Tabular excel editor for analysis of aligned nucleotide sequences

Excel platform was used for transition of results of multiple aligned nucleotide sequences obtained using the BLAST network service to the form appropriate for visual analysis and editing. Two macros operators for MS Excel 2007 were constructed. The array of aligned sequences transformed into Excel table and processed using macros operators is more appropriate for analysis than initial html data.     

Morphologic mutant of Escherichia coli K12 having disorders in morphology, division and cell wall biosynthesis]

A study was made of the properties of a spherical mutant obtained from the E. coli K12 HfrC strain under the effect of N-nitroso-N-methyl-urea. The growth of the mutant of full value media was characterized by a marked reduction of the cell division at the rest phase, but exponential growth phase failed to differ from the growth of the parental strain. Electron microscopic study of surface structures of the mutant cells which grew under physiological conditions permitted to distinguish two types: the first type had a typical structure of the cell wall characteristic of Gram negative microbes; the second type was framed by a bicontour membrane without any distinct structure. The presence of these two types of cells was also confirmed by their different sensitivity to the ionic detergents. On the basis of chemical analysis of peptidoglycan of the cell wall (which was markedly decreased in amount in the mutant cells), and also of the unsually high accumlation of the UDP-precursors of peptidoglycan under conditions of penicillin action it is supposed that normal regulation of metabolism of the cell walls was deranged. Mutation designated by 11rA symbol was plotted by phase PI transduction alongside of strA gene.     

The population structure of Mycobacterium tuberculosis in Mongolia as assessed using large sequence polymorphism analysis

112 strains of M. tuberculosis isolated from lung tuberculosis patients in Mongolia were genotyped using RD9, RD7, TbD1, RD105, and RD750 loci. The genotypes of all the strains studied were characterized using the conservation of RD7, RD9, and RD750 loci and the presence of the deletion in the locus TbD1. RD105 was detected in 65 isolates (58%). The isolate was classified into two groups--East-Asian and Euro-American.     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

Mapping the amino acid properties of constituent nucleoporins onto the yeast nuclear pore complex

Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules. Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the authors.     

The rickettsial genome studied by DNA restriction analysis

The restriction analysis of 6 Rickettsia prowazekii strains with the use of 8 restrictases (Cfr13I, EcoRI, HindIII, MSpI, MvaI, PstI, XhoI, BamHI) has been carried out. In the presence of considerable homology in the restriction pictures of DNA in these strains some differences in 1-2 fragments within the range of 8,000-20,000 nucleotide pairs have been established. The strains under study have been divided into two groups according to the character of differences in their restrictograms: the group of virulent typing strain Breinl (Breinl, G. Anan'ev) and the group of strain E with low pathogenicity (E, EVir, Katsinian). Differences in the restrictograms of DNA do not correlate with the virulence of R. prowazekii strains and the areas of their isolation.     

Estimation of the Total and Active Microbial Biomasses in Buried Subkurgan Paleosoils of Different Age

Microorganisms that were isolated from steppe soils buried below kurgans from 5800 to 750 years ago were analyzed for the completeness of isolation, total biomass (the sum of glucose-reactivated and resting microbial cells), and active biomass (metabolically active cells). The metabolic state of microbial communities in buried and modern background soils was estimated from the proportion of active and total biomasses. The paleosoils were found to be characterized by lower total and active biomasses and a lower proportion of active microorganisms as compared to the modern background soils. The age-dependent decrease in the content of active microorganisms in the microbial communities of paleosoils was not monotonic. For instance, the 4000-year-old paleosoil was characterized by a high total biomass and a relatively low content of active microorganisms, whereas the 1950-year-old paleosoil was characterized by a relatively low total biomass and a relatively high content of active microorganisms. This could reflect the temporal dynamics of paleoclimatic conditions in the geographic region under study.     

UV-inducibility of the LT-toxin operon

The plasmid elt-operon pVZ14 was constructed by fusing of the eltoperon of the plasmid pVZ357 with the lac-gene of the bacteriophage Mud1 (Amp, Lac). lacZ gene has been proven to be fused with an elt-promoter by the loss of toxin production coded by pVZ357 and acquiring of Lac+ phenotype by pVZ14 containing cells, as well as by HindIII fragments hybridization of pVZ357 and pVZ14 with the labelled elt-probe. The kinetics of beta-galactosidase synthesis in E. coli cells harboring pVZ14 shows an elt-operon promoter to have expressed constitutive activity and to be activated by a SOS-inducing agent, UV-light.     

Rd7 genotyping of M. tuberculosis strains isolated from patients with lung tuberculosis in different areas of Kazakhstan

A three-primer PCR assay was designed for detection of possible deletions in the RD7 region of the Mycobacterium tuberculosis complex chromosome. The assay produced amplicons of different size depending on the presence or absence of the deletions. The PCR assay was applied to 176 isolates from patients with lung tuberculosis collected in different areas of Kazakhstan in summer 2004. The isolates were initially characterized by culture and biochemical tests. The RD7 genotyping results demonstrated no polymorphism and the absence of deletions in the RD7 genome region. Some strains were additionally characterized using PCR-RFLP analysis of gyrB and hsp64 genes. The RFLP-patterns obtained corresponded to the M. tuberculosis genotypes. The results of this work are consistent with certain previous studies, indicating population stability of the RD7 region in M. tuberculosis strains. Species characterization of the isolates shows that M. tuberculosis sensu stricto is the principal causative agent of human lung tuberculosis in Kazakhstan.