The curvature of the conical intersection seam: an approximate second-order analysis

We present a method for analyzing the curvature (second derivatives) of the conical intersection hyperline at an optimized critical point. Our method uses the projected Hessians of the degenerate states after elimination of the two branching space coordinates, and is equivalent to a frequency calculation on a single Born-Oppenheimer potential-energy surface. Based on the projected Hessians, we develop an equation for the energy as a function of a set of curvilinear coordinates where the degeneracy is preserved to second order (i.e., the conical intersection hyperline). The curvature of the potential-energy surface in these coordinates is the curvature of the conical intersection hyperline itself, and thus determines whether one has a minimum or saddle point on the hyperline. The equation used to classify optimized conical intersection points depends in a simple way on the first- and second-order degeneracy splittings calculated at these points. As an example, for fulvene, we show that the two optimized conical intersection points of C2v symmetry are saddle points on the intersection hyperline. Accordingly, there are further intersection points of lower energy, and one of C2 symmetry - presented here for the first time - is found to be the global minimum in the intersection space

The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer.

Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR.

Autosomal Recessive Posterior Microphthalmos/Nanophthalmos is Caused by Loss-of-function Mutations in LOC646960, a Novel Gene Encoding a Trypsin-like Serine Protease

Purpose: Posterior microphthalmos (MCOP)/nanophthalmos (NNO) is a developmental anomaly characterized by extreme hyperopia due to short axial length. The population of the Faroe Islands shows a high prevalence of an autosomal recessive form (arMCOP). The gene mutated in arMCOP is not yet known.Methods: Genetic mapping by linkage analysis using microsatellite and single nucleotide polymorphisms, mutation analysis by PCR and sequencing, molecular modellingResults: Having refined the position of the disease locus (MCOP6) in an interval of 250 kb in chromosome 2q37.1 in Faroese families, we detected 3 mutations in a novel gene, LOC646960: Patients of 10 different Faroese families were either homozygous (n=22) for c.926G>C (p.Trp309Ser) or compound heterozygous (n=6) for c.926G>C and c.526C>G (p.Arg176Gly), whereas a homozygous 1 bp duplication (c.1066dupC) was identified in patients with arNNO from a Tunisian family. In two unrelated patients with MCOP, no LOC646960 mutation was found. LOC646960 is expressed in the human adult retina and RPE. The expression of the mouse homologue in the eye can be first detected at E17 and is highest in adults. The predicted protein is a 603 amino acid long secreted trypsin-like serine peptidase. c.1066dupC should result in a functional null allele. Molecular modelling of the p.Trp309Ser mutant suggests that both affinity and reactivity of the enzyme towards in vivo substrates are substantially reduced.Conclusions: Postnatal growth of the eye is important for proper development of the refractive components (emmetropization), and is mainly due to elongation of the posterior segment from 10-11 mm at birth to 15-16 mm at the age of 13 years. Optical defocus leads to changes in axial length by moving the retina towards the image plane. arMCOP may theoretically be explained, in line with the expression pattern of LOC646960, by a postnatal growth retardation of the posterior segment.

Characterization of PHO1 and PHO1;H1 gene function in Arabidopsis thaliana

Summary Phosphorus is one of the major macronutrients required for plant growth and development. Plant roots acquire phosphorus as inorganic phosphate (Pi), which is further distributed to the shoot, via the transpiration stream and root pressure, where Pi is imported again into cells. PHO1 in Arabidopsis has been identified as a protein involved in the loading of Pi into the root xylem. PHO1 does not have any homology to described Pi transporters including the Pht1 family of H+/ Pi cotransporters. PHO1 bears two domains, SPX and EXS domains, previously identified in Saccharomyces cerevisiae proteins involved in Pi transport and/or sensing, or in sorting proteins to endomembranes. Phylogenetic analysis of the PHO1 gene family revealed the presence of three clusters, with PHO1 and PHO1;H1 forming one cluster. The biological significance behind this cluster was demonstrated by the complementation of the pho1 mutant with only PHO1 and PHO1;H1, of all the PHO1 family members, when expressed under the PHO1 promoter. PHO1 has been shown to be expressed mostly in the root vascular cylinder and at low level in the shoot. PHO1;H1 had a different expression pattern, being expressed in both root and shoot vascular cylinder to the same level, with the levels in leaves increasing with the leaf maturity, suggesting additional role of PHO1;H1 in the Pi mobilization in leaves. In order to further explore the role of PHO1, Pi dynamics was studied on plants expressing PHO1 at different levels compared to the wild type: PHO1 overexpressors, PHO1 underexpressors and the pho1 mutant. Overexpression of the PHO1 protein in the shoot vascular tissue was shown to lead to increased Pi efflux out of the leaf cells and Pi accumulation in the shoot xylem apoplast compared to wild type, confirming the hypothesized role of PHO1 in xylem loading with Pi. The overexpression of PHO1 in the shoot was responsible far both changed Pi dynamic and stunted growth of PHO1 overexpressors, as shown by grafting experiments between wild type and PHO1 overexpressor. We found a ca. 2 fold decrease of shoot phosphorus and a 5-10 fold decrease in vacuolar Pi content in the PHO1 underexpressors and the pho1 null mutant compared to wild type, consistent with the role of PHO1 in the transfer of Pi from the root to the shoot. Shoot Pi deficiency results in a poor growth of the pho1 mutant. Grafting experiments between pho1 and wild type confirmed that both Pi deficiency and stunt growth of the pho1 mutant were dependent on the pho1 root, further supporting the importance of PHO1 in the root xylem loading with Pi. The pho1 mutant and the PHO1 underexpressors accumulated 8-15 fold more Pi in the root relative to wild type. In contrast to the pho1 mutant, the growth of PHO1 underexpressors was not impaired by the low shoat Pi content. This finding suggests that either PHO1 protein or root Pi concentration is important in Pi signaling and development of Pi deficiency symptoms leading to reduced growth. Résumé Le phosphore est l'un des nutriments essentiels à la croissance et au développement des plantes. Les racines absorbent le phosphore sous forme de phosphate inorganique (Pi) qui est dirigé, par la transpiration et la pression de la racine, vers les feuilles où le phosphate est acquis par les cellules. La protéine PHO1 a été démontrée indispensable au chargement du Pi dans le xylème des racines d'Arabidopsis. PHO1 ne démontre pas d'homologie aux transporteurs de Pi connus, incluant la famille Pht1 de cotransporteurs H+/Pi qui ont comme fonction le transport du phosphate à l'intérieur de la cellule. PHO1 contient deux domaines, SPX et EXS, aussi présents dans des protéines de Saccharomyces cerevisiae impliquées dans le transport ou la perception du phosphate, ou dans la localisation des protéines vers différentes membranes. Le génome d'Arabidopsis contient onze gènes homologues à PHO1. Neuf de ces homologues sont répartis en trois groupes. PHO1 et PHO1;H1 forment un de ces groupes. Nos travaux ont démontré que seuls PHO1;H1 et PHO1, sous contrôle du promoteur PHO1, peuvent complémenter le mutant pho1. PHO1 est exprimé principalement dans le cylindre vasculaire de la racine et faiblement dans la partie aérienne. Le degré d'expression de PHO1;H1 est similaire dans le cylindre vasculaire de la racine et des feuilles. Ceci suggère que PHO1;H1 est aussi impliqué dans la mobilisation du Pi dans les feuilles, en plus de son rôle dans le transfert du Pi dans le xylème des racines. Afin de mieux explorer le rôle de PHO1, la dynamique du phosphate a été observée dans trois lignées de plantes transgéniques: un sur-expresseur de PHO1, un sous-expresseur de PHO1 et le mutant pho1. La sur-expression de PHO1 dans le tissue vasculaire des feuilles a provoqué l'efflux du Pi vers l'espace apoplastic du xylème, ce qui confirme le rôle de PHO1 dans le chargement du Pi dans le xylème. La sur-expressìon de PHO1 dans la rosette est responsable d'un changement de la dynamique du Pi et de la diminution de la croissance, ce qui fut démontré par une expérience de greffe de la rosette du sur-expresseur de PHO1 sur les racines du sauvage. On a observé pour le sous-expresseur de PHO1 et le mutant pho1 une diminution du phosphore d'environ 2 fais au niveau des feuilles, et une diminution de 5-10 fois du Pi dans les vacuoles des feuilles, par rapport au sauvage. Ceci confirme le rôle proposé de PHO1 dans le transfert du Pi des racines aux feuilles. La carence de Pi chez pho1 implique une diminution de la taille de la rosette. Pour expliquer ce phénotype une autre expérience de greffe démontra que la cause de ce changement provenait des racines. Ceci renforce l'hypothèse de l'importance du rôle de PHO1 dans le xylème de la racine pour le chargement du Pi. Le mutant phot et le sous-expresseur de PHO1 accumulent 8-15 fois plus de Pi dans leurs racines comparé au sauvage. Cependant, contrairement au phot mutant, le sous-expresseur de PHO1 avait une croissance comparable au sauvage malgré le niveau bas du Pi dans les feuilles. Ceci suggère que la taille de la rosette lors d'une carence en Pi chez Arabidopsis serait la conséquence d'un changement de concentration de Pi dans les racines ou d'une influence de la protéine PHO1.

Homeostasis and in vivo effector function of antigen-specific CD4+CD25+ regulatory T cells in experimental transplantation.

CD4+CD25+ regulatory T cells (Tregs) play a critical role in the prevention of autoimmune diseases as well as in the induction and maintenance of dominant tolerance in transplantation models. While their suppressive function has been extensively studied in vitro, their homeostasis and mechanisms of immunoregulation still remain to be clarifi ed in vivo. Using a murine adoptive transfer and skin allograft model, we analysed the expansion, effector function and traffi cking of effector T cells in the presence or absence of donor-specifi c Tregs. Although hyporesponsive to allogeneic and polyclonal stimulation in vitro, transferred Tregs survived and expanded, in response to an allograft in vivo. When co-transferred with naive CD4+CD25- effector T cells, they specifi cally prevented donor but not 3rd party allograft rejection by inhibiting the production of effector cytokines rather than the proliferation of effector T cells in response to alloantigens. The co-transfer of donor-specifi c Tregs did not affect the homing of effector T cells towards the graft draining lymph nodes, but it markedly reduced the infi ltration of the allograft by these pathogenic cells. Furthermore, in recipients where donor-specifi c transplantation tolerance was induced, Tregs preferentially accumulated in the allograft draining lymph nodes and within the grafted skin itself. Taken together, our results suggest that the suppression of graft rejection is an active process that involves the persistent presence of Tregs at the site of antigenic challenge.

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

The extraordinarily bright optical afterglow of GRB 991208 and its host galaxy

Observations of the extraordinarily bright optical afterglow (OA) of GRB 991208 started 2.1 d after the event. The flux decay constant of the OA in the R-band is -2.30 +/- 0.07 up to 5 d, which is very likely due to the jet effect, and after that it is followed by a much steeper decay with constant -3.2 +/- 0.2, the fastest one ever seen in a GRB OA. A negative detection in several all-sky films taken simultaneously to the event implies either a previous additional break prior to 2 d after the occurrence of the GRB (as expected from the jet effect). The existence of a second break might indicate a steepening in the electron spectrum or the superposition of two events. Once the afterglow emission vanished, contribution of a bright underlying SN is found, but the light curve is not sufficiently well sampled to rule out a dust echo explanation. Our determination of z = 0.706 indicates that GRB 991208 is at 3.7 Gpc, implying an isotropic energy release of 1.15 x 10E53 erg which may be relaxed by beaming by a factor > 100. Precise astrometry indicates that the GRB coincides within 0.2' with the host galaxy, thus given support to a massive star origin. The absolute magnitude is M_B = -18.2, well below the knee of the galaxy luminosity function and we derive a star-forming rate of 11.5 +/- 7.1 Mo/yr. The quasi-simultaneous broad-band photometric spectral energy distribution of the afterglow is determined 3.5 day after the burst (Dec 12.0) implying a cooling frequency below the optical band, i.e. supporting a jet model with p = -2.30 as the index of the power-law electron distribution.

Optical response of Cu3Ge thin films

We report an investigation on the optical properties of Cu3Ge thin films displaying very high conductivity, with thickness ranging from 200 to 2000 Å, deposited on Ge substrates. Reflectance, transmittance, and ellipsometric spectroscopy measurements were performed at room temperature in the 0.01-6.0, 0.01-0.6, and 1.4-5.0 eV energy range, respectively. The complex dielectric function, the optical conductivity, the energy-loss function, and the effective charge density were obtained over the whole spectral range. The low-energy free-carrier response was well fitted by using the classical Drude-Lorentz dielectric function. A simple two-band model allowed the resulting optical parameters to be interpreted coherently with those previously obtained from transport measurements, hence yielding the densities and the effective masses of electrons and holes.

Optical-geometrical effects on the photoluminescence spectra of Si nanocrystals embedded in SiO2

We demonstrate that thickness, optical constants, and details of the multilayer stack, together with the detection setting, strongly influence the photoluminescence spectra of Si nanocrystals embedded in SiO2. Due to multiple reflections of the visible light against the opaque silicon substrate, an interference pattern is built inside the oxide layer, which is responsible for the modifications in the measured spectra. This interference effect is complicated by the depth dependence of (i) the intensity of the excitation laser and (ii) the concentration of the emitting nanocrystals. These variations can give rise to apparent features in the recorded spectra, such as peak shifts, satellite shoulders, and even splittings, which can be mistaken as intrinsic material features. Thus, they can give rise to an erroneous attribution of optical bands or estimate of the average particle size, while they are only optical-geometrical artifacts. We have analyzed these effects as a function of material composition (Si excess fraction) and thickness, and also evaluated how the geometry of the detection setup affects the measurements. To correct the experimental photoluminescence spectra and extract the true spectral shape of the emission from Si nanocrystals, we have developed an algorithm based on a modulation function, which depends on both the multilayer sequence and the experimental configuration. This procedure can be easily extended to other heterogeneous systems.

Linear and nonlinear optical properties of Si nanocrystals in SiO2 deposited by plasma-enhanced chemical-vapor deposition

Linear and nonlinear optical properties of silicon suboxide SiOx films deposited by plasma-enhanced chemical-vapor deposition have been studied for different Si excesses up to 24¿at.¿%. The layers have been fully characterized with respect to their atomic composition and the structure of the Si precipitates. Linear refractive index and extinction coefficient have been determined in the whole visible range, enabling to estimate the optical bandgap as a function of the Si nanocrystal size. Nonlinear optical properties have been evaluated by the z-scan technique for two different excitations: at 0.80¿eV in the nanosecond regime and at 1.50¿eV in the femtosecond regime. Under nanosecond excitation conditions, the nonlinear process is ruled by thermal effects, showing large values of both nonlinear refractive index (n2 ~ ¿10¿8¿cm2/W) and nonlinear absorption coefficient (ß ~ 10¿6¿cm/W). Under femtosecond excitation conditions, a smaller nonlinear refractive index is found (n2 ~ 10¿12¿cm2/W), typical of nonlinearities arising from electronic response. The contribution per nanocrystal to the electronic third-order nonlinear susceptibility increases as the size of the Si nanoparticles is reduced, due to the appearance of electronic transitions between discrete levels induced by quantum confinement.

Silicon nanocluster sensitization of erbium ions under low-energy optical excitation

The sensitizing action of amorphous silicon nanoclusters on erbium ions in thin silica films has been studied under low-energy (long wavelength) optical excitation. Profound differences in fast visible and infrared emission dynamics have been found with respect to the high-energy (shortwavelength) case. These findings point out to a strong dependence of the energy transfer process on the optical excitation energy. Total inhibition of energy transfer to erbium states higher than thefirst excited state (4I13/2) has been demonstrated for excitation energy below 1.82 eV (excitation wavelength longer than 680 nm). Direct excitation of erbium ions to the first excited state (4I13/2)has been confirmed to be the dominant energy transfer mechanism over the whole spectral range of optical excitation used (540 nm¿680 nm).

Analysis of leakage properties and guiding conditions of rib antiresonant reflecting optical waveguides

Power leakage properties and guiding conditions of rib antiresonant reflecting optical waveguides (rib-ARROW) have been theoretically and experimentally studied as a function of wavelength and polarization of the light for different geometrical and optical parameters that characterize the rib-ARROW structure. Obtained results show that rib-ARROWs can only be fabricated with low losses in a wavelength range when determined rib configurations are adopted. Furthermore, these waveguides exhibit a polarization sensitivity that largely depends on the core-substrate refractive index difference. Together with the experimental results, theoretical calculations from different modeling methods are also presented and discussed.

Size effects in the magneto-optical response of Co nanoparticles

A study of the magneto-optical (MO) spectral response of Co nanoparticles embedded in MgO as a function of their size and concentration in the spectral range from 1.4 to 4.3 eV is presented. The nanoparticle layers were obtained by sputtering at different deposition temperatures. Transmission electron microscopy measurements show that the nanoparticles have a complex structure which consists of a crystalline core having a hexagonal close-packed structure and an amorphous crust. Using an effective-medium approximation we have obtained the MO constants of the Co nanoparticles. These MO constants are different from those of continuous Co layers and depend on the size of the crystalline core. We associate these changes with the size effect of the intraband contribution to the MO constants, related to a reduction of the relaxation time of the electrons into the nanoparticles.

Domain Adaptation in remote sensing: increasing the portability of land-cover classifiers

Among the types of remote sensing acquisitions, optical images are certainly one of the most widely relied upon data sources for Earth observation. They provide detailed measurements of the electromagnetic radiation reflected or emitted by each pixel in the scene. Through a process termed supervised land-cover classification, this allows to automatically yet accurately distinguish objects at the surface of our planet. In this respect, when producing a land-cover map of the surveyed area, the availability of training examples representative of each thematic class is crucial for the success of the classification procedure. However, in real applications, due to several constraints on the sample collection process, labeled pixels are usually scarce. When analyzing an image for which those key samples are unavailable, a viable solution consists in resorting to the ground truth data of other previously acquired images. This option is attractive but several factors such as atmospheric, ground and acquisition conditions can cause radiometric differences between the images, hindering therefore the transfer of knowledge from one image to another. The goal of this Thesis is to supply remote sensing image analysts with suitable processing techniques to ensure a robust portability of the classification models across different images. The ultimate purpose is to map the land-cover classes over large spatial and temporal extents with minimal ground information. To overcome, or simply quantify, the observed shifts in the statistical distribution of the spectra of the materials, we study four approaches issued from the field of machine learning. First, we propose a strategy to intelligently sample the image of interest to collect the labels only in correspondence of the most useful pixels. This iterative routine is based on a constant evaluation of the pertinence to the new image of the initial training data actually belonging to a different image. Second, an approach to reduce the radiometric differences among the images by projecting the respective pixels in a common new data space is presented. We analyze a kernel-based feature extraction framework suited for such problems, showing that, after this relative normalization, the cross-image generalization abilities of a classifier are highly increased. Third, we test a new data-driven measure of distance between probability distributions to assess the distortions caused by differences in the acquisition geometry affecting series of multi-angle images. Also, we gauge the portability of classification models through the sequences. In both exercises, the efficacy of classic physically- and statistically-based normalization methods is discussed. Finally, we explore a new family of approaches based on sparse representations of the samples to reciprocally convert the data space of two images. The projection function bridging the images allows a synthesis of new pixels with more similar characteristics ultimately facilitating the land-cover mapping across images.

Energy transfer mechanism and Auger effect in Er3+ coupled silicon nanoparticle samples

We report a spectroscopic study about the energy transfer mechanism among silicon nanoparticles (Si-np), both amorphous and crystalline, and Er ions in a silicon dioxide matrix. From infrared spectroscopic analysis, we have determined that the physics of the transfer mechanism does not depend on the Si-np nature, finding a fast (< 200 ns) energy transfer in both cases, while the amorphous nanoclusters reveal a larger transfer efficiency than the nanocrystals. Moreover, the detailed spectroscopic results in the visible range here reported are essential to understand the physics behind the sensitization effect, whose knowledge assumes a crucial role to enhance the transfer rate and possibly employing the material in optical amplifier devices. Joining the experimental data, performed with pulsed and continuous-wave excitation, we develop a model in which the internal intraband recombination within Si-np is competitive with the transfer process via an Auger electron"recycling" effect. Posing a different light on some detrimental mechanism such as Auger processes, our findings clearly recast the role of Si-np in the sensitization scheme, where they are able to excite very efficiently ions in close proximity to their surface. (C) 2010 American Institute of Physics.