Functional diversification of duplicate genes through subcellular adaptation of encoded proteins.

BACKGROUND: Gene duplication is the primary source of new genes with novel or altered functions. It is known that duplicates may obtain these new functional roles by evolving divergent expression patterns and/or protein functions after the duplication event. Here, using yeast (Saccharomyces cerevisiae) as a model organism, we investigate a previously little considered mode for the functional diversification of duplicate genes: subcellular adaptation of encoded proteins. RESULTS: We show that for 24-37% of duplicate gene pairs derived from the S. cerevisiae whole-genome duplication event, the two members of the pair encode proteins that localize to distinct subcellular compartments. The propensity of yeast duplicate genes to evolve new localization patterns depends to a large extent on the biological function of their progenitor genes. Proteins involved in processes with a wider subcellular distribution (for example, catabolism) frequently evolved new protein localization patterns after duplication, whereas duplicate proteins limited to a smaller number of organelles (for example, highly expressed biosynthesis/housekeeping proteins with a slow rate of evolution) rarely relocate within the cell. Paralogous proteins evolved divergent localization patterns by partitioning of ancestral localizations ('sublocalization'), but probably more frequently by relocalization to new compartments ('neolocalization'). We show that such subcellular reprogramming may occur through selectively driven substitutions in protein targeting sequences. Notably, our data also reveal that relocated proteins functionally adapted to their new subcellular environments and evolved new functional roles through changes of their physico-chemical properties, expression levels, and interaction partners. CONCLUSION: We conclude that protein subcellular adaptation represents a common mechanism for the functional diversification of duplicate genes.

The role of energetic value in dynamic brain response adaptation during repeated food image viewing.

The repeated presentation of simple objects as well as biologically salient objects can cause the adaptation of behavioral and neural responses during the visual categorization of these objects. Mechanisms of response adaptation during repeated food viewing are of particular interest for better understanding food intake beyond energetic needs. Here, we measured visual evoked potentials (VEPs) and conducted neural source estimations to initial and repeated presentations of high-energy and low-energy foods as well as non-food images. The results of our study show that the behavioral and neural responses to food and food-related objects are not uniformly affected by repetition. While the repetition of images displaying low-energy foods and non-food modulated VEPs as well as their underlying neural sources and increased behavioral categorization accuracy, the responses to high-energy images remained largely invariant between initial and repeated encounters. Brain mechanisms when viewing images of high-energy foods thus appear less susceptible to repetition effects than responses to low-energy and non-food images. This finding is likely related to the superior reward value of high-energy foods and might be one reason why in particular high-energetic foods are indulged although potentially leading to detrimental health consequences.

A methodology for the adaptation of a PMP at the determination of a PMF

This paper presents a new type of very fine grid hydrological model based on the spatiotemporal repartition of a PMP (Probable Maximum Precipitation) and on the topography. The goal is to estimate the influence of this rain on a PMF (Probable Maximum Flood) on a catchment area in Switzerland. The spatiotemporal distribution of the PMP was realized using six clouds modeled by the advection-diffusion equation. The equation shows the movement of the clouds over the terrain and also gives the evolution of the rain intensity in time. This hydrological modeling is followed by a hydraulic modeling of the surface and subterranean flow, done considering the factors that contribute to the hydrological cycle, such as the infiltration, the resurgence and the snowmelt. These added factors make the developed model closer to reality and also offer flexibility in the initial condition that is added to the factors concerning the PMP, such as the duration of the rain, the speed and direction of the wind. All these initial conditions taken together offer a complete image of the PMF.

Genetic and phenotypic population divergence on a microgeographic scale in brown trout.

Salmonid populations of many rivers are rapidly declining. One possible explanation is that habitat fragmentation increases genetic drift and reduces the populations' potential to adapt to changing environmental conditions. We measured the genetic and eco-morphological diversity of brown trout (Salmo trutta) in a Swiss stream system, using multivariate statistics and Bayesian clustering. We found large genetic and phenotypic variation within only 40 km of stream length. Eighty-eight percent of all pairwise F(ST) comparisons and 50% of the population comparisons in body shape were significant. High success rates of population assignment tests confirmed the distinctiveness of populations in both genotype and phenotype. Spatial analysis revealed that divergence increased with waterway distance, the number of weirs, and stretches of poor habitat between sampling locations, but effects of isolation-by-distance and habitat fragmentation could not be fully disentangled. Stocking intensity varied between streams but did not appear to erode genetic diversity within populations. A lack of association between phenotypic and genetic divergence points to a role of local adaptation or phenotypically plastic responses to habitat heterogeneity. Indeed, body shape could be largely explained by topographic stream slope, and variation in overall phenotype matched the flow regimes of the respective habitats.

Life-history consequences of adaptation to larval nutritional stress in Drosophila.

Many animal species face periods of chronic nutritional stress during which the individuals must continue to develop, grow, and/or reproduce despite low quantity or quality of food. Here, we use experimental evolution to study adaptation to such chronic nutritional stress in six replicate Drosophila melanogaster populations selected for the ability to survive and develop within a limited time on a very poor larval food. In unselected control populations, this poor food resulted in 20% lower egg-to-adult viability, 70% longer egg-to-adult development, and 50% lower adult body weight (compared to the standard food on which the flies were normally maintained). The evolutionary changes associated with adaptation to the poor food were assayed by comparing the selected and control lines in a common environment for different traits after 29-64 generations of selection. The selected populations evolved improved egg-to-adult viability and faster development on poor food. Even though the adult dry weight of selected flies when raised on the poor food was lower than that of controls, their average larval growth rate was higher. No differences in proportional pupal lipid content were observed. When raised on the standard food, the selected flies showed the same egg-to-adult viability and the same resistance to larval heat and cold shock as the controls and a slightly shorter developmental time. However, despite only 4% shorter development time, the adults of selected populations raised on the standard food were 13% smaller and showed 20% lower early-life fecundity than the controls, with no differences in life span. The selected flies also turned out less tolerant to adult malnutrition. Thus, fruit flies have the genetic potential to adapt to poor larval food, with no detectable loss of larval performance on the standard food. However, adaptation to larval nutritional stress is associated with trade-offs with adult fitness components, including adult tolerance to nutritional stress.

Morphological and physiological species-dependent characteristics of the rodent Grueneberg ganglion.

In the mouse, the Grueneberg ganglion (GG) is an olfactory subsystem implicated both in chemo- and thermo-sensing. It is specifically involved in the recognition of volatile danger cues such as alarm pheromones and structurally-related predator scents. No evidence for these GG sensory functions has been reported yet in other rodent species. In this study, we used a combination of histological and physiological techniques to verify the presence of a GG and investigate its function in the rat, hamster, and gerbil comparing with the mouse. By scanning electron microscopy (SEM) and transmitted electron microscopy (TEM), we found isolated or groups of large GG cells of different shapes that in spite of their gross anatomical similarities, display important structural differences between species. We performed a comparative and morphological study focusing on the conserved olfactory features of these cells. We found fine ciliary processes, mostly wrapped in ensheating glial cells, in variable number of clusters deeply invaginated in the neuronal soma. Interestingly, the glial wrapping, the amount of microtubules and their distribution in the ciliary processes were different between rodents. Using immunohistochemistry, we were able to detect the expression of known GG proteins, such as the membrane guanylyl cyclase G and the cyclic nucleotide-gated channel A3. Both the expression and the subcellular localization of these signaling proteins were found to be species-dependent. Calcium imaging experiments on acute tissue slice preparations from rodent GG demonstrated that the chemo- and thermo-evoked neuronal responses were different between species. Thus, GG neurons from mice and rats displayed both chemo- and thermo-sensing, while hamsters and gerbils showed profound differences in their sensitivities. We suggest that the integrative comparison between the structural morphologies, the sensory properties, and the ethological contexts supports species-dependent GG features prompted by the environmental pressure.

Evidence for polygenic adaptation to pathogens in the human genome.

Most approaches aiming at finding genes involved in adaptive events have focused on the detection of outlier loci, which resulted in the discovery of individually "significant" genes with strong effects. However, a collection of small effect mutations could have a large effect on a given biological pathway that includes many genes, and such a polygenic mode of adaptation has not been systematically investigated in humans. We propose here to evidence polygenic selection by detecting signals of adaptation at the pathway or gene set level instead of analyzing single independent genes. Using a gene-set enrichment test to identify genome-wide signals of adaptation among human populations, we find that most pathways globally enriched for signals of positive selection are either directly or indirectly involved in immune response. We also find evidence for long-distance genotypic linkage disequilibrium, suggesting functional epistatic interactions between members of the same pathway. Our results show that past interactions with pathogens have elicited widespread and coordinated genomic responses, and suggest that adaptation to pathogens can be considered as a primary example of polygenic selection.

Le trouble de l'adaptation, un diagnostic anodin ? : une étude comparative avec le trouble dépressif majeur

Résumé Le trouble de l'adaptation est un diagnostic très fréquent, mais étonnamment peu étudié et controversé. Il est, selon les études, considéré comme une forme mineure d'un trouble psychiatrique spécifique, comme une fragilité psychologique révélée par un événement stressant pour le sujet ou encore comme une forme précoce annonçant un trouble psychiatrique majeur. Ces trois points de vue ramènent en fait tous à la question de fond concernant son étiologie. L'objectif de cette étude est de montrer si le trouble de l'adaptation est un diagnostic clairement différencié dont l'existence est justifiée. Afin de tenter de répondre à cette question, il nous est apparu intéressant de comparer cette catégorie diagnostique à une autre catégorie diagnostique psychiatrique importante, le trouble dépressif majeur. Dans cette étude rétrospective nous avons sélectionné tous les patients avec un diagnostic de trouble de l'adaptation ou un trouble dépressif majeur parmi les patients hospitalisés à l'hôpital psychiatrique de Malévoz en Valais en 1993 (580). Elle est basée sur des diagnostics cliniques. Nous avons comparé leurs données socio-démographiques (âge, sexe, nationalité, état civil, activité professionnelle), leurs antécédents psychiatriques (hospitalisations antérieures, suivi psychiatrique ambulatoire, antécédents de tentamen), leurs hospitalisations ultérieures dans les 5 ans, leur hospitalisation actuelle (durée, tentamens, comorbidité) et les traitements médicamenteux prescrits (leur nombre et leur classe). Notre étude met en évidence certaines distinctions entre le trouble de l'adaptation et le trouble dépressif majeur: les patients souffrant de trouble de l'adaptation diffèrent des troubles dépressifs majeurs par le fait qu'ils sont plus fréquemment des hommes, célibataires et plus jeunes que ceux souffrant de trouble dépressif majeur; leur durée d'hospitalisation est plus courte, leur évolution entre les hospitalisations est meilleure et ils reçoivent moins de psychotropes. Nous ne pouvons cependant pas conclure à une distinction claire de ces deux catégories diagnostiques, ni que le trouble de l'adaptation n'est pas simplement lié à une moindre gravité. Nos résultats confirment par contre que ce diagnostic n'est pas non plus un diagnostic anodin (nombre élevé d'antécédents psychiatriques, de tentamens, d'hospitalisations psychiatriques ultérieures, importance des comorbidités de même que la lourdeur des traitements psychotropes prescrits (notamment la fréquence des neuroleptiques). A notre avis, les trois hypothèses étiologiques (forme mineure, trouble précoce ou fragilité psychologique spécifique révélée par un événement stressant) qui ont été évoquées peuvent être considérées comme plausibles suivant le point de vue que l'on choisit. Le diagnostic de trouble de l'adaptation révèle une des limitations de l'approche du DSM-Ill-R qui se veut athéorique. Le fait que dans sa définition même, le DSM-111-R évoque "qu'il faut souvent se référer au seul jugement clinique" le montre bien, un tel diagnostic renvoie inévitablement à une référence psychopathologique. Nous pensons qu'il est illusoire de vouloir se passer d'une telle référence qui elle seule permet d'appréhender justement la portée symbolique d'un événement donné pour un individu. Summary In this retrospective study we selected all the patients with a diagnosis of adjustment disorder (77) or major depressive disorder (125) among the patients hospitalised in the psychiatric hospital of Malevoz in Valais during the year 1993 (580). It is based on clinical diagnosis. Their social and demographic characteristics (age, sex, nationality, marital status, professional activity), their past psychiatric history (earlier psychiatric hospitalisations, ambulatory treatment and attempted suicide), their hospitalisations during the next 5 years, their index hospitalisation (length, attempted suicide, comorbidity) and their drug treatment (number and class of prescribed drugs) were compared. This survey confirms certain differences be-tween adjustment disorder and major depression disorder: patients suffering from adjustment disorder were more often men, not married, younger than those suffering from major depression; their hospitalisations were shorter with a better evolution between hospitalisations and they received less medication. However, the study does not allow to clearly distinguish between the two diagnoses or to conclude that adjustment disorder is not only a minor form of a specific psychiatric disorder. Yet it confirms that adjustment disorder is not a light diagnosis (importance of the psychiatric past, high number of past attempted suicides, rehospitalisations, number of comorbid disorders and weight of the prescribed psychotropic treatments among which neuroleptics were frequent). The three aetiological hypotheses that have been proposed (minor form of a specific disorder, specific psychological vulnerability revealed by a stress factor or precursor manifestation of a major psychiatric disorder) can still be considered as plausible. The diagnosis of adjustment disorder points to methodological limitations of the atheoretical approach of the DSM-III-R. The fact that, in its DSM-III-R definition, it is stated that the diagnosis of adjustment disorder has often to be based only on clinical judgment shows very well that such a diagnosis inevitably refers to a psychopathological theory. Indeed, the authors consider an approach without such a reference as difficult, a reference which remains the only way to appreciate accurately the symbolic weight of a given event for an individual person.

Les groupes de parole de prévention de la récidive au sein des SPIP: une évolution centrée sur la gestion du risque, entre théorie et adaptation pratique

En France, les différentes réorientations pénales et les missions confiées au Service Pénitentiaire d'Insertion et de Probation (SPIP) placent l'évaluation des risques de récidive et leur prévention au centre de la pratique professionnelle des Conseillers Pénitentiaires d'Insertion et de Probation (CPIP). Les récentes évolutions législatives des missions des SPIP, les mutations identitaires et des pratiques qu'elles impliquent -en particulier les Groupes de Paroles de Prévention de la Récidive (GPPR)-, caractérisent une évolution centrée sur la gestion du risque. Partant de critiques dans la littérature sur la notion de gestion du risque de récidive dans les pratiques pénales et de ce qu'elle induit dans les modes d'appréhension des sujets et dans les interventions professionnelles, l'article met en relation les réorientations vers une gestion du risque telles qu'elles peuvent apparaître dans les textes, missions et référentiel du SPIP, avec une évaluation des pratiques professionnelles centrées sur les GPPR intégrés au sein des SPIP. Y a-t-il infiltration et remodelage des pratiques ? Si c'est bien le cas, on examine où se situe le niveau pertinent de cette influence et du réaménagement des pratiques.

Biochemical, morphological and content characterization of synaptobrevin 2-expressing vesicles in astrocytes

Neuron-astrocyte reciprocal communication at synapses has emerged as a novel signalling pathway in brain function. Astrocytes sense the level of synaptic activity and, in turn, influence its efficacy through the regulated release of ''glio- transmitters'' such as glutamate, ATP or D-serine. A calcium- dependent exocytosis is proposed to drive the release of gliotransmitters but its existence is still debated. To shed light onto the mechanisms controlling the storage and the release of gliotransmitters and namely D-serine, we have developed a new method for the immunoisolation of synaptobrevin 2-positive vesicles from rat cortical astrocytes in culture. The purified organelles are clear round shape vesicles of excellent purity as judged by electron microscopy. Immunoblotting analysis revealed that isolated vesicles contain most of the major proteins already described for neuron-derived vesicles. In addition, we have analyzed the content for various amino acids of these vesicles by means of chiral capillary electro- phoresis coupled to laser-induced fluorescence detection and liquid chromatography coupled to mass spectrometry. Post- embedding immunogold labelling of the rat neocortex and hippocampus further revealed the expression of D-serine and glutamate in astrocyte processes contacting excitatory sy- napses. Our results provide significant support for the existence of secretory glial vesicles storing chemical substances like D- serine and glutamate and thus point to the co-release of amino acids by exocytosis in astrocytes.

An analysis of visual adaptation and contrast perception for tone mapping

Tone Mapping is the problem of compressing the range of a High-Dynamic Range image so that it can be displayed in a Low-Dynamic Range screen, without losing or introducing novel details: The final image should produce in the observer a sensation as close as possible to the perception produced by the real-world scene. We propose a tone mapping operator with two stages. The first stage is a global method that implements visual adaptation, based on experiments on human perception, in particular we point out the importance of cone saturation. The second stage performs local contrast enhancement, based on a variational model inspired by color vision phenomenology. We evaluate this method with a metric validated by psychophysical experiments and, in terms of this metric, our method compares very well with the state of the art.

Neuronal adaptation effects in decision making

Recently, there has been an increased interest on the neural mechanisms underlying perceptual decision making. However, the effect of neuronal adaptation in this context has not yet been studied. We begin our study by investigating how adaptation can bias perceptual decisions. We considered behavioral data from an experiment on high-level adaptation-related aftereffects in a perceptual decision task with ambiguous stimuli on humans. To understand the driving force behind the perceptual decision process, a biologically inspired cortical network model was used. Two theoretical scenarios arose for explaining the perceptual switch from the category of the adaptor stimulus to the opposite, nonadapted one. One is noise-driven transition due to the probabilistic spike times of neurons and the other is adaptation-driven transition due to afterhyperpolarization currents. With increasing levels of neural adaptation, the system shifts from a noise-driven to an adaptation-driven modus. The behavioral results show that the underlying model is not just a bistable model, as usual in the decision-making modeling literature, but that neuronal adaptation is high and therefore the working point of the model is in the oscillatory regime. Using the same model parameters, we studied the effect of neural adaptation in a perceptual decision-making task where the same ambiguous stimulus was presented with and without a preceding adaptor stimulus. We find that for different levels of sensory evidence favoring one of the two interpretations of the ambiguous stimulus, higher levels of neural adaptation lead to quicker decisions contributing to a speed–accuracy trade off.

Three-dimensional morphological analysis of intracranial aneurysms: a fully automated method for aneurysm sac isolation and quantification

Morphological descriptors are practical and essential biomarkers for diagnosis andtreatment selection for intracranial aneurysm management according to the current guidelinesin use. Nevertheless, relatively little work has been dedicated to improve the three-dimensionalquanti cation of aneurysmal morphology, automate the analysis, and hence reduce the inherentintra- and inter-observer variability of manual analysis. In this paper we propose a methodologyfor the automated isolation and morphological quanti cation of saccular intracranial aneurysmsbased on a 3D representation of the vascular anatomy.