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Biomedical subjects

I V Babkin

Publications and source records attributed to I V Babkin.

At least 19 recordsLinked to original sources
PubMed2005

Multiplex PCR detection and species differentiation of orthopoxviruses pathogenic to humans.

A method for one-stage rapid identification of four orthopoxvirus species pathogenic to humans based on multiplex polymerase chain reaction (MPCR) was developed. Five pairs of oligonucleotide primers--one, genus-specific; and the rest, species-specific for variola, monkeypox, cowpox, and vaccinia viruses, respectively--were used concurrently for MPCR assay of orthopoxvirus DNAs. Specificity and sensitivity of the method developed were evaluated using DNAs of 57 orthopoxvirus strains, including the DNAs isolated from human case clinical materials.

Cowpox virus↗
PubMed2003

[Multiplex PCR analysis for species specific express-identification of orthopoxviruses].

A method for one-stage rapid identification of the four orthopovirus species, which are pathogenic to humans, involving multiplex polymerase chain reaction (MPCR) was developed. Five pairs of oligonucleotides primers were simultaneously used in the mentioned MPCR assay of orthopoxvirus DNA; one of the pairs was genus-specific, the remaining four primers were species-specific for variola, monkey-pox, cowpox and vaccine-pox. The specificity and sensitivity of the developed method were evaluated through analyzing the DNA samples of 55 orthopoxvirus strains, including samples isolated from human clinical materials.

Base Sequence↗
PubMed2002

Analysis of the monkeypox virus genome.

Monkeypox virus (MPV) belongs to the orthopoxvirus genus of the family Poxviridae, is endemic in parts of Africa, and causes a human disease that resembles smallpox. The 196,858-bp MPV genome was analyzed with regard to structural features and open reading frames. Each end of the genome contains an identical but oppositely oriented 6379-bp terminal inverted repetition, which similar to that of other orthopoxviruses, includes a putative telomere resolution sequence and short tandem repeats. Computer-assisted analysis was used to identify 190 open reading frames containing >/=60 amino acid residues. Of these, four were present within the inverted terminal repetition. MPV contained the known essential orthopoxvirus genes but only a subset of the putative immunomodulatory and host range genes. Sequence comparisons confirmed the assignment of MPV as a distinct species of orthopoxvirus that is not a direct ancestor or a direct descendent of variola virus, the causative agent of smallpox.

Animals↗
PubMed2002

[Genetic identification of the Crimean-Congo hemorrhagic fever virus during epidemic outbreak in Kazakhstan in 2000].

Sera samples from patients suspected of Crimean-Congo hemorrhagic fever (CCHF) taken during epidemic outbreak at the territory of Sarysusky and Moiynkumsky districts of the Zhambyl region in Kazakhstan, in 2000, were analysed by means of reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of virus genome fragments. Genome RNA of CCHF virus was found in 2 assays. Analysis of nucleotide sequences of fragments of S-segment of viral genome revealed in the Sarysusky districts circulation of CCHF virus, genetically resembled to close phylogenetically to CCHF virus strains from China.

Amino Acid Sequence↗
PubMed2001

Human monkeypox and smallpox viruses: genomic comparison.

Monkeypox virus (MPV) causes a human disease which resembles smallpox but with a lower person-to-person transmission rate. To determine the genetic relationship between the orthopoxviruses causing these two diseases, we sequenced the 197-kb genome of MPV isolated from a patient during a large human monkeypox outbreak in Zaire in 1996. The nucleotide sequence within the central region of the MPV genome, which encodes essential enzymes and structural proteins, was 96.3% identical with that of variola (smallpox) virus (VAR). In contrast, there were considerable differences between MPV and VAR in the regions encoding virulence and host-range factors near the ends of the genome. Our data indicate that MPV is not the direct ancestor of VAR and is unlikely to naturally acquire all properties of VAR.

Amino Acid Sequence↗
PubMed1991

[5-Variable genome sequence of the LIVP vaccinia virus. A possible role for short direct repeats in the formation of deletions].

HindIII-O/N DNA fragments of vaccinia virus (VV) of the LIVP strain were mapped using thirteen restriction endonucleases. Nucleotide sequences of the HindIII-O fragment (1530 bp) as well as of a site of the HindIII-N genome fragment 353 bp in size were determined. Comparison of restriction maps and nucleotide sequences of VV strains (WR and LIVP) demonstrated that DNA of VV LIVP contained % deletions and 2 insertions. "Reliable" short direct repeats were localized and their possible role in formation of DNA deletions was shown. It was suggested that VV endonuclease and DNA-ligase participate in replication and repair processes. Mechanism of formation of variable sequences of viral genomes is discussed.

Amino Acid Sequence↗
PubMed1991

[Cloning, sequencing and translation analysis of the Vaccinia virus LIVP HINDIII N genome fragment].

The sequence of vaccinia virus (VV) LIVP HindIII N DNA fragment has been determined to be 2215 b.p. Three open reading frames designated LN1, N1 and NO1 and coding polypeptides with the calculated molecular masses (32.5 kDa, 21.8 kDa and 47.8 kDa) were located. mRNAs selected by hybridization with the VV HindIII N were translated in rabbit reticulocyte lysate. Proteins of genes for host range and resistance to alpha-amanitin corresponding to 29 and 47 kDa were detected. Two forms of polypeptides of the ORF LN1 (32 and 29K), and anomalous electrophoresis mobility of the ORF LN1 are discussed.

Amino Acid Sequence↗
PubMed1988

[Chemical transformation of radioactive 4-(N-2-chloroethyl-N-methylamino)benzyl-5'-[32P]phosphamides of oligodeoxyribonucleotides during in vivo experiments].

The practical use of reactive oligonucleotide derivatives for complementarily addressed modification of nucleic acids in vivo includes several steps, at which side chemical reactions resulting in a decrease of the modification efficiency may take place. Chemical reactions of 4-(N-2-chloroethyl-N-methylamino)benzyl-5'-[32P]phosphamides of oligodeoxyribonucleotides were studied in vivo. The intermolecular self-alkylation at the reactive residue of the alkylating derivative was found in the precipitate of its lithium salt under acetone at-20 degrees C. The effects of pH, buffer solutions, salts, temperature, phenol, cell culture suspensions, tissue homogenates, etc., on the stability of the derivatives were studied. A sufficient cleavage of the phosphamide bond was observed at pH less than 3. In fresh liver homogenates the nucleolytic degradation of the oligonucleotide part of the reagent was shown to occur. After intraperitoneal injection of mice with radioactive alkylating derivatives up to 50% of the reagent was included into the blood biopolymers within one hour. The covalently linked to the biopolymers oligonucleotide appeared to be highly degraded thereby.

Alkylating Agents↗
PubMedDate not supplied

[The time scale in poxvirus evolution].

Unlike vertebrates and RNA-containing viruses, the objective estimate of molecular clock for DNA-containing viruses was so far absent. An extended central conservative genomic region of orthopoxviruses (about 102 kbp) and the sequence of DNA polymerase gene (about 3 kbp) of the viruses belonging to various genera from the family Poxviridae were analyzed. During this analysis, the known dating of variola virus (VARV) transfer from West Africa to South America (XVI century) and our own data on close phylogenetic relations between the modem West African and South American VARV isolates were used. As a result of this work, it was calculated for the first time that the rate of mutation accumulation in these DNA-containing viruses amounted to 0.9-1.2 x 10(-6) substitutions per site per year. The poxviruses started separating from the ancestor virus to form the modem genera approximately 500 thousand years ago; the ancestor of the genus Orthopoxvirus separated about 300 thousand years ago; and its division into the modem studied species took place approximately 14 thousand years ago.

DNA, Viral↗
PubMedDate not supplied

[Identification of orthopoxvirus species using oligonucleotide micro-chips].

A method for describing the Orthopoxviruses that are pathogenic both to man and animals is described in the article. The method is based on hybridization of a fluorescently labelled amplified DNA sample with oligonucleotides, which were immobilized in a microchip. Species-specific regions within the crmB gene encoding a viral analogue of the tumor necrosis factor receptor, i.e. an important gene determining the pathogenicity of the mentioned Orthopoxviruses type, were used as a target for identification. The identification procedure takes around 6 hours and does not demand any costly equipment (a portable fluorescent microscope can be used).

Animals↗
PubMedDate not supplied

[The study of orthopoxvirus genes for Kelch-like proteins. II. Construction of cowpox virus variants with targeted gene deletions].

Integrative plasmids p delta C, p delta D, and p delta G were designed to contain a selective marker beyond the region of homology to virus DNA and to allow construction of recombinant cowpox viruses (CPV) that lack C18L, D11L, or G3L coding for kelch-like proteins. CPV mutants lacking one (C18L, D11L, or G3L), two (D11L/G3L or C18L/D11L), or three (D11L/G3L/C18L, that is, all) kelch-like protein genes of the left variable region of the virus genome were obtained. Impaired reproduction was observed for the triple mutant. Pocks produced by the triple mutant and the original virus differed in size and morphology. In addition, the two CPV variants differed in destructive changes caused in the chorioallantoic membrane of chicken embryos.

Animals↗
PubMedDate not supplied

[Comparative restriction enzyme analysis of the genome in variola virus strains from the Russian collection].

Comparative RFLP analysis was for the first time performed for 21 variola virus (VARV) strains of the Russian collection with 20 amplicons covering the total VARV genome. The amplicons were synthesized in the long polymerase chain reaction. A database useful as a reference for identifying VARV strains was generated. VARV strains isolated in different geographical regions were compared and proved to vary mostly in variable genome regions. Each of the dendrograms constructed included three clusters of African, Asian, and VARV-alastrim isolates. The VARV-alastrim isolates differed to the greatest extent from the other strains. VARV strains isolated during an ecdemic variola burst in Moscow (1960) grouped with Asian isolates. Polymorphism of VARV strains was for the first time observed for a single variola burst with a few affected patients.

Base Sequence↗
PubMedDate not supplied

[Construction of DNA-fragments' libraries with complete genomes of different variola strains].

Libraries of hybrid plasmids carrying DNA fragments of complete genomes of 8 variola virus strain from the Russian Collection belonging to 2 epidemical types and isolated in various geographic regions of the world were obtained. Genomic sequences of variola virus can be thus preserved for a long time in a biologically safe form and provide the research work on studying the genetic organization of this unique virus and on developing modern methods for rapid detection of variola virus and other orthopoxviruses.

DNA, Viral↗