Leishmania major: differential regulation of the surface metalloprotease in amastigote and promastigote stages.

During its life cycle, the protozoan parasite Leishmania major alternates from an intracellular amastigote form in the mammalian host to a flagellated promastigote form in the insect vector. The expression of the surface metalloprotease (PSP) during differentiation in vitro was investigated by Western and Northern blots, by immunoprecipitation of cells metabolically labeled with [35S]methionine or labeled at the surface with radioactive iodine, and by quantification of the proteolytic activity in substrate-containing polyacrylamide gels. We report that the surface metalloprotease is down-regulated at both the mRNA and the protein level in amastigotes, where it represents less than 1% of the equivalent proteolytic activity detected in promastigotes. A significant amount of mRNA is detected 4 hr after the onset of differentiation. The expression of the protease begins at that time and reaches steady state 8 hr later. The synthesis of PSP precedes the complete morphological differentiation to the promastigote stage and the appearance of the lipophosphoglycan, another major promastigote surface component. In contrast to PSP, a family of mercaptoethanol-activated proteases present in the amastigote exists only at a reduced level in the promastigote. The confinement of the surface metalloprotease to the insect stage of the parasite suggests that it has no physiological function in the parasitism maintenance of mammalian host macrophages.

Mating does not influence reproductive investment, in a viviparous lizard.

Mating is crucial for females that reproduce exclusively sexually and should influence their investment into reproduction. Although reproductive adjustments in response to mate quality have been tested in a wide range of species, the effect of exposure to males and mating per se has seldom been studied. Compensatory mechanisms against the absence of mating may evolve more frequently in viviparous females, which pay higher direct costs of reproduction, due to gestation, than oviparous females. To test the existence of such mechanisms in a viviparous species, we experimentally manipulated the mating opportunity of viviparous female lizard, Lacerta (Zootoca) vivipara. We assessed the effect of mating on ovulation, postpartum body condition and parturition date, as well as on changes in locomotor performances and body temperatures during the breeding cycle. Female lizards ovulated spontaneously and mating had no influence on litter size, locomotor impairment or on selected body temperature. However, offspring production induced a more pronounced locomotor impairment and physical burden than the production of undeveloped eggs. Postpartum body condition and parturition dates were not different among females. This result suggests that gestation length is not determined by an embryonic signal. In the common lizard, viviparity is not associated with facultative ovulation and a control of litter size after ovulation, in response to the absence of mating.

Phyletic trends in uppermost Triassic (Rhaetian) Radiolaria: Two examples from Queen Charlotte Islands, British Columbia, Canada

Risella Carter and Laxtorum Blome, two genera from the diverse Rhaetian fauna of the Sandilands Formation, Queen Charlotte Islands, are used to illustrate phyletic trends in latest Triassic Radiolaria. Several distinct morphotypes constituting a lineage are recognized for each genus. These lineages are homogenous, evolved in situ, and show a continuum of variation through time. The evolution of Risella takes place entirely in the Rhaetian and all species disappear at the end of the Triassic. Earliest species of Laxtorum appear in the upper Norian and evolve rapidly in the Rhaetian. All Rhaetian species go extinct at the end of the Triassic but the genus survives marginally into the Lower Jurassic. Morphological transformations in Risella (a paronaellid) are manifest in the external/cortical shell as the shape changes from triangular to three-rayed. In Laxtorum, distal post abdominal chambers become constricted and eventually develop a terminal tube while, at the same time, an increase in size and sphericity is coupled with a reduction in the number of post abdominal chambers. Evolutionary transitions in the Risella lineage probably represent a reversion of the normal hypothesized trend for paronaellid radiolarians. In the Laxtorum lineage, comparisons with other groups and species displaying similar homeomorphies suggest the evolutionary trends are fundamental and occur repeatedly in faunas of all ages.

Climate and vegetation history of western Portugal inferred from Albian near-shore deposits (Gale Formation, Lusitanian Basin)

The late Early Cretaceous greenhouse climate has been studied intensively based on proxy data derived essentially from open marine archives. In contrast, information on continental climatic conditions and on the accompanying response of vegetation is relatively scarce, most notably owing to the stratigraphic uncertainties associated with many Lower Cretaceous terrestrial deposits. Here, we present a palynological record from Albian near-shore deposits of the Lusitanian Basin of W Portugal, which have been independently dated using Sr-isotope signals derived from low-Mg oyster shell calcite. Sr-87/Sr-86 values fluctuate between 0.707373 +/- 0.00002 and 0.707456 +/- 0.00003; absolute values and the overall stratigraphic trend match well with the global open marine seawater signature during Albian times. Based on the new Sr-isotope data, existing biostratigraphic assignments of the succession are corroborated and partly revised. Spore-pollen data provide information on the vegetation community structure and are flanked by sedimentological and clay mineralogical data used to infer the overall climatic conditions prevailing on the adjacent continent. Variations in the distribution of climate-sensitive pollen and spores indicate distinct changes in moisture availability across the studied succession with a pronounced increase in hygrophilous spores in late Early Albian times. Comparison with time-equivalent palynofloras from the Algarve Basin of southern Portugal shows pronounced differences in the xerophyte/hygrophyte ratio, interpreted to reflect the effect of a broad arid climate belt covering southern and southeastern Iberia during Early Albian times.

A generalization of Cope's rule

For numerous shelly invertebrates, Cope's rule is shown in this paper to merely describe the particular case where volume increase is strictly coupled with diameter or length. Allometries, which are frequently observed in the evolution of the shells' geometry, mean that their size, volume and surface can vary independently. The consequences of this can be summarized as follows : 1) volume increase not coupled with an increase of diameter or length of the organisms generates increasing involution and/or lateral width in the shell of cephalopods, foraminifera and radiolarians; 2) an increase of the biomineralizing surface, not coupled with volume increase, generates increasing apparent complexity in the sutures and growth lines in ammonites, and an increase in the complexity and number of chambers in foraminifera.

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

Exposure to bioaerosols in poultry houses at different stages of fattening; use of real-time PCR for airborne bacterial quantification

Previous studies have demonstrated that poultry house workers are exposed to very high levels of organic dust and consequently have an increased prevalence of adverse respiratory symptoms. However, the influence of the age of broilers on bioaerosol concentrations has not been investigated. To evaluate the evolution of bioaerosol concentration during the fattening period, bioaerosol parameters (inhalable dust, endotoxin and bacteria) were measured in 12 poultry confinement buildings in Switzerland, at three different stages of the birds' growth; samples of air taken from within the breathing zones of individual poultry house employees as they caught the chickens ready to be transported for slaughter were also analysed. Quantitative polymerase chain reaction (Q-PCR) was used to assess the quantity of total airborne bacteria and total airborne Staphylococcus species. Bioaerosol levels increased significantly during the fattening period of the chickens. During the task of catching mature birds, the mean inhalable dust concentration for a worker was 26 +/- 1.9 mg m(-3) and endotoxin concentration was 6198 +/- 2.3 EU m(-3) air, >6-fold higher than the Swiss occupational recommended value (1000 EU m(-3)). The mean exposure level of bird catchers to total bacteria and Staphylococcus species measured by Q-PCR is also very high, respectively, reaching values of 53 (+/-2.6) x 10(7) cells m(-3) air and 62 (+/-1.9) x 10(6) m(-3) air. It was concluded that in the absence of wearing protective breathing apparatus, chicken catchers in Switzerland risk exposure beyond recommended limits for all measured bioaerosol parameters. Moreover, the use of Q-PCR to estimate total and specific numbers of airborne bacteria is a promising tool for evaluating any modifications intended to improve the safety of current working practices

ConnectomeViewer - Multi-Modal Multi-Level Network Visualization and Analysis.

Introduction: The field of Connectomic research is growing rapidly, resulting from methodological advances in structural neuroimaging on many spatial scales. Especially progress in Diffusion MRI data acquisition and processing made available macroscopic structural connectivity maps in vivo through Connectome Mapping Pipelines (Hagmann et al, 2008) into so-called Connectomes (Hagmann 2005, Sporns et al, 2005). They exhibit both spatial and topological information that constrain functional imaging studies and are relevant in their interpretation. The need for a special-purpose software tool for both clinical researchers and neuroscientists to support investigations of such connectome data has grown. Methods: We developed the ConnectomeViewer, a powerful, extensible software tool for visualization and analysis in connectomic research. It uses the novel defined container-like Connectome File Format, specifying networks (GraphML), surfaces (Gifti), volumes (Nifti), track data (TrackVis) and metadata. Usage of Python as programming language allows it to by cross-platform and have access to a multitude of scientific libraries. Results: Using a flexible plugin architecture, it is possible to enhance functionality for specific purposes easily. Following features are already implemented: * Ready usage of libraries, e.g. for complex network analysis (NetworkX) and data plotting (Matplotlib). More brain connectivity measures will be implemented in a future release (Rubinov et al, 2009). * 3D View of networks with node positioning based on corresponding ROI surface patch. Other layouts possible. * Picking functionality to select nodes, select edges, get more node information (ConnectomeWiki), toggle surface representations * Interactive thresholding and modality selection of edge properties using filters * Arbitrary metadata can be stored for networks, thereby allowing e.g. group-based analysis or meta-analysis. * Python Shell for scripting. Application data is exposed and can be modified or used for further post-processing. * Visualization pipelines using filters and modules can be composed with Mayavi (Ramachandran et al, 2008). * Interface to TrackVis to visualize track data. Selected nodes are converted to ROIs for fiber filtering The Connectome Mapping Pipeline (Hagmann et al, 2008) processed 20 healthy subjects into an average Connectome dataset. The Figures show the ConnectomeViewer user interface using this dataset. Connections are shown that occur in all 20 subjects. The dataset is freely available from the homepage (connectomeviewer.org). Conclusions: The ConnectomeViewer is a cross-platform, open-source software tool that provides extensive visualization and analysis capabilities for connectomic research. It has a modular architecture, integrates relevant datatypes and is completely scriptable. Visit www.connectomics.org to get involved as user or developer.

Perinuclear Mlp proteins down-regulate gene expression in response to a defect in mRNA export

Résumé Une caractéristique des cellules eucaryotes est le confinement du matériel génétique (ADN/DNA) dans le noyau. Pour décoder cette information, un ARN messager (mRNA) est d'abord transcrit sous forme d'un ARN prémessager (pré-mRNA). Ce-dernier doit subir plusieurs étapes de maturation pour aboutir à une particule ribonucléoprotéique (mRNP) qui sera exportée vers le cytoplasme et traduite en protéine. La protéine de levure Mex67p et son homologue humain TAP sont des récepteurs d'export médiant la translocation du mRNP au travers des complexes du pore nucléaire (NPC). Mex67p/TAP ne se lient pas directement au mRNA, mais nécessitent la présence de protéines adaptatrices, telles que Yra1p et son homologue humain REF1. Afin d'identifier de nouveaux facteurs impliqués dans l'export des mRNPs ou de nouvelles fonctions pour Yra1p, nous avons effectué un crible génétique avec un mutant thermosensible de Yra1p, GFP-yra 1 -8. Ce mutant présente un défaut d'export des mRNAs et une diminution des niveaux de transcrits du gène rapporteur LacZ ainsi que de certains transcrits endogènes. Nous avons trouvé que la perte de Mlp2p, ou d'une protéine hautement similaire, Mlp1p, restaure la croissance du mutant GFP-yra1-8 à température restrictive. Mlp1p et Mlp2p sont des protéines nucléaires, dont l'homologue humain est TPR. Les Mlp (myosin¬like proteins) ainsi que TPR forment des structures filamenteuses ancrées aux NPC. Bien que la fonction des Mlp ne soit pas clairement définie, un rôle dans la biogenèse et la surveillance des mRNPs a été récemment proposé. Notre étude montre que la perte des Mlp, non seulement restaure la croissance de GFP-yra1-8, mais augmente aussi les niveaux des transcrits LacZ et facilite leur apparition dans le cytoplasme. Des expériences d'immunoprécipitations de la chromatine révèlent que Mlp2p diminue le taux de synthèse du transcrit LacZ dans GFP-yra1-8. Des analyses du transcriptome montrent que Mlp2p réduit aussi les niveaux d'une population de transcrits endogènes dans le mutant. Finalement, des localisations in situ suggèrent que la transcription du rapporteur LacZ a lieu à la périphérie du noyau, à proximité des Mlp. Ainsi, les protéines Mlp pourraient préférentiellement diminuer la transcription de gènes exprimés à la périphérie nucléaire. Nous montrons aussi que Yra1p interagit génétiquement avec Nab2p une protéine liée au mRNA et impliquée dans son export, mais non avec d'autres protéines également impliquées dans l'export des mRNAs. Les résultats obtenus soutiennent un modèle où les protéines Yra1p et Nab2p sont nécessaires à l'arrimage des mRNPs sur la plate-forme des Mlp. Si ces signaux manquent ou sont défectueux, les mRNPs ne peuvent pas poursuivre leur trajet vers le canal central du NPC. Ce bloc induirait par la suite une diminution de la transcription d'une population de gènes potentiellement localisée à la périphérie nucléaire. Dans son ensemble, cette étude suggère que les protéines Mlp établissent un lien entre la transcription de certains mRNAs et leur export au travers du pore nucléaire. Summary A hallmark of the eukaryotic cell is the packaging of DNA in the nucleus. To decode the genetic information, a messenger RNA (mRNA) is first synthesized as a pre-mRNA molecule, which undergoes different maturation steps resulting in an mRNP (messenger RNA ribonucleoprotein), which can be actively transported to the cytoplasm and translated into a protein. Yeast Mex67p and its human homologue TAP are export receptors mediating mRNP translocation through the nuclear pore complex (NPC). The recruitment of Mex67p/TAP to mRNA is mediated by mRNA export adaptors of the evolutionarily conserved REF (RNA and Export Factor binding) family: yeast Yra1p and human REF1. To uncover new functions of Yra1p or new factors implicated in mRNA export, we performed a genetic screen with a themiosensitive (ts) yra1 mutant, GFP-yra1-8. This mutant exhibits mRNA export defects and a decrease in the levels of LacZ reporter and certain endogenous transcripts. We found that the loss of Mlp2p, or the related Mlp1p protein, substantially rescues the growth defect of the GFP-yra1 -8 mutant. Mlp1p and M1p2p are large non-essential proteins, homologous to human TPR, proposed to form intra-nuclear filamentous structures anchored at the NPC. Their role is not clearly defined, but they have been implicated in mRNP biogenesis and surveillance. Our study shows that loss of Mlp proteins not only restores growth of GFP-yra1-8, but also rescues LacZ mRNA levels and increases their appearance in the cytoplasm. Chromatin immunoprecipitation and pulse chase experiments indicate that Mlp2p down-regulates LacZ mRNA synthesis in GFP-yra1-8. DNA micro- array analyses reveal that Mlp2p also reduces the levels of a subset of cellular transcripts in the yra1 mutant strain. In situ localizations suggest that LacZ transcription occurs at the nuclear periphery, in close proximity to Mlp proteins. Thus, Mlp proteins may preferentially down-regulate genes expressed at the nuclear periphery. Finally, we show that Yra1p genetically interacts with the shuttling mRNA-binding protein Nab2p and that loss of Mlp proteins rescues the growth defect of yra1 and nab2, but not other mRNA export mutants. The data support a model in which Nab2p and Yra1p are required for rnRNP docking to the Mlp platform. Lack of these signals prevents mRNPs from crossing the Mlp gate. This block may then negatively feed-back on the transcription of a subset of genes, potentially located at the nuclear envelope. Overall, this study suggests that perinuclear Mlp proteins establish a link between mRNA transcription and export.