Analysis of superfamily specific profile-profile recognition accuracy

Background  

Annotation of sequences that share little similarity to sequences of known function remains a major obstacle in genome annotation. Some of the best methods of detecting remote relationships between protein sequences are based on matching sequence profiles. We analyse the superfamily specific performance of sequence profile-profile matching. Our benchmark consists of a set of 16 protein superfamilies that are highly diverse at the sequence level. We relate the performance to the number of sequences in the profiles, the profile diversity and the extent of structural conservation in the superfamily.     

Classification of the forebrain striatum neurons in birds

Polymorphism of neurons in the basic fields of the forebrain striatum of birds was described using specially developed classification of neurons in Nissl preparations. Birds with different degrees of development of elementary rational activity were studied: Corvus monedula, Columba livia, Coturnix coturnix, and Melopsittacus undulatus. According to the proposed method, the neurons were classified in 3 basic types and 2 additional, 6 subtypes and 26 classes. It was found that in the higher brain regions of Corvus monedula, birds with advanced rational activity, there are a greater variety and number of complex associative stellate cells than in birds with poorly developed rational activity (Columba livia and Coturnix coturnix).     

Comparative embryology of nematodes and the law of embryo similarity

Two types of embryonic development can be distinguished within nematodes, with a variable (Enoplia) or invariant (remaining species) cleavage. In the case of invariant cleavage two main variants of cell lineage are presented in nematodes, with the posterior (Rhabditea) or anterior (Dorylaimida) localization of endoderm material at the two-cell stage. This classification is in a good agreement with some modern nematode taxonomy and it is supported by molecular phylogeny studies. The variable cleavage is plesiomorphic. Traditional concept of "mosaic" cleavage is not applicable for nematodes as inductive interactions and a regulation of experimental interventions are usual attributes of any mode of nematode development. The representatives of order Rhabditida have almost identical cell lineage, but at the same time they have strong interspecific differences in mechanisms of ooplasmic segregation any early inductive interactions. The diversity of geometric patterns in the early cleavage, often at the level of individual random variations, is a usual characteristic of nematodes including species with the invariant cleavage. Thus, the early stages of nematode development are evolutionary very flexible, but at the course of embryonic development similarity of different species is progressively increased up to the uniform morphogenetic stages. The dynamics of variation in nematode development contradict to the von Baer's law but are in an agreement with the modern "hourglass model" (Doboul, 1994; Raff, 1986).     

Diagnostic criteria for diabetes revisited: making use of combined criteria

Background  

Existing cut-offs for fasting plasma glucose (FPG) and post-load glucose (2hPG) criteria are not equivalent in the diagnosis of diabetes and glucose intolerance. Adjusting cut-offs of single measurements have not helped so we undertook this project to see if they could be complementary.     

Dephosphorylation of beta2-syntrophin and Ca2+/mu-calpain-mediated cleavage of ICA512 upon stimulation of insulin secretion

Islet cell autoantigen (ICA) 512 is a receptor-tyrosine phosphatase-like protein associated with the secretory granules of neuroendocrine cells, including pancreatic beta-cells. Binding of its cytoplasmic tail to beta2-syntrophin suggests that ICA512 connects secretory granules to the utrophin complex and the actin cytoskeleton. Here we show that stimulation of insulin secretion from INS-1 cells triggers the biosynthesis of pro-ICA512 and the degradation of its mature form. Inhibition of calpain, which is activated upon stimulation of insulin secretion, prevents the Ca2+-dependent proteolysis of ICA512. In vitro mu-calpain cleaves ICA512 between a putative PEST domain and the beta2-syntrophin binding site, whereas binding of ICA512 to beta2-syntrophin protects the former from cleavage. beta2-syntrophin and its F-actin-binding protein utrophin are enriched in subcellular fractions containing secretory granules. ICA512 preferentially binds phospho-beta2-syntrophin and stimulation of insulin secretion induces the Ca2+-dependent, okadaic acid-sensitive dephosphorylation of beta2-syntrophin. Similarly to calpeptin, okadaic acid inhibits ICA512 proteolysis and insulin secretion. Thus, stimulation of insulin secretion might promote the mobilization of secretory granules by inducing the dissociation of ICA512 from beta2-syntrophin-utrophin complexes and the cleavage of the ICA512 cytoplasmic tail by mu-calpain.     

Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys

Background  

The highly pathogenic H5N1 is a major avian pathogen that crosses species barriers and seriously affects humans as well as some mammals. It mutates in an intensified manner and is considered a potential candidate for the possible next pandemic with all the catastrophic consequences.     

Study of plasma confinement in the L-2M stellarator during the formation of an edge transport barrier

A plasma confinement mode characterized by the formation of an edge transport barrier (ETB) was discovered in the L-2M stellarator after boronization of the vacuum vessel wall. The transition into this mode is accompanied by a jump in the electron temperature by 100–200 eV at the plasma edge and a sharp increase in the gradient of the electron temperature T _e in this region. The threshold power for the transition into the ETB confinement mode with an increased electron temperature gradient is P _thr ^?Te = (60 ± 15)n _e [10¹⁹ m^?3] kW. The formation of the ETB manifests itself also in a substantial change in the electron density profile. A density peak with a steep gradient at the outer side forms at the plasma edge. The threshold power for the transition into the ETB confinement mode corresponding to a substantial increase in the plasma density gradient near r = a is P _thr ^?Te = (67 ± 9)n _e [10¹⁹ m^?3] kW, which agrees to within experimental error with the threshold power for the transition into the ETB confinement mode determined from the sharp increase in the gradient of the electron temperature T _e . The value of P _thr for the L-2M stellarator agrees to within 25% with that obtained from the tokamak scaling. In the ETB confinement mode, the plasma energy W and the energy confinement time τ _E determined from diamagnetic measurements increase by 20–30% as compared to those obtained from the stellarator scaling for the confinement mode without an ETB. When the heating power increases by a factor of 2–3 above the threshold value, the effects related to improved energy confinement disappear.     

IL‐1α and IL‐1β have different effects on formation and activity of large osteoclasts

Interleukin 1 (IL‐1) is a proinflammatory cytokine upregulated in conditions such as rheumatoid arthritis and periodontal disease. Both isoforms, IL‐1α and IL‐1β, have been shown to activate osteoclasts (OCs), the cells responsible for resorbing bone. Inflammatory conditions are also characterized by increased bone loss and by the presence of large OCs (10+ nuclei). We and others have previously shown that large OCs are more likely to be resorbing compared to small OCs (2–5 nuclei). Moreover, large OCs express higher levels of the IL‐1 activating receptor IL‐1RI, integrins αv and β3, RANK, and TNFR1, while small OCs have higher levels of the decoy receptor IL‐1RII. We hypothesized that IL‐1 would have different effects on large and small OCs due to these distinct receptor expression patterns. To test this hypothesis, RAW 264.7 cells were differentiated into populations of small and large OCs and treated with IL‐1α or IL‐1β (1 and 10 ng/ml). In the presence of sRANKL, both IL‐1α and IL‐1β increased total OC number and resorptive activity of large OCs. IL‐1α stimulated formation of large OCs and increased the number of resorption pits, while IL‐1β changed the morphology of large OCs and integrin‐β3 phosphorylation. No effects were seen in small OCs in response to either IL‐1 isoform. These results demonstrate that IL‐1 predominantly affects large OCs. The dissimilarity of responses to IL‐1α and IL‐1β suggests that these isoforms activate different signaling pathways within the two OC populations. J. Cell. Biochem. 109: 975–982, 2010. © 2010 Wiley‐Liss, Inc.