Comparative Analysis of Behavioral Reactions and Morphological Changes in the Rat Brain After Exposure to Ionizing Radiation with Different Physical Characteristics.

The aim of this research was to study behavioral reactions and morphological changes in the brain of adult female Sprague Dawley rats after exposure to 170 MeV and 70 MeV protons and gamma radiation (60Co) at a dose of 1 Gy. The analysis of the behavioral reactions in the T-maze showed that exposure to ionizing radiation with different LETs led to an increase in number of repeated entries into the arms of the maze in the spontaneous alternation test. In the Open Field test a decrease in overall motor activity in the group of irradiated animals (70 MeV protons at the Bragg peak) was observed. A decrease in the number of standing positions was seen in all groups of irradiated animals. Morphological analysis showed the development of early amyloidosis, autolysis of the ependymal layer, an increase in the number of neurodegenerative changes in various structures of the brain, and the development of neuronal hypertrophy on the 30th day after irradiation in the cerebellum and hippocampal hilus. Exposure to protons at a dose of 1 Gy leads to the development of structural and functional disorders of the central nervous system of animals on the 30th day after irradiation. These data indicate a damage of short-term memory, a decrease in motor activity and exploratory behavior of animals. With an increase in LET, there is an increase in the number of amyloid plaques in the forebrain of rats, autolysis of the ependymal layer of the ventricles, and the development of dystrophic changes. Investigations of behavioral reactions and morphological changes in various parts of the brain of adult rats on the 30th day after influence of ionizing radiation with different physical characteristics at a dose of 1 Gy. Various negative patho-morphological and cognitive-behavioral changes observed.

[The method of template construction for sequencing extended DNA fragments]. / Sposob prigotovleniia matrits dlia opredeleniia nukleotidnykh posledovatel'nostei protiazhennykh fragmentov DNK.

A rapid and convenient method was proposed for constructing insertional mutants in the sequencing of extended DNA fragments. The gist is insertion of an antibiotic resistance gene in plasmid DNA digested with DNase I. DNase I provides for a uniform distribution of insertion sites along the plasmid, and the background is low owing to antibiotic-based selection. The method requires neither high quality nor large amounts of plasmid DNA (which is especially important with low-copied plasmids), yields the results independent of the plasmid nucleotide sequence, and allows highly accurate analysis and ordering of the insertional mutants.

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

A probabilistic method for identifying start codons in bacterial genomes.

As the pace of genome sequencing has accelerated, the need for highly accurate gene prediction systems has grown. Computational systems for identifying genes in prokaryotic genomes have sensitivities of 98-99% or higher (Delcher et al., Nucleic Acids Res., 27, 4636-4641, 1999). These accuracy figures are calculated by comparing the locations of verified stop codons to the predictions. Determining the accuracy of start codon prediction is more problematic, however, due to the relatively small number of start sites that have been confirmed by independent, non-computational methods. Nonetheless, the accuracy of gene finders at predicting the exact gene boundaries at both the 5' and 3' ends of genes is of critical importance for microbial genome annotation, especially in light of the important signaling information that is sometimes found on the 5' end of a protein coding region. In this paper we propose a probabilistic method to improve the accuracy of gene identification systems at finding precise translation start sites. The new system, RBSfinder, is tested on a validated set of genes from Escherichia coli, for which it improves the accuracy of start site locations predicted by computational gene finding systems from the range 67-77% to 90% correct.

Synonymous codon usage in bacteria.

In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid conservation, protein hydropathy, transcriptional selection and even RNA stability. The review discusses these factors and their contribution to bias in synonymous codon usage in bacterial genomes.

Complete genome sequence of Caulobacter crescentus.

The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.

Prediction of operons in microbial genomes.

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P: >/= 0.98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.

Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.

Prediction of transcription terminators in bacterial genomes.

This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energy-scoring function that reflects hairpin stability, and a tail-scoring function based on the number of U nucleotides and their proximity to the stem, are computed. A confidence value can be assigned to each terminator by analyzing candidate terminators found both within and between genes, and taking into account the energy and tail scores. The confidence is an empirical estimate of the probability that the sequence is a true terminator. The algorithm was used to conduct a comprehensive analysis of 12 bacterial genomes to identify likely candidates for rho-independent transcription terminators. Four of these genomes (Deinococcus radiodurans, Escherichia coli, Haemophilus influenzae and Vibrio cholerae) were found to have large numbers of rho-independent terminators. Among the other genomes, most appear to have no transcription terminators of this type, with the exception of Thermotoga maritima. A set of 131 experimentally determined E. coli terminators was used to evaluate the sensitivity of the method, which ranges from 89 % to 98 %, with corresponding false positive rates of 2 % and 18 %.

[Molecular dynamics of oligopeptides. 3. Maps of levels of free energy of modified dipeptides and dynamic correlation in amino acid residues]. / Molekuliarnaia dinamika oligopeptidov. 3. Karty urovnei svobodnoi énergii modifitsirovannykh dipeptidov i dinamicheskie korreliatsii v aminokislotnykh ostatkakh.

A method of free energy maps for studying the dynamic correlations of fluctuations in molecules with conformational mobility is proposed. An agreement between the structure of the free energy level map and the type of the corresponding cross-correlation function (in the presence and absence of the correlation of fluctuations in conformational freedom degree in modified dipeptides) was established.

Multiple forms of the SH2-containing inositol phosphatase, SHIP, are generated by C-terminal truncation.

The SH2-containing inositol phosphatase, SHIP, often appears as multiple bands in anti-SHIP immunoblots. To characterize these bands, antisera were generated against the N-terminal (anti-N), mid-region (anti-M), and C-terminal (anti-C) portions of SHIP. Immunoprecipitation and immunoblotting studies showed that 145-, 135-, 125-, and 110-kD bands were detected in lysates from the murine hematopoietic cell line, DA-ER, with either anti-N or anti-M antisera, whereas only the 145- and 135-kD bands were recognized by the anti-C antiserum. This finding suggested that the smaller proteins might be C-terminal truncations of the full-length SHIP. To confirm this and determine if these proteins arose through alternate splicing or posttranslational cleavage, a 5'-hemagglutin (HA)-tagged full-length SHIP cDNA was expressed in these cells. We observed, via Western analysis with anti-HA antibodies, the same 4 bands with either anti-N or anti-M and only the 145- and 135-kD bands with anti-C immunoprecipitation. After interleukin-3 stimulation of HA-SHIP-expressing DA-ER cells, only the 145-kD form coprecipitated with Shc, raising the possibility that different forms of SHIP may have distinct intracellular sites. This was confirmed by subcellular fractionation, which showed that only the 110-kD form is present in the cytoskeleton of DA-ER cells. This 110-kD form possesses the same PIP3 5-ptase activity as the 145-kD form and can be generated from the latter in vitro by digestion with calpain. It is therefore possible that the different forms of SHIP are generated in vivo by calpain-mediated C-terminal truncations and perform distinct functions within hematopoietic cells.

[Dynamic surface tension of blood and synovial fluid in rheumatoid arthritis]. / Dinamicheskoe poverkhnostnoe natiazhenie krovi i sinovial'noi zhidkosti pri revmatoidnom artrite.

AIM: Assessment of the dynamic surface tension (DST) of blood serum (BS), synovial fluid (SF) in various courses of rheumatoid arthritis (RA). MATERIALS AND METHODS: Forty three patients with RA and 63 apparently healthy individuals were examined. DST of BS and SF was determined in the computer-aided tensiometer and some blood biochemical parameters were also measured. RESULTS: DST of BS in patients with RA were found to be higher than the normal values and some parameters c beta 2 and beta 3) of BS DST did not significantly differ from the normal values whereas others (beta 1 and gamma proved to be much lower. Depending on the disease course variants, there were some differences in these DST changes. There was a feedback between DST parameters and the levels of immunoglobulins, beta 2-microglobulin, and lipids in blood. CONCLUSION: Assessment of BS and SF DST may be useful in the differential diagnosis of RA, in the determination of its intensity and prognosis, and therapeutical efficiency.

[Changes in the dynamic surface tension of the blood and urine during the development of visceritis in patients with rheumatoid arthritis]. / Izmeneniia dinamicheskogo poverkhnosnogo natiazheniia krovi i mochi pri razvitii vistserita u bol'nykh revmatoidnym artritom.

The condition was studied of the dynamic surface tension of biologic fluids in patients with rheumatoid arthritis using a method of maximum pressure in the vesicle with the aid of computerized tensiometer MPT-1 "Lauda" (Germany). Rise in indices of blood serum surface tension with diminution of the slope of tensiogram curves may suggest the development of pathology of the heart and liver, while increase in the same parameters of urine might be indicative of the coming nephropathy.

Expression and hormonal regulation of transcription factors GATA-4 and GATA-6 in the mouse ovary.

Two members of the GATA-binding family of transcription factors, GATA-4 and GATA-6, are expressed in the vertebrate ovary. To gain insight into the role of these factors in ovarian cell differentiation and function, we used in situ hybridization to determine the patterns of expression of GATA-4 and GATA-6 in mouse ovary during development and in response to hormonal stimulation. GATA-4 messenger RNA (mRNA) was first evident in the ovary around the time of birth. In the adult ovary, abundant GATA-4 mRNA was detected in granulosa cells of primary and antral follicles, with lesser amounts of GATA-4 message detected in theca cells, germinal epithelium, and interstitial cells. Little or no GATA-4 mRNA was found in corpus luteum. GATA-6 message exhibited a different distribution in the ovary, with abundant expression evident in both granulosa cells and corpora lutea. Stimulation of 3-week-old females with PMSG or estrogen enhanced follicular expression of GATA-4 and GATA-6 transcripts. Subsequent induction of ovulation with human CG resulted in a decrease in GATA-4 mRNA expression in granulosa cells, whereas GATA-6 mRNA expression persisted in granulosa cells after ovulation and in corpora lutea. Moreover, follicular apoptosis was associated with a decrease in the expression of GATA-4 but not GATA-6 message. Stimulation of cultured gonadal cell lines with FSH resulted in increased expression of GATA-4 message, whereas GATA-6 mRNA expression was not affected. In light of these findings, the established role of other GATA-binding proteins in hematopoetic cell differentiation and apoptosis, and the presence of conserved GATA motifs in the promoters of genes expressed selectively in ovary, we propose that GATA-4 and GATA-6 play distinct roles in follicular development and luteinization.

[Molecular dynamics of oligopeptides. 2. Dynamic correlation functions of the conformational modes of the modified dipeptides]. / Molekuliarnaia dinamika oligopeptidov. 2.Korreliatsionnye funktsii vnutrennikh stepenei svobody modifitsirovannykh dipeptidov.

The method of investigation of dynamic correlation functions in molecules with conformational mobility on an example of modified dypeptides by molecular dynamics is proposed. Comparison of results for different types torsion angles and internuclear distances are carried out. Connection between the chemical structure of peptides and the peculiarities of internal dynamic correlations is established. A question about dynamic isomorphism of amino acids is discussed.

[Molecular dynamics of oligopeptides. 1. The use of long trajectory and high temperature data for determination of statistical weight of conformational substates]. / Molekuliarnaia dinamika oligopeptidov. 1. Ispol'zovanie dannykh traektorii i vysokikh temperatur dlia opredeleniia statisticheskogo vesa konformatsionnykh podsostoianii.

The method of molecular dynamics investigations of the particularities of macromolecule physical-chemical properties is discussed. The results, obtained from the calculations of modified dipeptides in different regimes (different temperatures, length of trajectories and ways of thermostat simulation) are compared. The optimal conditions for this peptides calculations are determined: collisional dynamics regime, trajectories not less than 5000 ps, temperature about 1000 K. In this case the figurative point is able to scan the molecule configuration space and the statistically reliable results could be obtained.

[The dynamic surface tension of the blood and urine in chronic glomerulonephritis]. / Dinamicheskoe poverkhnostnoe natiazhenie krovi i mochi pri khronicheskom glomerulonefrite.

Dynamic surface-tension (S-T) was investigated of blood and urine of healthy individuals and patients with chronic glomerulonephritis by the proposed method of maximum pressure in a bubble with the aid of the computer-assisted device tensometer MPT-1 (Lauda, Germany). Patterns of changes in dynamic and static S-T were found out as were those of the slope of the curve in patients with mesangioproliferative and mesangiocapillary variants of the condition, in nephrotic syndrome and chronic renal insufficiency. Correlation type comparison was performed of physical-and-chemical properties of biological fluids to parameters characterizing protein and fat exchange. Relationship between dynamic S-T and biochemical composition of blood and urine was revealed. Diagnostic value of results of the studies made is discussed.

Efficient interaction with a receptor requires a specific type of prenyl group on the G protein gamma subunit.

Post-translational prenylation of the carboxyl-terminal cysteine is a characteristic feature of the guanine nucleotide-binding protein (G protein) gamma subunits. Recent findings show that the farnesylated COOH-terminal tail of the gamma 1 subunit is a specific determinant of rhodopsin-transducin coupling. We show here that when synthetic peptides specific to the COOH-terminal tail of gamma 1 are chemically modified with geranyl, farnesyl, or geranylgeranyl groups and tested for their ability to interact with light activated rhodopsin, the farnesylated peptide is significantly more effective. These results show that an appropriate isoprenoid on the G protein gamma subunit serves not only a membrane anchoring function but in combination with the COOH-terminal domain specifies receptor-G protein coupling.

Receptor-G protein coupling is established by a potential conformational switch in the beta gamma complex.

Receptor-G protein interaction is characterized by cycles of association and dissociation. We present evidence which indicates that during receptor-G protein interaction, the C-terminal tail of the G protein gamma subunit, which is masked in the beta gamma complex, is exposed and establishes high-affinity contact with the receptor. This potential conformational switch provides a mechanism to regulate receptor-G protein coupling. This switch may also be significant for the role of the beta gamma complex in regulation of effector function.