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PubMed2002

Antigenic and genetic characterization of influenza C viruses which caused two outbreaks in Yamagata City, Japan, in 1996 and 1998.

During the 3 years from January 1996 to December 1998, a total of 33 strains of influenza C virus were isolated from 10,726 throat swab specimens collected from children with acute respiratory illness who visited two pediatric clinics in Yamagata City, Japan. These 33 strains were isolated in clusters during two different periods, 20 strains in May to August 1996 and the remaining 13 in March to June 1998. Antigenic analysis with monoclonal antibodies to the hemagglutinin-esterase (HE) glycoprotein and phylogenetic analysis of seven RNA segments showed that the 33 influenza C viruses isolated were antigenically and genetically similar and that they were reassortant viruses which had obtained PB2, PB1, HE, M, and NS genes from a C/pig/Beijing/115/81-like virus and P3 and NP genes from a C/Mississippi/80-like virus. These observations suggest strongly that during the survey period of 3 years, two outbreaks of influenza C occurred in Yamagata City, both of which were caused by a reassortant virus having the genome composition described above.

Adolescent↗

PubMed2001

Genetic characterization of six species of diplozoids (Monogenea; Diplozoidae).

The second internal transcribed spacer (ITS2) of the ribosomal RNA gene array of 6 species of diplozoids; Eudiplozoon nipponicum, Paradiplozoon bliccae, P. homoion, P. megan, P. pavlovskii and P. sapae, was amplified by PCR and sequenced. These sequences clearly demonstrate discrimination at the species level and confirm the validity of species determined by morphological identification. No intraspecific variation was found in the ITS2 sequences. There were no differences in the ITS2 sequences of P. homoion from populations parasitizing different host species. The length of the PCR product allowed discrimination of E. nipponicum from the Paradiplozoon species. Digestion of the amplified ITS2 fragment with enzymes AluI, HaeIII and HinfI provided useful genetic markers for species identification. The genetic relationships between diplozoids again demonstrated that E. nipponicum was the most genetically distinct species, whereas P. bliccae and P. sapae were the species most closely related. This represents the first molecular taxonomic study of these interesting parasites and demonstrates the utility of these methods for addressing questions of systematics.

Animals↗

PubMed1999

Escherichia coli O157:H7 and O157:H(-) strains that do not produce Shiga toxin: phenotypic and genetic characterization of isolates associated with diarrhea and hemolytic-uremic syndrome.

We have isolated one sorbitol-nonfermenting (SNF) Escherichia coli O157:H7 isolate and five sorbitol-fermenting (SF) E. coli O157:H(-) isolates that do not contain Shiga toxin (Stx) genes (stx). Isolates originated from patients with diarrhea (n = 4) and hemolytic-uremic syndrome (HUS) (n = 2). All isolates harbored a chromosomal eae gene encoding gamma-intimin as well as the plasmid genes E-hly and etp. The E. coli O157:H7 isolate was katP and espP positive. Respective sera obtained from the patient with HUS contained antibodies to the O157 lipopolysaccharide antigen. The stx-negative E. coli O157:H7 isolate is genetically related to stx-positive SNF E. coli O157:H7. All stx-negative SF E. coli O157:H(-) isolates belong to the same genetic cluster and are closely related to stx-positive SF E. coli O157:H(-) isolates. Our data indicate that stx-negative E. coli O157:H7/H(-) variants may occur at a low frequency and cannot be recognized by diagnostic methods that target Stx.

Antibodies, Bacterial↗

PubMed1976

[Mice of southern France: genetic characterization of two groups of sympatric populations].

An electrophoretic survey of five proteins (lactate dehydrogenase, isocitrate dehydrogenase, esterase-1, esterase-2, albumin) shows that there are two groups of populations strongly (or completely) reproductively isolated. The first group does not differ from Mus musculus L. The second exhibits several new biochemical traits and should probably be considered a different species.

Animals↗

PubMed1992

Physical and genetic characterization of the distal segment of the myotonic dystrophy area on 19q.

The mutation involved in myotonic dystrophy (DM) has been mapped to the region between the ERCC1 DNA repair gene and the anonymous D19S51 locus on 19q13.3. Starting at locus D19S112 (probe pX75b), which served as a novel entry site for this chromosome region, we have established a cosmid contig of approximately 200 kb. In the contig, a gene expressed in the brain and a highly informative, 12-allele (TG)n variable simple sequence motif (VSSM) were identified. With this marker, designated X75b-VSSM, a highly characteristic size distribution of alleles linked with DM, which differed significantly from that on normal chromosomes, was observed. Combining our physical mapping and genetic data, we show that the X75b-VSSM marker is the closest distal to DM, thus excluding the DM mutation from the entire telomeric portion of the ERCC1-D19S51 region.

Base Sequence↗

PubMed1982

Antigenic and genetic characterization of a novel hemagglutinin subtype of influenza A viruses from gulls.

Influenza A virus isolates from ring-billed, Franklin, blackback, and herring gulls in the United States possess a hemagglutinin (HA) distinct from the 12 reference HA subtypes. Serological assays (hemagglutination inhibition and double-immunodiffusion) with specific antisera to reference strains and to a representative gull isolate showed that the HA of the gull virus was not antigenically related to that of any known subtype. The gull virus did not replicate in ducks or chickens but did replicate in ferrets. Comparison of the nucleotide sequences (and deduced amino acid sequences) of the 3' 20% of the HA genes of these viruses indicates that the gull viruses represent a genetically distinct group. We propose that this HA, which has been detected only in gull isolates thus far, be called the H13 subtype.

Animals↗

PubMed2006

Genetic characterization of fas-associated phosphatase-1 as a putative tumor suppressor gene on chromosome 4q21.3 in hepatocellular carcinoma.

PURPOSE: Allelic loss at chromosome 4q21-23 occurs frequently in human hepatocellular carcinoma, and the putative tumor suppressor gene (TSG) has not yet been identified. We studied the Fas-associated phosphatase-1 (FAP-1) gene as a potential candidate TSG in this region. EXPERIMENTAL DESIGN: The expression level of FAP-1 RNA in hepatocellular carcinomas was evaluated by RNase protection and quantitative PCR. Sodium bisulfite modification and subsequent single-strand conformational polymorphism and sequence analyses were used to assay the methylation of CpGs at FAP-1 promoter. Direct sequencing of the FAP-1 coding region was conducted for detecting the genetic mutations. Two common single nucleotide polymorphisms of FAP-1 were selected for evaluating their association with the hepatocellular carcinoma trait in sporadic and familial hepatocellular carcinomas. Moreover, the functional effect of FAP-1 on cellular proliferation has been evaluated by small interfering RNA approach. RESULTS: Around 50% of hepatocellular carcinomas showed significantly decreased expression of FAP-1 compared with the corresponding nontumorous liver tissues. In most cases, the RNA level was well correlated with the methylation status of promoter CpGs, suggesting that the promoter methylation may contribute to the down-regulation. Several genetic mutations of FAP-1 have been identified in hepatocellular carcinomas. The G/G genotype of FAP-1 cSNP6304 was significantly associated with the increased risk of multiplex familial hepatocellular carcinomas (odds ratio, 2.44; 95% confidence interval, 1.19-5.01). Finally, knockdown expression of FAP-1 was shown to enhance the cellular proliferation in PLC5 cells. CONCLUSIONS: FAP-1 could be inactivated during hepatocarcinogenesis, mainly attributed by allelic loss and promoter methylation. The genetic mutations and polymorphisms may also confront with the higher hepatocellular carcinoma risk. These results first suggested FAP-1 as a putative TSG in hepatocarcinogenesis.

Alleles↗

PubMed1995

A large pedigree with early-onset Alzheimer's disease: clinical, neuropathologic, and genetic characterization.

We present clinical, neuropsychological, and neuropathologic data on a large pedigree including 34 subjects with early-onset progressive dementia. The mean (+/- SD) age at onset was 46 +/- 3.5 years and the mean age at death 52.6 +/- 5.7 years. Twelve patients were clinically diagnosed as having probable Alzheimer's disease (AD) according to the NINCDS-ADRDA criteria. Neuropsychological evaluation, performed at a moderate stage of the disease, was available in six subjects and showed a classic pattern of cognitive deficit. Myoclonus and extrapyramidal signs were common, and seizures were present in all affected subjects. There were neuropathologic changes typical of AD in two brains. A significant lod score of 5.48 was observed at a recombination fraction of theta = 0.0 with the genetic marker D14S43, thereby establishing that the responsible gene was located on chromosome 14q24.3. These results suggest that epilepsy could represent a particular feature in AD families linked to chromosome 14q.

Age of Onset↗

PubMed2004

Risk of Plasmodium vivax malaria reintroduction in Uzbekistan: genetic characterization of parasites and status of potential malaria vectors in the Surkhandarya region.

Plasmodium vivax malaria was eradicated from Uzbekistan in 1961. Due to resurgence of the disease in neighbouring states and massive population migration, there has been an increase of P. vivax malaria, imported from Tajikistan, resulting in a number of indigenous cases being identified in areas bordering that country. A molecular study using the merozoite surface protein 1 (msp-1) gene as a marker was performed on 24 P. vivax genomic isolates from 12 indigenous and 10 imported malaria cases that occurred in the Surkhandarya region during the summer of 2002. Results have shown a significant difference in the frequency of msp-1 types between indigenous and imported isolates, the latter showing greater genetic heterogeneity. An entomological investigation in the area suggested that three Anopheles species, namely A. superpictus, A. pulcherrimus and A. hyrcanus may have a potential role in the endemic transmission of P. vivax.

Adolescent↗

PubMed2002

Genetic characterization of hepatitis A virus isolates from Buenos Aires, Argentina.

The Hepatitis A virus (HAV) has been classified in seven different genotypes, which include human (I, II, III, and VII) and simian (IV, V, and VI) groups. The sequence analysis of HAV strains contributes to the molecular epidemiology of the virus. Although the infection with HAV is endemic in Argentina and vaccination is being implemented in this country, using both IA and IB strains, there are very few data on the genotypes of the circulating viruses. On the basis of the sequences of 20 isolates collected in Buenos Aires during a 2-year period (extended to 3 years by two additional specimens), we observed the presence of a single sub-genotype, IA, but with a high genetic diversity. We analyzed the VP1-2A junction and also the VP3-VP1 region. Most of the Argentine isolates grouped in at least two clusters. One of these was related to South American strains, thus suggesting a co-circulation of related isolates in neighbor countries. The other cluster was composed only of Argentine specimens. Other sequences were more scattered along the phylogenetic tree. However, we demonstrated that a consistent genetic relatedness of sequences could only be inferred on the basis of a more extensive sequencing of each isolate.

Adult↗

PubMed2002

Isolation and genetic characterization of a novel filamentous bacteriophage, a deleted form of phage f237, from a pandemic Vibrio parahaemolyticus O4:K68 strain.

We isolated a filamentous bacteriophage, VfO4K68, from the pandemic Vibrio parahaemolyticus strain belonging to 04:K68 serovar. The VfO4K68 DNA lacked a 1,893-bp fragment present in that of the distinctive region of f237, a filamentous phage isolated from a pandemic 03:K6 strain (Nasu, H. et al., J. Clin. Microbiol., 38, 2156-2161, 2000). The deletion resulted in the formation of a novel open reading frame (ORF) that possesses homology to the ORF 27 of ETA phage and staphylococcal enterotoxin E (SEE) of Staphylococcus aureus. VfO4K68 was able to infect the recipient 03:K6 serovar strains. These results suggest that VfO4K68 might act as a genetic transmitter and play some roles in the pandemic V. parahaemolyticus infection.

Amino Acid Sequence↗

PubMed2005

Genetic characterization of a caprine pestivirus as the first member of a putative novel pestivirus subgroup.

Currently, the genus Pestivirus comprises four approved species, namely bovine viral diarrhoea viruses 1 and 2 (BVDV-1, BVDV-2), classical swine fever virus and border disease virus (BDV). Recently, three major genotypes have been identified within the species BDV and termed as subgroups BDV-1, BDV-2 and BDV-3. Here, an isolate from animals in a herd showing BD-like syndromes, which occurred in central Italy was analysed. A reverse transcriptase polymerase chain reaction was performed using primers that specifically amplify a fragment of the 5'-non-coding region (5'-NCR) from BDV. Both the 5'-NCR fragment and the entire Npro gene were sequenced and used for genetic typing. The 5'-NCR sequence revealed that the newly isolated Pestivirus could be allocated to the BDV species. Interestingly, the Npro sequence of this virus isolate significantly differed from all the ovine pestiviruses previously described, providing evidence for the presence of an additional subgroup within the species BDV.

Animals↗

PubMed2006

[Molecular genetic characterization of chronic lymphocytic leukemia aggressivity in Czech patients: a nucleotide variability of genes coding for heavy chain of immunoglobulin].

BACKGROUND: Chronic lymphocytic leukemia is a heterogeneous disease manifesting with a variable clinical course. It is evident from many studies, that the division into two main prognostic categories is possible on the basis of mutation status of the immunoglobulin heavy-chain gene. The objective of our work was to identify a presence or absence of IgVH gene mutations in B-CLL patients which are monitored or treated on hematological clinics and to determine the presence of individual D and J, subgenes in malignant population of B-cells. METHODS AND RESULTS: A nucleotide sequence of IgVH gene of neoplastic cells was analyzed by appropriate molecular-genetic methods. RNA/cDNA was collected from 358 patients and a spectrum of individual subgenes translocations was identified. Our results show that 56.3% of patients manifested an unmutated variable (VH) segment. It is expected from the published data that this group of patients will suffer from aggressive course of the disease and will exhibit a substantially shorter survival in comparison to patients possessing somatic hypermutations. An expanded population of leukemic B-cells showed increased occurrence of clones whose variable segments belong to three different families. VH3 alleles are the ones most frequently used. A frequency of unmutated alleles is prominently shifted into families with V I homology. The preferred "diversity and joining" segments are D3, D2 and JH 4 and JH 6. CONCLUSIONS: The analysis of heavy chain immunoglobulin gene after recombinant VH-D-J11 segments translocation belongs to a standard hematooncological investigation. The results are an important prognostic criterion for prediction of expected disease aggressivity and for a minimal residual disease monitoring.

Base Sequence↗

PubMed1981

Physical and genetic characterization of the glnA--glnG region of the Escherichia coli chromosome.

We have cloned and characterized a fragment of the Escherichia coli chromosome spanning glnA, the structural gene for glutamine synthetase (L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2]. The fragment also carriers glnG, whose product is necessary for regulation of glnA expression, and a previously unidentified gene whose function we have not discovered. Transcription of glnA and the newly identified gene occurs divergently from a region between the two genes. Transcription of glnA proceeds toward glnG, which is transcribed in the same direction. A region of DNA between glnA and glnG contains genetic information whose loss may result in the inability to reduce expression of glnA and other operons in response to ammonia (the GlnC phenotype).

Bacteriophage lambda↗

PubMed1997

Genetic characterization of the chromosomal rearrangements that accompany the transgene insertion in the chakragati mouse mutant.

We have previously reported that the circling phenotype of the chakragati mouse segregates with the transgene integration event as an autosomal recessive trait. It was unclear, however, whether the phenotype was linked to the transgene integration point near D16Ros1 or to a potential disruption at D16Ros2, 10 cM away. We report here that animals recombinant between D16Ros1 and D16Ros2, homozygous for the transgene insertion at D16Ros1, but wildtype for D16Ros2, do indeed show the phenotype. We conclude that any potential disruption at the D16Ros2 locus is not responsible for the circling phenotype. We further show that recombination between D16Ros1 and D16Ros2 occurs at a greatly reduced level in the chakragati mouse compared to wildtype strains. Detailed genetic analysis of recombinants indicates that the proximal-most 4.5 cM shows no recombination in over 1400 meioses. We propose that this is due to an inversion in this region, and we genetically define the proposed distal inversion break point to a 1.3-cM region between D16Mit63 and D16Mit169.

Animals↗

PubMed2003

Pharmacological and genetic characterization of two selective serotonin transporter ligands: 2-[2-(dimethylaminomethylphenylthio)]-5-fluoromethylphenylamine (AFM) and 3-amino-4-[2-(dimethylaminomethyl-phenylthio)]benzonitrile (DASB).

The expression and function of the serotonin transporter (SERT) is important in the regulation of mood and emotion. Determination of SERT alterations in physiological and pathological states is essential for understanding the role of SERT in mood regulation, and in the etiology and therapy of psychiatric disorders. Two SERT ligands, AFM ([(3)H]2-[2-(dimethylaminomethylphenylthio)]-5-fluoromethylphenylamine) and DASB ([(3)H]3-amino-4-[2-(dimethylaminomethylphenylthio)]benzonitrile), have recently been developed for positron emission tomography (PET) imaging. The aim of the present study was to determine the selectivity of these compounds for SERT. Autoradiography of AFM or DASB binding was compared in the brains of mice with genetically normal, diminished, or absent SERT. In addition, the pharmacodynamic profile of [(3)H]AFM was examined in the mouse brain. The distribution of [(3)H]AFM and [(3)H]DASB binding in the normal brains was consistent with that of previously studied serotonin reuptake inhibitors. Both ligands had negligible binding in the brain of SERT knockout mice, and binding was reduced approximately 50% in heterozygote SERT mice. The K(d) of [(3)H]AFM binding in the cortex and midbrain was 1.6 and 1.0 nM, respectively. Competition studies showed that [(3)H]AFM has very low affinity for norepinephrine and dopamine transporters as well as 5-HT receptors, including 5-HT(1A), 5-HT(1B), 5-HT(2A), and 5-HT(2C) receptors. In addition, fenfluramine showed a low capability to compete with [(3)H]AFM. The present results suggest that both AFM and DASB are highly selective SERT ligands potentially suitable for use in human PET studies of SERT.

Aniline Compounds↗

PubMed2003

Genetic characterization of stress responsiveness in Japanese quail. 1. Analyses of line effects and combining abilities by diallel crosses.

The inheritance of stress responsiveness (line effects and combining abilities) was phenotypically studied in progeny from diallel crosses of randombred (RB) quail and quail selected for exaggerated (high stress, HS) or reduced (low stress, LS) plasma corticosterone (CS) response to brief immobilization. The three genotypes were crossed in a 3 x 3 factorial arrangement of treatments that allowed all possible crosses between RB, LS, and HS males with RB, LS, and HS females. The nine crosses produced 479 progeny. At 28 d of age, quail of each cross were stressed by immobilization, and blood was sampled. Plasma CS was used to estimate stress responsiveness in the progeny of each cross. Estimates of the following genetic effects were made: average post-immobilization plasma CS response within each cross, general combining ability (GCA), and specific combining ability (SCA). Differences (P < 0.05) in plasma CS response to immobilization between crosses involving the LS and HS lines (HS crosses > LS crosses) were commonly observed. There were no significant differences in the means of plasma CS responses between males and females within each of the crosses except for the marginal (P = 0.07) sex difference (male > female) found within the LL cross (LS male with LS female). The GCA estimates were -1.23, -2.89, and 5.08 for the RB, LS, and HS quail, respectively. The SCA was not significant for any diallel mating except HH (P < 0.007). Line effects on plasma CS response were different from zero for the LS and HS lines.

Alleles↗

PubMed1983

Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides.

The polA1 mutation of Escherichia coli K12 and two further mutations, resA1 and resA2, characterized in E. coli B have been shown to produce enzymatically active nonsense (amber) peptides. These enzymes can be purified to virtual homogeneity by use of the lambda polA transducing phage system. The peptides are immunologically related and react weakly but specifically with antibody to whole DNA polymerase I. In their purified form the peptides are less heat-labile than the whole enzyme or the Klenow fragment produced by proteolysis. Physiological studies indicate that all three alleles are compatible with a number of different streptomycin resistance mutations (rpsL alleles) in a variety of genetic backgrounds. There is, however, clear evidence for slight amounts of "read-through" of these mutations under these conditions. DNA sequence studies have indicated the exact nucleotides that have been mutated to produce the amber alleles. The resA1 and resA2 alleles appear to be independent isolates of the same mutation both resulting in CAG (Gln) leads to TAG (amber) at amino acid residue 298. The polA1 mutation results in TGC (Trp) leads to TAG (amber) at amino acid residue 342. The significance of these findings is discussed with reference to the structure of the whole enzyme as shown by the DNA sequence data of Joyce et al. (1982) and protein chemistry of Brown et al. (1982).

Antigens, Bacterial↗