferenced sample elements. The comparison measures derived from the error matrix indicated that despite some similarity on the maps, they are different. The difference between the estimated production by the reference map and the actual production was of 350 kilograms. The same difference calculated with the mode map was of 50 kilograms, indicating that the study of influential points is of fundamental importance to obtain a more reliable estimative and use of measures obtained from the error matrix is a good option to make comparisons between thematic maps.

Hydro-physical characterization of soils under tropical semi-deciduous forest

The study of the hydro-physical behavior in soils using toposequences is of great importance for better understanding the soil, water and vegetation relationships. This study aims to assess the hydro-physical and morphological characterization of soil from a toposequence in Galia, state of São Paulo, Brazil). The plot covers an area of 10.24 ha (320 × 320 m), located in a semi-deciduous seasonal forest. Based on ultra-detailed soil and topographic maps of the area, a representative transect from the soil in the plot was chosen. Five profiles were opened for the morphological description of the soil horizons, and hydro-physical and micromorphological analyses were performed to characterize the soil. Arenic Haplustult, Arenic Haplustalf and Aquertic Haplustalf were the soil types observed in the plot. The superficial horizons had lower density and greater hydraulic conductivity, porosity and water retention in lower tensions than the deeper horizons. In the sub-superficial horizons, greater water retention at higher tensions and lower hydraulic conductivity were observed, due to structure type and greater clay content. The differences observed in the water retention curves between the sandy E and the clay B horizons were mainly due to the size distribution, shape and type of soil pores.

Regularizing a set of unstructured 3D points from a sequence of stereo images

[EN] In this paper we present a method for the regularization of a set of unstructured 3D points obtained from a sequence of stereo images. This method takes into account the information supplied by the disparity maps computed between pairs of images to constraint the regularization of the set of 3D points. We propose a model based on an energy which is composed of two terms: an attachment term that minimizes the distance from 3D points to the projective lines of camera points, and a second term that allows for the regularization of the set of 3D points by preserving discontinuities presented on the disparity maps. We embed this energy in a 2D finite element method. After minimizing, this method results in a large system of equations that can be optimized for fast computations. We derive an efficient implicit numerical scheme which reduces the number of calculations and memory allocations.

Studio molecolare dei meccanismi dell'autoincompatibilità gametofitica in pero europeo (Pyrus communis)

Self-incompatibility (SI) systems have evolved in many flowering plants to prevent self-fertilization and thus promote outbreeding. Pear and apple, as many of the species belonging to the Rosaceae, exhibit RNase-mediated gametophytic self-incompatibility, a widespread system carried also by the Solanaceae and Plantaginaceae. Pear orchards must for this reason contain at least two different cultivars that pollenize each other; to guarantee an efficient cross-pollination, they should have overlapping flowering periods and must be genetically compatible. This compatibility is determined by the S-locus, containing at least two genes encoding for a female (pistil) and a male (pollen) determinant. The female determinant in the Rosaceae, Solanaceae and Plantaginaceae system is a stylar glycoprotein with ribonuclease activity (S-RNase), that acts as a specific cytotoxin in incompatible pollen tubes degrading cellular RNAs. Since its identification, the S-RNase gene has been intensively studied and the sequences of a large number of alleles are available in online databases. On the contrary, the male determinant has been only recently identified as a pollen-expressed protein containing a F-box motif, called S-Locus F-box (abbreviated SLF or SFB). Since F-box proteins are best known for their participation to the SCF (Skp1 - Cullin - F-box) E3 ubiquitine ligase enzymatic complex, that is involved in protein degradation through the 26S proteasome pathway, the male determinant is supposed to act mediating the ubiquitination of the S-RNases, targeting them for the degradation in compatible pollen tubes. Attempts to clone SLF/SFB genes in the Pyrinae produced no results until very recently; in apple, the use of genomic libraries allowed the detection of two F-box genes linked to each S haplotype, called SFBB (S-locus F-Box Brothers). In Japanese pear, three SFBB genes linked to each haplotype were cloned from pollen cDNA. The SFBB genes exhibit S haplotype-specific sequence divergence and pollen-specific expression; their multiplicity is a feature whose interpretation is unclear: it has been hypothesized that all of them participate in the S-specific interaction with the RNase, but it is also possible that only one of them is involved in this function. Moreover, even if the S locus male and female determinants are the only responsible for the specificity of the pollen-pistil recognition, many other factors are supposed to play a role in GSI; these are not linked to the S locus and act in a S-haplotype independent manner. They can have a function in regulating the expression of S determinants (group 1 factors), modulating their activity (group 2) or acting downstream, in the accomplishment of the reaction of acceptance or rejection of the pollen tube (group 3). This study was aimed to the elucidation of the molecular mechanism of GSI in European pear (Pyrus communis) as well as in the other Pyrinae; it was divided in two parts, the first focusing on the characterization of male determinants, and the second on factors external to the S locus. The research of S locus F-box genes was primarily aimed to the identification of such genes in European pear, for which sequence data are still not available; moreover, it allowed also to investigate about the S locus structure in the Pyrinae. The analysis was carried out on a pool of varieties of the three species Pyrus communis (European pear), Pyrus pyrifolia (Japanese pear), and Malus × domestica (apple); varieties carrying S haplotypes whose RNases are highly similar were chosen, in order to check whether or not the same level of similarity is maintained also between the male determinants. A total of 82 sequences was obtained, 47 of which represent the first S-locus F-box genes sequenced from European pear. The sequence data strongly support the hypothesis that the S locus structure is conserved among the three species, and presumably among all the Pyrinae; at least five genes have homologs in the analysed S haplotypes, but the number of F-box genes surrounding the S-RNase could be even greater. The high level of sequence divergence and the similarity between alleles linked to highly conserved RNases, suggest a shared ancestral polymorphism also for the F-box genes. The F-box genes identified in European pear were mapped on a segregating population of 91 individuals from the cross 'Abbé Fétel' × 'Max Red Bartlett'. All the genes were placed on the linkage group 17, where the S locus has been placed both in pear and apple maps, and resulted strongly associated to the S-RNase gene. The linkage with the RNase was perfect for some of the F-box genes, while for others very rare single recombination events were identified. The second part of this study was focused on the research of other genes involved in the SI response in pear; it was aimed on one side to the identification of genes differentially expressed in compatible and incompatible crosses, and on the other to the cloning and characterization of the transglutaminase (TGase) gene, whose role may be crucial in pollen rejection. For the identification of differentially expressed genes, controlled pollinations were carried out in four combinations (self pollination, incompatible, half-compatible and fully compatible cross-pollination); expression profiles were compared through cDNA-AFLP. 28 fragments displaying an expression pattern related to compatibility or incompatibility were identified, cloned and sequenced; the sequence analysis allowed to assign a putative annotation to a part of them. The identified genes are involved in very different cellular processes or in defense mechanisms, suggesting a very complex change in gene expression following the pollen/pistil recognition. The pool of genes identified with this technique offers a good basis for further study toward a better understanding of how the SI response is carried out. Among the factors involved in SI response, moreover, an important role may be played by transglutaminase (TGase), an enzyme involved both in post-translational protein modification and in protein cross-linking. The TGase activity detected in pear styles was significantly higher when pollinated in incompatible combinations than in compatible ones, suggesting a role of this enzyme in the abnormal cytoskeletal reorganization observed during pollen rejection reaction. The aim of this part of the work was thus to identify and clone the pear TGase gene; the PCR amplification of fragments of this gene was achieved using primers realized on the alignment between the Arabidopsis TGase gene sequence and several apple EST fragments; the full-length coding sequence of the pear TGase gene was then cloned from cDNA, and provided a precious tool for further study of the in vitro and in vivo action of this enzyme.

Perceptual maps analysis for organic food consumers in China: a study on Shanghai consumers

Although in Europe and in the USA many studies focus on organic, little is known on the topic in China. This research provides an insight on Shanghai consumers’ perception of organic, aiming at understanding and representing in graphic form the network of mental associations that stems from the organic concept. To acquire, process and aggregate the individual networks it was used the “Brand concept mapping” methodology (Roedder et al., 2006), while the data analysis was carried out also using analytic procedures. The results achieved suggest that organic food is perceived as healthy, safe and costly. Although these attributes are pretty much consistent with the European perception, some relevant differences emerged. First, organic is not necessarily synonymous with natural product in China, also due to a poor translation of the term in the Chinese language that conveys the idea of a manufactured product. Secondly, the organic label has to deal with the competition with the green food label in terms of image and positioning on the market, since they are easily associated and often confused. “Environmental protection” also emerged as relevant association, while the ethical and social values were not mentioned. In conclusion, health care and security concerns are the factors that influence most the food consumption in China (many people are so concerned about food safety that they found it difficult to shop), and the associations “Safe”, “Pure and natural”, “without chemicals” and “healthy” have been identified as the best candidates for leveraging a sound image of organic food .

Characterization of fold-related fractures in the carbonate rocks of the Cingoli anticline, northern Apennines, Italy

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different structures, such as joints, faults, pressure solution seams, and deformation bands. Defining the development of fracture systems related to the folding process is significant both for theoretical and practical purposes. Fracture systems are useful constrains in order to understand the kinematical evolution of the fold. Furthermore, understanding the relationships between folding and fracturing provides a noteworthy contribution for reconstructing the geodynamic and the structural evolution of the studied area. Moreover, as fold-related fractures influence fluid flow through rocks, fracture systems are relevant for energy production (geothermal studies, methane and CO2 , storage and hydrocarbon exploration), environmental and social issues (pollutant distribution, aquifer characterization). The PhD project shows results of a study carried out in a multilayer carbonate anticline characterized by different mechanical properties. The aim of this study is to understand the factors which influence the fracture formation and to define their temporal sequence during the folding process. The studied are is located in the Cingoli anticline (Northern Apennines), which is characterized by a pelagic multilayer characterized by sequences with different mechanical stratigraphies. A multi-scale analysis has been made in several outcrops located in different structural positions. This project shows that the conceptual sketches proposed in literature and the strain distribution models outline well the geometrical orientation of most of the set of fractures observed in the Cingoli anticline. On the other hand, the present work suggests the relevance of the mechanical stratigraphy in particular controlling the type of fractures formed (e.g. pressure solution seams, joints or shear fractures) and their subsequent evolution. Through a multi-scale analysis, and on the basis of the temporal relationship between fracture sets and their orientation respect layering, I also suggest a conceptual model for fracture systems formation.

Hydrogeochemical characterization of Seehausen territory - Bremen

The aim of this thesis is to provide a geochemical characterization of the Seehausen territory (a neighborhood) of Bremen, Germany. In this territory it is hosted a landfill of dredged sediments coming both from Bremerhaven (North See) and Bremen harbor (directly on the river Weser). For this reason this work has been focused also on possible impacts of the landfill on the groundwaters (shallow and deep aquifer). The Seehausen landfill uses the dewatering technique to manage the dredged sediments: incoming sediments are put into dewatering fields until they are completely dried (it takes almost a year). Then they are randomly sampled and analyzed: if the pollutants content is acceptable, sediments are treated with other materials and used instead of raw material for embankment, bricks, etc., otherwise they are disposed in the landfill. During this work it has been made a study of the natural geology and hydrogeology of the whole area of interest, especially because it is characterized by ancient natural salt deposits. Then, together with the Geological Survey of Bremen and the Harbor Authority of Bremen there have been identified all useful piezometers for a monitoring net around the landfill. During the sampling campaign there have been collected data of the principal anions and cations, physical parameters and stable water isotopes. Data analysis has been focused particularly on Cl, Na, SO4 and EC because these parameters might be helpful to attribute geochemical trends to the landfill or to a natural background. Furthermore dataloggers have been installed for a month in some piezometers and EC, pressure, dissolved oxygen and temperature data have been collected. Finally there has been made a deep comparison between current and historical data (1996 – 2011) and between old interpolation maps and current ones in order to see time trends of the aquifer geochemistry.

Diffusion maps in the Subriemannian motion group and perceptual grouping

Il presente lavoro è motivato dal problema della constituzione di unità percettive a livello della corteccia visiva primaria V1. Si studia dettagliatamente il modello geometrico di Citti-Sarti con particolare attenzione alla modellazione di fenomeni di associazione visiva. Viene studiato nel dettaglio un modello di connettività. Il contributo originale risiede nell'adattamento del metodo delle diffusion maps, recentemente introdotto da Coifman e Lafon, alla geometria subriemanniana della corteccia visiva. Vengono utilizzati strumenti di teoria del potenziale, teoria spettrale, analisi armonica in gruppi di Lie per l'approssimazione delle autofunzioni dell'operatore del calore sul gruppo dei moti rigidi del piano. Le autofunzioni sono utilizzate per l'estrazione di unità percettive nello stimolo visivo. Sono presentate prove sperimentali e originali delle capacità performanti del metodo.