Search for functional domain boundaries and localization of functional sites based on oligopeptide vocabularies]

A new method based on the analysis of oligopeptide composition of the amino acid sequences from different protein families is presented. We assume, that any protein family can be characterized by the set of oligopeptides (oligopeptides vocabulary). We demonstrate, that oligopeptides vocabulary comparison can distinguish different families from each other and from random sequences. It should be noted, that this comparison can be successfully performed on the set of only 25 dipeptides and without preliminary alignment. We demonstrate, that characteristic peptides are localized in the regions of functional significance, as shown on the example of GTP-binding domain of translation elongation factors. We suggest how to use this method to localize the boundaries of functional domains in amino sequences. On the example of few functional domains we demonstrate, that the average error of prediction does not exceed 3-4 amino acid residue.     

Mechanisms of immunodeficiency in HIV infection and ways of overcoming it]

Though antibodies against HIV-1 appearing in the course of infection are successfully used for the diagnostic purposes, their accumulation on the earlier step leads to: firstly, to the rapid generation of the immunodeficiency by different mechanisms and secondly, to inefficiency of immunotherapy. One of the causes for immunodeficiency seems to be antibodies which are induced in the HIV-infected person by the HIV peptides homologous to the MHC class II molecules by their amino acid sequences. 73% of HIV-1 positive sera are shown to react with human B-lymphoma cells expressing surface class II molecule. The binding is caused by the antibodies preventing the murine monoclonal anti-HLA.DR Ab interaction with B-lymphoma. Three amino acid sequences are identified in both alpha- and beta-chain of the HLA.DR antigen, these sequences being homologous to HIV-1 gp120 or gp42 molecules for 50 to 70%. Using synthetic peptides it was shown that HIV-1-infected persons contain antibodies which cross-react to the homologous peptides of the HIV-1 and of the MHC class II. It is supposed that such antibodies shield the class II molecule on the surface of their own antigen-presenting cell which may lead to immunodeficiency caused by the anti-HIV-1 antibody.     

Effect of the stereoisomers of glutamic acid on the vital activity of auxotrophic mutant producers of lysine]

Studies of L, D and DL-forms of glutamic acid as the sole nitrogen source or as a supplement to the major nitrogen source--ammonium sulphate have demonstrated that in the first case all forms of glutamic acid are assimilated by auxotrophic mutants--lysine producers. However, the lysine synthesis was very low, when L-glutamic acid was used as the only nitrogen source. Glutamic acid at a concentration of 0.01 M applied as a supplement to the major source of nitrogen acted as a stimulator of lysine synthesis, slightly inhibiting biomass increment. That was true of every form of glutamic acid, especially of DL-glutamic acid.     

The epidemiology of epidemic parotitis in the USSR.

Morbidity from epidemic parotitis in the USSR in the period from 1958 to 1972 ranged within the limits of 266.6 and 521.7 cases per 100 000 inhabitants. A 3--4 years cyclic recurrence of rises and falls in morbidity was observed. The bulk of cases of disease occur in the winter-spring period. In towns, parotitis is registered 3 times more frequently, in the mean, than in rural districts. More than 95% of patients in the USSR consisted of children under 15, while in Moscow, children aged 3--5 years were the most affected group. In Moscow in the period from February 1, 1972 to January 31, 1973, the morbidity in men was 493.2 per 100 000 and in women 339.5 per 100 000 (ratio 1:1.45).     

The human U5 snRNP 52K protein (CD2BP2) interacts with U5-102K (hPrp6), a U4/U6.U5 tri-snRNP bridging protein, but dissociates upon tri-snRNP formation

The U5 snRNP plays an essential role in both U2- and U12-dependent splicing. Here, we have characterized a 52-kDa protein associated with the human U5 snRNP, designated U5-52K. Protein sequencing revealed that U5-52K is identical to the CD2BP2, which interacts with the cytoplasmic portion of the human T-cell surface protein CD2. Consistent with it associating with an snRNP, immunofluorescence studies demonstrated that the 52K protein is predominantly located in the nucleoplasm of HeLa cells, where it overlaps, at least in part, with splicing-factor compartments (or "speckles"). We further demonstrate that the 52K protein is a constituent of the 20S U5 snRNP, but is not found in U4/U6.U5 tri-snRNPs. Thus, it is the only 20S U5-specific protein that is not integrated into the tri-snRNP and resembles, in this respect, the U4/U6 di-snRNP assembly factor Prp24p/p110. Yeast two-hybrid screening and pulldown assays revealed that the 52K protein interacts with the U5-specific 102K and 15K proteins, suggesting that these interactions are responsible for its integration into the U5 particle. The N-terminal two-thirds of 52K interact with the 102K protein, whereas its C-terminal GYF-domain binds the 15K protein. As the latter lacks a proline-rich tract, our data indicate that a GYF-domain can also engage in specific protein-protein interactions in a polyproline-independent manner. Interestingly, the U5-102K protein has been shown previously to play an essential role in tri-snRNP formation, binding the U4/U6-61K protein. The interaction of 52K with a tri-snRNP bridging protein, coupled with its absence from the tri-snRNP, suggests it might function in tri-snRNP assembly.     

Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking

Oenococcus oeni is an acidophilic member of the Leuconostoc branch of lactic acid bacteria indigenous to wine and similar environments. O. oeni is commonly responsible for the malolactic fermentation in wine and due to its positive contribution is frequently used as a starter culture to promote malolactic fermentation. In collaboration with the Lactic Acid Bacteria Genome Consortium the genome sequence of O. oeni PSU-1 has been determined. The complete genome is 1,780,517 nt with a GC content of 38%. 1701 ORFs could be predicted from the sequence of which 75% were functionally classified. Consistent with its classification as an obligately heterofermentative lactic acid bacterium the PSU-1 genome encodes all the enzymes for the phosphoketolase pathway. Moreover, genes related to flavor modification in wine, such as malolactic fermentation capacity and citrate utilization were readily identified. The completion of the O. oeni genome marks a significant new phase for wine-related research on lactic acid bacteria in which the physiology, genetic diversity and performance of O. oeni starter cultures can be more rigorously examined.     

Detection of IgG binding to Schistosoma mansoni recombinant protein RP26 is a sensitive and specific method for acute schistosomiasis diagnosis

We recently described the first recombinant Schistosoma mansoni protein RP26, which was capable of acute infection diagnosis. The aim of the present work was to further characterize the RP26 diagnostic properties in immunoblot and enzyme-linked immunosorbent (ELISA) assays. Testing sera from uninfected donors and sera from patients with acute or chronic Schistosoma infection by Western blot immunoassay revealed 100% specificity and 100% sensitivity for acute infection identification. Sera from uninfected, acute, and chronic schistosomiasis were also probed for IgG, IgG4, IgA, and IgM reactivity to RP26 plus soluble egg antigens (SEA) in ELISA. The mean IgG reactivity to RP26 by sera from acute schistosomiasis patients was significantly higher than the chronic ones. The IgG4, IgA, and IgM reactivities to RP26 were low and similar in both infected groups. The mean IgA and IgM reactivities to SEA were significantly higher in the group of acute compared to chronic group, whereas mean IgG4 reactivity was higher in chronic group. To estimate the specificity of Schistosoma infection diagnosis sera from patients infected with other different parasites were tested to detect IgG reactivity to RP26 and IgA and IgM reactivity to SEA. For IgA against SEA detection, 72% of sera were positive and 48% of sera were positive for IgM detection. Based on these results we can suggest that detection of sera IgG binding to RP26 is a sensitive and specific method for acute schistosomiasis diagnosis. Therefore, RP26 is a candidate for immunodiagnostic kit development.     

Evolutionary and functional genomics of the Archaea

In the past two years, archaeal genomics has achieved several breakthroughs. On the evolutionary front the most exciting development was the sequencing and analysis of the genome of Nanoarchaeum equitans, a tiny parasitic organism that has only approximately 540 genes. The genome of Nanoarchaeum shows signs of extreme rearrangement including the virtual absence of conserved operons and the presence of several split genes. Nanoarchaeum is distantly related to other archaea, and it has been proposed to represent a deep archaeal branch that is distinct from Euryarchaeota and Crenarchaeota. This would imply that many features of its gene repertoire and genome organization might be ancestral. However, additional genome analysis has provided a more conservative suggestion - that Nanoarchaeum is a highly derived euryarchaeon. Also there have been substantial developments in functional genomics, including the discovery of the elusive aminoacyl-tRNA synthetase that is involved in both the biosynthesis of cysteine and its incorporation into proteins in methanogens, and the first experimental validation of the predicted archaeal exosome.