Prediction and assessment of the time-varying effective pulmonary vein area via cardiac MRI and Doppler echocardiography

Accurately estimating left atrial (LA) volume with Doppler echocardiography remains challenging. Using angiography for validation, Marino et al. (Marino P, Prioli AM, Destro G, LoSchiavo I, Golia G, and Zardini P. Am Heart J 127: 886-898, 1994) determined LA volume throughout the cardiac cycle by integrating the velocity-time integrals of Doppler transmitral and pulmonary venous flow, assuming constant mitral valve and pulmonary vein areas. However, this LA volume determination method has never been compared with three-dimensional LA volume data from cardiac MRI, the gold standard for cardiac chamber volume measurement. Previously, we determined that the effective mitral valve area is not constant but varies as a function of time. Therefore, we sought to determine whether the effective pulmonary vein area (EPVA) might be time varying as well and also assessed Marino's method for estimating LA volume. We imaged 10 normal subjects using cardiac MRI and concomitant transthoracic Doppler echocardiography. LA and left ventricular (LV) volumes were measured by MRI, transmitral and pulmonary vein flows were measured by Doppler echocardiography, and time dependence was synchronized via the electrocardiogram. LA volume, estimated using Marino's method, was compared with the MRI measurements. Differences were observed, and the discrepancy between the echocardiographic and MRI methods was used to predict EPVA as a function of time. EPVA was also directly measured from short-axis MRI images and was found to be time varying in concordance with predicted values. We conclude that because EPVA and LA volume time dependence are in phase, LA filling in systole and LV filling in diastole are both facilitated. Application to subjects in select pathophysiological states is in progress.     

A temporal approach to linking aboveground and belowground ecology

Ecologists are becoming increasingly aware of the role of aboveground-belowground relationships in controlling ecosystem processes and properties. Here, we review recent studies that show that relationships between aboveground and belowground communities operate over a hierarchy of temporal scales, ranging from days to seasons, to millennia, with differing consequences for ecosystem structure and function. We propose that a temporal framework is crucial to our understanding of the nature and ecological significance of relationships between aboveground and belowground communities.     

Cryo-electron microscopy of the giant Mimivirus

Mimivirus is the largest known virus. Using cryo-electron microscopy, the virus was shown to be icosahedral, covered by long fibers, and appears to have at least two lipid membranes within its protein capsid. A unique vertex, presumably for attachment and infection of the host, can be seen for particles that have a suitable orientation on the micrographs.     

Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates

Four yellow-pigmented, gram-negative, chemoorganotrophic aerobic bacteria were isolated from starfish Stellaster equestris (strains 022-2-10T, 022-2-9, and 022-2-12) and soft coral (unidentified species) (strain 022-4-7) collected in the South China Sea. 16S rRNA gene sequence-based analyses of the new organisms revealed that Erythrobacter spp. were the closest relatives and shared the highest similarity of 98.7% to E. citreus, 98.5% to E. flavus, 97.9% to E. litoralis and 97.6% to E. longus. The novel organisms were tolerant to 3-6% NaCl, grew between 10 degrees C and 40 degrees C, and were not able to degrade gelatin, casein, and agar, while degraded Tween 80. Two strains (022-2-9 and 022-2-12) could weakly degrade starch. All strains produced a large pool of carotenoids and did not have Bacteriochlorophyll a. Phosphatidylethanolamine (30-36%), phosphatidylglycerol (39-46%), and phosphatidylcholine (21-27%) were the predominant phospholipids. Sphingoglycolipid was not detected. The major fatty acids were 16:0 (6-11%), 16:1omega7 (12-15%), and 18:1omega7 (46-49%). The two-hydroxy fatty acids, 13:0-2OH, 14:0-2OH, 15:0-2OH, 16:0-2OH were also present. The G + C content of the DNAs ranged from 61 to 62 mol%. The level of DNA similarity among four strains was conspecific and ranged from 94% to 98%. Even though new strains and other species of the genus had rather high level of 16S rRNA gene sequence similarities, DNA-DNA hybridization experiments showed only 33-39% of binding with the DNA of the type strains. On the basis of these results and the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the new organisms be classified as a novel species; the name Erythrobacter vulgaris sp. nov. is proposed. The type strain is 022-2-10T (= KMM 3465T = CIP 107841T).     

Comparative methods for multiplex analysis of cytokine protein expression in plasma of lipopolysaccharide-treated mice

Changes in circulating cytokines might serve as predictors of compound-evoked inflammatory responses. CD-1 mice were treated with lipopolysaccharide (LPS; 0.2 ml of 0.25 mg/ml, intraperitoneal) for subsequent expression measurement of plasma cytokine protein expression at 24-h post-treatment using multiple antibody Western blot, and at both 2-h and 24-h post-treatment using antibody array and suspension bead array. Antibody array provided a semi-qualitative assessment and suggested significantly increased expression of GCSF at 2-h post-treatment and GCSF, IL-6, IL-12, MCP-1, MCP-5, RANTES and sTNFR1 at 24-h post-treatment. Densitometric analysis of multiple antibody Western blots provided a semi-quantitative assessment and indicated significantly increased expression of IL-6, IL-12, IL-17, GCSF, eotaxin, and MCP-2 at 24-h post-treatment. The suspension bead array yielded statistically significant cytokine protein expression increases for IL-6, IL-10, IFNgamma and TNFalpha at both 2-h and 24-h post-treatments, while significant expression at 24-h post-treatment only was noted for IL-1beta, IL-5, IL-12 and GM-CSF. Suspension bead array provided the greatest range of detection, revealing subtle increased expression of GM-CSF, IL-1beta, IL-5, IL-10, TNFalpha and IFNgamma at 24-h post-treatment, not detected by antibody array or multiple antibody Western blot. Suspension bead array proved to be the best method for detection of LPS-evoked changes in plasma cytokine levels.     

Spatio-temporal modeling of localized brain activity

Functional neuroimaging, including positron emission tomography (PET) and functional magnetic resonance imaging (fMRI), plays an important role in identifying specific brain regions associated with experimental stimuli or psychiatric disorders such as schizophrenia. PET and fMRI produce massive data sets that contain both temporal correlations from repeated scans and complex spatial correlations. Several methods exist for handling temporal correlations, some of which rely on transforming the response data to induce either a known or an independence covariance structure. Despite the presence of spatial correlations between the volume elements (voxels) comprising a brain scan, conventional methods perform voxel-by-voxel analyses of measured brain activity. We propose a two-stage spatio-temporal model for the estimation and testing of localized activity. Our second-stage model specifies a spatial auto-regression, capturing correlations within neural processing clusters defined by a data-driven cluster analysis. We use maximum likelihood methods to estimate parameters from our spatial autoregressive model. Our model protects against type-I errors, enables the detection of both localized and regional activations (including volume of interest effects), provides information on functional connectivity in the brain, and establishes a framework to produce spatially smoothed maps of distributed brain activity for each individual. We illustrate the application of our model using PET data from a study of working memory in individuals with schizophrenia.     

Bacterial Exopolysaccharides from Extreme Marine Environments with Special Consideration of the Southern Ocean, Sea Ice, and Deep-Sea Hydrothermal Vents: A Review

Exopolysaccharides (EPSs) are high molecular weight carbohydrate polymers that make up a substantial component of the extracellular polymers surrounding most microbial cells in the marine environment. EPSs constitute a large fraction of the reduced carbon reservoir in the ocean and enhance the survival of marine bacteria by influencing the physicochemical environment around the bacterial cell. Microbial EPSs are abundant in the Antarctic marine environment, for example, in sea ice and ocean particles, where they may assist microbial communities to endure extremes of temperature, salinity, and nutrient availability. The microbial biodiversity of Antarctic ecosystems is relatively unexplored. Deep-sea hydrothermal vent environments are characterized by high pressure, extreme temperature, and heavy metals. The commercial value of microbial EPSs from these habitats has been established recently. Extreme environments offer novel microbial biodiversity that produces varied and promising EPSs. The biotechnological potential of these biopolymers from hydrothermal vent environments as well as from Antarctic marine ecosystems remains largely untapped.     

Core formation and the acquisition of fusion competence are linked during secretory granule maturation in Tetrahymena

The formation of dense core secretory granules is a multistage process beginning in the trans Golgi network and continuing during a period of granule maturation. Direct interactions between proteins in the membrane and those in the forming dense core may be important for sorting during this process, as well as for organizing membrane proteins in mature granules. We have isolated two mutants in dense core granule formation in the ciliate Tetrahymena thermophila, an organism in which this pathway is genetically accessible. The mutants lie in two distinct genes but have similar phenotypes, marked by accumulation of a set of granule cargo markers in intracellular vesicles resembling immature secretory granules. Sorting to these vesicles appears specific, since they do not contain detectable levels of an extraneous secretory marker. The mutants were initially identified on the basis of aberrant proprotein processing, but also showed defects in the docking of the immature granules. These defects, in core assembly and docking, were similarly conditional with respect to growth conditions, and therefore are likely to be tightly linked. In starved cells, the processing defect was less severe, and the immature granules could dock but still did not undergo stimulated exocytosis. We identified a lumenal protein that localizes to the docking-competent end of wildtype granules, but which is delocalized in the mutants. Our results suggest that dense cores have functionally distinct domains that may be important for organizing membrane proteins involved in docking and fusion.     

Study of primary amines for nucleophilic cleavage of cyanylated cystinyl proteins in disulfide mass mapping methodology

In a study of primary (methyl to butyl) amines as nucleophiles for cyano-induced cleavage of cysteinyl proteins, methylamine was found to be superior to ammonia for cyanylation (CN)-based disulfide mass mapping methodology. Reaction conditions such as nucleophile concentration, temperature, and reaction time were systematically studied using ribonuclease A as a model protein. The CN-induced cleavage products were monitored using reverse-phase chromatography and matrix-assisted laser desorption ionization mass spectrometry. Results showed that low temperature, short reaction time, and high nucleophile concentration optimize the cleavage reaction and minimize side reactions. These conditions shorten the analysis time and substantially improve the yield of cleavage products. Further, the concurrent use of homologous nucleophiles (e.g., ammonia and methylamine) facilitates recognition and identification of cleavage products.