Spectral mixture analysis of EELS spectrum-images

Recent advances in detectors and computer science have enabled the acquisition and the processing of multidimensional datasets, in particular in the field of spectral imaging. Benefiting from these new developments, earth scientists try to recover the reflectance spectra of macroscopic materials (e.g., water, grass, mineral types...) present in an observed scene and to estimate their respective proportions in each mixed pixel of the acquired image. This task is usually referred to as spectral mixture analysis or spectral unmixing (SU). SU aims at decomposing the measured pixel spectrum into a collection of constituent spectra, called endmembers, and a set of corresponding fractions (abundances) that indicate the proportion of each endmember present in the pixel. Similarly, when processing spectrum-images, microscopists usually try to map elemental, physical and chemical state information of a given material. This paper reports how a SU algorithm dedicated to remote sensing hyperspectral images can be successfully applied to analyze spectrum-image resulting from electron energy-loss spectroscopy (EELS). SU generally overcomes standard limitations inherent to other multivariate statistical analysis methods, such as principal component analysis (PCA) or independent component analysis (ICA), that have been previously used to analyze EELS maps. Indeed, ICA and PCA may perform poorly for linear spectral mixture analysis due to the strong dependence between the abundances of the different materials. One example is presented here to demonstrate the potential of this technique for EELS analysis.Comment: Manuscript accepted for publication in Ultramicroscop

Variable selection in near infrared spectra for the biological characterization of soil and earthworm casts

International audienceNear infrared reflectance spectroscopy (NIRS) was used to predict six biological properties of soil and earthworm casts including extracellular soil enzymes, microbial carbon, potential nitrification and denitrification. Partial least squares regression (PLSR) models were developed with a selection of the most important near infrared wavelengths. They reached coefficients of determination ranging from 0.81 to 0.91 and ratios of performance-to-deviation above 2.3. Variable selection with the variable importance in the projection (VIP) method increased dramatically the prediction performance of all models with an important contribution from the 1750–2500 nm region. We discuss whether selected wavelengths can be attributed to macronutrient availability or to microbial biomass. Wavelength selection in NIR spectra is recommended for improving PLSR models in soil research

HIV-1-associated PKA acts as a cofactor for genome reverse transcription

BACKGROUND: Host cell proteins, including cellular kinases, are embarked into intact HIV-1 particles. We have previously shown that the Cα catalytic subunit of cAMP-dependent protein kinase is packaged within HIV-1 virions as an enzymatically active form able to phosphorylate a synthetic substrate in vitro (Cartier et al. J. Biol. Chem. 278:35211 (2003)). The present study was conceived to investigate the contribution of HIV-1-associated PKA to the retroviral life cycle. RESULTS: NL4.3 viruses were produced from cells cultured in the presence of PKA inhibitors H89 (H89-NL4.3) or Myr-PKI (PKI-NL4.3) and analyzed for viral replication. Despite being mature and normally assembled, and containing expected levels of genomic RNA and RT enzymatic activity, such viruses showed poor infectivity. Indeed, infection generated reduced amounts of strong-strop minus strand DNA, while incoming RNA levels in target cells were unaffected. Decreased cDNA synthesis was also evidenced in intact H89-NL4.3 and PKI-NL4.3 cell free particles using endogenous reverse transcription (ERT) experiments. Moreover, similar defects were reproduced when wild type NL4.3 particles preincubated with PKA inhibitors were subjected to ERT reactions. CONCLUSIONS: Altogether, our results indicate that HIV-1-associated PKA is required for early reverse transcription of the retroviral genome both in cell free intact viruses and in target cells. Accordingly, virus-associated PKA behaves as a cofactor of an intraviral process required for optimal reverse transcription and for early post-entry events

Interspecific competition between entomopathogenic nematodes (Steinernema) is modified by their bacterial symbionts (Xenorhabdus)

BACKGROUND: Symbioses between invertebrates and prokaryotes are biological systems of particular interest in order to study the evolution of mutualism. The symbioses between the entomopathogenic nematodes Steinernema and their bacterial symbiont Xenorhabdus are very tractable model systems. Previous studies demonstrated (i) a highly specialized relationship between each strain of nematodes and its naturally associated bacterial strain and (ii) that mutualism plays a role in several important life history traits of each partner such as access to insect host resources, dispersal and protection against various biotic and abiotic factors. The goal of the present study was to address the question of the impact of Xenorhabdus symbionts on the progression and outcome of interspecific competition between individuals belonging to different Steinernema species. For this, we monitored experimental interspecific competition between (i) two nematode species: S. carpocapsae and S. scapterisci and (ii) their respective symbionts: X. nematophila and X. innexi within an experimental insect-host (Galleria mellonella). Three conditions of competition between nematodes were tested: (i) infection of insects with aposymbiotic IJs (i.e. without symbiont) of both species (ii) infection of insects with aposymbiotic IJs of both species in presence of variable proportion of their two Xenorhabdus symbionts and (iii) infection of insects with symbiotic IJs (i.e. naturally associated with their symbionts) of both species. RESULTS: We found that both the progression and the outcome of interspecific competition between entomopathogenic nematodes were influenced by their bacterial symbionts. Thus, the results obtained with aposymbiotic nematodes were totally opposite to those obtained with symbiotic nematodes. Moreover, the experimental introduction of different ratios of Xenorhabdus symbionts in the insect-host during competition between Steinernema modified the proportion of each species in the adults and in the global offspring. CONCLUSION: We showed that Xenorhabdus symbionts modified the competition between their Steinernema associates. This suggests that Xenorhabdus not only provides Steinernema with access to food sources but also furnishes new abilities to deal with biotic parameters such as competitors

A recurrent 14q32.2 microdeletion mediated by expanded TGG repeats

Nearly all recurrent microdeletion/duplication syndromes described to date are characterized by the presence of flanking low copy repeats that act as substrates for non-allelic homologous recombination (NAHR) leading to the loss, gain or disruption of dosage sensitive genes. We describe an identical 1.11 Mb heterozygous deletion of 14q32.2 including the DLK1/GTL2 imprinted gene cluster in two unrelated patients. In both patients, the deleted chromosome 14 was of paternal origin, and consistent with this both exhibit clinical features compatible with uniparental disomy (UPD) (14)mat. Using a high-resolution oligonucleotide array, we mapped the breakpoints of this recurrent deletion to large flanking (TGG)n tandem repeats, each approximately 500 bp in size and sharing ≥88% homology. These expanded (TGG)n motifs share features with known fragile sites and are predicted to form strong guanine quadruplex secondary structures. We suggest that this recurrent deletion is mediated either by NAHR between the TGG repeats, or alternatively results from their inherent instability and/or strong secondary structure. Our results define a recurrent microdeletion of the 14q32.2 imprinted gene cluster mediated by flanking (TGG)n repeats, identifying a novel mechanism of recurrent genomic rearrangement. Our observation that expanded repeats can act as catalysts for genomic rearrangement extends the role of triplet repeats in human disease, raising the possibility that similar repeat structures may act as substrates for pathogenic rearrangements genome-wid

VSV-G pseudotyping rescues HIV-1 CA mutations that impair core assembly or stability

<p>Abstract</p> <p>Background</p> <p>The machinery of early HIV-1 replication still remains to be elucidated. Recently the viral core was reported to persist in the infected cell cytoplasm as an assembled particle, giving rise to the reverse transcription complex responsible for the synthesis of proviral DNA and its transport to the nucleus. Numerous studies have demonstrated that reverse transcription of the HIV-1 genome into proviral DNA is tightly dependent upon proper assembly of the capsid (CA) protein into mature cores that display appropriate stability. The functional impact of structural properties of the core in early replicative steps has yet to be determined.</p> <p>Results</p> <p>Here, we show that infectivity of HIV-1 mutants bearing S₁₄₉A and S₁₇₈A mutations in CA can be efficiently restored when pseudotyped with vesicular stomatitis virus envelope glycoprotein, that addresses the mutant cores through the endocytic pathway rather than by fusion at the plasma membrane. The mechanisms by which these mutations disrupt virus infectivity were investigated. S₁₄₉A and S₁₇₈A mutants were unable to complete reverse transcription and/or produce 2-LTR DNA. Morphological analysis of viral particles and <it>in vitro </it>uncoating assays of isolated cores demonstrated that infectivity defects resulted from disruption of the viral core assembly and stability for S₁₄₉A and S₁₇₈A mutants, respectively. Consistent with these results, both mutants failed to saturate TRIM-antiviral restriction activity.</p> <p>Conclusion</p> <p>Defects generated at the level of core assembly and stability by S₁₄₉A and S₁₇₈A mutations are sensitive to the way of delivery of viral nucleoprotein complexes into the target cell. Addressing CA mutants through the endocytic pathway may compensate for defects generated at the reverse transcription/nuclear import level subsequent to impairment of core assembly or stability.</p

Technical and pedagogical feedback on the deployment of an ePortfolio. Models of the uses, analysis and perspectives

ISBN: 9782954014418International audienceThis paper asks how are being designed and expected modes of integration of students during and after their university studies in the specific context of development on private and public markets for applications such as e-digital portfolios. She also questioned the manner in which to deploy the strategies and institutional policies regarding the choice of digital interfaces for the enhancement of learning and using the integration of students and in particular the way is taken into account the research dimension a tool to select and deploy. To do this, it relies on a study conducted as part of e-inclusion project supported by the Office for Students professional insertion (BAIP) and funded by the University of Lorraine and the Regional Council of Lorraine. This study is based on monitoring of a panel of about 250 students and fifteen teachers experimenting "Lorfolio" in their regular educational setting. Lorfolio is a portfolio of digital skills remotely accessible, for all the assets of a territory, and being developed in Lorraine at the initiative of the Regional Council. We propose in particular to highlight the returns through the use of specific questions that are generated when it comes to decide on their wide deployment of an institution, consortium or territory. What models to use is based does? What actual uses generates does? How to use these models and are they related to the digital strategies of institutions? After recalling the context of the study, the actors and the methodology adopted, we will build on the first qualitative and quantitative analyzes performed to establish the first profiles of the perception of the tool from the point of view of students as teachers to measure the impact of such a deployment at institutional level

Impact of anatase and rutile titanium dioxide nanoparticles on uptake carriers and efflux pumps in Caco-2 gut epithelial cells

International audienceTiO2 microparticles are widely used in food products, where they are added as a white food colouring agent. This food additive contains a significant amount of nanoscale particles; still the impact of TiO2 nanoparticles (TiO2-NPs) on gut cells is poorly documented. Our study aimed at evaluating the impact of rutile and anatase TiO2-NPs on the main functions of enterocytes, i.e. nutrient absorption driven by solute-liquid carriers (SLC transporters) and protection against other xenobiotics driven by efflux pumps from the ATP-binding cassette (ABC) family. We show that acute exposure of Caco-2 cells to both anatase (12 nm) and rutile (20 nm) TiO2-NPs induce early upregulation of a battery of efflux pumps and nutrient transporters. In addition they cause overproduction of reactive oxygen species and misbalance redox repair systems, without inducing cell mortality or DNA damage. Taken together, these data suggest that TiO2-NPs may increase the functionality of gut epithelial cells, particularly their property to form a protective barrier against exogenous toxicants and to absorb nutrients

Reconstruction of randomly and partially sampled STEM spectrum-images

Scanning transmission electron microscopy (STEM) offers the ability to acquire several single- and multi-channels signals generated simultaneously for each probe position: cathodoluminescence (CL), electron energy loss spectroscopy (EELS) and high-angle annular dark-field imaging (HAADF). However, in some cases, sensitive samples (e.g., biological samples or molecular structures) may suffer from irradiation damages during acquisition. As a consequence, it is often necessary to reduce probe current or dwell time, which could significantly lower the signal-to-noise ratio. Another approach consists in acquiring only a subset of pixels randomly chosen in a given region of interest. This particular experimental set-up has been implemented on the STEM VG HB501 (LPS, Orsay, France), with the beam following a predetermined random path. The reconstruction of HAADF images is then straightforward with well known algorithms. However, when reconstructing the associated spectrum image, the high number of energy bands makes the problem computationally expensive