Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells

Proteomics strategies based on nanoflow (nano-) LC-MS/MS allow the identification of hundreds to thousands of proteins in complex mixtures. When combined with protein isotopic labeling, quantitative comparison of the proteome from different samples can be achieved using these approaches. However, bioinformatics analysis of the data remains a bottleneck in large scale quantitative proteomics studies. Here we present a new software named Mascot File Parsing and Quantification (MFPaQ) that easily processes the results of the Mascot search engine and performs protein quantification in the case of isotopic labeling experiments using either the ICAT or SILAC (stable isotope labeling with amino acids in cell culture) method. This new tool provides a convenient interface to retrieve Mascot protein lists; sort them according to Mascot scoring or to user-defined criteria based on the number, the score, and the rank of identified peptides; and to validate the results. Moreover the software extracts quantitative data from raw files obtained by nano-LC-MS/MS, calculates peptide ratios, and generates a non-redundant list of proteins identified in a multisearch experiment with their calculated averaged and normalized ratio. Here we apply this software to the proteomics analysis of membrane proteins from primary human endothelial cells (ECs), a cell type involved in many physiological and pathological processes including chronic inflammatory diseases such as rheumatoid arthritis. We analyzed the EC membrane proteome and set up methods for quantitative analysis of this proteome by ICAT labeling. EC microsomal proteins were fractionated and analyzed by nano-LC-MS/MS, and database searches were performed with Mascot. Data validation and clustering of proteins were performed with MFPaQ, which allowed identification of more than 600 unique proteins. The software was also successfully used in a quantitative differential proteomics analysis of the EC membrane proteome after stimulation with a combination of proinflammatory mediators (tumor necrosis factor-alpha, interferon-gamma, and lymphotoxin alpha/beta) that resulted in the identification of a full spectrum of EC membrane proteins regulated by inflammation.     

A multiple biomarker approach to tracking the fate of an ice algal bloom to the sea floor

In ice-covered Arctic seas, the ice algal production can be the main input of organic matter to the ecosystem. Pelagic–benthic coupling is thought to be particularly tight in those areas. The increase in ice algal production in Franklin Bay from January/February to April/May 2004 paralleled an increase in benthic oxygen demand. However, sedimentary chlorophyll a, which is usually an indicator of “fresh” organic matter inputs to the sea floor, did not increase. Consequently, it was asked what was the fate of the ice algal phytodetritus arriving at the sea floor? To answer this question, photosynthetic pigments from the sea ice, water column particulate organic matter, and sediment, as well as diatom frustules in the sediment, were studied from January to May 2004. The number of ice diatom cells in the sediment showed an increase in April/May, confirming higher inputs of fresh ice algae to the sediment. Changes in sedimentary pigment profiles in the first 10 cm suggested an increase in bioturbation due to enhanced benthic activities. Finally, the decrease in the ratio of chlorophyll a to phaeophorbide a implied an increase in macrobenthic activity. Benthic macrofauna consumed some of the deposited material and mixed some within the top five cm of sediment. The response of sedimentary pigments to an ice algal input can be studied at different levels and it is only the combination of these studies that will allow an understanding of the overall fate of phytodetritus in the benthic compartment.     

Mba1, a membrane-associated ribosome receptor in mitochondria

The genome of mitochondria encodes a small number of very hydrophobic polypeptides that are inserted into the inner membrane in a cotranslational reaction. The molecular process by which mitochondrial ribosomes are recruited to the membrane is poorly understood. Here, we show that the inner membrane protein Mba1 binds to the large subunit of mitochondrial ribosomes. It thereby cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C-terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70. We propose that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane.     

Biogeochemical mass-balances (C, N, P, Si) in three large reservoirs of the Seine Basin (France)

Three major reservoirs (Marne, Seine and Aube), situated in the upstream basin of the river Seine represent a storage capacity of 800 10⁶ m³. In order to quantify the possible role of these reservoirs as a sink or source of nutrients and organic matter for the river system, an input/output mass-balance of suspended matter, organic carbon, inorganic nitrogen forms, phosphorus and reactive silica was established, providing reliable estimates of their retention/elimination and export. The study was carried out over 3 years (1993, 1994 and 1995) in differing hydrological conditions. The retention times varied from 0.3 to 0.8 year, depending on the reservoir and the year, but was longer in 1993 that was a drier year than 1994 and 1995, hydrologically quite similar.Regarding retention (or elimination) and export, the behaviour of the three studied reservoirs was similar. A clear loss or retention of nitrogen, phosphorus and silica was observed in the reservoirs and represented about 40% of the incoming flux of nitrate, 50% of silica, and 60% of phosphate. The retention was lower for total phosphorus than for phosphate. The reservoirs are also sites of suspended matter deposition except during the decennial drawdown, when suspended matter is exported. For inorganic nitrogen, the average amount of nitrate retained in the Seine basin reservoirs upstream from Paris is 5000 tonnes y^–1 that is almost equal to the estimated retention by deposition or denitrification in river channel sediments for the whole drainage network. The retention in the reservoirs represents about 12% of the total flux of nitrate at the outlet of the basin upstream from Paris, and 5% at the mouth of the Seine River.We also calculated inlake C, N, P, Si budgets on the basis of direct process measurements. Measurements of planktonic primary and bacterial activity production led to annual net production of 4200 and 580 tonnes of carbon, respectively. A reasonable value (450 tonnes of carbon) of grazing was calculated. Corresponding N, P, Si fluxes were drawn from appropriate C:N:P:Si ratios. Benthic fluxes were measured with bell jars. The retention of P and Si represents a small fraction of important internal fluxes of phytoplanktonic uptake and recycling, while inorganic nitrogen retention depends mostly on benthic denitrification. The behaviour of P and Si differs in that P is mainly recycled in the water column, while Si dissolution occurs at the sediment interface. Nitrogen is recycled in both the planktonic and the benthic phase.     

Toxoplasma gondii and mucosal immunity

Toxoplasma gondii, an intracellular parasite infects the host through the oral route. Infection induces a cascade of immunological events that involve both the components of the innate and adaptative immune responses. Alteration of the homeostatic balance of infected intestine results in an acute inflammatory ileitis in certain strains of inbred mice. Both the infected enterocytes as well as the CD4 T cells from the lamina propria produce chemokines and cytokines that are necessary to clear the parasite whereas CD8 intraepithelial lymphocytes secrete transforming growth factor beta that reduces the inflammation. In this review, we describe the salient features of this complex network of interactions among the different components of the gut-associated lymphoid tissue cell population that are induced after oral infection with T. gondii.     

Timing and abundance as key mechanisms affecting trophic interactions in variable environments

Climatic changes are disrupting otherwise tight trophic interactions between predator and prey. Most of the earlier studies have primarily focused on the temporal dimension of the relationship in the framework of the match–mismatch hypothesis. This hypothesis predicts that predator's recruitment will be high if the peak of the prey availability temporally matches the most energy‐demanding period of the predators breeding phenology. However, the match–mismatch hypothesis ignores the level of food abundance while this can compensate small mismatches. Using a novel time‐series model explicitly quantifying both the timing and the abundance component for trophic relationships, we here show that timing and abundance of food affect recruitment differently in a marine (cod/zooplankton), a marine–terrestrial (puffin/herring) and a terrestrial (sheep/vegetation) ecosystem. The quantification of the combined effect of abundance and timing of prey on predator dynamics enables us to come closer to the mechanisms by which environment variability may affect ecological systems.     

Gut microflora is a key player in host energy homeostasis

Gut microflora is now considered as a key organ involved in host energy homeostasis. Recent data suggest that the alterations of the gut bacteria ecosystem could contribute to the development of metabolic disorders such as type 2 diabetes and obesity. First, gut microflora may increase energy efficiency of non digested food via the fermentation, thus providing more energy to the host. Secondly, fatty acids flux and storage in the adipose tissue is under the control of the fasting-induced adipocyte factor FIAF, which expression depends on gut microflora. Third, high-fat diet feeding changes gut bacteria profile, leading to a drop in bifidobacteria content, which correlates with a higher LPS plasma levels, thereby participating to the onset of inflammation, insulin resistance and type 2 diabetes associated with obesity. Changing gut microflora composition could be a useful tool to prevent or to treat high-fat/low fibres diet-induced metabolic syndrome. double dagger.