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A A Mironov

Publications and source records attributed to A A Mironov.

At least 19 recordsLinked to original sources
PubMed2006

[How to measure structures, or new stereology: III. Stereology and electron microscopy].

This review describes modern stereological approaches and methods for estimation of subcellular structures dimensions. These estimators could be used for determination of number- and volume-weighted parameters of particle size. Very often they do not require the application of the disector at the first stage of sampling of images. Additionally, the modified version of the rotator for point counting is demonstrated, which significantly accelerates the morphometric procedure.

Cellular Structures↗
PubMed2005

Alternative splicing and protein function.

BACKGROUND: Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data. RESULTS: We have developed a method that generates possible mRNA isoforms for human genes contained in the EDAS database, taking into account the effects of nonsense-mediated decay and translation initiation rules, and a procedure for offsetting the effects of uneven EST coverage. Then we computed the number of mRNA isoforms for genes from different functional categories. Genes encoding ribosomal proteins and genes in the category "Small GTPase-mediated signal transduction" tend to have fewer isoforms than the average, whereas the genes in the category "DNA replication and chromosome cycle" have more isoforms than the average. Genes encoding proteins involved in protein-protein interactions tend to be alternatively spliced more often than genes encoding non-interacting proteins, although there is no significant difference in the number of isoforms of alternatively spliced genes. CONCLUSION: Filtering for functional isoforms satisfying biological constraints and accounting for uneven EST coverage allowed us to describe differences in alternative splicing of genes from different functional categories. The observations seem to be consistent with expectations based on current biological knowledge: less isoforms for ribosomal and signal transduction proteins, and more alternative splicing of interacting and cell cycle proteins.

Algorithms↗
PubMed2005

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.

MOTIVATION: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency for highly divergent motifs as well as estimation of motif geometric parameters. RESULT: We present a modification of the Gibbs sampling motif extraction algorithm, SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo), which finds structured motifs of these types, as well as non-structured motifs, in a set of unaligned DNA sequences. It employs improved estimators of motif and spacer lengths. The probability that a sequence does not contain any motif is accounted for in a rigorous Bayesian manner. We have applied the algorithm to a set of upstream regions of genes from two Escherichia coli regulons involved in respiration. We have demonstrated that accounting for a symmetric motif structure allows the algorithm to identify weak motifs more accurately. In the examples studied, ArcA binding sites were demonstrated to have the structure of a direct spaced repeat, whereas NarP binding sites exhibited the palindromic structure. AVAILABILITY: The WWW interface of the program, its FreeBSD (4.0) and Windows 32 console executables are available at http://bioinform.genetika.ru/SeSiMCMC

Algorithms↗
PubMed2005

[Myringoplasty and its effect on a vestibular function in patients with otitis media purulenta chronica (OMPC)].

A complex vestibulologic and audiologic examination was made in 25 patients with OMPC free of mesotympanitis before and after experimental myringoplasty with hen's egg amnion. The patients were divided into two groups depending on the presence of vestibular complaints. Partial or complete disappearance of subjective vestibular symptoms, reduced stimulation of the vestibular receptors (by 19%, on the average) were detected by experimental vestibular tests on the side of the affected ear. The asymmetry coefficient by labyrinth lowered by 31.1%, on the average.

Caloric Tests↗
PubMed2005

[How to measure the structures, or new stereology. I. Sampling and orientation of samples].

This article presents a brief review of newly developed methods of modern stereology for measurement of biostructures, which allow to avoid problems of uncertainty and technical difficulties peculiar to old stereology. In the first part of the review, a brief historical report on the development of new stereological approaches and their practical application to the selection and orientation of samples, is given. In particular, Cavalieri's principle, random systematic isotropic sampling, fractionator, isector, orientator and principle of vertical sections are described. Some details for practical aspects of measurements have been provided.

Histocytological Preparation Techniques↗
PubMed2005

[How to measure the structures, or new stereology. II. Methods of stereological estimation of the absolute dimensions of cell structures in light microscopy].

This review describes modern stereological estimators used for the counting of histological structures and their parameters determination at the light microscopic level. All of these estimators, as a rule, require the preliminary application of a disector for the sampling of images. Nucleator and rotator not only allow unbiased determination of structures absolute dimensions, but also help to save the time used for these operations. In the last years, these stereological estimators are being increasingly used in clinical practice and in electron microscopical analysis.

Cell Count↗
PubMed2004

Structural aspects of Golgi function.

Since its discovery, the Golgi complex has attracted the attention of cell biologists because of its 'fashionable' morphology and central position within the secretory system of the cell. Here, we discuss how the three-dimensional architecture of the Golgi complex relates to its multiple functions in protein sorting and processing, and how an analysis of the morphology of the Golgi complex can help to provide an understanding of the mechanisms involved in transport through this unique organelle.

Animals↗
PubMed2002

[Purine regulon of gamma-proteobacteria: a detailed description].

The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of gamma-proteobacteria: Escherichia coli, Salmonella typhi, Yersinia pestis, Haemophilus influenzae, Pasteurella multocida, Actinobacillus actinomycetemcomitans, and Vibrio cholerae. The palindromic binding site of the purine repressor (consensus ACGCAAACGTTTGCGT) is fairly well retained of genes encoding enzymes that participate in the synthesis of inosinemonophosphate from phosphoribozylpyrophosphate and in transfer of unicarbon groups, and also upstream of some transport protein genes. These genes may be regarded as the main part of the purine regulon. In terms of physiology, the regulation of the purC and gcvTHP/folD genes seems to be especially important, because the PurR site was found upstream of nonorthologous but functionally replaceable genes. However, the PurR site is poorly retained in front of orthologs of some genes belonging to the E. coli purine regulon, such as genes involved in general nitrogen metabolism, biosynthesis of pyrimidines, and synthesis of AMP and GMP from IMP, and also upstream of the purine repressor gene. It is predicted that purine regulons of the examined bacteria include the following genes: upp participating in synthesis of pyrimidines; uraA encoding an uracil transporter gene; serA involved in serine biosynthesis; folD responsible for the conversion of N5,N10-methenyl tetrahydrofolate into N10-formyltetrahydrofolate; rpiA involved in ribose metabolism; and protein genes with an unknown function (yhhQ and ydiK). The PurR site was shown to have different structure in different genomes. Thus, the tendency for a decline of the conservatism of site positions 2 and 15 was observed in genomes of bacteria belonging to the Pasteurellaceae and Vibrionaceae groups.

Adenosine Monophosphate↗
PubMed2001

Small cargo proteins and large aggregates can traverse the Golgi by a common mechanism without leaving the lumen of cisternae.

Procollagen (PC)-I aggregates transit through the Golgi complex without leaving the lumen of Golgi cisternae. Based on this evidence, we have proposed that PC-I is transported across the Golgi stacks by the cisternal maturation process. However, most secretory cargoes are small, freely diffusing proteins, thus raising the issue whether they move by a transport mechanism different than that used by PC-I. To address this question we have developed procedures to compare the transport of a small protein, the G protein of the vesicular stomatitis virus (VSVG), with that of the much larger PC-I aggregates in the same cell. Transport was followed using a combination of video and EM, providing high resolution in time and space. Our results reveal that PC-I aggregates and VSVG move synchronously through the Golgi at indistinguishable rapid rates. Additionally, not only PC-I aggregates (as confirmed by ultrarapid cryofixation), but also VSVG, can traverse the stack without leaving the cisternal lumen and without entering Golgi vesicles in functionally relevant amounts. Our findings indicate that a common mechanism independent of anterograde dissociative carriers is responsible for the traffic of small and large secretory cargo across the Golgi stack.

Animals↗
PubMed2001

Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.

In Bacillus subtilis, utilisation of xylose, arabinose and ribose is controlled by the transcriptional factors XylR, AraR and RbsR, respectively. Here we apply the comparative approach to the analysis of these regulons in the Bacillus/Clostridium group. Evolutionary variability of operon structures is demonstrated and operator sites for the main transcription factors are predicted. The consensus sequences for the XylR and RbsR binding sites vary in different subgroups of genomes. The functional coupling of gene clusters and the conservation of regulatory sites allow for detection of non-orthologous gene displacement of ribulose kinase in Enterococcus faecium and Clostridium acetobutylicum. Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression.

AraC Transcription Factor↗
PubMed2001

Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria.

The comparative approach to the recognition of transcription regulatory sites is based on the assumption that as long as a regulator is conserved in several genomes, one can expect that sets of co-regulated genes (regulons) and regulatory sites for the regulator in these genomes are conserved as well. We used this approach to analyze the ribose (RbsR), arabinose (AraC), and xylose (XylR) regulons of gamma Proteobacteria for which (almost) completely sequenced genomes were available. Candidate binding sites for RbsR and AraC were detected. The improved XylR site consensus was proposed. Potential new members of the xylose regulons were found in the Escherichia coli, Salmonella typhi, and Klebsiella pneumoniae genomes. The function of these new xylose-regulated operons is likely to be the utilization of oligosaccharides containing xylose. Finally, candidate cAMP receptor-protein sites were identified in the regulatory regions of the majority of RbsR-, AraC-, and XylR-regulated operons.

AraC Transcription Factor↗
PubMed2001

Comparative analysis of FUR regulons in gamma-proteobacteria.

Iron is an essential element for the survival and pathogenesis of bacteria. The strict control of iron homeostasis is mediated by the FUR repressor, which is highly conserved among various bacterial species. Here we apply the comparative genomics approach to analyze candidate Fur-binding sites in the genomes of Escherichia coli (K12 and O157:H7), Salmonella typhi, Yersinia pestis and Vibrio cholerae. We describe a number of new loci encoding siderophore biosynthesis and transport proteins. A new regulator of iron-acquisition systems was found in S.typhi. We predict FUR regulation for several virulence systems. We also predict FUR regulation for the chemotaxis system of V.cholerae that is probably involved in the process of pathogenesis.

Amino Acid Sequence↗
PubMed2001

Recruitment of protein kinase D to the trans-Golgi network via the first cysteine-rich domain.

Protein kinase D (PKD) is a cytosolic protein, which upon binding to the trans-Golgi network (TGN) regulates the fission of transport carriers specifically destined to the cell surface. We have found that the first cysteine-rich domain (C1a), but not the second cysteine-rich domain (C1b), is sufficient for the binding of PKD to the TGN. Proline 155 in C1a is necessary for the recruitment of intact PKD to the TGN. Whereas C1a is sufficient to target a reporter protein to the TGN, mutation of serines 744/748 to alanines in the activation loop of intact PKD inhibits its localization to the TGN. Moreover, anti-phospho-PKD antibody, which recognizes only the activated form of PKD, recognizes the TGN-bound PKD. Thus, activation of intact PKD is important for binding to the TGN.

Amino Acid Substitution↗
PubMed2001

Conservation of the binding site for the arginine repressor in all bacterial lineages.

BACKGROUND: The arginine repressor ArgR/AhrC is a transcription factor universally conserved in bacterial genomes. Its recognition signal (the ARG box), a weak palindrome, is also conserved between genomes, despite a very low degree of similarity between individual sites within a genome. Thus, the arginine repressor is different from two other universal transcription factors - HrcA, whose recognition signal is very strongly conserved both within and between genomes, and LexA/DinR, whose signal is strongly conserved within, but not between, genomes. The arginine regulon is well studied in Escherichia coli and to some extent in Bacillus subtilis and some other genomes. Here, we apply the comparative genomic approach to the prediction of the ArgR-binding sites in all completely sequenced bacterial genomes. RESULTS: Orthologs of ArgR/AhrC were identified in the complete genomes of E. coli, Haemophilus influenzae, Vibrio choleras, B. subtilis, Mycobacterium tuberculosis, Thermotoga maritima, Chlamydia pneumoniae and Deinococcus radiodurans. Candidate arginine repressor binding sites were identified upstream of arginine transport and metabolism genes. CONCLUSIONS: We found that the ArgR/AhrC recognition signal is conserved in all genomes that contain genes encoding orthologous transcription factors of this family. All genomes studied except M. tuberculosis contain ABC transport cassettes (related to the Art system of E. coli) belonging to the candidate arginine regulons.

Bacteria↗
PubMed2001

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.

Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts. It tolerates up to 5% of sequencing errors without considerable drop of prediction reliability when a sufficiently close homologous protein is available (normalized evolutionary distance similarity score 50% or higher).

Algorithms↗