Constrained variable clustering and the best basis problem in functional data analysis

International audienceFunctional data analysis involves data described by regular functions rather than by a finite number of real valued variables. While some robust data analysis methods can be applied directly to the very high dimensional vectors obtained from a fine grid sampling of functional data, all methods benefit from a prior simplification of the functions that reduces the redundancy induced by the regularity. In this paper we propose to use a clustering approach that targets variables rather than individual to design a piecewise constant representation of a set of functions. The contiguity constraint induced by the functional nature of the variables allows a polynomial complexity algorithm to give the optimal solution

A new Late Agenian (MN2a, Early Miocene) fossil assemblage from Wallenried (Molasse Basin, Canton Fribourg, Switzerland)

Excavations of two fossiliferous layers in the Wallenried sand- and marl pit produced a very diversified vertebrate fauna. New material allows the reassessment of the taxonomic position of the ruminant taxa Andegameryx andegaviensis and endemic Friburgomeryx wallenriedensis. An emended diagnosis for the second species is provided and additional material of large and small mammals, as well as ectothermic vertebrates, is described. The recorded Lagomorpha show interesting morphological deviations from other Central European material, and probably represent a unique transitional assemblage with a co-occurrence of Titanomys, Lagopsis and Prolagus. Rodentia and Eulipotyphla belong to typical and well-known species of the Agenian of the Swiss Molasse Basin. Abundant small mammal teeth have allowed us to pinpoint the biostratigraphic age of Wallenried to late MN2a. The biostratigraphic age conforms to data derived from the charophyte assemblages and confirms the oldest occurrence of venomous snake fangs. The palaeoenvironmental context is quite complex. Sedimentary structures and fauna (fishes, frogs, salamanders, ostracods) are characteristic for a humid, lacustrine environment within a flood plain system

Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape

The onset of ripening involves changes in sugar metabolism, softening, and color development. Most understanding of this process arises from work in climacteric fruits where the control of ripening is predominately by ethylene. However, many fruits such as grape are nonclimacteric, where the onset of ripening results from the integration of multiple hormone signals including sugars and abscisic acid (ABA). In this study, we identified ten orthologous gene families in Vitis vinifera containing components of sugar and ABA-signaling pathways elucidated in model systems, including PP2C protein phosphatases, and WRKY and homeobox transcription factors. Gene expression was characterized in control- and deficit-irrigated, field-grown Cabernet Sauvignon. Sixty-seven orthologous genes were identified, and 38 of these were expressed in berries. Of the genes expressed in berries, 68% were differentially expressed across development and/or in response to water deficit. Orthologs of several families were induced at the onset of ripening, and induced earlier and to higher levels in response to water deficit; patterns of expression that correlate with sugar and ABA accumulation during ripening. Similar to field-grown berries, ripening phenomena were induced in immature berries when cultured with sucrose and ABA, as evidenced by changes in color, softening, and gene expression. Finally, exogenous sucrose and ABA regulated key orthologs in culture, similar to their regulation in the field. This study identifies novel candidates in the control of nonclimacteric fruit ripening and demonstrates that grape orthologs of key sugar and ABA-signaling components are regulated by sugar and ABA in fleshy fruit

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae).

BACKGROUND: Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. RESULTS: Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. CONCLUSIONS: Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups supports a previously proposed headwater origin hypothesis for aquatic insects

A comprehensive review on the colorless carotenoids phytoene and phytofluene

Carotenoids and their derivatives are versatile isoprenoids involved in many varied actions, hence their importance in the agri-food industry, nutrition, health and other fields. All carotenoids are derived from the colorless carotenes phytoene and phytofluene, which are oddities among carotenoids due to their distinct chemical structure. They occur together with lycopene in tomato and other lycopene-containing foods. Furthermore, they are also present in frequently consumed products like oranges and carrots, among others. The intake of phytoene plus phytofluene has been shown to be higher than that of lycopene and other carotenoids in Luxembourg. This is likely to be common in other countries. However, they are not included in food carotenoid databases, hence they have not been linked to health benefits in epidemiological studies. Interestingly, there are evidences in vitro, animal models and humans indicating that they may provide health benefits. In this sense, the study of these colorless carotenes in the context of food science, nutrition and health should be further encouraged. In this work, we review much of the existing knowledge concerning their chemical characteristics, physico-chemical properties, analysis, distribution in foods, bioavailability and likely biological activities

Uma promenade nos trópicos: os barões do café sob as palmeiras-imperiais, entre o Rio de Janeiro e São Paulo

This paper proposes to discuss the transformation of urban landscapes in the Paraíba River Valley as members of the coffee elite emerged in this area and a specific landscape configuration was projected there based on the use of imperial palms (Roystonea oleracea). Chronologically speaking, the paper covers a period from 1808 to 1911; with regard to space, it focuses on the stretch between Rio de Janeiro and São Paulo, with a closer look at the case of the city of Lorena (SP), so as to encompass all the changes that took place in this region from the introduction to the decline of coffee growing as an economic activity. The urban changes during this period were accompanied by the advent and consolidation of landscapes typical of the society of coffee growers: streets lined with palm trees, a token of their close connections with the royal court, a display of their adherence to "Frenchified customs". Such configurations were used to characterize public areas and raise them to the same status as the new buildings that gradually replaced those built in colonial style. The paper is structured around three key moments, namely: the introduction of imperial palms in Rio de Janeiro and their association with the idea of nobility and rank, and consequently with neoclassical architecture, which was brought to the colony by the 1816 French Mission; the dissemination of the use of imperial palms as a landscaping resource typical of public spaces from the royal court to the capital of São Paulo, particularly by the coffee barons during the second period of monarchic rule; and, finally, the hypothesis that the use of imperial palms to embellish public areas in São Paulo may have been introduced by a Lorena citizen associated with the coffee elite, albeit later, when Brazil was already a republic.O presente trabalho propõe-se a discutir a transformação da paisagem urbana das cidades vale-paraibanas, a partir do estabelecimento de uma elite ligada à cultura do café nessa região e do surgimento de uma configuração paisagística específica, apoiada na utilização da palmeira-imperial (Roystonea oleracea). Seu recorte cronológico abrange o período entre 1808 e 1911, enquanto espacialmente seu foco direciona-se para o eixo Rio de Janeiro-São Paulo, com estudo mais aproximado do caso da cidade de Lorena, São Paulo, de modo a cobrir as transformações aí ocorridas desde a chegada do café até o esgotamento dessa cultura. Acompanhando as transformações urbanas do período, surgiram e consolidaram-se exemplos paisagísticos próprios da sociedade do café: ruas arborizadas com renques de palmeiras, a demonstrar a proximidade com a Corte, a sinalizar os novos "modos afrancesados". Utilizaram-se tais configurações com o propósito de qualificar os logradouros públicos, a fim de equipará-los aos novos edifícios que substituíam aqueles da tradição colonial. O texto desenvolve-se em três momentos principais: a introdução da palmeira-imperial no Rio de Janeiro, sua vinculação à idéia de nobreza e classe, e conseqüente aproximação com a arquitetura neoclássica trazida pela Missão Francesa de 1816; a difusão de sua utilização como recurso paisagístico qualificador dos espaços públicos desde a Corte até a capital paulista, principalmente pelo baronato do Segundo Império; e, finalmente, a possibilidade de sua introdução nos espaços públicos paulistanos ter sido viabilizada por um lorenense, vinculado à elite cafeeira, embora já sob a República

Model Plants and Functional Genomic Approaches Applied to the Characterization ofGenes Involved in Floral Scent Biosynthesis

International audienceFlower scents have been subjected to extensive chemical characterization for many years, providing detailed analyses of the complex mixture of volatiles emitted by flowers. However, the past ten years have seen a rapid acceleration of progress in flower scent research, with the characterization of numerous genes involved in scent biosynthesis. This review focuses on the evolution of flower scent research, from the early biochemical to the present genomic approaches, illustrating how the use of different plant models, combined with functional genomic approaches, contributed to the present knowledge in this field

Impact of iron limitation on primary production (dissolved and particulate) and secondary production in cultured Trichodesmium sp.

International audienceDiazotrophic cyanobacteria play an important role in biogeochemical cycles of carbon and nitrogen and, hence, in oceanic productivity in the tropical and subtropical regions of the ocean. Although many studies have examined the impact of iron (Fe) limitation on particulate primary production and dinitrogen (N2) fixation in the colonial cyanobacterium Trichodesmium, none have looked at the impact of Fe limitation on the percentage extracellular release (PER) and secondary production (SP) in Fe-limited cultures of this cyanobacterium. Here, we present the results of a series of culture experiments during which we examined the impact of 3 concentrations of dissolved iron (DFe) on total primary production (TPP = dissolved + particulate primary production, i.e. DPP + PPP), PER and on SP. Under severe Fe limitation (5 nM DFe), biomass, growth rates, TPP and N2 fixation were strongly reduced, while PER increased relative to the rates ob served at the highest Fe concentration. Moreover, reducing Fe concentration induced an increase in the percentage of photosynthetically fixed C used for algal growth, while the percentage of C used to support algal respiration decreased. Reduced Fe concentrations also induced a decrease in SP and in the SP:DPP ratio, indicating that the efficiency of transfer of fixed carbon from autotrophic to heterotrophic processes is reduced. This suggests that Fe, either directly through influencing cellular processes or indirectly through influencing organic matter structure or nitrogen availability, is controlling SP and, thus, microbial carbon utilization. These results suggest that the amount of carbon entering into the microbial loop may be reduced under Fe limitation, thus leading to an accumulation of dissolved organic carbon with potentially important impacts on microbial carbon cycling and, ultimately, on the biological carbon pum