A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

Post-print version of the article.

Evolution and challenges of dynamic global vegetation models for some aspects of plant physiology and elevated atmospheric CO2.

Dynamic global vegetation models (DGVMs) simulate surface processes such as the transfer of energy, water, CO2, and momentum between the terrestrial surface and the atmosphere, biogeochemical cycles, carbon assimilation by vegetation, phenology, and land use change in scenarios of varying atmospheric CO2 concentrations. DGVMs increase the complexity and the Earth system representation when they are coupled with atmospheric global circulation models (AGCMs) or climate models. However, plant physiological processes are still a major source of uncertainty in DGVMs. The maximum velocity of carboxylation (Vcmax), for example, has a direct impact over productivity in the models. This parameter is often underestimated or imprecisely defined for the various plant functional types (PFTs) and ecosystems. Vcmax is directly related to photosynthesis acclimation (loss of response to elevated CO2), a widely known phenomenon that usually occurs when plants are subjected to elevated atmospheric CO2 and might affect productivity estimation in DGVMs. Despite this, current models have improved substantially, compared to earlier models which had a rudimentary and very simple representation of vegetation?atmosphere interactions. In this paper, we describe this evolution through generations of models and the main events that contributed to their improvements until the current state-of-the-art class of models. Also, we describe some main challenges for further improvements to DGVMs.

Wheat proteins evolution and environmental triggers of Wheat-related diseases

Cereals, and in particular wheat, have always been recognized as a fundamental food worldwide. In particular, the success of wheat is linked with unique properties of the gluten protein fraction used in bread making process to obtain products that are widely used in traditional and modern diets. The rapid increase in the world population let to a parallel increases in food production, particularly of wheat. Increasing yield potential and selection of cultivars much more resistant to plant disease and to environmental factors could have negatively affected the quality of the grain. Moreover, the “green revolution” was characterized by a widespread use of agricultural chemicals and by industrialization of food production that led to a huge rise in the consumption of refined products. Modern baking practices have shortened bread leavening, increased the use of chemical/yeast leavening agents and there is well-documented scientific evidence of the negative effects of ultra-processed food in human healthy. All this changes profoundly modified the human diet and, as a result, may have affected Gluten-related disease (GRDs) that has arisen in the whole word populations. Gluten-related diseases (GRDs) are multifactorial pathologies in which environmental factors and genetic background contribute to a low-grade chronic inflammation of the gastrointestinal tract. Here, I investigated the potential pro-inflammatory effect of different wheat varieties and whether bread making processing are involved in the onset or worsening of gut inflammation. In vitro, ex vivo and in vivo studies conducted throughout my Phd period have shown a pro-inflammatory effect of wheat especially marked in modern varieties and a higher inflammatory response linked to the use of common raising agent as Saccharomyces Cerevisiae and to the addiction of chemical bakery improver substances.

A contribuição do pensamento de Rousseau na construção da antropologia como disciplina acadêmica no século XIX

Pós-graduação em Ciências Sociais - FFC

Jurassic sedimentary record and tectonic evolution of the northwestern corner of Africa

The history of the opening seaway from the westernmost Tethys to the Central Atlantic is traced by the analysis of the sedimentary facies development in the external Rif basin of Northern Morocco and the geological and seismic data from the Moroccan Atlantic continental margin. In the Rif basin, after the early Sinemurian, sedimentary facies dated by ammonites, foraminifers and brachiopods, indicate a progression of rapid subsidence resulting from extensional tectonic (tilted blocks, escarpment fault breccias, neptunian dykes etc.) from the N and NE to the S and SW. From the Toarcian to the Bajocian, deltas progress from the W and SW into the `'Rides sud-rifaines'' realm. From the late Bathonian to the Oxfordian, deep-sea fans develop in the external Rif. During the same period, deltaic sediments fill in the Middle Atlas basin of Eastern Morocco and progress into the external Rif. The top of the Jurassic is characterised by carbonate deposits. At the northwestern corner of Africa, the subsidence of the sedimentary basins by rifting is initiated in the late Triassic; however, at the Mazagan transect of the Atlantic continental margin, the tectonic pattern characteristic of a passive continental margin appears clearly only in the early Jurassic. At the foot of the Mazagan escarpment, the sedimentary record shows a foundering of the first bloc during early to middle Lias. A thermal uplift phase is indicated by emersion of the African margin shoulder in late Liassic, and thermal relaxation starts in the middle Jurassic. The morphology of this transect, compared with the conjugate side of the American continent is most easily explained by the uniform sense simple shear model.

Silene as a model system in ecology and evolution.

The genus Silene, studied by Darwin, Mendel and other early scientists, is re-emerging as a system for studying interrelated questions in ecology, evolution and developmental biology. These questions include sex chromosome evolution, epigenetic control of sex expression, genomic conflict and speciation. Its well-studied interactions with the pathogen Microbotryum has made Silene a model for the evolution and dynamics of disease in natural systems, and its interactions with herbivores have increased our understanding of multi-trophic ecological processes and the evolution of invasiveness. Molecular tools are now providing new approaches to many of these classical yet unresolved problems, and new progress is being made through combining phylogenetic, genomic and molecular evolutionary studies with ecological and phenotypic data.

Progress in observing and modelling the urban boundary layer

The urban boundary layer (UBL) is the part of the atmosphere in which most of the planet’s population now lives, and is one of the most complex and least understood microclimates. Given potential climate change impacts and the requirement to develop cities sustainably, the need for sound modelling and observational tools becomes pressing. This review paper considers progress made in studies of the UBL in terms of a conceptual framework spanning microscale to mesoscale determinants of UBL structure and evolution. Considerable progress in observing and modelling the urban surface energy balance has been made. The urban roughness sub-layer is an important region requiring attention as assumptions about atmospheric turbulence break down in this layer and it may dominate coupling of the surface to the UBL due to its considerable depth. The upper 90% of the UBL (mixed and residual layers) remains under-researched but new remote sensing methods and high resolution modelling tools now permit rapid progress. Surface heterogeneity dominates from neighbourhood to regional scales and should be more strongly considered in future studies. Specific research priorities include humidity within the UBL, high-rise urban canopies and the development of long-term, spatially extensive measurement networks coupled strongly to model development.

Galaxy distribution and evolution around a sample of 2dF groups

Context. We study galaxy evolution and spatial patterns in the surroundings of a sample of 2dF groups. Aims. Our aim is to find evidence of galaxy evolution and clustering out to 10 times the virial radius of the groups and so redefine their properties according to the spatial patterns in the fields and relate them to galaxy evolution. Methods. Group members and interlopers were redefined after the identification of gaps in the redshift distribution. We then used exploratory spatial statistics based on the the second moment of the Ripley function to probe the anisotropy in the galaxy distribution around the groups. Results. We found an important anticorrelation between anisotropy around groups and the fraction of early-type galaxies in these fields. Our results illustrate how the dynamical state of galaxy groups can be ascertained by the systematic study of their neighborhoods. This is an important achievement, since the correct estimate of the extent to which galaxies are affected by the group environment and follow large-scale filamentary structure is relevant to understanding the process of galaxy clustering and evolution in the Universe.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Distribution and evolution of the Anopheles punctulatus group (Diptera : Culicidae) in Australia and Papua New Guinea

The members of the Anopheles punctulatus group are major vectors of malaria and Bancroftian filariasis in the southwest Pacific region. The group is comprised of 12 cryptic species that require DNA-based tools for species identification. From 1984 to 1998 surveys were carried out in northern Australia, Papua New Guinea and on islands in the southwest Pacific to determine the distribution of the A. punctulatus group. The results of these surveys have now been completed and have generated distribution data from more than 1500 localities through this region. Within this region several climatic and geographical barriers were identified that restricted species distribution and gene flow between geographic populations. This information was further assessed in light of a molecular phylogeny derived from the ssrDNA (18S). Subsequently, hypotheses have been generated on the evolution and distribution of the group so that future field and laboratory studies may be approached more systematically. This study suggested that the ability for widespread dispersal was found to have appeared independently in species that show niche-specific habitat preference (Anopheles farauti s.s. and A. punctulatus) and conversely in species that showed diversity in their larval habitat (Anopheles farauti 2). Adaptation to the monsoonal climate of northern Australia and southwest Papua New Guinea was found to have appeared independently in A. farauti s.s., A. farauti 2 and Anopheles farauti 3. Shared or synapomorphic characters were identified as saltwater tolerance (A. farauti s.s. and Anopheles farauti 7) and elevational affinities above 1500 m (Anopheles farauti 5, Anopheles farauti 6 and A. farauti 2). (C) 2002 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.

Fractional coins and fractional derivatives

This paper discusses the fundamentals of negative probabilities and fractional calculus. The historical evolution and the main mathematical concepts are discussed, and several analogies between the two apparently unrelated topics are established. Based on the new conceptual perspective, some experiments are performed shading new light into possible future progress.

The domestic architecture of Bracara Augusta and its evolution

The excavations carried out under the rescue “Project of Bracara Augusta” have generated significant amounts of data that enabled the reconstruction of Bracara Augusta urban evolution and the characterization of its buildings and blocks. This paper aims to enhance the existing data related with the domestic architecture of the roman town, which was mainly represented by the houses of domus type.

Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model.

The t(8;21) chromosomal translocation activates aberrant expression of the AML1-ETO (AE) fusion protein and is commonly associated with core binding factor acute myeloid leukaemia (CBF AML). Combining a conditional mouse model that closely resembles the slow evolution and the mosaic AE expression pattern of human t(8;21) CBF AML with global transcriptome sequencing, we find that disease progression was characterized by two principal pathogenic mechanisms. Initially, AE expression modified the lineage potential of haematopoietic stem cells (HSCs), resulting in the selective expansion of the myeloid compartment at the expense of normal erythro- and lymphopoiesis. This lineage skewing was followed by a second substantial rewiring of transcriptional networks occurring in the trajectory to manifest leukaemia. We also find that both HSC and lineage-restricted granulocyte macrophage progenitors (GMPs) acquired leukaemic stem cell (LSC) potential being capable of initiating and maintaining the disease. Finally, our data demonstrate that long-term expression of AE induces an indolent myeloproliferative disease (MPD)-like myeloid leukaemia phenotype with complete penetrance and that acute inactivation of AE function is a potential novel therapeutic option.

Conflict resolution and evolution of social structures in insect societies

In colonies of social Hymenoptera (which include all ants, as well as some wasp and bee species), only queens reproduce whereas workers generally perform other tasks. The evolution of worker's reproductive altruism can be explained by kin selection, which states that workers can indirectly transmit copies of their genes by helping the reproduction of relatives. The relatedness between queens and workers may however be low, particularly when there are multiple queens per colony, which limits the transmission of copies of workers genes and increases potential conflicts between colony members. In this thesis, we investigated the link between social structure variations and conflicts, and explored the mechanisms involved in variation of colony queen number in ants. According to kin selection, workers should rear the brood they are most related to. In social Hymenoptera, males are haploid whereas females (workers and queens) are diploid. As a result, workers can be up to three times more related to females than males in some colonies, where they should consequently favour the production of females. In contrast, queens are equally related to daughters and sons in all types of colonies and therefore should favour a balanced sex ratio. In a meta-analysis across all studies of social Hymenoptera, we showed that colony sex ratio is generally largely influenced by workers. Hence, the evolution of social structures where queens and workers are equally related to males and females may contribute to decrease the conflict between the two castes over colony sex ratio. Another conflict between queens and workers can occur over male production. Many species contain workers that still have the ability to lay haploid eggs. In some social structures, workers are on average more related to sons of queens than to sons of other workers. As a result, workers should eliminate worker-laid eggs to favour queen-laid eggs. We showed that in the ant Formica selysi, workers eliminate more worker-laid than queen-laid eggs, independently of colony social structure. These results therefore suggest that worker policing can evolve independently from relatedness, potentially because of costs of worker reproduction at the colony-level. Colony queen number is a key parameter that influences relatedness between group members. Queen body size is generally linked to the success of independent colony foundation by single queens and may influence the number of queens in the new colony. In the ant F. selysi, single-queen colonies produce larger queens than multiple-queen colonies. We showed that this association results from genes or maternal effects transmitted to the eggs. However, we also found that queens produced in colonies of the two social forms did not differ in their general ability to found new colonies independently. Queen body size may also influence queen dispersal ability and constrain small queens to be re-adopted in their original nest after mating at proximity. We tested the acceptance of new queens in another ant species, Formica paralugubris, which has numerous queens per colony. Our results show that workers do not discriminate between nestmate and foreign queens, and more generally accept new queens at a limited rate. To conclude, this thesis shows that mechanisms influencing variation in colony queen number and the influence of these changes on conflict resolution are complex. Data gathered in this thesis therefore constitute a solid background for further research on the evolution and the maintenance of complex organisations in insect societies.