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1.
Epidemiol Infect ; 145(15): 3154-3167, 2017 11.
Article in English | MEDLINE | ID: mdl-29061202

ABSTRACT

Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. (hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.


Subject(s)
Chiroptera/microbiology , Mycoplasma Infections/veterinary , Mycoplasma/genetics , Animals , Belize , DNA, Bacterial/genetics , Disease Reservoirs/microbiology , Genetic Variation/genetics , Mycoplasma Infections/microbiology , Mycoplasma Infections/transmission , Peru , Phylogeny , Polymerase Chain Reaction/veterinary , RNA, Ribosomal, 16S/genetics
2.
J Appl Microbiol ; 116(1): 100-8, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24112653

ABSTRACT

AIMS: The aim of this study was to optimize conditions for preparation and cryopreservation of mycoplasma reference materials suitable to evaluate alternative nucleic acid testing (NAT)-based assays and to compare their limits of detection (LODs) with those of conventional culture-based methods. METHODS AND RESULTS: Acholeplasma laidlawii, Mycoplasma gallisepticum and Mycoplasma arginini stocks with low ratios of genomic copies to colony forming units (12, 8 and 4, respectively) harvested in early stationary phases of growth were preserved with different cryoprotective agents (CPAs) under slow (1°C min(-1)), moderate (8°C min(-1)), fast (13°C min(-1)) and 'snapshot' (60°C min(-1)) cooling rates. Depending on mycoplasma species, increasing the cooling rate from slow to snapshot enhanced cell survival up to 5-fold. The addition of 10% (v/v) dimethyl sulfoxide (DMSO) and 15% (v/v) glycerol significantly improved cell survival of all tested strains. Cryoprotected stocks maintained high and stable titres for at least 1 year during storage at -80°C. Sonication of cell cultures prior to cryopreservation enhanced cell dispersion and reduced of GC/CFU ratios. CONCLUSIONS: It is feasible to prepare stable reference stocks of cryopreserved mycoplasma cells suitable to reliably compare NAT- and culture-based mycoplasma testing methods. SIGNIFICANCE AND IMPACT OF THE STUDY: This study describes experimental results demonstrating the preparation and storage of highly viable and dispersed mycoplasma reference stocks suitable for comparing alternative NAT-and conventional culture-based mycoplasma detection methods.

3.
J Appl Microbiol ; 111(4): 904-14, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21794032

ABSTRACT

AIMS: To optimize growth conditions for preparation of stocks of mycoplasma reference strains to obtain highly viable and disperse samples with low ratios of genomic copy (GC) number to that of colony forming units (CFU). These stocks are required for assessment of relative limits of detection (LOD) of alternative nucleic acid testing (NAT)-based methods in comparison to the conventional microbiological methods. METHODS AND RESULTS: A kinetics study was used to assess the changes in ratios between the numbers of GC and CFU at different growth phases of six different mycoplasma cultures Acholeplasma laidlawii, Mycoplasma gallisepticum, Mycoplasma arginini, Mycoplasma fermentans, Mycoplasma orale and Mycoplasma pneumoniae. All tested mycoplasmas demonstrated low GC/CFU ratios (≤ 10) within the log and early stationary growth phases. A significant increase in GC/CFU ratios was observed at the very late stationary and death phases, when the titre of cultures has declined. Similar patterns of GC/CFU profiles were observed for A. laidlawii and Myc. gallisepticum co-cultured with suspension of Chinese hamster ovary (CHO) cells. CONCLUSIONS: Tested mycoplasma strains harvested at the exponential-early stationary phases of growth demonstrated the lowest GC/CFU ratios and low propensity to form filamentous structures or aggregates under proposed conditions and can be used for the preparation of a mycoplasma reference panel for methods comparability study. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that the preparation and use of viable mycoplasma reference strains with low CG/CFU ratios is the most reliable way to adequately evaluate the LOD of alternative NAT-based mycoplasma testing methods.


Subject(s)
Bacteriological Techniques/methods , Mycoplasma/growth & development , Animals , CHO Cells , Coculture Techniques , Colony Count, Microbial/methods , Cricetinae , Cricetulus , DNA, Bacterial/genetics , Evaluation Studies as Topic , Gene Dosage , Limit of Detection , Mycoplasma/genetics , Polymerase Chain Reaction , Reference Standards , Validation Studies as Topic
4.
J Microbiol Methods ; 86(3): 383-6, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21693139

ABSTRACT

A novel application of mid-infrared chemical imaging (IRCI) for the fluorophore-free detection and identification of mycoplasma species is reported for the first time. The PCR-amplified biotinylated targets hybridized to microarray probes were treated with streptavidin-gold nanoparticles followed by silver enhancement. This modification has the potential to expand the implementation of DNA microarray techniques in laboratories involved in the detection of cell substrates, other biological products, and clinical materials for the presence of mycoplasmas.


Subject(s)
Mycoplasma/isolation & purification , Oligonucleotide Array Sequence Analysis/methods , Polymerase Chain Reaction/methods , DNA, Bacterial/analysis , DNA, Bacterial/chemistry , Gold/chemistry , Infrared Rays , Metal Nanoparticles/chemistry , Mycoplasma/genetics , Silver/chemistry , Spectrophotometry, Infrared , Streptavidin/chemistry
5.
J Appl Microbiol ; 110(1): 54-60, 2011 Jan.
Article in English | MEDLINE | ID: mdl-20854458

ABSTRACT

AIMS: To assess the limit of detection (LOD) and the feasibility of 16S rRNA-based reverse transcription-PCR (RT-PCR) assays for advanced detection of mycoplasma contamination in cell substrates. MATERIALS AND METHODS: The RT-PCR approach is based on detecting the 16S rRNA molecules that, in contrast to genomic bacterial DNA, are represented by multiple copies in mycoplasma cell. The number of 16S rRNA molecules in mycoplasma cells of five species i.e. Mycoplasma arginini, Myc. fermentans, Myc. hyorhinis, Myc. orale and Acholeplasma laidlawii, all known to be frequent cell line contaminants in industrial and research laboratories, was measured using molecular methods. The results of two independently prepared mycoplasma cultures harvested at the stationary phase of their growth showed that the 16S rRNA copy number per cell varied in the range from about 400 to 2000 copies, depending on species, but stayed close between different preparations of one species. The assessment of the LOD of the in-house 16S rRNA-based RT-PCR was performed using samples of MDCK cell culture spiked with different amounts of five aforementioned mycoplasma species. To minimize the bias in methods comparison, the LOD of the RT-PCR assay was expressed in terms of genome equivalents (GEs) and compared with that determined for highly optimized 16S rDNA-based mycoplasma testing methods previously described in scientific literature. CONCLUSIONS: The results of the study showed that the in-house 16S rRNA-based RT-PCR assay was able to reliably detect the presence of less than one mycoplasma GE that is at least 10-fold higher of the LOD previously determined for well-optimized 16S rDNA-based assays developed and described by other researchers. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of the study showed that rapid RT-PCR methods based on the detection of bacterial 16S rRNA are able to expedite mycoplasma testing of cell cultures (1-2 days vs 28 days) and to ensure the limits of detection comparable to that of currently used culture-based mycoplasma testing methods.


Subject(s)
Mycoplasma/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , Animals , Cell Line , Limit of Detection , Mycoplasma/genetics , RNA, Ribosomal, 16S/analysis
6.
Mol Gen Mikrobiol Virusol ; (4): 23-30, 2006.
Article in Russian | MEDLINE | ID: mdl-17094655

ABSTRACT

An oligonucleotide microarray for detection and identification of orthopoxviruses was developed. Genus specific and orthopoxvirus species-specific regions of the genes encoding chemokine binding and alpha/beta-interferon binding proteins were used as a target. The developed microarray allows the variola, monkeypox, cowpox, vaccinia, camel-pox and ectromelia (mousepox) viruses to be distinguished with a high degree of reliability.


Subject(s)
Gene Amplification , Genes, Viral , Oligonucleotide Array Sequence Analysis , Orthopoxvirus/classification , In Situ Hybridization, Fluorescence , Orthopoxvirus/genetics , Phylogeny
7.
Mol Cell Probes ; 18(6): 359-67, 2004 Dec.
Article in English | MEDLINE | ID: mdl-15488374

ABSTRACT

A microarray-based method for characterization of six Clostridium perfringens toxin genes: iA (iota toxin), cpa (alpha toxin), cpe (enterotoxin E), etxD (epsilon toxin), cpb1 (beta toxin 1),and cpb2 (beta toxin 2) was developed and evaluated using 17 C. perfringens isolates. Three individual oligonucleotide probes (oligoprobes), complementary to the unique sequences of each toxin gene, were designed and immobilized on a surface of aldehyde-coated glass slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all six genes. Single-stranded DNA (ssDNA) samples for microarray analysis were prepared by following a primer extension of amplicons in the presence of one primer. Fluorescent moieties (Cy3) were incorporated into the ssDNA by chemical modification of guanine bases. The presence of toxin genes in C. perfringens was established by hybridization of the fluorescently labeled ssDNA representing different samples to the microarray gene-specific oligoprobes. Results of the study showed sensitivity and specificity of genotyping C. perfringens using multiple microarray-based assays.


Subject(s)
Bacterial Toxins/genetics , Clostridium perfringens/classification , Oligonucleotide Array Sequence Analysis , ADP Ribose Transferases/genetics , Bacterial Typing Techniques , Base Sequence , Calcium-Binding Proteins/genetics , Clostridium perfringens/genetics , Clostridium perfringens/pathogenicity , Enterotoxins/genetics , Genotype , Oligonucleotide Probes , Polymerase Chain Reaction , Type C Phospholipases/genetics
8.
Appl Opt ; 43(23): 4590-7, 2004 Aug 10.
Article in English | MEDLINE | ID: mdl-15376437

ABSTRACT

We present data on the linear (transmission, index of refraction) and nonlinear (second-order susceptibility) optical properties of the quaternary semiconductor AgGaGe5Se12 with orthorhombic symmetry--a solid solution in the AgxGaxGe1-xSe2 system with x = 0.17. The nonlinear coefficients are estimated from phase-matched second-harmonic generation near 3 microm. After numerical analysis of the phase-matching configurations for three-wave nonlinear interactions, the first experimental results on difference-frequency mixing, producing tunable (4-7.5-microm) femtosecond pulses at a 1-kHz repetition rate, are described. The pulses of only five optical cycles (FWHM = 84 fs) are generated near 5 microm with energy of 0.5 microJ. Because of its higher damage threshold, larger birefringence and bandgap, and greater variety of phase-matching schemes, AgGaGe5Se12 could become an alternative to AgGaS2 and AgGaSe2, more widely used in high-power and specific applications.

9.
Appl Environ Microbiol ; 70(7): 4256-66, 2004 Jul.
Article in English | MEDLINE | ID: mdl-15240309

ABSTRACT

Identification of bona fide Listeria isolates into the six species of the genus normally requires only a few tests. Aberrant isolates do occur, but even then only one or two extra confirmatory tests are generally needed for identification to species level. We have discovered a hemolytic-positive, rhamnose and xylose fermentation-negative Listeria strain with surprising recalcitrance to identification to the species level due to contradictory results in standard confirmatory tests. The issue had to be resolved by using total DNA-DNA hybridization testing and then confirmed by further specific PCR-based tests including a Listeria microarray assay. The results show that this isolate is indeed a novel one. Its discovery provides the first fully documented instance of a hemolytic Listeria innocua strain. This species, by definition, is typically nonhemolytic. The L. innocua isolate contains all the members of the PrfA-regulated virulence gene cluster (Listeria pathogenicity island 1) of L. monocytogenes. It is avirulent in the mouse pathogenicity test. Avirulence is likely at least partly due to the absence of the L. monocytogenes-specific allele of iap, as well as the absence of inlA, inlB, inlC, and daaA. At least two of the virulence cluster genes, hly and plcA, which encode the L. monocytogenes hemolysin (listeriolysin O) and inositol-specific phospholipase C, respectively, are phenotypically expressed in this L. innocua strain. The detection by PCR assays of specific L. innocua genes (lin0198, lin0372, lin0419, lin0558, lin1068, lin1073, lin1074, lin2454, and lin2693) and noncoding intergenic regions (lin0454-lin0455 and nadA-lin2134) in the strain is consistent with its L. innocua DNA-DNA hybridization identity. Additional distinctly different hemolytic L. innocua strains were also studied.


Subject(s)
Genes, Bacterial , Listeria monocytogenes/genetics , Listeria monocytogenes/pathogenicity , Listeria/genetics , Animals , Base Sequence , Listeria monocytogenes/classification , Mice , Molecular Sequence Data , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , Phylogeny , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics , Serotyping , Virulence
10.
J Appl Microbiol ; 95(4): 787-98, 2003.
Article in English | MEDLINE | ID: mdl-12969293

ABSTRACT

AIMS: To develop a DNA microarray for analysis of genes encoding resistance determinants to erythromycin and the related macrolide, lincosamide and streptogramin B (MLS) compounds. METHODS AND RESULTS: We developed an oligonucleotide microarray containing seven oligonucleotide probes (oligoprobes) for each of the six genes (ermA, ermB, ermC, ereA, ereB and msrA/B) that account for more than 98% of MLS resistance in Staphylococcus aureus clinical isolates. The microarray was used to test reference and clinical S. aureus and Streptococcus pyrogenes strains. Target genes from clinical strains were amplified and fluorescently labelled using multiplex PCR target amplification. The microarray assay correctly identified the MLS resistance genes in the reference strains and clinical isolates of S. aureus, and the results were confirmed by direct DNA sequence analysis. Of 18 S. aureus clinical strains tested, 11 isolates carry MLS determinants. One gene (ermC) was found in all 11 clinical isolates tested, and two others, ermA and msrA/B, were found in five or more isolates. Indeed, eight (72%) of 11 clinical isolate strains contained two or three MLS resistance genes, in one of the three combinations (ermA with ermC, ermC with msrA/B, ermA with ermC and msrA/B). CONCLUSIONS: Oligonucleotide microarray can detect and identify the six MLS resistance determinants analysed in this study. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggest that microarray-based detection of microbial antibiotic resistance genes might be a useful tool for identifying antibiotic resistance determinants in a wide range of bacterial strains, given the high homology among microbial MLS resistance genes.


Subject(s)
Erythromycin/pharmacology , Oligonucleotide Array Sequence Analysis/methods , Staphylococcus/genetics , Anti-Bacterial Agents/pharmacology , Base Sequence , Culture Media , DNA, Bacterial/biosynthesis , Drug Resistance, Bacterial , Lincosamides , Macrolides/pharmacology , Polymerase Chain Reaction/methods , Sequence Analysis, DNA/methods , Staphylococcus/drug effects , Staphylococcus aureus/drug effects , Staphylococcus aureus/genetics , Streptogramin B/pharmacology
11.
Vaccine ; 21(25-26): 3867-74, 2003 Sep 08.
Article in English | MEDLINE | ID: mdl-12922121

ABSTRACT

The yield of influenza virus in eggs is critical to influenza vaccine production and availability, but the contribution of specific genes to the growth properties of influenza B viruses is not well understood. Influenza B/Beijing/184/93 and B/Shangdong/7/97 were chosen for study because B/Shangdong/7/97 replicated to several fold higher titers in eggs than B/Beijing/184/93 as demonstrated by hemagglutination titers and EID50. A reassortant with the HA, NP and PB2 genes from B/Beijing/184/93 and all other genes from B/Shangdong/7/97 had the high growth phenotype of B/Shangdong/7/97 in eggs, which suggests that NS, M, NA, PB1 or PA, or a combination of these genes derived from B/Shangdong/7/97 were needed for the high growth phenotype of the reassortants. A high degree of homology was found among the genetic sequences of B/Beijing/184/93, B/Shangdong/7/97, and other influenza B viruses. However, differences potentially related to growth characteristics were suggested by analysis of the deduced amino acid (AA) sequences of four genes: NS (NS1, NS2), M (BM2), NA (NA, NB) and PB1. The studies identify multiple genes that may affect growth of influenza B viruses in eggs.


Subject(s)
Influenza B virus/growth & development , Influenza B virus/genetics , Animals , Cell Line , Chick Embryo , DNA, Viral/analysis , DNA, Viral/biosynthesis , Genotype , Hemagglutination, Viral , Influenza Vaccines/immunology , Kinetics , Neuraminidase/analysis , Neuraminidase/metabolism , Phenotype , RNA, Viral/analysis , RNA, Viral/biosynthesis , Reverse Transcriptase Polymerase Chain Reaction , Species Specificity
12.
Genetika ; 39(5): 694-701, 2003 May.
Article in Russian | MEDLINE | ID: mdl-12838617

ABSTRACT

Allele distribution at a highly polymorphic minisatellite adjacent to the c-Hras1 gene as well as deletions of microsatellite markers, D3S966, D3S1298, D9S171, and a microsatellite within p53 gene, were examined in bronchial epithelium specimens obtained from 53 chronic obstructive pulmonary disease (COPD) patients and healthy donors. A higher frequency of rare Hras1 minisatellite alleles in COPD patients than in the individuals without pulmonary pathology (6.6% versus 2.2%; P < 0.05) was shown. This difference was most pronounced in the group of ten COPD patients with idiopathic pulmonary fibrosis. Three of these patients had rare Hras1 minisatellite allele (P < 0.02 in comparison with healthy controls). Alterations in at least one of the microsatellite markers (deletions or microsatellite instability) were detected in bronchial epithelium samples obtained from: 4 of 10 COPD patients with pneumofibrosis (40%); 15 of 43 COPD patients (34.9%) without pneumofibrosis; and 8 of 20 tobacco smokers (40%) without pulmonary pathology. These defects were not observed in the analogous samples obtained from healthy nonsmoking individuals. No statistically significant differences were revealed between COPD patients and healthy smokers upon comparison of both the total number of molecular defects and the number of defects in the individual chromosomal loci. The total number of molecular defects revealed in bronchial epithelium samples from the individuals of two groups examined correlated with the intensity of exposure to tobacco smoke carcinogens (r = 0.28; P < 0.05). These findings suggest that rare alleles at the Hras1 locus may be associated with hereditary predisposition to COPD and the development of pneumofibrosis, while mutations in microsatellite markers result from exposure to tobacco smoke carcinogens and are not associated with the appearance of these pathologies.


Subject(s)
Microsatellite Repeats , Minisatellite Repeats , Pulmonary Disease, Chronic Obstructive/genetics , Adult , Aged , DNA, Satellite , Genes, p53 , Humans , Male , Middle Aged , Pulmonary Disease, Chronic Obstructive/pathology , Pulmonary Fibrosis/genetics , Smoking/adverse effects , Smoking/genetics
13.
J Clin Microbiol ; 40(7): 2398-407, 2002 Jul.
Article in English | MEDLINE | ID: mdl-12089254

ABSTRACT

A rapid and reliable method for the identification of five clinically relevant G genotypes (G1 to G4 and G9) of human rotaviruses based on oligonucleotide microarray hybridization has been developed. The genotype-specific oligonucleotides immobilized on the surface of glass slides were selected to bind to the multiple target regions within the VP7 gene that are highly conserved among individual rotavirus genotypes. Rotavirus cDNA was amplified in a PCR with primers common to all group A rotaviruses. A second round of nested PCR amplification was performed in the presence of indodicarbocyanine-dCTP and another pair of degenerate primers also broadly specific for all genotypes. The use of one primer containing 5'-biotin allowed us to prepare fluorescently labeled single-stranded hybridization probe by binding of another strand to magnetic beads. The identification of rotavirus genotype was based on hybridization with several individual genotype-specific oligonucleotides. This approach combines the high sensitivity of PCR with the selectivity of DNA-DNA hybridization. The specificity of oligonucleotide microchip hybridization was evaluated by testing 20 coded rotavirus isolates from different geographic areas for which genotypes were previously determined by conventional methods. Analysis of the coded specimens showed that this microarray-based method is capable of unambiguous identification of all rotavirus strains. Because of the presence of random mutations, each individual virus isolate produced a unique hybridization pattern capable of distinguishing different isolates of the same genotype and, therefore, subgenotype differentiation. This strain information indicates one of several advantages that microarray technology has over conventional PCR techniques.


Subject(s)
Antigens, Viral , Capsid Proteins , Oligonucleotide Array Sequence Analysis/methods , Rotavirus/genetics , Rotavirus/isolation & purification , Base Sequence , Capsid/genetics , DNA Primers/genetics , DNA, Viral/genetics , DNA, Viral/isolation & purification , Drug Design , Genes, Viral , Genotype , Humans , Molecular Probe Techniques , Mutation , Oligonucleotide Probes/genetics , Rotavirus/classification , Species Specificity , Virology/methods
15.
Appl Environ Microbiol ; 67(7): 3258-63, 2001 Jul.
Article in English | MEDLINE | ID: mdl-11425749

ABSTRACT

Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of Escherichia coli and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (eaeA, slt-I, slt-II, fliC, rfbE, and ipaH) encoding bacterial antigenic determinants and virulence factors of bacterial strains was monitored by multiplex PCR followed by hybridization of the denatured PCR product to the gene-specific oligonucleotides on the microchip. The assay was able to detect these virulence factors in 15 Salmonella, Shigella, and E. coli strains. The results of the chip analysis were confirmed by hybridization of radiolabeled gene-specific probes to genomic DNA from bacterial colonies. In contrast, gel electrophoretic analysis of the multiplex PCR products used for the microarray analysis produced ambiguous results due to the presence of unexpected and uncharacterized bands. Our results suggest that microarray analysis of microbial virulence factors might be very useful for automated identification and characterization of bacterial pathogens.


Subject(s)
Enterobacteriaceae/genetics , Enterobacteriaceae/pathogenicity , Oligonucleotide Array Sequence Analysis/methods , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Enterobacteriaceae Infections/microbiology , Fluorescent Dyes , Food Microbiology , Humans , Nucleic Acid Hybridization , Polymerase Chain Reaction/methods , Virulence/genetics
16.
Mol Carcinog ; 30(3): 151-8, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11301475

ABSTRACT

Allelic losses at 1p32-pter have been reported as frequent events in human non-small cell lung cancer (NSCLC). To further characterize the region of deletions, we studied loss of heterozygosity on a panel of 102 microdissected NSCLC samples with 20 polymorphic markers spanning 1p32-pter. Two shortest regions of the overlap of the deletions (SROs) were found: SRO 2a (D1S417--D1S57) and SRO 2b (D1S450--D1S243). Allelic losses at either region correlated independently with advanced stage of disease and with postoperative metastasis and relapse (P < 0.05), suggesting that crucial genes in these regions are involved in NSCLC progression. Mol. Carcinog. 30:151--158, 2001.


Subject(s)
Carcinoma, Non-Small-Cell Lung/genetics , Chromosomes, Human, Pair 1 , Loss of Heterozygosity , Lung Neoplasms/genetics , Carcinoma, Non-Small-Cell Lung/mortality , Female , Humans , Lung Neoplasms/mortality , Male , Microsatellite Repeats , Middle Aged , Minisatellite Repeats
17.
J Clin Microbiol ; 39(3): 1157-60, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11230448

ABSTRACT

Human rotavirus strains belonging to genotype G9 or P[9] were detected in a collection of stool specimens from children with diarrhea in two cities of the state of Rio de Janeiro, Brazil, between March 1997 and December 1999. G9 strains were first detected in April 1997 and remained prevalent until the end of the study, at a frequency of 15.9% (n = 157). A high percentage of VP7 nucleotide (99.0 to 99.5%) and deduced amino acid identity (98.6 to 99.1%) was found between three randomly selected Brazilian G9 strains and the American G9 strain US1205. A novel G9:P[4] genotype combination was detected in addition to G9:P[8] and G9:P[6], demonstrating that this G genotype may undergo constant genetic reassortment in nature. The P[9] rotavirus strains constituted 10.2%, the majority of which were detected between April and July 1997. The RNA electrophoretic migration pattern of the G3:P[9] strains resembled that of AU-1 virus (G3:P3[9]), suggesting a genetic similarity between the Brazilian G3:P[9] strains and the Japanese virus, which is similar to a feline rotavirus genetically.


Subject(s)
Antigens, Viral , Capsid Proteins , Diarrhea/virology , Rotavirus Infections/virology , Rotavirus/classification , Rotavirus/genetics , Bacterial Typing Techniques , Brazil/epidemiology , Capsid/genetics , Child, Preschool , Diarrhea/epidemiology , Electrophoresis, Polyacrylamide Gel , Genotype , Humans , Molecular Sequence Data , Rotavirus/isolation & purification , Rotavirus Infections/epidemiology , Sequence Analysis, DNA
18.
J Virol ; 75(5): 2076-86, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11160712

ABSTRACT

The nonpolyadenylated mRNAs of rotavirus are templates for the synthesis of protein and the segmented double-stranded RNA (dsRNA) genome. During serial passage of simian SA11 rotaviruses in cell culture, two variants emerged with gene 5 dsRNAs containing large (1.1 and 0.5 kb) sequence duplications within the open reading frame (ORF) for NSP1. Due to the sequence rearrangements, both variants encoded only C-truncated forms of NSP1. Comparison of these and other variants encoding defective NSP1 with their corresponding wild-type viruses indicated that the inability to encode authentic NSP1 results in a small-plaque phenotype. Thus, although nonessential, NSP1 probably plays an active role in rotavirus replication in cell culture. In determining the sequences of the gene 5 dsRNAs of the SA11 variants and wild-type viruses, it was unexpectedly found that their 3' termini ended with 5'-UGAACC-3' instead of the 3' consensus sequence 5'-UGACC-3', which is present on the mRNAs of nearly all other group A rotaviruses. Cell-free assays indicated that the A insertion into the 3' consensus sequence interfered with its ability to promote dsRNA synthesis and to function as a translation enhancer. The results provide evidence that the 3' consensus sequence of the gene 5 dsRNAs of SA11 rotaviruses has undergone a mutation causing it to operate suboptimally in RNA replication and in the expression of NSP1 during the virus life cycle. Indeed, just as rotavirus variants which encode defective NSP1 appear to have a selective advantage over those encoding wild-type NSP1 in cell culture, it may be that the atypical 3' end of SA11 gene 5 has been selected for because it promotes the expression of lower levels of NSP1 than the 3' consensus sequence.


Subject(s)
Consensus Sequence/genetics , Rotavirus/physiology , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , Virus Replication , Amino Acid Sequence , Animals , Base Sequence , Cell Line , DNA, Complementary/genetics , Gene Expression Regulation, Viral , Genome, Viral , Molecular Sequence Data , RNA, Double-Stranded/genetics , RNA, Double-Stranded/metabolism , Rotavirus/genetics , Rotavirus Infections/virology , Sequence Analysis, DNA , Viral Plaque Assay
19.
Genetika ; 37(10): 1388-95, 2001 Oct.
Article in Russian | MEDLINE | ID: mdl-11761616

ABSTRACT

PCR-based typing of Hras1 minisatellite alleles was carried out in 226 non-small cell lung cancer (NSCLC) patients and 207 unaffected controls. Application of this method permitted detection of four common (a1 to a4) and 25 other alleles, differing from any common allele by one or more repeat units. Depending on their frequency in control group, these alleles were defined as intermediate or rare (the frequency over 0.5% or less than 0.5%, respectively). It was established that the frequency of rare alleles in the group of NSCLC patients (7.1%) was statistically significantly higher than in healthy individuals (2.2%, p = 0.002), while the difference in the distribution of common and intermediate alleles between the compared groups was not statistically significant. In addition, rare Hras1 alleles were more frequent (p = 0.02) among nonsmoking patients compared to the patients subjected to of tobacco carcinogens. The presence of "heavy" (a3-a4) alleles was associated with an increased risk of low-differentiated and/or actively metastasizing tumors and also with the risk of lung cancer in the patients under 50 years of age (p < 0.05). These data indicate that an approach including application of modern highly sensitive techniques of Hras1 allele typing in combination with preliminary examination of healthy control population can be employed for identifying carcinogenic risk groups as well as for prognosis of the NSCLC clinical course.


Subject(s)
Alleles , Carcinoma, Non-Small-Cell Lung/genetics , Genes, ras , Lung Neoplasms/genetics , Minisatellite Repeats/genetics , Smoking/genetics , Base Sequence , Carcinogens , Carcinoma, Non-Small-Cell Lung/pathology , DNA Primers , Humans , Lung Neoplasms/pathology , Middle Aged , Polymerase Chain Reaction , Prognosis
20.
Virus Res ; 70(1-2): 31-44, 2000 Sep.
Article in English | MEDLINE | ID: mdl-11074123

ABSTRACT

To identify the hantaviruses causing hemorrhagic fever with renal syndrome (HFRS) in the Far East of Russia, blood samples collected from HFRS patients in 1994-1998, were examined by reverse transcription-polymerase chain reaction. In addition, 36 sera were tested by an immunofluorescence assay for antibodies against Hantaan, Seoul, Puumala, and Khabarovsk viruses, and 54 samples were tested by plaque reduction neutralization test. With both serological assays, the highest antibody titers were to Hantaan and/or Seoul viruses. Of 110 blood samples 36 were found RT-PCR positive. Phylogenetic analysis the sequences of a 256-nucleotide (nt) fragment of the hantavirus M genome segment revealed at least 3 genetically distinct hantavirus lineages. Nucleotide sequence comparison showed that two of the lineages, designated as FE and Amur (AMR), differed from one another by 15.9-21.2% and from Hantaan virus by 9.8-17.5%. The third lineage, VDV, differed from Seoul virus by 2.6-5.1%. All S segment sequences were from FE lineage, and differed from Hantaan virus by 10.7-12.6%. Thirty of the 36 (83%) analyzed sequences were found to be the FE genotype, which is very similar to that of Hantaan virus, strain 76-118. Of the remaining hantaviruses, 11% were the AMR genotype, and 6% the VDV genotype, which are genetically novel genotypes of Hantaan or Seoul viruses, respectively.


Subject(s)
Genetic Variation , Hantaan virus/genetics , Hemorrhagic Fever with Renal Syndrome/virology , Amino Acid Sequence , DNA, Viral/analysis , DNA, Viral/blood , Hantaan virus/isolation & purification , Hemorrhagic Fever with Renal Syndrome/epidemiology , Humans , Molecular Sequence Data , Phylogeny , Reverse Transcriptase Polymerase Chain Reaction , Russia/epidemiology , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
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