Quorum-sensing-negative (lasR) mutants of Pseudomonas aeruginosa avoid cell lysis and death.

In Pseudomonas aeruginosa, N-acylhomoserine lactone signals regulate the expression of several hundreds of genes, via the transcriptional regulator LasR and, in part, also via the subordinate regulator RhlR. This regulatory network termed quorum sensing contributes to the virulence of P. aeruginosa as a pathogen. The fact that two supposed PAO1 wild-type strains from strain collections were found to be defective for LasR function because of independent point mutations in the lasR gene led to the hypothesis that loss of quorum sensing might confer a selective advantage on P. aeruginosa under certain environmental conditions. A convenient plate assay for LasR function was devised, based on the observation that lasR mutants did not grow on adenosine as the sole carbon source because a key degradative enzyme, nucleoside hydrolase (Nuh), is positively controlled by LasR. The wild-type PAO1 and lasR mutants showed similar growth rates when incubated in nutrient yeast broth at pH 6.8 and 37 degrees C with good aeration. However, after termination of growth during 30 to 54 h of incubation, when the pH rose to > or = 9, the lasR mutants were significantly more resistant to cell lysis and death than was the wild type. As a consequence, the lasR mutant-to-wild-type ratio increased about 10-fold in mixed cultures incubated for 54 h. In a PAO1 culture, five consecutive cycles of 48 h of incubation sufficed to enrich for about 10% of spontaneous mutants with a Nuh(-) phenotype, and five of these mutants, which were functionally complemented by lasR(+), had mutations in lasR. The observation that, in buffered nutrient yeast broth, the wild type and lasR mutants exhibited similar low tendencies to undergo cell lysis and death suggests that alkaline stress may be a critical factor providing a selective survival advantage to lasR mutants.

Cyclooxygenase-2 controls energy homeostasis in mice by de novo recruitment of brown adipocytes.

Obesity results from chronic energy surplus and excess lipid storage in white adipose tissue (WAT). In contrast, brown adipose tissue (BAT) efficiently burns lipids through adaptive thermogenesis. Studying mouse models, we show that cyclooxygenase (COX)-2, a rate-limiting enzyme in prostaglandin (PG) synthesis, is a downstream effector of beta-adrenergic signaling in WAT and is required for the induction of BAT in WAT depots. PG shifted the differentiation of defined mesenchymal progenitors toward a brown adipocyte phenotype. Overexpression of COX-2 in WAT induced de novo BAT recruitment in WAT, increased systemic energy expenditure, and protected mice against high-fat diet-induced obesity. Thus, COX-2 appears integral to de novo BAT recruitment, which suggests that the PG pathway regulates systemic energy homeostasis.

Monitoring and predicting crop growth and analysing agricultural ecosystems by remote sensing

Selostus: Maatalousekosysteemien analysointi ja sadon ennustaminen kaukokartoituksen avulla

PPARbeta/delta regulates paneth cell differentiation via controlling the hedgehog signaling pathway.

BACKGROUND & AIMS: All 4 differentiated epithelial cell types found in the intestinal epithelium derive from the intestinal epithelial stem cells present in the crypt unit, in a process whose molecular clues are intensely scrutinized. Peroxisome proliferator-activated receptor beta (PPARbeta) is a nuclear hormone receptor activated by fatty acids and is highly expressed in the digestive tract. However, its function in intestinal epithelium homeostasis is understood poorly. METHODS: To assess the role of PPARbeta in the small intestinal epithelium, we combined various cellular and molecular approaches in wild-type and PPARbeta-mutant mice. RESULTS: We show that the expression of PPARbeta is particularly remarkable at the bottom of the crypt of the small intestine where Paneth cells reside. These cells, which have an important role in the innate immunity, are strikingly affected in PPARbeta-null mice. We then show that Indian hedgehog (Ihh) is a signal sent by mature Paneth cells to their precursors, negatively regulating their differentiation. Importantly, PPARbeta acts on Paneth cell homeostasis by down-regulating the expression of Ihh, an effect that can be mimicked by cyclopamine, a known inhibitor of the hedgehog signaling pathway. CONCLUSIONS: We unraveled the Ihh-dependent regulatory loop that controls mature Paneth cell homeostasis and its modulation by PPARbeta. PPARbeta currently is being assessed as a drug target for metabolic diseases; these results reveal some important clues with respect to the signals controlling epithelial cell fate in the small intestine.

Oxygen consumption in collagenase-liberated rat adipocytes in relation to cell size and age.

Oxygen consumption of collagenase-liberated rat adipocytes was measured by two different techniques: a microspectrophotometric method using hemoglobin as indicator of respiration and a technique using the oxygen electrode. These two completely different techniques gave similar values for oxygen consumption. With the spectrophotometric method, the oxygen consumption of single fat cells was determined. A close positive correlation (r = greater than 0.90) between oxygen consumption and fat cell size was observed in each tissue examined. With the oxygen electrode technique, oxygen consumption of adipocyte suspensions from young (40 days, 180 g) and old (90 days, 480 g) rats was examined. Fat cells of the suspensions were separated into classes of different size by a flotation technique. A significant positive correlation between fat cell size and oxygen consumption was observed in both young (r = 0.88) and old (r = 0.95) rats. However, the slope was much steeper in young rats. At a cell weight of 0.1 microgram the oxygen consumption was 0.364 and 0.086 microL O2/10(6) cells/min-1 in young and old rats, respectively. In the literature, a number of separate metabolic pathways have been found to be related positively to fat cell size and negatively to age. We conclude that these scattered metabolic observations are in agreement with integrated data on energy expenditure as evaluated from oxygen consumption. Estimations of the energy expenditure of adipose tissue indicates that this tissue is responsible for about 1% and 0.5% of the total energy expenditure in young and old rats, respectively.

The nNOS-p38MAPK Pathway Is Mediated by NOS1AP during Neuronal Death.

Neuronal nitric oxide synthase (nNOS) and p38MAPK are strongly implicated in excitotoxicity, a mechanism common to many neurodegenerative conditions, but the intermediary mechanism is unclear. NOS1AP is encoded by a gene recently associated with sudden cardiac death, diabetes-associated complications, and schizophrenia (Arking et al., 2006; Becker et al., 2008; Brzustowicz, 2008; Lehtinen et al., 2008). Here we find it interacts with p38MAPK-activating kinase MKK3. Excitotoxic stimulus induces recruitment of NOS1AP to nNOS in rat cortical neuron culture. Excitotoxic activation of p38MAPK and subsequent neuronal death are reduced by competing with the nNOS:NOS1AP interaction and by knockdown with NOS1AP-targeting siRNAs. We designed a cell-permeable peptide that competes for the unique PDZ domain of nNOS that interacts with NOS1AP. This peptide inhibits NMDA-induced recruitment of NOS1AP to nNOS and in vivo in rat, doubles surviving tissue in a severe model of neonatal hypoxia-ischemia, a major cause of neonatal death and pediatric disability. The highly unusual sequence specificity of the nNOS:NOS1AP interaction and involvement in excitotoxic signaling may provide future opportunities for generation of neuroprotectants with high specificity.

Genome-wide meta-analysis for serum calcium identifies significantly associated SNPs near the calcium-sensing receptor (CASR) gene.

Calcium has a pivotal role in biological functions, and serum calcium levels have been associated with numerous disorders of bone and mineral metabolism, as well as with cardiovascular mortality. Here we report results from a genome-wide association study of serum calcium, integrating data from four independent cohorts including a total of 12,865 individuals of European and Indian Asian descent. Our meta-analysis shows that serum calcium is associated with SNPs in or near the calcium-sensing receptor (CASR) gene on 3q13. The top hit with a p-value of 6.3 x 10(-37) is rs1801725, a missense variant, explaining 1.26% of the variance in serum calcium. This SNP had the strongest association in individuals of European descent, while for individuals of Indian Asian descent the top hit was rs17251221 (p = 1.1 x 10(-21)), a SNP in strong linkage disequilibrium with rs1801725. The strongest locus in CASR was shown to replicate in an independent Icelandic cohort of 4,126 individuals (p = 1.02 x 10(-4)). This genome-wide meta-analysis shows that common CASR variants modulate serum calcium levels in the adult general population, which confirms previous results in some candidate gene studies of the CASR locus. This study highlights the key role of CASR in calcium regulation.

Estimation of soil moisture in the root-zone from remote sensing data

Field-based soil moisture measurements are cumbersome. Thus, remote sensing techniques are needed because allows field and landscape-scale mapping of soil moisture depth-averaged through the root zone of existing vegetation. The objective of the study was to evaluate the accuracy of an empirical relationship to calculate soil moisture from remote sensing data of irrigated soils of the Apodi Plateau, in the Brazilian semiarid region. The empirical relationship had previously been tested for irrigated soils in Mexico, Egypt, and Pakistan, with promising results. In this study, the relationship was evaluated from experimental data collected from a cotton field. The experiment was carried out in an area of 5 ha with irrigated cotton. The energy balance and evaporative fraction (Λ) were measured by the Bowen ratio method. Soil moisture (θ) data were collected using a PR2 - Profile Probe (Delta-T Devices Ltd). The empirical relationship was tested using experimentally collected Λ and θ values and was applied using the Λ values obtained from the Surface Energy Balance Algorithm for Land (SEBAL) and three TM - Landsat 5 images. There was a close correlation between measured and estimated θ values (p<0.05, R² = 0.84) and there were no significant differences according to the Student t-test (p<0.01). The statistical analyses showed that the empirical relationship can be applied to estimate the root-zone soil moisture of irrigated soils, i.e. when the evaporative fraction is greater than 0.45.

Oxygen content and inhomogeneity effects on the electrical properties of YBa2Cu3Oy thin films

Oxygen content is a very important factor influencing the electrical properties of YBa2Cu3Oy. In this work the electrical properties of laser deposited YBa2Cu3Oy thin films on LaAlO3(100), in the whole range 6 y 7, are studied. An electrical network model, which randomly assigns oxygen contents and R(T) characteristics to the different elements in the circuit according to an arbitrary distribution, is used to analyze several features in the measured R(T) characteristics as a function of oxygen homogeneity. The model takes into account both short-range and long-range oxygen inhomogeneities. Good agreement between estimated oxygen contents from x-ray diffraction data in our samples and the average oxygen contents used to reproduce their R(T) characteristics is found. The model points out that oxygen homogeneity is very important in order to get the best and reproducible properties, and for conduction and superconductivity analysis through the shape or derivatives of R(T) characteristics.

Active uptake of dendritic cell-derived exovesicles by epithelial cells induces the release of inflammatory mediators through a TNF-alpha-mediated pathway.

Dendritic cells (DCs) can release hundreds of membrane vesicles, called exovesicles, which are able to activate resting DCs and distribute antigen. Here, we examined the role of mature DC-derived exovesicles in innate and adaptive immunity, in particular their capacity to activate epithelial cells. Our analysis of exovesicle contents showed that exovesicles contain major histocompatibility complex-II, CD40, and CD83 molecules in addition to tumor necrosis factor (TNF) receptors, TNFRI and TNFRII, and are important carriers of TNF-alpha. These exovesicles are rapidly internalized by epithelial cells, inducing the release of cytokines and chemokines, but do not transfer an alloantigen-presenting capacity to epithelial cells. Part of this activation appears to involve the TNF-alpha-mediated pathway, highlighting the key role of DC-derived exovesicles, not only in adaptive immunity, but also in innate immunity by triggering innate immune responses and activating neighboring epithelial cells to release cytokines and chemokines, thereby amplifying the magnitude of the innate immune response.

Advanced Kernel Methods For Remote Sensing Image Classification

Résumé Suite aux recentes avancées technologiques, les archives d'images digitales ont connu une croissance qualitative et quantitative sans précédent. Malgré les énormes possibilités qu'elles offrent, ces avancées posent de nouvelles questions quant au traitement des masses de données saisies. Cette question est à la base de cette Thèse: les problèmes de traitement d'information digitale à très haute résolution spatiale et/ou spectrale y sont considérés en recourant à des approches d'apprentissage statistique, les méthodes à noyau. Cette Thèse étudie des problèmes de classification d'images, c'est à dire de catégorisation de pixels en un nombre réduit de classes refletant les propriétés spectrales et contextuelles des objets qu'elles représentent. L'accent est mis sur l'efficience des algorithmes, ainsi que sur leur simplicité, de manière à augmenter leur potentiel d'implementation pour les utilisateurs. De plus, le défi de cette Thèse est de rester proche des problèmes concrets des utilisateurs d'images satellite sans pour autant perdre de vue l'intéret des méthodes proposées pour le milieu du machine learning dont elles sont issues. En ce sens, ce travail joue la carte de la transdisciplinarité en maintenant un lien fort entre les deux sciences dans tous les développements proposés. Quatre modèles sont proposés: le premier répond au problème de la haute dimensionalité et de la redondance des données par un modèle optimisant les performances en classification en s'adaptant aux particularités de l'image. Ceci est rendu possible par un système de ranking des variables (les bandes) qui est optimisé en même temps que le modèle de base: ce faisant, seules les variables importantes pour résoudre le problème sont utilisées par le classifieur. Le manque d'information étiquétée et l'incertitude quant à sa pertinence pour le problème sont à la source des deux modèles suivants, basés respectivement sur l'apprentissage actif et les méthodes semi-supervisées: le premier permet d'améliorer la qualité d'un ensemble d'entraînement par interaction directe entre l'utilisateur et la machine, alors que le deuxième utilise les pixels non étiquetés pour améliorer la description des données disponibles et la robustesse du modèle. Enfin, le dernier modèle proposé considère la question plus théorique de la structure entre les outputs: l'intègration de cette source d'information, jusqu'à présent jamais considérée en télédétection, ouvre des nouveaux défis de recherche. Advanced kernel methods for remote sensing image classification Devis Tuia Institut de Géomatique et d'Analyse du Risque September 2009 Abstract The technical developments in recent years have brought the quantity and quality of digital information to an unprecedented level, as enormous archives of satellite images are available to the users. However, even if these advances open more and more possibilities in the use of digital imagery, they also rise several problems of storage and treatment. The latter is considered in this Thesis: the processing of very high spatial and spectral resolution images is treated with approaches based on data-driven algorithms relying on kernel methods. In particular, the problem of image classification, i.e. the categorization of the image's pixels into a reduced number of classes reflecting spectral and contextual properties, is studied through the different models presented. The accent is put on algorithmic efficiency and the simplicity of the approaches proposed, to avoid too complex models that would not be used by users. The major challenge of the Thesis is to remain close to concrete remote sensing problems, without losing the methodological interest from the machine learning viewpoint: in this sense, this work aims at building a bridge between the machine learning and remote sensing communities and all the models proposed have been developed keeping in mind the need for such a synergy. Four models are proposed: first, an adaptive model learning the relevant image features has been proposed to solve the problem of high dimensionality and collinearity of the image features. This model provides automatically an accurate classifier and a ranking of the relevance of the single features. The scarcity and unreliability of labeled. information were the common root of the second and third models proposed: when confronted to such problems, the user can either construct the labeled set iteratively by direct interaction with the machine or use the unlabeled data to increase robustness and quality of the description of data. Both solutions have been explored resulting into two methodological contributions, based respectively on active learning and semisupervised learning. Finally, the more theoretical issue of structured outputs has been considered in the last model, which, by integrating outputs similarity into a model, opens new challenges and opportunities for remote sensing image processing.

Evidence for catabolic pathway of propionate metabolism in CNS: expression pattern of methylmalonyl-CoA mutase and propionyl-CoA carboxylase alpha-subunit in developing and adult rat brain.

Methylmalonyl-CoA mutase (MCM) and propionyl-CoA carboxylase (PCC) are the key enzymes of the catabolic pathway of propionate metabolism and are mainly expressed in liver, kidney and heart. Deficiency of these enzymes leads to two classical organic acidurias: methylmalonic and propionic aciduria. Patients with these diseases suffer from a whole spectrum of neurological manifestations that are limiting their quality of life. Current treatment does not seem to effectively prevent neurological deterioration and pathophysiological mechanisms are poorly understood. In this article we show evidence for the expression of the catabolic pathway of propionate metabolism in the developing and adult rat CNS. Both, MCM and PCC enzymes are co-expressed in neurons and found in all regions of the CNS. Disease-specific metabolites such as methylmalonate, propionyl-CoA and 2-methylcitrate could thus be formed autonomously in the CNS and contribute to the pathophysiological mechanisms of neurotoxicity. In rat embryos (E15.5 and E18.5), MCM and PCC show a much higher expression level in the entire CNS than in the liver, suggesting a different, but important function of this pathway during brain development.

Muscle protein waste in tumor-bearing rats is effectively antagonized by a beta 2-adrenergic agonist (clenbuterol). Role of the ATP-ubiquitin-dependent proteolytic pathway.

Tissue protein hypercatabolism (TPH) is a most important feature in cancer cachexia, particularly with regard to the skeletal muscle. The rat ascites hepatoma Yoshida AH-130 is a very suitable model system for studying the mechanisms involved in the processes that lead to tissue depletion, since it induces in the host a rapid and progressive muscle waste mainly due to TPH (Tessitore, L., G. Bonelli, and F. M. Baccino. 1987. Biochem. J. 241:153-159). Detectable plasma levels of tumor necrosis factor-alpha associated with marked perturbations in the hormonal homeostasis have been shown to concur in forcing metabolism into a catabolic setting (Tessitore, L., P. Costelli, and F. M. Baccino. 1993. Br. J. Cancer. 67:15-23). The present study was directed to investigate if beta 2-adrenergic agonists, which are known to favor skeletal muscle hypertrophy, could effectively antagonize the enhanced muscle protein breakdown in this cancer cachexia model. One such agent, i.e., clenbuterol, indeed largely prevented skeletal muscle waste in AH-130-bearing rats by restoring protein degradative rates close to control values. This normalization of protein breakdown rates was achieved through a decrease of the hyperactivation of the ATP-ubiquitin-dependent proteolytic pathway, as previously demonstrated in our laboratory (Llovera, M., C. García-Martínez, N. Agell, M. Marzábal, F. J. López-Soriano, and J. M. Argilés. 1994. FEBS (Fed. Eur. Biochem. Soc.) Lett. 338:311-318). By contrast, the drug did not exert any measurable effect on various parenchymal organs, nor did it modify the plasma level of corticosterone and insulin, which were increased and decreased, respectively, in the tumor hosts. The present data give new insights into the mechanisms by which clenbuterol exerts its preventive effect on muscle protein waste and seem to warrant the implementation of experimental protocols involving the use of clenbuterol or alike drugs in the treatment of pathological states involving TPH, particularly in skeletal muscle and heart, such as in the present model of cancer cachexia.

The auditory pathway in cat corpus callosum.

The cortical auditory fields of the two hemispheres are interconnected via the corpus callosum. We have investigated the topographical arrangement of auditory callosal axons in the cat. Following circumscribed biocytin injections in the primary (AI), secondary (AII), anterior (AAF) and posterior (PAF) auditory fields, labelled axons have been found in the posterior two-thirds of the corpus callosum. Callosal axons labelled by small individual cortical injections did not form a tight bundle at the callosal midsagittal plane but spread over as much as one-third of the corpus callosum. Axons originating from different auditory fields were roughly topographically ordered, reflecting to some extent the rostro-caudal position of the field of origin. Axons from AAF crossed on average more rostrally than axons from AI; the latter crossed more rostrally than axons from PAF and AII. Callosal axons originating in a discrete part of the cortex travelled first in a relatively tight bundle to the telo-diencephalic junction and then dispersed progressively. In conclusion, the cat corpus callosum does not contain a sector reserved for auditory axons, nor a strictly topographically ordered auditory pathway. This observation is of relevance to neuropsychological and neuropathological observations in man.