Ensemble-based data assimilation and the localisation problem

The “butterfly effect” is a popularly known paradigm; commonly it is said that when a butterfly flaps its wings in Brazil, it may cause a tornado in Texas. This essentially describes how weather forecasts can be extremely senstive to small changes in the given atmospheric data, or initial conditions, used in computer model simulations. In 1961 Edward Lorenz found, when running a weather model, that small changes in the initial conditions given to the model can, over time, lead to entriely different forecasts (Lorenz, 1963). This discovery highlights one of the major challenges in modern weather forecasting; that is to provide the computer model with the most accurately specified initial conditions possible. A process known as data assimilation seeks to minimize the errors in the given initial conditions and was, in 1911, described by Bjerkness as “the ultimate problem in meteorology” (Bjerkness, 1911).

Viral nucleolar localisation signals determine dynamic trafficking within the nucleolus

Localisation of both viral and cellular proteins to the nucleolus is determined by a variety of factors including nucleolar localisation signals (NoLSs), but how these signals operate is not clearly understood. The nucleolar trafficking of wild type viral proteins and chimeric proteins, which contain altered NoLSs, were compared to investigate the role of NoLSs in dynamic nucleolar trafficking. Three viral proteins from diverse viruses were selected which localised to the nucleolus; the coronavirus infectious bronchitis virus nucleocapsid (N) protein, the herpesvirus saimiri ORF57 protein and the HIV-1 Rev protein. The chimeric proteins were N protein and ORF57 protein which had their own NoLS replaced with those from ORF57 and Rev proteins, respectively. By analysing the sub-cellular localisation and trafficking of these viral proteins and their chimeras within and between nucleoli using confocal microscopy and photo-bleaching we show that NoLSs are responsible for different nucleolar localisations and trafficking rates.

Localisation studies of cell-wall degrading enzymes in soybean

Postembedding immunoelectron microscopy has been used to investigate the diffusibility of an endo-beta-1,4-glucanase and a xylanase from A. niger in soybean. The results showed more specific localisation of the enzymes into the protein and lipid bodies of soybean cells. This was against our hypothesis that suggested that the enzymes should be localised in the cell wall.

Cell motility and SCAR localisation in axenically growing Dictyostelium cells.

Dictyostelium is a popular experimental organism, in particular for studies of actin dynamics, cell motility and chemotaxis. We find that the motility of axenic cells is unexpectedly different from other strains during growth. In particular, vegetative AX3 cells do not show detectable localisation of SCAR and its regulatory complex to actin-rich protrusions such as filopodia and pseudopodia. Similarly, a range of different mutations, in particular knockouts of members of the SCAR complex and Ras proteins, cause different phenotypes during vegetative growth in different parental strains. Development reverses this unusual behaviour; aggregation-competent AX3 cells localise SCAR in the same way as cells of other strains and species. Studies on cell motility using vegetative cells should therefore be interpreted with caution.

Circuitos espaciais de produção da atividade boneleira: o uso dos territórios de Caicó, Serra Negra do Norte e São José do Seridó

Cette étude a été fondée sur la reconaissance, la description et l'analyse du circuit spatial de la production de l activité des fabriques des casquettes dans la région du Seridó Potiguar. L activité des fabriques des casquettes est située dans les villes de Caicó, Serra Negra do Norte e São José do Seridó, qui forment le pôle de fabriques de casquettes, composé de soixante-quatre (64) unités de fabrication, le deuxième plus grand producteur de casquettes au Brésil. Dans la condition de base géographique, l'opérationnalisation du concept de circuits spatiales de la production a été essentielle à la compréhension de l'utilisation du territoire et de l'indivisibilité de l'espace, du fournisseur de matières premières au consommateur final, comprenant les étapes des matières premières, la main-d'oeuvre, le stockage, les transports, le commerce et la consommation dans la période actuelle, dans laquelle les instances de la production, la circulation, la distribution et de la consommation sont spatialement diffus. Sur la base de l'identification et de la localisation de ces étapes et des principaux acteurs impliqués dans la activité des fabriques de casquettes, une configuration de circuit spatial de la production a été élaborée, en s'interprétant l'utilisation des territoires par les instances productives. L'interprétation des étapes de production a identifié que les entreprises liées à l'Association Seridoense des Fabricants de Casquettes agissent plus efficacement sur le territoire que celles nonassociées, alors que toujours elles investissent dans des nouveaux équipements, en augmentant sa puissance technique pour se renforcer avant un marché si compétitif comme celui des casquettes. En examinant la contribution de la fabrication des casquettes à l'utilisation actuelle des territoires de la coupe, nous avons appris que les activités complémentaires et des matières premiéres nécessaires à sa réalisation se trouvent dans leur environnement géographique. Ainsi, la proximité spatiale entre les étapes de la fabrication des casquettes fait entrevoir la matérialité du territoire, conférée dans la coexistence des techniques passées et présentes, et l'ensemble des actions effectuées par un certain nombre de travailleurs sociaux qui collaborent à la création du circuit spatial de la production de l activité des fabriques des casquettes. Cette étude a confirmé que les fabriques des casquettes sont organisées sous la forme de cellules de production, continues ou discontinues, dont les équipements et les machines à coudre industrielles obéissent à la logique d'une production de plus en plus standardisée. Ce circuit spatial de la production contribue à l'utilisation actuelle des territoires de Caicó, Serra Negra do Norte et de São José do Seridó car il amplifie le mouvement du commerce et des relations entre les lieux, à travers la dynamique des flux des personnes, des biens et des produits, en constante circulation, guidées par la division du travail entre les étapes productives

Collenchyma in Panicum maximum (Poaceae): localisation and possible role

This work relates the occurrence and distribution of collenchyma in Panicum maximum Jacq. P. maximum leaves were collected at different phases of development and sampled from both the base of the sheath and from the sheath-leaf blade transition area. For the stems, the study was made by using hand-cut sections of the internodal base. In the leaves, analyses of serial sections showed, at the base and sheath-leaf blade transition area, a sudden change of tissue at vascular bundle. The vascular bundles are surrounded by sclerenchyma, both in the sheath and the leaf blade, as well as by fibrous threads that occur on the adaxial side of the central bundles. However, at the base of the sheath and at the sheath-leaf blade transition area, sclerenchyma was substituted for collenchyma. In the stem, the substitution of sclerenchyma associated with vascular bundles for collenchyma occurs at the base of the internode, in the pulvinus region. The analyses from transmission electron microscopy showed the presence of lamellated cell wall and active protoplast in collenchyma cells.

Annexin 1 localisation in tissue eosinophils as detected by electron microscopy

BACKGROUND: Human and rodent leukocytes express high levels of the glucocorticoid-inducible protein annexin 1 ( ANXA1) ( previously referred to as lipocortin 1). Neutrophils and monocytes have abundant ANXA1 levels.Aim: We have investigated, for the first time, ANXA1 ultrastructural expression in rat eosinophils and compared it with that of extravasated neutrophils. The effect of inflammation ( carrageenin peritonitis) was also monitored.Methods: Electron microscopy was used to define the sub-cellular localisation of ANXA1 in rat eosinophils and neutrophils extravasated in the mesenteric tissue. A pair of antibodies raised against the ANXA1 N-terminus (i.e. able to recognise intact ANXA1, termed LCPS1) or the whole protein ( termed LCS3) was used to perform the ultrastructural analysis.Results: the majority of ANXA1 was localised in the eosinophil cytosol (similar to 60%) and nucleus (30-40%), whereas a small percentage was found on the plasma membrane (< 10%). Within the cytosol, the protein was equally distributed in the matrix and in the granules, including those containing the typical crystalloid. The two anti-ANXA1 antibodies gave similar results, with the exception that LCPS1 gave a lower degree of immunoreactivity in the plasma membrane. Inflammation (i.e. carrageenin injection) produced a modest increase in eosinophil-associated ANXA1 reactivity ( significant only in the cytoplasm compartment). Extravasated neutrophils, used for comparative purposes, displayed a much higher degree of immunoreactivity for the protein.Conclusion: We describe for the first time ANXA1 distribution in rat eosinophil by ultrastructural analysis, and report a different protein mobilisation from extravasated neutrophils, at least in this acute model of peritonitis.

Oligomerisation, localisation and interaction of the sensor histidine kinases DcuS and CitA in Escherichia coli

The two-component system DcuSR of Escherichia coli regulates gene expression of anaerobic fumarate respiration and aerobic C4-dicarboxylate uptake. C4-dicarboxylates and citrate are perceived by the periplasmic domain of the membrane-integral sensor histidine kinase DcuS. The signal is transduced across the membrane by phosphorylation of DcuS and of the response regulator DcuR, resulting in activation of DcuR and transcription of the target genes.rnIn this work, the oligomerisation of full-length DcuS was studied in vivo and in vitro. DcuS was genetically fused to derivatives of the green fluorescent protein (GFP), enabling fluorescence resonance energy transfer (FRET) measurements to detect protein-protein interactions in vivo. FRET measurements were also performed with purified His6-DcuS after labelling with fluorescent dyes and reconstitution into liposomes to study oligomerisation of DcuS in vitro. In vitro and in vivo fluorescence resonance energy transfer showed the presence of oligomeric DcuS in the membrane, which was independent of the presence of effector. Chemical crosslinking experiments allowed clear-cut evaluation of the oligomeric state of DcuS. The results showed that detergent-solubilised His6-DcuS was mainly monomeric and demonstrated the presence of tetrameric DcuS in proteoliposomes and in bacterial membranes.rnThe sensor histidine kinase CitA is part of the two-component system CitAB of E. coli, which is structurally related to DcuSR. CitAB regulates gene expression of citrate fermentation in response to external citrate. The sensor kinases DcuS and CitA were fused with an enhanced variant of the yellow fluorescent protein (YFP) and expressed in E. coli under the control of an arabinose-inducible promoter. The subcellular localisation of DcuS-YFP and CitA-YFP within the cell membrane was studied by means of confocal laser fluorescence microscopy. Both fusion proteins were found to accumulate at the cell poles. The polar accumulation was slightly increased in the presence of the stimulus fumarate or citrate, respectively, but independent of the expression level of the fusion proteins. Cell fractionation demonstrated that polar accumulation was not related to inclusion bodies formation. The degree of polar localisation of DcuS-YFP was similar to that of the well-characterised methyl-accepting chemotaxis proteins (MCPs), but independent of their presence. To enable further investigations on the function of the polar localisation of DcuS under physiological conditions, the sensor kinase was genetically fused to the flavin-based fluorescent protein Bs2 which shows fluorescence under aerobic and anaerobic conditions. The resulting dcuS-bs2 gene fusion was inserted into the chromosome of various E. coli strains.rnFurthermore, a protein-protein interaction between the related sensor histidine kinases DcuS and CitA, regulating common metabolic pathways, was detected via expression studies under anaerobic conditions in the presence of citrate and by in vivo FRET measurements.