Proteomics analysis of the neurodegeneration in the brain of tau transgenic mice

Protein tau, a major microtubule-binding protein in the brain, comprises six isoforms generated through alternative mRNA splicing. A dysfunctional form of mutant and normal tau is associated or implicated in the pathogenesis of several neurodegenerative disorders. The neuropathological hallmark of these tau-opathies are intraneuronal depositions of fibrillary aggregates of which neurofibrillary tangles are most common. Several distinct transgene mouse models confirmed that tau protein can cause neurodegeneration directly. This study was aimed at identifying proteins that might play a role in the cellular disturbances caused by overexpression of the longest isoform of human tau in the brain of transgenic mice. We found 34 proteins which differed in integrated intensity by a factor of at least 1.5. These proteins could be sorted into several categories. Some of the phenotypic characteristics found in the htau transgenic mice could be related to proteins found in this study. Several proteins are linked to processes involving apoptosis and neuronal death and have been discussed in papers describing neurodegenerative disorders.     

A homogeneous fluorometric assay for measuring cell adhesion to immobilized ligand using V-well microtiter plates

We have developed a homogeneous high-capacity assay format for measuring integrin- and selectin-dependent cell binding to immobilized ligand using V-well microtiter plates. 2',7'-Bis(2-carboxyethyl)-5-(and-6)-carboxylfluorescence, acetoxymethylester-labeled cells are added to ligand-coated V-shaped microtiter wells. Bound cells are separated from free cells using centrifugal force to produce shear stress. Nonadherent cells accumulate in the nadir of the well and are measured using a fluorescence plate reader. Antibody or low-molecular-weight inhibitors of either the ligand or the cell surface receptor result in less cell binding, more cells in the pellet, and increased signal. The optimization and validation of the very late antigen-4/vascular cell adhesion molecule-1 assay is described in detail. We demonstrate that this assay can be rapidly adapted to measure other integrin- and selectin-mediated interactions. This assay format has several advantages over conventional assays. The centrifugal process is biologically relevant and eliminates the washing steps to remove nonadherent cells that can cause well-to-well and plate-to-plate variation. Because the assay is robust with a high signal-to-noise ratio and low variability, it is ideally suited for studying multiple parameters of cell adhesion and for high capacity screening.     

Distribution and trophic ecology of chaetognaths in the western Mediterranean in relation to an inshore-offshore gradient

This study examines the distribution patterns and feeding ecologyof chaetognaths in the Catalan Sea in relation to mesoscalefeatures along an inshore–offshore gradient. The studywas conducted during two different periods of the year: latespring of 1995 and late summer of 1996. The two periods differedin hydrographic conditions and mesoscale processes, which affectedthe distribution patterns of the different species of chaetognathsfound. The diet of the chaetognaths was mainly composed of copepodsand differed between species. Prey size was not always stronglyrelated to chaetognath size and for certain species, there wasan overlap in prey size spectrum. Trophic niche breadth (ona ratio scale) appeared to be constant with growth. Ingestionrates and predation pressure by chaetognaths did not followa clear trend related to the mesoscale features in the area,such as the presence of a density front. The impact of chaetognathson copepod standing stock appeared to be extremely low (<1%),but it became more relevant when the species and prey size specificityof the chaetognaths was taken into account.     

Optimal allocation between nutrient uptake and growth in a microbial trichome

 A microbial trichome grows by assimilating nutrients from its environment, and converting these into catalytic macro-molecular machinery. This machinery may be divided into assimilatory machinery and proliferative machinery. The former type is involved in nutrient uptake, whereas the latter type enables the trichome to grow. The cells in the trichome are faced with an allocation problem: given the availability of nutrients in the environment, how many macro-molecular building blocks should be allocated to the synthesis of assimilatory machinery, and how many to the synthesis of proliferative machinery? We answer this question for a particular model, which is a generalization of the Droop quota model. We formulate a two-dimensional non-linear optimal control problem, corresponding to this model. An optimal allocation regime with a singular segment is derived, based on Pontryagin’s maximum principle. We give a direct proof of optimality. We discuss how actual biological cells might implement this optimal regime. Received: 16 December 1996 / Revised version: 14 September 1997     

Distribution of introduced and native fish in Patagonia (Argentina): patterns and changes in fish assemblages

The interaction between native fishes and salmonids introduced in Patagonia at the beginning of the 20th Century, developed at the same time as the environmental change. The phenomenon of global warming has led to the formulation of predictions in relation to changes in the distribution of species, in the latitudinal dimension, both at intralacustrine, or small streams levels. The aim of the present work includes three main objectives: a) to compose a general and updated picture of the latitudinal distribution range of native and alien fishes, b) to analyze the historical changes in the relative abundance of Percichthys trucha, Odontesthes sp., and salmonids in lakes and reservoirs, and c) to relate the diversity and relative abundance of native and salmonid fishes to the environmental variables of lakes and reservoirs. We analysed previous records and an ensemble of data about new locations along the northern border of the Patagonian Province. We compared current data about the relative abundance of native fishes and salmonids in lakes and reservoirs, with previous databases (1984–1987). All samplings considered were performed during spring-summer surveys and include relative abundance, as proportions of salmonids, P. trucha, and Odontesthes sp. For the first time, we found changes in fish assemblages from twenty years back up to the present: a significant decline in the relative abundances of salmonids and an increase of P. trucha. We studied the association between the diversity and relative abundance of native and salmonid fishes and the environmental variables of lakes and reservoirs using Canonical Correspondence Analysis. Relative abundance showed mainly geographical cues and the diversity relied largely on morphometric characteristics. Relative abundance and diversity seem to have a common point in the lake area, included into the PAR concept. Native abundance and alien diversity were negatively related with latitude. Greater native diversity was observed in lakes with high PAR compared with salmonids. Historical changes such as southward dispersion, relative abundance changes, and geographical patterns for relative abundance and diversity are basic concepts needed not only in future research but also in management design for Patagonian fish populations.     

An arrangement of changes along gradients,with examples from successions in boreal peatland

Summary A multidimensional arrangement of various gradients referring to the nature of ecosystem changes is presented (Table 1). Examples are given, some of them from boreal peatlands (mires) which show both convergence from different origin and divergence in the local development. Some successions in wetlands are retrogressive, and the changes are usually at the same time biotically generated and environmentally conditioned, sometimes (e.g. shores, deltas, palsas) mainly the latter.     

GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets

Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding the interpretation of actual functional similarity and overall functional coherence of such a group. One way to mitigate such issues is through the use of visualization and statistical techniques. Therefore, in order to help interpret this annotation heterogeneity we created a web application that generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and Information Content based metrics. The publicly accessible website http://xldb.di.fc.ul.pt/gryfun/ currently accepts lists of UniProt accession numbers in order to create user-defined protein sets for subsequent annotation visualization and statistical assessment. GRYFUN is a freely available web application that allows GO annotation visualization of protein sets and which can be used for annotation coherence and cohesiveness analysis and annotation extension assessments within under-annotated protein sets.     

Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome

The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.