Analysis and visualization of H7 influenza using genomic,evolutionary and geographic information in a modular web service

We have reported previously on use of a web‐based application, Supramap ( http://supramap.org ) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug‐resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY ( http://poyws.org ) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes ( http://geogenes.org ). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.     

Interaction of soil moisture and elevated CO2 on the above-ground growth rate, root length density and gas exchange of turves from temperate pasture

Interactions between water availability and elevated atmosphericCO₂ concentrations have the potential to be important factorsin determining future forage supply from temperate pastures.Using large turves from an established pasture, the responseof these communities at 350 or 700 l l^–1 CO₂ to a soilmoisture deficit and to recovery from the deficit in comparisonto turves that were well-watered throughout was measured. Priorto this experiment the turves had been exposed to the CO₂ treatmentsfor 324 d. Net CO₂ exchange continued at elevated CO₂ even when the volumetricsoil moisture content was less than 0.10 m³ m^–3 soil;at the same moisture deficit gas exchange at ambient CO₂ waszero. The additional carbon fixed by the elevated CO₂ turveswas primarily allocated below-ground as shown by the maintenanceof root length density at the same level as in well-wateredturves. When the dry turves were rewatered there was compensatorygrowth at ambient CO₂ so that the above-ground growth rate exceededthat of turves that had not experienced a moisture deficit.At the start of this experiment, the turves that were growingat 700 l I^–1 CO₂ had a greater proportion of legume (principallywhite clover, Trifolium repens L.) in the harvested herbage.There was a trend for the legume content at elevated CO₂ tobe reduced under a soil moisture deficit. The results indicate different strategies in response to soilmoisture deficits depending on the CO₂ concentration. At ambientCO₂, growth stopped, but plants were able to respond stronglyon rewatering; while at elevated CO₂ growth continued (particularlybelow-ground), but no additional growth was evident on rewatering.Ecosystem gas exchange measurements taken at the end of theexperiment (after 429 d of exposure to CO₂) showed 33% moreCO₂ was fixed at elevated CO₂ with only a small (12%) and nonsignificantdownward regulation. Key words: Carbon dioxide, climate change, grassland, gas exchange, soil moisture deficit     

Evidence for the expression of two distinct MHC class II DRβ like molecules in the sheep

This study used monoclonal antibodies to sheep MHC class II molecules as well as an L cell transfectant (T8.1) which expresses DRA and DRB genes to show that two distinct DRβ chains are expressed in the sheep. Two anti-β chain specific monoclonal antibodies VPM37 and VPM43 react with DR antigen but not DQ antigen by ELISA. These two antibodies do not react with the DRβ chain expressed in the T8.1 cell line. Two-dimensional immunoblotting shows that these antibodies recognize a subgroup of the spots recognized by the DR-specific monoclonal antibody VPM57 which does react with the T8.1 β chain. Amino-terminal sequence analysis of the α chain associated with VPM37β chain shows that this α chain is homologous to the human DRα chain strongly indicating that the β chain is DR-like. VPM37 and VPM43 are shown to be directed against different epitopes on sheep MHC class II molecules so it is highly unlikely that the data can be explained by the presence of posttranslational modifications or the existence of a very common allele. These data provide clear evidence for the expression of two distinct DRP chains in the sheep.     

Retrograde Traffic Out of the Yeast Vacuole to the TGN Occurs via the Prevacuolar/Endosomal Compartment

A large number of trafficking steps occur between the last compartment of the Golgi apparatus (TGN) and the vacuole of the yeast Saccharomyces cerevisiae. To date, two intracellular routes from the TGN to the vacuole have been identified. Carboxypeptidase Y (CPY) travels through a prevacuolar/endosomal compartment (PVC), and subsequently on to the vacuole, while alkaline phosphatase (ALP) bypasses this compartment to reach the same organelle. Proteins resident to the TGN achieve their localization despite a continuous flux of traffic by continually being retrieved from the distal PVC by virtue of an aromatic amino acid–containing sorting motif. In this study we report that a hybrid protein based on ALP and containing this retrieval motif reaches the PVC not by following the CPY sorting pathway, but instead by signal-dependent retrograde transport from the vacuole, an organelle previously thought of as a terminal compartment. In addition, we show that a mutation in VAC7, a gene previously identified as being required for vacuolar inheritance, blocks this trafficking step. Finally we show that Vti1p, a v-SNARE required for the delivery of both CPY and ALP to the vacuole, uses retrograde transport out of the vacuole as part of its normal cellular itinerary.     

Timm-staining intensity is correlated with the density of Timm-positive presynaptic structures in the cerebral cortex of lizards

In cortical areas of the lizard, Podarcis hispanica, Timm staining reveals a distinct pattern of lamination. At the electron-microscope level, virtually all of the reaction product is located in the synaptic vesicles of Timm-positive boutons. Using linear-regression analysis, the area density of Timm-positive bouton profiles as well as the numerical and volume density of stained vesicles were found to be closely correlated with the light-microscopic densitometric values obtained for each Timm-positive cortical zone. We discuss the possibility of estimating stereological electron-microscopic data parameters from densitometric measurements at the light-microscope level.