Clustering proteins from interaction networks for the prediction of cellular functions

BACKGROUND: Developing reliable and efficient strategies allowing to infer a function to yet uncharacterized proteins based on interaction networks is of crucial interest in the current context of high-throughput data generation. In this paper, we develop a new algorithm for clustering vertices of a protein-protein interaction network using a density function, providing disjoint classes. RESULTS: Applied to the yeast interaction network, the classes obtained appear to be biological significant. The partitions are then used to make functional predictions for uncharacterized yeast proteins, using an annotation procedure that takes into account the binary interactions between proteins inside the classes. We show that this procedure is able to enhance the performances with respect to previous approaches. Finally, we propose a new annotation for 37 previously uncharacterized yeast proteins. CONCLUSION: We believe that our results represent a significant improvement for the inference of cellular functions, that can be applied to other organism as well as to other type of interaction graph, such as genetic interactions

Mechanisms of remanent optical alignment of dyes in a gel matrix

International audienceWe present the mechanisms of a remanent alignment of polarizable molecules dispersed in a solid silica gel matrix, when submitted to powerful, femtosecond, linearly polarized, optical pulses emitted from a dye laser. This alignment can be related to third-order nonlinearities of the dopants through an orientational optical Kerr effect. Its remanence results from the strong interactions the dopants share with their host matrix, particularly through hydrogen bonds. We expose here the detailed mechanism of this phenomenon, considering that such a rotation of large chromophores may not be compatible at first sight with subpicosecond pulse durations. Through several experiments, we show that this apparent contradiction is solved once analyzed, by the structure of the excitation pulses, which cannot be simply described as ''femtosecond pulses'', but consist of two temporal components--a femtosecond one and a nanosecond one--playing different but essential roles in the proces

Inhibition of the post-translational processing of microvillar hydrolases is associated with a specific decreased expression of sucrase-isomaltase and an increased turnover of glucose in Caco-2 cells treated with monensin

AbstractThe biosynthesis and post-translational processing of sucrase-isomaltase and dipeptidylpeptidase IV were studied by L-[35S]methionine labeling, immunoisolation with monoclonal antibodies and SDS-PAGE in post-confluent Caco-2 cells treated with monensin (10 μM, 48 h). In addition to its classical effect on the post-translational processing of both hydrolases, i.e. an inhibition of the conversion of the high-mannose to the complex glycosylated form of the enzymes, monensin was found to have two other effects: a marked decrease of sucrase-isomaltase expression, but not of dipeptidylpeptidase IV; an increased turnover of glucose, as substantiated by increased rates of glucose consumption and lactic acid production and a decreased glycogen content. Whether these two effects are related to the particular differentiation and metabolic status of Caco-2 cells is discussed, as well as a possible role for the drug-induced modifications of glucose turnover on the decreased expression of sucrase-isomaltase

Assessment of the susceptibility to pests and diseases of 36 apple cultivars in four low-input organic orchards in France

One of the keystones of the organic orchard is the cultivar choice as one element of pest and disease control. However, few exhaustive data sets concerning the cultivar susceptibility to pests and diseases are available for growers. In order to identify cultivars adapted to organic production methods, the susceptibility to scab, aphids and powdery mildew and the agronomic properties of 36 cultivars were assessed in four French sites under different pedo-climatic conditions. Different levels of susceptibility to scab were observed for 23 scab Vf-resistant and 13 other cultivars. In the North of France where Vf resistance is overcome, the Vf cultivars displayed different levels of scab severity. A high variability in the susceptibility to aphids was observed whereas susceptibility to powdery mildew varied less. The analysis of susceptibility properties, yield and fruit quality, fruit storability and tree behaviour permitted to identify a set of interesting cultivars according to the site

Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network

We here describe PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method, assessed biologically and statistically, enabled us to classify 11% of the Saccharomyces cerevisiae proteome into several groups, the majority of which contained proteins involved in the same biological process(es), and to predict a cellular function for many otherwise uncharacterized proteins