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PubMed1999

Cloning and functional characterization of a Caenorhabditis elegans muscarinic acetylcholine receptor.

A cDNA clone encoding a muscarinic acetylcholine receptor (mAChR) has been isolated from the nematode Caenorhabditis elegans. The nematode mAChR, consisted of 585 amino acids, displays a high degree of amino acid sequence homology to other invertebrate and vertebrate mAChRs. Excluding a highly variable middle portion of the third intracellular loop, the C. elegans mAChR shares about 51% amino acid sequence identity with a Drosophila mAChR and 42-44% identity with human m1-m5 mAChR subtypes. Comparison of the cDNA sequence with the corresponding genomic sequence reveals that the C. elegans mAChR gene contains ten introns, eight of them in the coding region. Pharmacological profiles of the C. elegans mAChR expressed in Chinese hamster ovary (CHO) cells were shown to be similar to those of mammalian counterparts, indicating that ligand binding domains of the receptor have been conserved during evolution. When this cloned receptor was expressed in Xenopus oocytes, acetylcholine evoked a transient Cl- current. Furthermore, activation of the receptor with oxotremorine, acetylcholine or carbachol resulted in the stimulation of phosphatidylinositol metabolism in CHO cells, suggesting that the receptor is coupled to phospholipase C activation.

Acetylcholine↗

PubMed2001

A rapid and highly sensitive method for diagnosis of equine influenza by antigen detection using immuno-PCR.

A rapid and highly sensitive method for diagnosis of influenza by detecting viral antigens using immuno-PCR has been developed. The sensitivity of the immuno-PCR for the detection of the nonstructural protein 1 (NS 1) antigenically common among influenza A viruses was 10(1.0-2.0) times higher than that of RT-PCR for the detection of the viral genome. For the detection of the hemagglutinin (HA) subtype-specific antigen, this assay using anti-HA monoclonal antibodies attained a sensitivity of up to 10(7.0-8.0) times higher than those by virus isolation or by RT-PCR.

Animals↗

PubMed1994

Genetic analysis of alpha 2-adrenergic receptors and blood pressure using Dahl salt-sensitive rats.

OBJECTIVE: To evaluate the role of alpha 2-adrenergic receptors in genetic hypertension by cosegregation analysis using Dahl rats. DESIGN: Inbred Dahl salt-sensitive (SS/Jr) rats were crossed with inbred Dahl salt-resistant (SR/Jr) rats; also, SS/Jr rats were crossed with several control strains, and large F2 populations were subsequently produced from each cross. All F2 populations were raised on a high-salt diet. The rats were genotyped, where possible, at the loci for three different subtypes of alpha 2-adrenergic receptors designated as classes I, II and III. The blood pressures of the rats classified by genotype at each alpha 2-adrenergic receptor subtype locus were compared using analysis of variance. METHODS: Genomic clones of three classes of alpha 2-adrenergic receptors were isolated from genomic lambda-phage libraries of SS/Jr or SR/Jr rat strains, or both, by screening with complementary DNA for human alpha 2-adrenergic receptors. Fragments of the rat genomic clones obtained were used for genotyping by restriction fragment length polymorphism. Also, cloned genomic DNA flanking the alpha 2-adrenergic receptors and containing microsatellites was sequenced; genotyping at informative microsatellite markers was performed using the polymerase chain reaction. Two of the three classes of rat alpha 2-adrenergic receptors were localized to rat chromosomes by linkage analysis or using a panel of mouse-rat hybrid somatic cell lines. RESULTS: Rat alpha 2-adrenergic receptor classes I and III genes were assigned to rat chromosomes 14 and 3, respectively. These correspond to alpha 2-adrenergic receptor genes on human chromosomes 4 and 2, respectively. Extensive cosegregation analysis, involving five alleles in six segregating populations for class I alpha 2-adrenergic receptors, yielded no evidence of an effect of these loci on blood pressure. Classes II and III alpha 2-adrenergic receptors could each be tested in only one population and there was no evidence for an effect of either receptor gene on genetic differences in blood pressure. The dopamine-1B receptor was closely linked to the class I alpha 2-adrenergic receptor on rat chromosome 14. Thus, the negative cosegregation of the class I receptor with blood pressure applies equally to the dopamine-1B receptor. CONCLUSIONS: Genetic analysis in segregating populations involving crosses of inbred Dahl salt-sensitive rats with five other strains provides no evidence for a genetic effect of class I alpha 2-adrenergic receptors, or of the dopamine-1B receptor, on blood pressure. Classes II and III alpha 2-adrenergic receptors also failed to cosegregate with blood pressure but, because only limited testing was possible with the classes II and III receptors, this negative result is not definitive.

Animals↗

PubMed1993

Nucleotide sequence of a cloned human HBV mutant (pDKHBV) in duck hepatoma of Qidong County.

This is the first report to describe the presence of an HBV-like DNA sequence in two hepatoma and their tumor surrounding liver tissues, one precancerous and one non-malignant liver tissue of ducks collected from Qidong County of China. The HBV-like sequences were either in an episomal form of 3.2 kb or in an integrated form of various sizes, while the DHBV DNA sequences (3.0 kb) were either present or absent in these tissues and in different size pattern. Furthermore, there was no evidence of cross-hybridization between HBV-like DNA sequences in duck and DHBV DNA. A 3.2 kb HBV-like DNA sequence has been cloned from one duck hepatoma (40 K), designated as pDKHBV. The 3218 bp full-length nucleotide sequence of this clone has been determined, which had no apparent homology with Duck Hepatitis B Virus (DHBV) genome, but was highly homologous to human HBV adw2 subtype (99.0%). The sequence was composed of four open reading frames for HBV gene Pre-S/S, X, C and P respectively. In addition to multiple sites of point mutation, one nt and two nt deletion were detected downstream the initiation codon of Pre-S1 gene and at the 3' end of C gene respectively, thereby suggesting a frameshift mutation in Pre-S gene and C gene. Based on these results, it was implicated that an unusual HBV variant might exist in Qidong County, which might have transmitted into duck through some yet unknown mechanisms. The possibility from exogenous contamination could be thus excluded.

Amino Acid Sequence↗

PubMed1997

[Viremia in influenza: detection by polymerase chain reaction].

Gastroenteritis, arthralgia and myalgia are frequently associated with influenza virus infections in humans. One explanation for these symptoms may be that they are due to extra respiratory transmission of virus by viremia. We tried to detect genomic viral RNA of the nucleoprotein (NP) and H3 subtype hemagglutinin (HA) genes by method of RT-PCR in peripheral blood mononuclear cells (PBMC) of 18 children aged 1-14 who suffered from an influenza outbreak in the Kansai district of Japan between December 1992 and February 1993. Three of the 18 samples were RT-PCR positive. The NP gene sequence observed in one patient's PBMC was identical to that obtained from his throat swab fluid. The HA gene sequences observed in the two other PBMC differed from those of RT-PCR amplified DNA from throat swabs by an order of 3-9 nucleotides. Moreover we tried to isolate virus by co-culture with MDCK cells and RBC or WBC of the patients from an influenza outbreak between December 1993 and March 1994. No virus was isolated from 9 patients suffering from H3 subtype but virus was isolated from 5 of 17 patients suffering from type B influenza virus. We believe these results suggest that the viremia on influenza infection is not so rare.

Adolescent↗

PubMed2001

A complex human immunodeficiency virus type 1 A/G/J recombinant virus isolated from a seronegative patient with AIDS from Benin, West Africa.

A human immunodeficiency virus type 1 (HIV-1(B76)) originating from Benin (West Africa) was isolated and characterized. The patient had severe clinical AIDS and presented an unusual serological profile. Only one out of five different detection assays was able to demonstrate the presence of antibodies to HIV, whereas confirmatory assays remained indeterminate. In contrast, both plasma viral load and p24 antigen level were unusually high. HIV-1 infection was proved by viral RNA and proviral DNA amplification. HIV-1(B76) partially purified lysate reacted strongly with all anti-HIV-1-positive sera from the region but B76 plasma did not react with subtype A control viral antigen. This patient is likely to have had severe acquired immune dysfunction explaining her lack of immunological reactivity. Phylogenetic analysis of the genome identified a complex HIV-1 A/G/J recombinant. The gag and pol genes, and the majority of nef,are characteristic of subtype A; the gag/pol junction, the 3' end of pol, vpu and env genes were characteristic of subtype G; vif, vpr and the 5' end of nef were subtype J. In addition, part of the HIV-1(B76) genome had considerable sequence similarity with the previously described CRF06 cpx (BFP90) isolate. HIV-1(B76) did not exhibit any remarkable replication properties or cell tropism in vitro.

Acquired Immunodeficiency Syndrome↗

PubMed1993

cDNA sequence diversity and genomic clusters of major surface glycoprotein genes of Pneumocystis carinii.

The major surface glycoprotein (MSG) of Pneumocystis carinii plays a crucial role in the pathobiology of P. carinii, which often causes fatal pneumonia in AIDS patients. The cDNAs encoding MSG antigens were cloned from a lambda gt11 expression library of rat-derived P. carinii by immunoscreening. The cloned cDNAs constituted a gene family containing approximately 70% amino acid identity between subtypes. The diversity of MSG cDNAs was high and reflected the genomic structure of MSG genes clustered in the P. carinii chromosomes. These multiple genes may account for the high-level expression of MSG that could generate potential variations in the cell surface. Moreover, the MSG sequences have significant sequence homology to tropomyosins and myosins, suggesting physical or functional association with the membrane cytoskeleton.

Amino Acid Sequence↗

PubMed2003

The influence of the expanding HIV genetic diversity on molecular diagnosis in the Philippines.

Since the discovery in the Philippines of the first AIDS case in 1984, several subtypes of HIV-1 have been discovered. From the persons diagnosed in the early 1980s only subtype B was found and thereafter other subtypes, C, D, E, and F were also identified although HIV was not particularly prevalent at that time. In this paper, we determine whether the rapid expansion of genetic diversity will influence molecular diagnosis by polymerase chain reaction (PCR). First, we determine HIV-1 subtype on env (V3) and gag (p24) gene as a means of rapid genetic diversity. Secondly, we tried to analyse and identify homologous regions of gag (p24) gene of HIV genome for diagnostic purposes of designing primers. Out of 46 samples analysed, six subtypes were classified based on gag and env gene subtyping namely: 33 subtype B/B (71.2%), nine subtype A/E and one each subtype C/C, A/B and G/A (2.2% each). As a result, occurrence of non-subtype B and inter-subtype recombinant contributed to expanding genetic diversity. Based on inter- and intra-subtype gag alignment, oligonucleotides (>10 bases in length) could be easily selected as a universal primer to produce the PCR product composed of more than 100bp. This indicates that the PCR technology can be safely used with limited length of primers for the diagnosis of HIV infection in this country.

Base Sequence↗

PubMed1998

Genes for polymorphic H1 histones are linked in the Japanese quail genome.

In a previous report (Pałyga, J., Biochem. Genet. 29, 431-445, 1991), three subtypes of erythrocyte histone H1 were found to vary in a Japanese quail population. While H1.b and H1.z histones were each represented by two electromorphs differing in apparent molecular weights, a polymorphism of histone H1.a was connected with a lack of this protein in some birds. As a genetic basis for this variability was demonstrated only in H1.b, here genetic data are provided which indicate that both H1.a and H1.z are encoded by two codominant alleles at a locus. A linkage analysis of family data in 13 quail pedigrees has revealed a significant linkage between H1.a and H1.z and between H1.b and H1.z (lod scores about 12 and 5, respectively). Thus, a gene for histone H1.z is located between H1.a and H1.b in the quail genome.

Alleles↗

PubMed1986

Subtypes of bovine adenovirus type 2 exhibit major differences in region E3.

The genomes of two adenovirus type 2 strains which were isolated from different hosts have been investigated. One of these strains designated ORT-111 was originally isolated from a lamb in Hungary during an outbreak of pneumoenteritis. This isolate was typed as bovine adenovirus type 2 (Ad bos 2) in a neutralization assay. The genome of ORT-111 was compared to that of the prototype strain of Ad bos 2, a virus which exclusively has been isolated from cattle. Electron microscopic heteroduplex analysis showed that 95% of the genomes were well matched, forming stable duplexes at Tm -6 degrees. Two distinct substitution loops were, however, seen which were approximately 0.5 and 1.0 kbp long. The centers of the two loops were located 5.3 and 7.7 kbp from one end of the Ad bos 2 genome. In order to map these regions relative to the gene map of human adenovirus type 2 (Ad2), restriction enzyme cleavage fragments of the two bovine viruses were cloned and hybridized to different sets of restriction fragments of human Ad2. From these results it was apparent that the centers of the two substitution loops were located at coordinates 76 and 83, respectively; thus at positions which fall within region E3 and the adjacent gene for polypeptide VIII of human Ad2. The observed differences between the genomes of the two Ad bos 2 strains are in sharp contrast to those previously observed when the genomes of different human adenovirus serotypes were compared. In the latter case the hexon and the fiber genes showed the most pronounced variation.

Adenoviridae↗

PubMed2006

euHCVdb: the European hepatitis C virus database.

The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a given host. A database allowing researchers to investigate the genetic and structural variability of all available HCV sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development. We describe here the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as well as three-dimensional (3D) molecular models of proteins. A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses. As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses.

Databases, Protein↗

PubMed2001

The genomic organization of the gene encoding the vanilloid receptor: evidence for multiple splice variants.

Vanilloid receptor subtype-1 (VR1) is a nonselective cation channel that is expressed in sensory neurons and is activated by multiple noxious stimuli. Rat Vr1, stretch-inactivated channel (SIC), and vanilloid receptor 5' splice variant (VR.5'sv) have been hypothesized to be derived from a common VR gene. Characterization of the genomic structure encoding the 5' portion of rat Vr1 confirmed that VR.5'sv is derived from the VR gene; however, SIC seemed to be derived from two related but independent genes. We also deduced the genomic organization of the human gene VR1. Comparative studies of rat and human VR genes showed substantial conservation in genomic organization. The splice site flanking exon-intron 7 in rat and human VR1 diverged from the expected consensus sequence; this may help to explain the skipping of exon 7 within VR.5'sv and other VR splice variants.

5' Untranslated Regions↗

PubMed1998

Various types of HIV mixed infections in Cameroon.

In order to assess the incidence of HIV mixed infection as well as to clarify the molecular epidemiology of HIV in central Africa, we investigated 43 HIVs obtained from 211 Cameroonian AC, ARC, and AIDS patients in 1994 and 1995. Part of the pol region and part of the env region were phylogenetically analyzed. The genotypes observed were varied: of 43 specimens, 28 (65%) were subtype A, 1 (2%) was subtype B, 2 (5%) were subtype D, 3 (7%) were subtype F, and 2 (5%) were group O. Of the remaining 7 specimens, 3 were mixed infections with HIV-1 subtypes A and C, HIV-1 subtypes C and F, and HIV-2 subtype A and HIV-1 subtype A; 1 was a mixed infection with HIV-1 subtypes A and D and the highly divergent group O (triple infection); another 3 appeared to consist of mosaic genomes (A/G, A/E, and B/A recombinant). These data show that various types of mixed infection, such as between different subtypes of HIV-1 group M, between HIV-1 and HIV-2, and even between HIV-1 groups O and M, were confirmed at a rather high frequency (approximately 10%). The mixed infection is particularly significant where there is a greater variety of HIV-1 subtypes circulating, since it results in new genetic diversity generated by intersubtype recombination.

Adolescent↗

PubMed2003

PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions.

The classical Mycobacterium tuberculosis complex (MtbC) subspecies include Mycobacterium tuberculosis, Mycobacterium africanum (subtypes I and II), Mycobacterium bovis (along with the attenuated M. bovis bacillus Calmette-Guérin [BCG]), and Mycobacterium microti; increasingly recognized MtbC groupings include Mycobacterium bovis subsp. caprae and "Mycobacterium tuberculosis subsp. canettii." Previous investigations have documented each MtbC subspecies as a source of animal and/or human tuberculosis. However, study of these organisms is hindered by the lack of a single protocol that quickly and easily differentiates all of the MtbC groupings. Towards this end we have developed a rapid, simple, and reliable PCR-based MtbC typing method that makes use of MtbC chromosomal region-of-difference deletion loci. Here, seven primer pairs (which amplify within the loci 16S rRNA, Rv0577, IS1561', Rv1510, Rv1970, Rv3877/8, and Rv3120) were run in separate but simultaneous reactions. Each primer pair either specifically amplified a DNA fragment of a unique size or failed, depending upon the source mycobacterial DNA. The pattern of amplification products from all of the reactions, visualized by agarose gel electrophoresis, allowed immediate identification either as MtbC composed of M. tuberculosis (or M. africanum subtype II), M. africanum subtype I, M. bovis, M. bovis BCG, M. caprae, M. microti, or "M. canettii" or as a Mycobacterium other than MtbC (MOTT). This MtbC PCR typing panel provides an advanced approach to determine the subspecies of MtbC isolates and to differentiate them from clinically important MOTT species. It has proven beneficial in the management of Mycobacterium collections and may be applied for practical clinical and epidemiological use.

Algorithms↗

PubMed1991

Detection of Epstein-Barr virus genomes in Hodgkin's disease: relation to age.

An investigation as to whether any particular subgroup of patients with Hodgkin's disease was particularly likely to be Epstein-Barr virus (EBV) genome positive was made on samples from 95 patients. These were grouped according to age and Hodgkin's disease subtype, and analysed using Southern blot analysis. Most samples from children or adults aged 50 years or over contained detectable EBV genomes; samples from young adults were only rarely positive. The differences in EBV positivity by age were highly significant, but there was no significant association between EBV and histological subtype after allowing for the effect of age. The results support the hypothesis that Hodgkin's disease in different age groups may have different aetiologies, and suggest that EBV does have a pathogenetic role in Hodgkin's disease in children and older age groups.

Adolescent↗

PubMed2006

HIV-specific T cell immunity across the entire HIV genome in Chinese men who have sex with men.

BACKGROUND: Man who has sex with man (MSM) is one of the high risk groups for spreading HIV/AIDS. It was reported that the most prevalent human immunodeficiency virus type 1 (HIV-1) strain among MSM is subtype B; however, T cell immunity remains unknown across the HIV-1 B genome in this population. METHODS: Using Elispot assay with synthetic peptides spanning the sequence of HIV-1 consensus B, HIV-1-specific cytotoxic T-cell lymphocyte responses were quantified among 3 treated and 19 untreated HIV-1 infected MSM from Beijing, China. Cross-sectional association between viral loads and cellular immune responses were analyzed. RESULTS: Peptide pools corresponding to each HIV-1 protein were used for Env, Gag, Pol, Nef, Tat/Rev, Vpr/Vpu and Vif. The results showed that the magnitude of T cell responses in the 3 treated HIV(+) MSM group [median, 770 spot forming cells (SFCs) per 10(6) peripheral blood mononuclear cells (PBMCs)] might be significantly lower than that in the 19 untreated HIV(+) MSM group (median, 6175 SFCs per 10(6) PBMCs). Nef, Gag and Pol are the most frequently targeted HIV-1 antigens; and 16 subjects (73%) were identified with vigorous T cell immunity against each of these three proteins. The overall magnitude of T cell immunity closely related to its breadth (r = 0.72, P < 0.05) and was inversely but weakly associated with viral loads (r = -0.15). Further analysis showed that both Gag (r = -0.24) and Pol specific T cells (r = -0.12) contributed to this inverse association whereas Nef specific T cells showed no association with viral loads. CONCLUSIONS: The magnitude of HIV-1 specific T cells is inversely but weakly associated with viral loads among MSM; HIV-specific T cell responses against conservative sequences (Gag and Pol) are the main contributors to this association among Chinese HIV(+) MSM. These findings have important implications for vaccine design.

Adult↗

PubMed1997

Classification of hepatitis C virus variants in six major types based on analysis of the envelope 1 and nonstructural 5B genome regions and complete polyprotein sequences.

The phylogenetic status of recently described isolates of hepatitis C virus (HCV) from Vietnam, Thailand and Indonesia (previously classified as types 7, 8, 9, 10 and 11) was re-analysed by the neighbour-joining method instead of the unweighted pair-group method with arithmetic mean (UPGMA) that was first used by the discoverers of these strains. The analysis of complete amino acid sequences and of nucleotide sequences of the envelope 1 (672 nt) and nonstructural 5B (1092 nt) genomic regions permitted the re-assignment of the type 7, 8, 9 and 1 1 isolates to type 6, and that of type 10 strains to type 3. Finally, this study made possible the classification of the previously described HCV strains (including these South-East Asian isolates) in six major types and at least 30 subtypes. It confirms that analysis of the E 1 and NS5B genomic regions using the neighbour-joining method is a reliable tool for the assignment of most new isolates.

Genome, Viral↗

PubMed2006

Increasing HIV type 1 polymorphic diversity but no resistance to antiretroviral drugs in untreated patients from Central African Republic: a 2005 study.

As the HIV-1 pandemic becomes increasingly complex and as new countries acceed to antiretroviral drugs, the molecular characterization of HIV-1 strains circulating has important implications for vaccine research and for the efficacy of treatments. To follow the evolution of HIV-1 diversity in African countries, we have carried out a molecular analysis of HIV-1 strains collected from 150 HIV-1-positive pregnant women recruited in Bangui, Central African Republic (CAR). We have sequenced reverse transcriptase (RT) and protease (PROT) genes to (1) characterize the subtypes and CRFs, (2) describe the polymorphism of RT and PROT, particularly at the positions of drug resistance mutations in subtype B, and (3) observe potential drug resistance mutations and evaluate the prevalence of isolates bearing such mutations in this untreated population. The results showed that there is a very high and increasing diversity of HIV-1 strains circulating in CAR; out of 117 samples sequenced, we have observed 45 CRF11_cpx, 22 subtypes A1, 13 subtypes G, 7 subtypes CRF01_AE, 3 subtypes B, 3 subtypes CRF02_AG, 2 of each subtype F2 and CRF09_cpx, and one of each subtype D, J, C, H, CRF06_cpx, CRF13_cpx, and CRF19_cpx; the remaining 13 strains showed discordant genomic results suggesting multiple recombinations leading to mosaic viruses. The polymorphism of RT and PROT was high compared to subtype B, particularly at some positions that have been involved in antiretroviral resistance in subtype B, but we could not observe any major resistance mutation in this sample of untreated patients. The prevalence of drug resistance mutations in this population was therefore clearly under the WHO 5% threshold.

Central African Republic↗