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PubMed1989

The genetic predisposition to fibrocalculous pancreatic diabetes.

Fibrocalculous pancreatic diabetes (previously known as tropical pancreatic diabetes) is a rare cause of diabetes confined to countries within the tropical belt. The aetiology of fibrocalculous pancreatic diabetes is thought to be environmental although the agent(s) is unknown. We have investigated a possible genetic basis of this disease by looking for restriction fragment length polymorphisms of genes implicated in the aetiology of diabetes mellitus. Seventy-six Dravidian patients with fibrocalculous pancreatic diabetes were studied, and the restriction fragment length polymorphisms obtained compared to racially matched control subjects (n = 94), patients with Type 2 (non-insulin-dependent) diabetes (n = 87) and Type 1 (insulin-dependent) diabetes (n = 58). No association of fibrocalculous pancreatic diabetes was found with restriction fragment length polymorphisms of the insulin receptor gene. Although no association of fibrocalculous pancreatic diabetes was found with polymorphism of the HLA DR alpha/DQ alpha/DX alpha genes, an association was found with the Taq 1 restriction fragment length polymorphisms of the DQ beta gene (DQ beta T2/T6 present in 39% of patients with fibrocalculous pancreatic diabetes compared to 19% in control subjects; p = 0.01; corrected p value = 0.04) which is similar to that found in Type 1 but not Type 2 diabetes. An association of fibrocalculous pancreatic diabetes was also found with the hypervariable region in the 5-prime flanking region of the insulin gene; 40% of patients possessed the class 3 allele compared to 9.5% of control subjects p = 0.0001; corrected p value = 0.0008).(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

PubMed1987

Human alpha-globin maps to pter-p13.3 in chromosome 16 distal to PGP.

Fibroblasts from a fetus with an unbalanced karyotype 46(XY), -16,+(16qter-16p13.3::4q31.1-4qter) were found to possess only one allele at the 3' hypervariable region (3'HVR) close to the alpha-globin locus and two alleles at the PGP locus. This places the alpha-globin locus at the very tip of 16p, distal to PGP.

Chromosome Banding↗

PubMed1987

Allele-specific DNA identity patterns.

A method of genetic analysis is presented which involves digestion of DNA with a single restriction enzyme (PvuII) and hybridisation with a mixture of five probes. Four of the five probes chosen recognise hypervariable regions (HVRs) of the human genome and hence an allele-specific DNA identity pattern results. An advantage of this approach to genetic characterisation is that the complex identity patterns may be broken down into simple allelic systems of known chromosomal localization by hybridisation with the individual probes. Also different probes may be included in a combined probe designed for particular types of investigation.

DNA Restriction Enzymes↗

PubMed1989

Strain variation in Campylobacter pylori detected by numerical analysis of one-dimensional electrophoretic protein patterns.

A total of 21 clinical isolates of Campylobacter pylori from Peru and the United Kingdom and two reference strains (from Australia), including the type strain (NCTC 11637T), were characterized by high resolution one-dimensional SDS-polyacrylamide gel electrophoresis of cellular proteins. The protein patterns contained more than 40 discrete bands and the approximate molecular weights of the major bands were 22, 27, 46, 57, 60, 65 and 93 kD. The total patterns were used as the basis of numerical analysis. Most strains were clustered in four phenons at 91% similarity with the exception of six ungrouped strains. Overall similarity was high with all strains linked in the phenogram at greater than or equal to 81%. Variation among strains was attributable principally to qualitative and quantitative band differences in the 47 to 56 kD (hypervariable) region of the C. pylori protein profile. From the analysis, ten different electropherotypes (EP-types) were identified. We demonstrated that differences were detectable among isolates from widely separated geographical locations as well as from the same location, although multiple isolates from two Peruvian patients had the same electropherotype. Our results indicate that determination of protein profiles provides the basis of a reproducible method for characterization of C. pylori isolates.

Bacterial Proteins↗

PubMed1991

A genetic study of retinopathy in south Indian type 2 (non-insulin-dependent) diabetic patients.

Genetic marker studies in diabetic retinopathy are controversial and frequently complicated by possible independent associations of Type 1 (insulin-dependent) diabetes mellitus with the markers so far analysed. We have looked for associations of candidate genes with retinopathy in South Indian Type 2 (non-insulin-dependent) diabetic patients; patients were subdivided into those with exudative maculopathy (n = 53), proliferative retinopathy (n = 40) and patients free from diabetic retinopathy with a minimum disease duration of 15 years (n = 45). DNA was extracted from blood samples and studied by Southern blot hybridisation techniques and the following probe enzyme combinations: HLA-DQB1; Taq 1, HLA-DQA1; Taq 1, HLA-DRA; Bgl II, insulin gene hypervariable region; Pvu II and the switch region of the immunoglobulin IgM heavy chain gene (S mu); Sac I. Differences in genotype distributions between the study groups were only detected with the S mu probe which detects polymorphism of both S mu and S alpha 1 (the switch region of IgA). Two alleles of S alpha 1 were detected sized 7.4 kilobase and 6.9 kilobase. The frequency of 6.9 kilobase homozygotes was lower in proliferative retinopathy (19%) compared to patients free from diabetic retinopathy (54%, p = 0.005) and exudative maculopathy (46%, p = 0.03). This data suggests that there is a genetic predisposition to proliferative retinopathy in Type 2 (non-insulin-dependent) diabetes of South Indian origin and that this is determined by polymorphism of the heavy chain immunoglobulin genes located on chromosome 14.

Aged↗

PubMed1987

The control mechanism of opacity protein expression in the pathogenic Neisseriae.

The expression of Neisseria gonorrhoeae opacity protein shows frequent phase transitions. The genome contains at least twelve copies of the opa gene. Each copy is complete and different from most of the others in certain hypervariable regions. All opa genes are constitutively transcribed. Part of the leader peptide of all Op's is encoded by repetitive CTTCT pentameric units, the so-called coding repeat (CR). The number of repeat units found in the genes and mRNA is subject to frequent and precise changes. Such changes affect the expression of individual opa genes at the translational level. This control mechanism is common also to the class 5 proteins of N. meningitidis and the Op-related proteins of N. lactamica.

Antigens, Bacterial↗

PubMed1991

Conservation genetics of the koala (Phascolarctos cinereus). II. Limited variability in minisatellite DNA sequences.

We have examined variability in TaqI and EcoRI restriction fragment sizes of DNA from the koala (Phascolarctos cinereus) using six HVR (hypervariable region) probes which reveal complex, individual-specific restriction patterns in humans and other species. Frequency of band-sharing among unrelated koalas was extremely high. This result is likely to be a consequence of the history of near-extinction and artificial recolonization of the populations we have studied, rather than a general marsupial or koala-wide phenomenon.

Animals↗

PubMed1990

Expression of foreign epitopes in P-fimbriae of Escherichia coli.

Hypervariable regions (HRs) of the major subunit of F11 fimbriae were exploited for insertion of foreign epitopes. Two insertion vectors were created that contain a unique cloning site in HR1 or HR4 respectively. Several oligonucleotides, coding for antigenic determinants derived from different pathogens, were cloned in both insertion vectors. Hybrid fimbrial subunits were generally shown to be assembled in fimbriae when the length of the inserted peptide did not exceed 14 amino acids. The inserted peptides appeared to be exposed in the fimbrial filament. One hybrid fimbrial protein induced detectable levels of antibodies against the inserted epitope if injected into mice.

Amino Acid Sequence↗

PubMed1990

The development of new radiopharmaceuticals.

The development of new radiopharmaceuticals is the basis of the continuing growth of nuclear medicine. Chemical interactions of electron clouds in their three-dimensional conformations bring together, in the process of molecular recognition, the reaction of antibody and antigen, receptor and ligand, enzyme and substrate, hormone and response site. This convergence enables the computer design of molecules such as ligands to fit computer-displayed conformational models showing active centres, positive and negative charges and other interactions. Indeed, given a particular molecule, a complementary binding structure can be devised. The hybridoma approach to monoclonal antibody production is being superceded by the bacterial bioengineer. The gene for the hypervariable region from the spleen cells of immunized mouse can be coupled with the myeloma gene. The polymerase chain reaction can duplicate the DNA a million times over in 20 min and the result transfected into a bacterial plasmid to produce the antibody. These scientific problems are soluble in principle and are being solved. However, so much damage to this developing biological field is being done by regulatory authorities that one must ask who should or can regulate the regulators. These problems have to be overcome in order to provide the new radiopharmaceuticals that are the food and wine of nuclear medicine.

Animals↗

PubMed1992

Serum antibodies to HIV-1 in recombinant vaccinia virus recipients boosted with purified recombinant gp160. NIAID AIDS Vaccine Clinical Trials Network.

Serum antibody responses were studied in detail in four vaccinia-naive volunteers in a phase I trial evaluating primary vaccination with a recombinant vaccinia virus expressing the HIV-1 gp160 envelope glycoprotein (HIVAC-1e, Oncogen/Bristol-Myers Squibb), followed by booster immunization with baculovirus-derived rgp160 (VaxSyn, MicroGeneSys). Prior to boosting, low-titer Fc receptor (FcR)-mediated, antibody-dependent enhancing (ADE) activity was detected in two of four volunteers but no IgM, IgG, IgA, neutralizing activity, or complement-mediated ADE activity was detected. Two weeks after boosting, all four volunteers developed HIV-1-specific IgG with titers of 1:160 to 1:640 by immunofluorescence assay. IgG1 was present in sera from each individual, while IgG2 and IgG3 were present in sera from two individuals, and IgG4 was present in serum from one individual. IgM and IgA were undetectable in all sera. Only one volunteer had IgG to the heterologous HIV-1 isolates, RF, MN, and SF2, after boosting. Serum from this volunteer neutralized the vaccine strain, LAV/IIIB, but not the heterologous strains, RF, MN, and SF2. Antibodies from the remaining volunteers had no neutralizing activity. The neutralizing serum had a positive reaction in a peptide-based ELISA utilizing a peptide corresponding to the principal neutralizing domain of the third hypervariable region (i.e., V3 loop) of the envelope glycoprotein. Neutralizing activity was partially removed by adsorption to this peptide, suggesting that it contained a type-specific neutralizing vaccine epitope. A low titer (1:40 to 1:80) of complement-mediated ADE activity to HIV-1 IIIB was present in sera from three vaccinees after boosting. FcR-ADE activity for HIV-1 SF2 and SF-128A were present in sera from two of these three vaccinees. None of the volunteers developed antisyncytial antibodies. These results indicate that inoculation with recombinant vaccinia followed by rgp160 boosting is the most effective strategy to date for inducing serum antibodies to the envelope glycoproteins of HIV-1, but further study is needed to optimize the functionality and cross-reactivity of these responses.

AIDS Vaccines↗

PubMed1988

Amino acid sequences of pilins from serologically distinct strains of Bacteroides nodosus.

Amino acid sequences of pilin from a strain of Bacteroides nodosus from serogroup B (234) and serogroup C (217) were determined. The amino-terminal N-methylphenlalanine residue of both proteins was followed by a hydrophobic sequence of 30 residues closely related to the N-terminal sequence of other pili having an amino-terminal residue of N-methylphenylalanine. These data lend support to the hypothesis that in pilins of this type, the amino-terminal sequence functions as a transport signal necessary for pilin to reach its external environment, as well as promoting intersubunit interactions for maintenance of the structural integrity of the pilus. Two hydrophilic hypervariable regions can be discerned across the pilin sequences, indicating possible locations of antigenic domains.

Amino Acid Sequence↗

PubMed1995

Selective transmission of hepatitis C virus in vivo and in vitro.

A human plasma containing quasi-species of hepatitis C virus (HCV) was inoculated to a chimpanzee and to human lymphocytic cell lines, HPB-Ma clone 10-2, AD HPB, and Daudi, which support replication of HCV. Among six different hypervariable region (HVR) sequences detected in the inoculum, the same two were recovered both in vivo and in vitro.

Amino Acid Sequence↗

PubMed1996

DNA typing from human faeces.

A method has been developed for the forensic analysis of faeces by DNA amplification and direct sequencing of a polymorphic segment of mitochondrial DNA. Starting from as little as 10 mg wet weight of faeces, DNA was extracted by a variety of protocols and amplified using primers specific to hypervariable region 1 of the mitochondrial control region. The resulting amplification products were sequenced in solid phase using an automated DNA sequencer. In total, mtDNA sequences were generated from the faeces of nine Caucasians and compared with sequences generated from their respective blood samples. Sequences of faeces and blood samples from the same individual were identical in every case, but a range of 1-10 nucleotide differences was observed between individuals, with an average sequence variation of approximately 4.88 per 400 bp. Of the various extraction protocols assessed in this study, greatest success rates were achieved using magnetisable beads to bind and purify the DNA. STR analysis of DNA extracted from faeces was not routinely possible.

Animals↗

PubMed1995

Sequence and genomic organization of a rabbit hemorrhagic disease virus isolated from a wild rabbit.

Rabbit hemorrhagic disease virus (RHDV) is a member of the caliciviridae family. The nucleotidic sequence of a full-length cDNA of one RHDV isolate (RHDV-SD) is reported. The genome is 7437 bases long and includes two ORFs, ORF1 (7034 b) and ORF2 (353 b), coding for the polyprotein and the Vp12, respectively. The coding sequence for the second structural protein (the capsid protein, Vp60) is located at the 3' end of ORF1. Comparison of RHDV-SD with the German RHDV isolated revealed 470 nucleotide substitutions (96% homology). The deduced amino acid sequences of the two isolates are closely related (98% identity), and no hypervariable region could be identified either in the structural or nonstructural proteins.

Amino Acid Sequence↗

PubMed1996

Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan.

In order to differentiate recent isolates of avian infectious bronchitis virus (IBV) in Taiwan, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and direct sequencing methods were used to type 25 IBV Taiwan isolates. Two conserved sequences that flank the hypervariable region I (HVR I) in the N-terminus of S1 protein gene were chosen as primers. Sequences of 228-231 base pairs (bp) were amplified by PCR from 25 Taiwan isolates and 4 reference strains (H120, Conn, JMK, Holte). PCR products were digested with 5 restriction endonucleases, BsoFI, DdeI, MboII, AluI, RsaI, and different IBV isolates were grouped according to their RFLP patterns. The RFLP patterns of the 4 reference strains in this study matched the published sequences in GenBank. Except 1 vaccine strain, the other 24 Taiwan isolates were different from these 4 and 18 other IBV strains whose sequences were published. The data from PCR-RFLP and sequencing of IBV genomes showed that the 24 Taiwan isolates can be divided into 2 distinct groups, I and II. Seven RFLP patterns are identified in group I and only 1 in group II.

Animals↗

PubMed1990

Allelic variation in the DR subregion of the canine major histocompatibility complex.

Allelic variation in the DR subregion of the canine major histocompatibility complex (DLA) has been analyzed by nucleic acid sequencing of cDNA clones of DRB genes amplified in vitro by the reverse transcriptase-polymerase chain reaction (RT-PCR). Sequence analysis of a panel of 19 homozygous typing cell dogs representing 12 different DLA-D types (defined by mixed leucocyte reaction) demonstrated the presence of one expressed DRB locus with at least nine distinct alleles in the dog. Unique DLA-DRB alleles were found in the DLA-D types Dw1, Dw3, Dw4, Dw8 (workshop assignments) and D4, D6, D7, D8, and D9 (Seattle assignments). In contrast, the DRB genes of the remaining three DLA-D types (D1, D10, and D16) were identical to those of Dw3/Dw4 (for D1), Dw8 (for D10), and D6 (for D16). The nucleotide sequences of all nine DLA-DRB alleles were typical of functional major histocompatibility complex (MHC) class II beta chains and contained three allelic hypervariable regions (HVRs) in the beta 1 domain at positions 8-16, 26-39, and 57-74. At each variable residue, two to five amino acid substitutions were found. The most polymorphic residues were located at positions 37 (with five amino acid substitutions), 11, 13, 28, and 71 (each with four substitutions). The DLA-DRB alleles had 96%-99% overall nucleotide sequence similarity and 93%-99% amino acid sequence similarity with each other. Cluster analysis of the nucleotide and predicted amino acid sequences subdivided the DLA-DRB alleles into three major allelic groups which may represent the canine counterparts of the supertypic groups described in man.

Alleles↗

PubMed1995

A detection assay for Campylobacter fetus in bovine semen by restriction analysis of PCR amplified DNA.

A rapid screening assay for Campylobacter fetus in bull semen was developed using the polymerase chain reaction (PCR) and restriction endonuclease analysis (REA) to complement isolation by culture. An oligonucleotide primer pair (C1/C2) from the hypervariable region of 16S rRNA of C. fetus was used to amplify a 362 base pair fragment by PCR. The PCR/REA assay, which is completed in 10 hours, detected as few as three C. fetus subsp. venerealis cells in experimentally infected raw bull semen and in semen diluted with milk or egg yolk Tris (EYT). All the strains tested, of both subspecies of C. fetus, were amplified, as were some other Campylobacter species. Restricting the amplified products by AluI differentiated C. fetus from the other organisms. There was no visible product generated by PCR from C. sputorum subsp. bubulus, a saprophytic organism found in the prepuce of bulls, or from seven other species of bacteria found in semen. A modification of the PCR assay, using another primer pair (C3/C2) and two temperature PCR cycling conditions, increased the probability of detecting C. fetus subsp. venerealis. PCR amplification followed by REA could be used to screen bovine semen rapidly for C. fetus. In most cases, sequencing of C1/C2 PCR generated products would be preferable for distinguishing between the two subspecies of C. fetus.

Animals↗

PubMed1996

Predictors of response to interferon therapy.

An optimal treatment schedule is the first factor that influences sustained responses to interferon (IFN) therapy. There is growing evidence that prolonged IFN therapy (at least 12 months or longer) increases the sustained response rate. A low viremia at baseline favorably affects the long-term response to IFN. High viral replication does not preclude response, but highly viremic patients tend not to sustain their response. Patients with genotypes 2 and 3 (Simmonds classification) have an improved likelihood of responding compared to patients with genotype 1; unfortunately, genotype 1 predominates in Western countries. The "quasispecies" diversity of hepatitis C virus (HCV) may play a role in determining response to IFN, which is more likely in patients with lesser degrees of HCV diversity. However, studying the nucleotide diversity of the hypervariable region 1 of HCV is a very complex and expensive process that cannot be applied to a large number of patients. The sustained response rate is higher in patients with mild disease than in cirrhotic patients. Cirrhotics should be treated with caution, since IFN therapy could induce serious side effects and decompensation. Baseline predictive factors of response are useful to improve the cost-benefit ratio of IFN therapy but cannot be considered inclusion/exclusion criteria. The decision on how to treat should be based upon the individual characteristics of each patient.

Chronic Disease↗