Optimized Null Model for Protein Structure Networks

Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model for RIGs, by comparing various RIG definitions against a series of network models.     

Maturation and persistence of the anti-SARS-CoV-2 memory B cell response

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Epidermal growth factor inhibits both cholecystokinin octapeptide-induced inositol 1,4,5-trisphosphate production and [CA2+]i increase in rat pancreatic acinar cells

We have studied the effects of epidermal growth factor (EGF) on both cholecystokinin octapeptide (CCK-OP)-induced inositol-1,4,5 trisphosphate (IP3) production and on cytosolic free calcium concentrations [Ca2+]i by fluorescence measurements in fura-2-loaded pancreatic acini. Our data show that EGF inhibits CCK-OP induced IP3 production by 40 +/- 9% and decreases CCK-OP induced rise in cytosolic Ca2+ by 41 +/- 9%. These data indicate that activation of EGF receptors leads to inhibition of CCK-OP induced stimulation of phospholipase C (PLC).     

Intracellular localization of lipoprotein lipase in adipose cells

Subcellular localization of lipoprotein lipase has been examined in differentiated Ob17 adipose cells. No patent activity is detectable in carefully homogenized cells. All latent activity can be unmasked by disrupting membrane structures with neutral detergents. The sequestration of lipoprotein lipase in closed membrane structures is supported by experiments of immunotitration with anti-lipoprotein lipase antibodies and by experiments showing a full protection of the masked activity against proteolytic attack by trypsin. The intracellular distribution of lipoprotein lipase investigated by immunofluorescence staining and by isopycnic centrifugation indicates that a large proportion of the enzyme is located in the Golgi apparatus, in which the activation of the enzyme is likely to take place (C. Vannier et al. (1985) J. Biol. Chem. 260, 4424-4431). Altogether, the results are in favor of a localization of lipoprotein lipase in adipose cells as being typical of that of a secretory protein and underline the absence of lipoprotein lipase in the cell cytoplasm.     

Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein,APUM9

Plant Molecular Biology - Here we demonstrate that the APUM9 RNA-binding protein and its co-factors play a role in mRNA destabilization and how this activity might regulate early plant development....     

Characterization of a monoclonal antibody to human proacrosin and its use in acrosomal status evaluation.

Among the monoclonal antibodies (MAb) selected after immunization of mice with a detergent-insoluble fraction from human spermatozoa, MAb 4D4 was found to stain in immunofluorescence the principal part of the acrosome of human spermatozoa. Acrosome reaction induced decreased and spotty 4D4 immunofluorescence staining. Immunoelectron microscopy before or after embedding revealed that the epitope defined by MAb 4D4 was sequestered in the anterior acrosomal matrix and, after the acrosome reaction, remained partly bound on matrix elements attached to the inner acrosomal membrane. Western blot analysis of sperm extracts showed that the epitope defined by MAb 4D4 was located on a 55 KD polypeptide in whole cells and on 55 and 50 KD polypeptides in non-ionic detergent fractions. Human proacrosin-enriched fraction obtained by FPLC purification exhibited several proteolytic activities against gelatin in gel enzymography: a 50 KD major band and two minor bands in the 20-30 KD area; the 50 KD polypeptide reacted with MAb 4D4 in Western blots. Furthermore, the 4D4-immunoprecipitated polypeptide from sperm extract showed that the 50 KD band exhibited proteolytic activity with an optimal pH at 8.0 that was strongly inhibited by soybean trypsin inhibitor and ZnCl2. MAb 4D4 also reacted with the acrosome of the monkey Macaca fascicularis but not with the acrosome of any of the other non-primate mammalian species examined so far. Various shape defects of the acrosomal principal region were revealed by 4D4 labeling of spermatozoa with head anomalies from infertile patients. MAb 4D4 also recognized proacrosin in paraffin-embedded human testis sections. These data make the monoclonal antiproacrosin antibody 4D4 an efficient tool for evaluation of the acrosomal status of human spermatozoa and spermatids.     

Plagiochila virginica A.Evans rather than P. dubia Lindenb. & Gottsche occurs in Macaronesia; placement in sect. Contiguae Carl is supported by ITS sequences of nuclear ribosomal DNA

 Plagiochila dubia Lindenb. & Gottsche is reduced to a synonym of the Neotropical P. patula (Sw.) Lindenb. Specimens from the Canary Islands and Madeira proved to belong to the eastern North American P. virginica A.Evans, new to Europe. Phylogenetic analyses of the internal transcribed spacer regions (ITS1-5.8S-ITS2) of nuclear ribosomal DNA of ten Plagiochila species produced four independent lineages that are well supported by all bootstrap analyses (maximum likelihood, maximum parsimony, and distance). These lineages correspond with the Plagiochila sections Arrectae, Contiguae, Cucullatae and Glaucescentes. Spruce's “Ramiflorae” and “Cauliflorae” may no longer be regarded as monophyletic units of Plagiochila. Received August 19, 2001 Accepted October 11, 2001     

Analysis of wet edaphic riparian communities of a Mediterranean hydrographic network: the Arc (Bouches-du-Rhône,France)

The composition of benthic communities is a good criterion to estimate water quality. Is this also true of the wet edaphic riparian invertebrates, less directly exposed to the impact of the water? What abiotic factors determine the distribution of species within a hydrosystem? These questions were addressed, using the River Arc and its hydrographic network, subject to various anthropogenic aggressions (urbanization, industry, agriculture) and offering varied hydrochemical situations. The riparian population (158 taxa) was analysed, using Reciprocal Averaging (9 sampling points on the main course and its tributaries). Results show that spatial variation of the edaphic riparian zoocenosis is chiefly determined by the nature of the substratum and, to a lesser extent, by the hydrologic instability of the water course. However, it can respond to some constraints of the environment like benthic macroinvertebrates.     

Computational Modelling of Metastasis Development in Renal Cell Carcinoma

The biology of the metastatic colonization process remains a poorly understood phenomenon. To improve our knowledge of its dynamics, we conducted a modelling study based on multi-modal data from an orthotopic murine experimental system of metastatic renal cell carcinoma. The standard theory of metastatic colonization usually assumes that secondary tumours, once established at a distant site, grow independently from each other and from the primary tumour. Using a mathematical model that translates this assumption into equations, we challenged this theory against our data that included: 1) dynamics of primary tumour cells in the kidney and metastatic cells in the lungs, retrieved by green fluorescent protein tracking, and 2) magnetic resonance images (MRI) informing on the number and size of macroscopic lesions. Critically, when calibrated on the growth of the primary tumour and total metastatic burden, the predicted theoretical size distributions were not in agreement with the MRI observations. Moreover, tumour expansion only based on proliferation was not able to explain the volume increase of the metastatic lesions. These findings strongly suggested rejection of the standard theory, demonstrating that the time development of the size distribution of metastases could not be explained by independent growth of metastatic foci. This led us to investigate the effect of spatial interactions between merging metastatic tumours on the dynamics of the global metastatic burden. We derived a mathematical model of spatial tumour growth, confronted it with experimental data of single metastatic tumour growth, and used it to provide insights on the dynamics of multiple tumours growing in close vicinity. Together, our results have implications for theories of the metastatic process and suggest that global dynamics of metastasis development is dependent on spatial interactions between metastatic lesions.