Plant Functional Type (PFT) map over Siberia derived from GlobCover 2005 dataset, link to dataset in NetCDF format

High-latitude ecosystems play an important role in the global carbon cycle and in regulating the climate system and are presently undergoing rapid environmental change. Accurate land cover data sets are required to both document these changes as well as to provide land-surface information for benchmarking and initializing Earth system models. Earth system models also require specific land cover classification systems based on plant functional types (PFTs), rather than species or ecosystems, and so post-processing of existing land cover data is often required. This study compares over Siberia, multiple land cover data sets against one another and with auxiliary data to identify key uncertainties that contribute to variability in PFT classifications that would introduce errors in Earth system modeling. Land cover classification systems from GLC 2000, GlobCover 2005 and 2009, and MODIS collections 5 and 5.1 are first aggregated to a common legend, and then compared to high-resolution land cover classification systems, vegetation continuous fields (MODIS VCFs) and satellite-derived tree heights (to discriminate against sparse, shrub, and forest vegetation). The GlobCover data set, with a lower threshold for tree cover and taller tree heights and a better spatial resolution, tends to have better distributions of tree cover compared to high-resolution data. It has therefore been chosen to build new PFT maps for the ORCHIDEE land surface model at 1 km scale. Compared to the original PFT data set, the new PFT maps based on GlobCover 2005 and an updated cross-walking approach mainly differ in the characterization of forests and degree of tree cover. The partition of grasslands and bare soils now appears more realistic compared with ground truth data. This new vegetation map provides a framework for further development of new PFTs in the ORCHIDEE model like shrubs, lichens and mosses, to represent the water and carbon cycles in northern latitudes better. Updated land cover data sets are critical for improving and maintaining the relevance of Earth system models for assessing climate and human impacts on biogeochemistry and biophysics.

Yersinia enterocolitica induces apoptosis in macrophages by a process requiring functional type III secretion and translocation mechanisms and involving YopP, presumably acting as an effector protein

Yersiniae, causative agents of plague and gastrointestinal diseases, secrete and translocate Yop effector proteins into the cytosol of macrophages, leading to disruption of host defense mechanisms. It is shown in this report that Yersinia enterocolitica induces apoptosis in macrophages and that this effect depends on YopP. Functional secretion and translocation mechanisms are required for YopP to act, strongly suggesting that this protein exerts its effect intracellularly, after translocation into the macrophages. YopP shows a high level of sequence similarity with AvrRxv, an avirulence protein from Xanthomonas campestris, a plant pathogen that induces programmed cell death in plant cells. This indicates possible similarities between the strategies used by pathogenic bacteria to elicit programmed cell death in both plant and animal hosts.

Morphologie évolutive et fonctionnelle des hémichordés

L’embranchement Hemichordata regroupe les classes Enteropneusta et Pterobranchia. Hemichordata constitue, avec l’embranchement Echinodermata, le groupe-frère des chordés. Les entéropneustes sont des organismes vermiformes solitaires qui vivent sous ou à la surface du substrat et s’alimentent généralement par déposivorie, alors que les ptérobranches sont des organismes coloniaux filtreurs habitant dans un réseau de tubes appelé coenecium. Ce mémoire présente trois études dont le point commun est l’utilisation des hémichordés actuels pour répondre à des questions concernant l’évolution des hémichordés, des chordés, et du super-embranchement qui les regroupe, Deuterostomia. Notre première étude démontre que les fentes pharyngiennes, l’organe pré-oral cilié (POCO) et le pharynx de l’entéropneuste Protoglossus graveolens sont utilisés pour l’alimentation par filtration. Le système de filtration de P. graveolens permet la capture de particules jusqu’à 1.3 um, à un débit de 4.05 mm.s-1, pour une demande énergétique de 0.009 uW. Les similarités structurales et fonctionnelles avec le système de filtration des céphalochordés suggèrent que la filtration pharyngienne est ancestrale aux deutérostomes. Lors de notre deuxième étude, nous avons exploré l’hypothèse selon laquelle le POCO des entéropneustes, une structure ciliée pré-buccale au rôle possiblement chémorécepteur, serait homologue au « wheel organ » des céphalochordés et à l’adénohypophyse des vertébrés. Pour cela, nous avons déterminé par immunohistochimie l’expression de Pit-1, un facteur de transcription spécifique à ces deux structures, chez l’entéropneuste Saccoglossus pusillus. Pit-1 est exprimé dans des cellules sensorielles du POCO, mais aussi dans des cellules épithéliales distribuées dans le proboscis, collet et tronc. Ce patron d’expression ne permet pas de confirmer ou rejeter l’homologie du POCO et de l’adénohypophyse des vertébrés. Lors de notre troisième étude, nous avons caractérisé l’ultrastructure du coenecium des ptérobranches Cephalodiscus hodgsoni, Cephalodiscus nigrescens et Cephalodiscus densus par microscopie électronique à transmisison et à balayage. Cephalodiscus est le groupe frère de Graptolithina, un groupe qui inclut les graptolithes éteints ainsi que les ptérobranches du genre Rhabdopleura. Nous avons décrit les types de fibrilles de collagène présents, leur taille et leur organisation, ainsi que l’organisation globale du coenecium. Nous avons ainsi démontré la présence chez Cephalodiscus d’une organisation similaire au paracortex, pseudocortex et eucortex des graptolithes. La présence chez Cephalodiscus de ce type d’organisation suggère que le cortex est ancestral à la classe Pterobranchia. Ces trois études illustrent plusieurs axes importants de la recherche sur les hémichordés, qui en intégrant des données morphologiques, fonctionnelles et moléculaires permet de reconstruire certains évènements clés de l’évolution des deutérostomes.

Periostin as a modulator of chronic cardiac remodeling after myocardial infarction

OBJECTIVE: After acute myocardial infarction, during the cardiac repair phase, periostin is released into the infarct and activates signaling pathways that are essential for the reparative process. However, the role of periostin in chronic cardiac remodeling after myocardial infarction remains to be elucidated. Therefore, the objective of this study was to investigate the relationship between tissue periostin and cardiac variables in the chronic cardiac remodeling induced by myocardial infarction. METHODS: Male Wistar rats were assigned to 2 groups: a simulated surgery group (SHAM; n = 8) and a myocardial infarction group (myocardial infarction; n = 13). After 3 months, morphological, functional and biochemical analyses were performed. The data are expressed as means±SD or medians (including the lower and upper quartiles). RESULTS: Myocardial infarctions induced increased left ventricular diastolic and systolic areas associated with a decreased fractional area change and a posterior wall shortening velocity. With regard to the extracellular matrix variables, the myocardial infarction group presented with higher values of periostin and types I and III collagen and higher interstitial collagen volume fractions and myocardial hydroxyproline concentrations. In addition, periostin was positively correlated with type III collagen levels (r = 0.673, p = 0.029) and diastolic (r = 0.678, p = 0.036) and systolic (r = 0.795, p = 0.006) left ventricular areas. Considering the relationship between periostin and the cardiac function variables, periostin was inversely correlated with both the fractional area change (r = -0.783, p = 0.008) and the posterior wall shortening velocity (r = -0.767, p = 0.012). CONCLUSIONS: Periostin might be a modulator of deleterious cardiac remodeling in the chronic phase after myocardial infarction in rats.

AopP, a type III effector protein of Aeromonas salmonicida, inhibits the NF-kappaB signalling pathway

Aeromonas salmonicida subsp. salmonicida contains a functional type III secretion system that is responsible for the secretion of the ADP-ribosylating toxin AexT. In this study, the authors identified AopP as a second effector protein secreted by this system. The aopP gene was detected in both typical and atypical A. salmonicida isolates and was found to be encoded on a small plasmid of approximately 6.4 kb. Sequence analysis indicates that AopP is a member of the YopJ family of effector proteins, a group of proteins that interfere with mitogen-activated protein kinase (MAPK) and/or nuclear factor kappa B (NF-kappaB) signalling pathways. AopP inhibits the NF-kappaB pathway downstream of IkappaB kinase (IKK) activation, while a catalytically inactivated mutant, AopPC177A, does not possess this inhibitory effect. Unlike other effectors of the YopJ family, such as YopJ and VopA, AopP does not inhibit the MAPK signalling pathway.

Global distributions of epipelagic macrozooplankton abundance and biomass - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

Macrozooplankton are an important link between higher and lower trophic levels in the oceans. They serve as the primary food for fish, reptiles, birds and mammals in some regions, and play a role in the export of carbon from the surface to the intermediate and deep ocean. Little, however, is known of their global distribution and biomass. Here we compiled a dataset of macrozooplankton abundance and biomass observations for the global ocean from a collection of four datasets. We harmonise the data to common units, calculate additional carbon biomass where possible, and bin the dataset in a global 1 x 1 degree grid. This dataset is part of a wider effort to provide a global picture of carbon biomass data for key plankton functional types, in particular to support the development of marine ecosystem models. Over 387 700 abundance data and 1330 carbon biomass data have been collected from pre-existing datasets. A further 34 938 abundance data were converted to carbon biomass data using species-specific length frequencies or using species-specific abundance to carbon biomass data. Depth-integrated values are used to calculate known epipelagic macrozooplankton biomass concentrations and global biomass. Global macrozooplankton biomass has a mean of 8.4 µg C l-1, median of 0.15 µg C l-1 and a standard deviation of 63.46 µg C l-1. The global annual average estimate of epipelagic macrozooplankton, based on the median value, is 0.02 Pg C. Biomass is highest in the tropics, decreasing in the sub-tropics and increasing slightly towards the poles. There are, however, limitations on the dataset; abundance observations have good coverage except in the South Pacific mid latitudes, but biomass observation coverage is only good at high latitudes. Biomass is restricted to data that is originally given in carbon or to data that can be converted from abundance to carbon. Carbon conversions from abundance are restricted in the most part by the lack of information on the size of the organism and/or the absence of taxonomic information. Distribution patterns of global macrozooplankton biomass and statistical information about biomass concentrations may be used to validate biogeochemical models and Plankton Functional Type models.

Global distributions of Phaeocystis sp. abundance and biomass - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The planktonic haptophyte Phaeocystis has been suggested to play a fundamental role in the global biogeochemical cycling of carbon and sulphur, but little is known about its global biomass distribution. We have collected global microscopy data of the genus Phaeocystis and converted abundance data to carbon biomass using species-specific carbon conversion factors. Microscopic counts of single-celled and colonial Phaeocystis were obtained both through the mining of online databases and by accepting direct submissions (both published and unpublished) from Phaeocystis specialists. We recorded abundance data from a total of 1595 depth-resolved stations sampled between 1955-2009. The quality-controlled dataset includes 5057 counts of individual Phaeocystis cells resolved to species level and information regarding life-stages from 3526 samples. 83% of stations were located in the Northern Hemisphere while 17% were located in the Southern Hemisphere. Most data were located in the latitude range of 50-70° N. While the seasonal distribution of Northern Hemisphere data was well-balanced, Southern Hemisphere data was biased towards summer months. Mean species- and form-specific cell diameters were determined from previously published studies. Cell diameters were used to calculate the cellular biovolume of Phaeocystis cells, assuming spherical geometry. Cell biomass was calculated using a carbon conversion factor for Prymnesiophytes (Menden-Deuer and Lessard, 2000). For colonies, the number of cells per colony was derived from the colony volume. Cell numbers were then converted to carbon concentrations. An estimation of colonial mucus carbon was included a posteriori, assuming a mean colony size for each species. Carbon content per cell ranged from 9 pg (single-celled Phaeocystis antarctica) to 29 pg (colonial Phaeocystis globosa). Non-zero Phaeocystis cell biomasses (without mucus carbon) range from 2.9 - 10?5 µg l-1 to 5.4 - 103 µg l-1, with a mean of 45.7 µg l-1 and a median of 3.0 µg l-1. Highest biomasses occur in the Southern Ocean below 70° S (up to 783.9 µg l-1), and in the North Atlantic around 50° N (up to 5.4 - 103 µg l-1).

Seed rain in areas with and without bamboo dominance within an urban fragment of the Atlantic Forest

Understanding the flow of diaspores is fundamental for determining plant population dynamics in a particular habitat, and a lack of seeds is a limiting factor in forest regeneration, especially in isolated forest fragments. Bamboo dominance affects forest structure and dynamics by suppressing or delaying the recruitment of and colonization by tree species as well as by inhibiting the survival and growth of adult trees. The goal of the present study was to determine whether dominance of the bamboo species Aulonemia aristulata (Döll) McClure in the forest understory influences species abundance and composition. We examined the seed rain at two noncontiguous sites (1.5 km apart) within an urban forest fragment, with and without bamboo dominance (BD+ and BD- areas, respectively). Sixty seed traps (0.5 m², with a 1-mm mesh) were set in the BD+ and BD- areas, and the seed rain was sampled from January to December 2007. Diaspores were classified according to dispersal syndrome, growth form and functional type of the species to which they belonged. There were significant differences between the two areas in terms of seed density, species diversity and dispersal syndrome. The BD+ area showed greater seed density and species diversity. In both areas, seed distribution was limited primarily by impaired dispersal. Bamboo dominance and low tree density resulted in fewer propagules in the seed rain. Our results suggest that low availability of seeds in the rain does not promote the maintenance of a degraded state, characterized by the presence of bamboo.

Effects of Mg2+ on Ca2+ release from sarcoplasmic reticulum of skeletal muscle fibres from yabby (crustacean) and rat

1. The role of myoplasmic [Mg2+] on Ca2+ release from the sarcoplasmic reticulum (SR) was examined in the two major types of crustacean muscle fibres, the tonic, long sarcomere fibres and the phasic, short sarcomere fibres of the fresh mater decapod crustacean Cherax: destructor (yabby) and in the fast-twitch rat muscle fibres using the mechanically skinned muscle fibre preparation. 2. A robust Ca2+-induced Ca2+-release (CICR) mechanism was present in both long and short sarcomere fibres and 1 mM Mg2+ exerted a strong inhibitory action on the XR Ca2+ release in both fibre types. 3. The XR displayed different properties with respect to Ca2+ loading in the long and the short sarcomere fibres and marked functional differences were identified with respect to Mg2+ inhibition between the two crustacean fibre types. Thus, in long sarcomere fibres, the submaximally loaded XR was able to release Ca2+ when [Mg2+] was lowered from 1 to 0.01 mw in the presence of 8 mM ATP(total) and in the virtual absence of Ca2+ (< 5 nM) even when the CICR was suppressed. In contrast, negligible Ca2+ was released from the submaximally loaded SR of short sarcomere yabby fibres when [Mg2+] was lowered from 1. to 0.01 mM under the same conditions as for the long sarcomere fibres. Nevertheless, the rate of XR Ca2+ release in short sarcomere fibres increased markedly when [Mg2+] was lowered in the presence of [Ca2+] approaching the normal resting levels (50-100 nM). 4. Rat fibres were able to release SR Ca2+ at a faster rate than the long sarcomere yabby fibres when [Mg2+] was lowered from 1 to 0.01 mM in the virtual absence of Ca2+ but, unlike with yabby fibres, the net rate of Ca2+ release was actually increased for conditions that were considerably less favourable to CICR. 5. In summary it is concluded that crustacean skeletal muscles have more that one functional type of Ca2+-release channels, that these channels display properties that are intermediate between those of mammalian skeletal and cardiac isoforms, that the inhibition exerted by Mg2+ at rest on the crustacean SR Ca2+-release channels must be removed during excitation-contraction coupling and that, unlike in crustacean fibres, CICR cannot play the major role in the activation of XR Ca2+-release channels in the rat skeletal muscle.

A influência da idade nos parâmetros metabólicos durante a marcha com andarilho

Introdução: Estruturalmente, a marcha é modificada de acordo com as características de cada individuo, sua natureza morfológica, tipo de atividade, idade e a presença de determinadas doenças, entre outros fatores. Devidas as alterações fisiológicas de envelhecimento, o custo energético da marcha normal por si só é superior nos idosos comparativamente com os jovens. Objetivo: Analisar a influência do uso de andarilho com rodas e fixo nos parâmetros metabólicos de indivíduos com mais de 60 anos e em jovens. Metodologia: realizou-se um estudo analítico transversal numa amostra de 21 voluntários, sendo 11adultos jovens (idade compreendida entre 18 e 25 anos) e 10 são adultos com idade superior a 60 anos. Utilizou-se o sistema K4b2 COSMED de forma a recolher os dados relativos ao consumo energético, quociente respiratório e volume de CO2 produzido. Os participantes realizaram os diferentes tipos de marcha (marcha normal, a três pontos com andarilho fixo, a três pontos modificada com andarilho fixo, a três pontos com andarilho com rodas e a três pontos modificada com andarilho com rodas) durante 10 minutos num percurso rectilíneo de 20 metros. Para a análise estatística recorreu-se ao software IBM SPSS Statistics v20 com um nível de significância de 0,05. Resultados: observou-se que á exceção da marcha normal em todos os outros tipos de marcha com andarilho, os participantes com mais de 60 anos, apresentam valores significativamente superiores aos dos jovens, nomeadamente nas marchas com andarilho fixo, a 3 pontos e a 3 pontos modificada e com andarilho de rodas, na marcha a 3ponto modificada. Verificaram-se diferenças apenas no grupo dos jovens, pois a marcha normal apresentou valores significativamente maiores que as restantes. Conclusão: A idade influenciou os parâmetros metabólicos da marcha normal e com andarilhos fixo e móvel apresentando os idosos um maior gasto energético, bem como os METS utilizados.

Local Distance-Based Generalized Linear Models using the dbstats package for R

This paper introduces local distance-based generalized linear models. These models extend (weighted) distance-based linear models firstly with the generalized linear model concept, then by localizing. Distances between individuals are the only predictor information needed to fit these models. Therefore they are applicable to mixed (qualitative and quantitative) explanatory variables or when the regressor is of functional type. Models can be fitted and analysed with the R package dbstats, which implements several distancebased prediction methods.