Geographic patterns in the distribution of social systems in terrestrial arthropods.

The role of ecology in the evolution and maintenance of arthropod sociality has received increasing research attention in recent years. In some organisms, such as halictine bees, polistine wasps, and social spiders, researchers are investigating the environmental factors that may contribute to high levels of variation in the degree of sociality exhibited both among and within species. Within lineages that include only eusocial members, such as ants and termites, studies focus more on identifying extrinsic factors that may contribute to the dramatic variation in colony size, number of queens, and division of labour that is evident across these species. In this review, I propose a comparative approach that seeks to identify environmental factors that may have a common influence across such divergent social arthropod groups. I suggest that seeking common biogeographic patterns in the distribution of social systems or key social traits may help us to identify ecological factors that play a common role in shaping the evolution of sociality across different organisms. I first review previous studies of social gradients that form along latitudinal and altitudinal axes. Within families and within species, many organisms show an increasing degree of sociality at lower latitudes and altitudes. In a smaller number of cases, organisms form larger groups or found nests cooperatively at higher latitudes and altitudes. I then describe several environmental factors that vary consistently along such gradients, including climate variables and abundance of predators, and outline their proposed role in the social systems of terrestrial arthropods. Finally, I map distributions of a social trait against several climatic factors in five case studies to demonstrate how future comparative studies could inform empirical research.

A framework for assessing the scale of influence of environmental factors on ecological patterns

The distribution of living organisms, habitats and ecosystems is primarily driven by abiotic environmental factors that are spatially structured. Assessing the spatial structure of environmental factors, e.g., through spatial autocorrelation analyses (SAC), can thus help us understand their scale of influence on the distribution of organisms, habitats, and ecosystems. Yet SAC analyses of environmental factors are still rarely performed in biogeographic studies. Here, we describe a novel framework that combines SAC and statistical clustering to identify scales of spatial patterning of environmental factors, which can then be interpreted as the scales at which those factors influence the geographic distribution of biological and ecological features. We illustrate this new framework with datasets at different spatial or thematic resolutions. This framework is conceptually and statistically robust, providing a valuable approach to tackle a wide range of issues in ecological and environmental research and particularly when building predictors for ecological models. The new framework can significantly promote fundamental research on all spatially-structured ecological patterns. It can also foster research and application in such fields as global change ecology, conservation planning, and landscape management.

Patterns of Subject Mix in Higher Education Institutions : A First Empirical Analysis Using the AQUAMETH Database

Teaching and research are organised differently between subject domains: attempts to construct typologies of higher education institutions, however, often do not include quantitative indicators concerning subject mix which would allow systematic comparisons of large numbers of higher education institutions among different countries, as the availability of data for such indicators is limited. In this paper, we present an exploratory approach for the construction of such indicators. The database constructed in the AQUAMETH project, which includes also data disaggregated at the disciplinary level, is explored with the aim of understanding patterns of subject mix. For six European countries, an exploratory and descriptive analysis of staff composition divided in four large domains (medical sciences, engineering and technology, natural sciences and social sciences and humanities) is performed, which leads to a classification distinguishing between specialist and generalist institutions. Among the latter, a further distinction is made based on the presence or absence of a medical department. Preliminary exploration of this classification and its comparison with other indicators show the influence of long term dynamics on the subject mix of individual higher education institutions, but also underline disciplinary differences, for example regarding student to staff ratios, as well as national patterns, for example regarding the number of PhD degrees per 100 undergraduate students. Despite its many limitations, this exploratory approach allows defining a classification of higher education institutions that accounts for a large share of differences between the analysed higher education institutions.

Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking approaches

Aim This study compares the direct, macroecological approach (MEM) for modelling species richness (SR) with the more recent approach of stacking predictions from individual species distributions (S-SDM). We implemented both approaches on the same dataset and discuss their respective theoretical assumptions, strengths and drawbacks. We also tested how both approaches performed in reproducing observed patterns of SR along an elevational gradient.Location Two study areas in the Alps of Switzerland.Methods We implemented MEM by relating the species counts to environmental predictors with statistical models, assuming a Poisson distribution. S-SDM was implemented by modelling each species distribution individually and then stacking the obtained prediction maps in three different ways - summing binary predictions, summing random draws of binomial trials and summing predicted probabilities - to obtain a final species count.Results The direct MEM approach yields nearly unbiased predictions centred around the observed mean values, but with a lower correlation between predictions and observations, than that achieved by the S-SDM approaches. This method also cannot provide any information on species identity and, thus, community composition. It does, however, accurately reproduce the hump-shaped pattern of SR observed along the elevational gradient. The S-SDM approach summing binary maps can predict individual species and thus communities, but tends to overpredict SR. The two other S-SDM approaches the summed binomial trials based on predicted probabilities and summed predicted probabilities - do not overpredict richness, but they predict many competing end points of assembly or they lose the individual species predictions, respectively. Furthermore, all S-SDM approaches fail to appropriately reproduce the observed hump-shaped patterns of SR along the elevational gradient.Main conclusions Macroecological approach and S-SDM have complementary strengths. We suggest that both could be used in combination to obtain better SR predictions by following the suggestion of constraining S-SDM by MEM predictions.

Predicting spatial patterns of plant biodiversity : from species to communities

Understanding the distribution and composition of species assemblages and being able to predict them in space and time are highly important tasks io investigate the fate of biodiversity in the current global changes context. Species distribution models are tools that have proven useful to predict the potential distribution of species by relating their occurrences to environmental variables. Species assemblages can then be predicted by combining the prediction of individual species models. In the first part of my thesis, I tested the importance of new environmental predictors to improve species distribution prediction. I showed that edaphic variables, above all soil pH and nitrogen content could be important in species distribution models. In a second chapter, I tested the influence of different resolution of predictors on the predictive ability of species distribution models. I showed that fine resolution predictors could ameliorate the models for some species by giving a better estimation of the micro-topographic condition that species tolerate, but that fine resolution predictors for climatic factors still need to be ameliorated. The second goal of my thesis was to test the ability of empirical models to predict species assemblages' characteristics such as species richness or functional attributes. I showed that species richness could be modelled efficiently and that the resulting prediction gave a more realistic estimate of the number of species than when obtaining it by stacking outputs of single species distribution models. Regarding the prediction of functional characteristics (plant height, leaf surface, seed mass) of plant assemblages, mean and extreme values of functional traits were better predictable than indices reflecting the diversity of traits in the community. This approach proved interesting to understand which environmental conditions influence particular aspects of the vegetation functioning. It could also be useful to predict climate change impacts on the vegetation. In the last part of my thesis, I studied the capacity of stacked species distribution models to predict the plant assemblages. I showed that this method tended to over-predict the number of species and that the composition of the community was not predicted exactly either. Finally, I combined the results of macro- ecological models obtained in the preceding chapters with stacked species distribution models and showed that this approach reduced significantly the number of species predicted and that the prediction of the composition is also ameliorated in some cases. These results showed that this method is promising. It needs now to be tested on further data sets. - Comprendre la manière dont les plantes se répartissent dans l'environnement et s'organisent en communauté est une question primordiale dans le contexte actuel de changements globaux. Cette connaissance peut nous aider à sauvegarder la diversité des espèces et les écosystèmes. Des méthodes statistiques nous permettent de prédire la distribution des espèces de plantes dans l'espace géographique et dans le temps. Ces modèles de distribution d'espèces, relient les occurrences d'une espèce avec des variables environnementales pour décrire sa distribution potentielle. Cette méthode a fait ses preuves pour ce qui est de la prédiction d'espèces individuelles. Plus récemment plusieurs tentatives de cumul de modèles d'espèces individuelles ont été réalisées afin de prédire la composition des communautés végétales. Le premier objectif de mon travail est d'améliorer les modèles de distribution en testant l'importance de nouvelles variables prédictives. Parmi différentes variables édaphiques, le pH et la teneur en azote du sol se sont avérés des facteurs non négligeables pour prédire la distribution des plantes. Je démontre aussi dans un second chapitre que les prédicteurs environnementaux à fine résolution permettent de refléter les conditions micro-topographiques subies par les plantes mais qu'ils doivent encore être améliorés avant de pouvoir être employés de manière efficace dans les modèles. Le deuxième objectif de ce travail consistait à étudier le développement de modèles prédictifs pour des attributs des communautés végétales tels que, par exemple, la richesse en espèces rencontrée à chaque point. Je démontre qu'il est possible de prédire par ce biais des valeurs de richesse spécifiques plus réalistes qu'en sommant les prédictions obtenues précédemment pour des espèces individuelles. J'ai également prédit dans l'espace et dans le temps des caractéristiques de la végétation telles que sa hauteur moyenne, minimale et maximale. Cette approche peut être utile pour comprendre quels facteurs environnementaux promeuvent différents types de végétation ainsi que pour évaluer les changements à attendre au niveau de la végétation dans le futur sous différents régimes de changements climatiques. Dans une troisième partie de ma thèse, j'ai exploré la possibilité de prédire les assemblages de plantes premièrement en cumulant les prédictions obtenues à partir de modèles individuels pour chaque espèce. Cette méthode a le défaut de prédire trop d'espèces par rapport à ce qui est observé en réalité. J'ai finalement employé le modèle de richesse en espèce développé précédemment pour contraindre les résultats du modèle d'assemblage de plantes. Cela a permis l'amélioration des modèles en réduisant la sur-prédiction et en améliorant la prédiction de la composition en espèces. Cette méthode semble prometteuse mais de nouveaux tests sont nécessaires pour bien évaluer ses capacités.

Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta.

Males in many animal species differ greatly from females in morphology, physiology and behaviour. Ants, bees and wasps have a haplodiploid mechanism of sex determination whereby unfertilized eggs become males while fertilized eggs become females. However, many species also have a low frequency of diploid males, which are thought to develop from diploid eggs when individuals are homozygous at one or more sex determination loci. Diploid males are morphologically similar to haploids, though often larger and typically sterile. To determine how ploidy level and sex-locus genotype affect gene expression during development, we compared expression patterns between diploid males, haploid males and females (queens) at three developmental timepoints in Solenopsis invicta. In pupae, gene expression profiles of diploid males were very different from those of haploid males but nearly identical to those of queens. An unexpected shift in expression patterns emerged soon after adult eclosion, with diploid male patterns diverging from those of queens to resemble those of haploid males, a pattern retained in older adults. The finding that ploidy level effects on early gene expression override sex effects (including genes implicated in sperm production and pheromone production/perception) may explain diploid male sterility and lack of worker discrimination against them during development.

Mammalian genes are transcribed with widely different bursting kinetics.

In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis in mammalian cells. To monitor transcription at high temporal resolution, we established various gene trap cell lines and transgenic cell lines expressing a short-lived luciferase protein from an unstable mRNA, and recorded bioluminescence in real time in single cells. Mathematical modeling identified gene-specific on- and off-switching rates in transcriptional activity and mean numbers of mRNAs produced during the bursts. Transcriptional kinetics were markedly altered by cis-regulatory DNA elements. Our analysis demonstrated that bursting kinetics are highly gene-specific, reflecting refractory periods during which genes stay inactive for a certain time before switching on again.

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a "covarion-like" pattern of correlated changes in evolutionary rates, and switches in conserved residues ("conserved but different"). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than "constant but different," but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.

Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e. g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

Similar patterns of local barn owl adaptation in the Middle East and Europe with respect to melanic coloration

The maintenance of phenotypic variation is a central question in evolutionary biology. A commonly suggested mechanism is that of local adaptation, whereby different phenotypes are adapted to alternative environmental conditions. A recent study in the European barn owl (Tyto alba) has shown that natural selection maintains a strong clinal variation in reddish pheomelanin-based coloration. Studies in the region where phenotypic variation in this owl is the highest in Europe have further demonstrated that dark-reddish and pale-reddish owls exploit open and wooded habitats, predate voles and wood mice, and are long-tailed and short-tailed, respectively. However, it remains unclear as to whether these traits evolved as a consequence of allopatric evolution of dark colour in northern Europe and white colour in southern Europe, during which owls could have also evolved different morphologies and foraging behaviour. This scenario implies that covariation between coloration and foraging behaviour could be a specificity of the European continent, which is not found in other worldwide-distributed populations. To investigate this issue we studied a barn owl population in the Middle East. Our results show that, as in Central Europe, dark-reddish female owls breed more often in the open landscape than their pale-reddish female conspecifics, their offspring are fed with more voles than Muridae, and they are longer-winged and longer-tailed. These findings indicate that in the barn owl the association in females between pheomelanin-based coloration and foraging behaviour and morphology is not restricted to the European continent but may well evolve in sympatry in many barn owl populations worldwide.

Splenic hypereosinophilia in anaphylaxis-related death: different assessments depending on different types of allergens?

The aim of this study was to evaluate splenic eosinophil and mast cell accumulation using pagoda red stain in a series of anaphylaxis-related deaths that underwent medico-legal investigations. Our goal was to assess whether fatal reactions to insect stings, intramuscularly administered antibiotics and intravenously injected contrast media are responsible for specific patterns of eosinophil and mast cell accumulation. Two study groups were prospectively formed, an anaphylaxis-related death group and a control group. Autopsy, histology (haematoxylin-eosin stain, pagoda red stain and immunohistochemistry using anti-tryptase antibodies), toxicology and postmortem biochemistry (beta-tryptase, total IgE and specific IgE) were performed in all cases. All tested parameters (spleen weight, beta-tryptase and total IgE levels as well as eosinophil, mast cell and degranulated mast cell numbers in the spleen) were significantly higher in the anaphylaxis-related death group. No statistically significant differences were observed among the various groups (intramuscular antibiotic injection, intravenous contrast medium administration and stinging insects) in any combination, suggesting that mast cell and eosinophil accumulation in the spleen during anaphylaxis does not have any specific pattern related to the triggering allergen. Despite a lower sensitivity than immunohistochemical staining in discriminating eosinophil and mast cells, pagoda red stain allowed these cells to be identified and could therefore be proposed as a low-cost, first-line diagnostic procedure in those situations where immunohistochemistry is not systematically performed or cannot be carried out.

The polymorphic nature of HIV type 1 env V4 affects the patterns of potential N-glycosylation sites in proviral DNA at the intrahost level.

We have previously shown that env V4 from HIV-1 plasma RNA is highly heterogeneous within a single patient, due to indel-associated polymorphism. In this study, we have analyzed the variability of V4 in proviral DNA from unfractionated PBMC and sorted T and non-T cell populations within individual patients. Our data show that the degree of sequence variability and length polymorphism in V4 from HIV provirus is even higher than we previously reported in plasma. The data also show that the sequence of V4 depends largely on the experimental approach chosen. We could observe no clear trend for compartmentalization of V4 variants in specific cell types. Of interest is the fact that some variants that had been found to be predominant in plasma were not detected in any of the cell subsets analyzed. Consistently with our observations in plasma, V3 was found to be relatively conserved at both interpatient and intrapatient level. Our data show that V4 polymorphism involving insertions and deletions in addition to point mutations results in changes in the patterns of sequons in HIV-1 proviral DNA as well as in plasma RNA. These rearrangements may result in the coexistence, within the same individual, of a swarm of different V4 regions, each characterized by a different carbohydrate surface shield. Further studies are needed to investigate the mechanism responsible for the variability observed in V4 and its role in HIV pathogenesis.

Inflammatory responses in aggregating rat brain cell cultures subjected to different demyelinating conditions.

To study inflammatory reactions occurring in relation to demyelination, aggregating rat brain cell cultures were subjected to three different demyelinating insults, i.e., (i) lysophosphatidylcholine (LPC), (ii) interferon-gamma combined with lipopolysaccharide (IFN-gamma+LPS), and (iii) anti-MOG antibodies plus complement (alpha-MOG+C). Demyelination was assessed by measuring the expression of myelin basic protein (MBP) and myelin oligodendrocyte glycoprotein (MOG), and the activity of 2',3'-cyclic nucleotide 3'-phosphohydrolase (CNP). The accompanying inflammatory reactions were examined by the quantification of microglia-specific staining, by immunostaining for glial fibrillary acidic protein (GFAP), and by measuring the mRNA expression of a panel of inflammation-related genes. It was found that all three demyelinating insults decreased the expression of MBP and MOG, and induced microglial reactivity. LPC and alpha-MOG+C, but not IFN-gamma+LPS, decreased CNP activity; they also caused the appearance of macrophagic microglia, and increased GFAP staining indicating astrogliosis. LPC affected also the integrity of neurons and astrocytes. LPC and IFN-gamma+LPS upregulated the expression of the inflammation-related genes IL-6, TNF-alpha, Ccl5, Cxcl1, and iNOS, although to different degrees. Other inflammatory markers were upregulated by only one of the three insults, e.g., Cxcl2 by LPC; IL-1beta and IL-15 by IFN-gamma+LPS; and IFN-gamma by alpha-MOG+C. These findings indicate that each of the three demyelinating insults caused distinct patterns of demyelination and inflammatory reactivity, and that of the demyelinating agents tested only LPC exhibited general toxicity.

Lipoprotein lipase and leptin are accumulated in different secretory compartments in rat adipocytes.

Adipose cells produce and secrete several physiologically important proteins, such as lipoprotein lipase (LPL), leptin, adipsin, Acrp30, etc. However, secretory pathways in adipocytes have not been characterized, and vesicular carriers responsible for the accumulation and transport of secreted proteins have not been identified. We have compared the intracellular localization of two proteins secreted from adipose cells: leptin and LPL. Adipocytes accumulate large amounts of both proteins, suggesting that neither of them is targeted to the constitutive secretory pathway. By means of velocity centrifugation in sucrose gradients, equilibrium density centrifugation in iodixanol gradients, and immunofluorescence confocal microscopy, we determined that LPL and leptin were localized in different membrane structures. LPL was found mainly in the endoplasmic reticulum with a small pool being present in low density membrane vesicles that may represent a secretory compartment in adipose cells. Virtually all intracellular leptin was localized in these low density secretory vesicles. Insulin-sensitive Glut4 vesicles did not contain either LPL or leptin. Thus, secretion from adipose cells is controlled both at the exit from the endoplasmic reticulum as well as at the level of "downstream" secretory vesicles.

Age-associated modulations of cerebral oscillatory patterns related to attention control.

Visual attention depends on bottom-up sensory activation and top-down attentional guidance. Although aging is known to affect sensory processing, its impact on the top-down control of attention remains a matter of debate. We investigated age-related modulations of brain oscillatory activity during visual attention using a variant of the attention network test (ANT) in 20 young and 28 elderly adults. We examined the EEG oscillatory responses to warning and target signals, and explored the correlates of temporal and spatial orienting as well as conflict resolution at target presentation. Time-frequency analysis was performed between 4 and 30Hz, and the relationship between behavioral and brain oscillatory responses was analyzed. Whereas temporal cueing and conflict had similar reaction time effects in both age groups, spatial cueing was more beneficial to older than younger subjects. In the absence of cue, posterior alpha activation was drastically reduced in older adults, pointing to an age-related decline in anticipatory attention. Following both cues and targets, older adults displayed pronounced motor-related activation in the low beta frequency range at the expense of attention-related posterior alpha activation prominent in younger adults. These findings support the recruitment of alternative motor-related circuits in the elderly, in line with the dedifferentiation hypothesis. Furthermore, older adults showed reduced midparietal alpha inhibition induced by temporal orienting as well as decreased posterior alpha activation associated with both spatial orienting and conflict resolution. Altogether, the results are consistent with an overall reduction of task-related alpha activity in the elderly, and provide functional evidence that younger and older adults engage distinct brain circuits at different oscillatory frequencies during attentional functions.