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PubMed2000

Molecular investigation of African isolates of Trichinella reveals genetic polymorphism in Trichinella nelsoni.

Molecular genetic studies were carried out on three isolates of Trichinella nelsoni (from Kenya, Tanzania and South Africa) and three isolates of Trichinella T8 (from South Africa and Namibia) from sylvatic carnivores and from a sylvatic swine. A probe (pT7.3) specific for T. nelsoni was obtained by screening a pUC18 genomic library. The pT7.3 sequence was 346 bp in length with an AT content of 70%. The sequence is present approximately 200 times per haploid genome. Southern blot analysis of Hind III digested DNAs of the three isolates of T. nelsoni revealed that the hybridisation patterns of the isolates from Kenya and Tanzania were identical and that they differed from that of the isolate from South Africa, indicating the presence of polymorphism in this species. A pUC18 genomic library of Trichinella T8 was also screened, and one clone (pT8.3) was found to be specific for homologous DNA by dot blot, but Southern blot analysis of DNA samples from eight genotypes showed different hybridisation signals for both Trichinella T8 and Trichinella britovi DNAs. No differences in the nucleotide sequences of the expansion segment V were observed for the T. nelsoni isolates. However, they differed from those of Trichinella T8. The presence of Trichinella T8 in Africa south of the Sahara and its genetic relationship with T. britovi remain unclear and warrant detailed investigations.

Animals↗

PubMed1995

Three novel sequence variations in the 5' upstream region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene: two polymorphisms and one putative molecular defect.

More than 400 sequence alterations have been identified in the whole coding sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene corresponding to the 27 exons and their exon-intron boundaries. However, in some CF chromosomes, no mutation has yet been detected. In such cases, we have explored the promoter and the sequence up to position -1000 from the cap site, by using denaturing gradient gel electrophoresis. This study concerning 35 CF chromosomes has allowed us to identify three novel sequence variations located in the 5' upstream region of the gene. The T to G substitution located at position -895 from the cap site could be considered as a polymorphic variation. The second substitution (C to T at position -816) has been detected on only one CF chromosome, but does not concern a regulatory DNA element previously described. Conversely, the third substitution (a T to G substitution at position -741 from the cap site) is located at a potential AP-1 binding site. We have investigated, by electrophoretic mobility shift assay, the ability of this region to bind nuclear factors. We have found that the normal sequence between -740/-745 does not bind either the AP-1 transcription factor or AP-1 related proteins, and that the T to G-741 mutated sequence exhibits an abnormal binding pattern suggesting the possible deleterious effect of still unknown negative trans-acting factors.

Base Sequence↗

PubMed2002

A single nucleotide polymorphism of the low molecular mass polypeptide 7 gene influences the interferon response in patients with chronic hepatitis C.

Transporter associated with antigen processing (TAP) and low molecular mass polypeptides (LMP) play crucial roles in the human leukocyte antigen (HLA) class I-restricted antigen presenting systems. This study was performed to elucidate whether these antigen-presenting gene polymorphisms could influence the response to interferon (IFN) treatment in patients with chronic hepatitis C. Polymorphisms of TAP and LMP genes in 175 hepatitis C virus (HCV) patients were determined by polymerase chain reaction-restriction fragment length polymorphism. The frequencies of these genes were compared between sustained-responders (n=49) and nonresponders (n=126), classified by biochemical and virological responses to IFN. The distributions of TAP1*, TAP2*, and LMP2 genes between sustained-responders and nonresponders did not differ. However, LMP7-K gene frequency in sustained-responders was higher than that in nonresponders [odds ratio 2.3 (95% confidence interval 1.1-4.6); 16%vs 7.9%]. Multivariate analysis revealed that LMP7-K and HCV-RNA quantity were independent factors influencing the outcome of IFN therapy [4.5 (1.4-14); P=0.011, 0.40 (0.24-0.65); P=0.0003, respectively]. Furthermore, among patients with a low viral load (< or = 2.0 Meq/mL), the LMP7-K positive patients had an even higher ratio of sustained response compared to those without LMP7-K [5.9 (1.6-22); 82%vs 44%; P=0.0062]. These findings suggest that a single nucleotide polymorphism of LMP7 gene is one of the important host factors which independently influence the response to IFN in patients with chronic hepatitis C.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1991

Molecular basis for allelic polymorphism of the maize Globulin-1 gene.

An abundant protein in maize (Zea mays L.) embryos is a storage globulin encoded by the polymorphic Glb1 gene. Several Glb1 protein size alleles and a null allele have been described. Here we report the isolation and nucleotide sequence analysis of genomic clones corresponding to two Glb1 size alleles (Glb1-L and Glb1-S) and to the Glb1-0 null allele. The Glb1-L and Glb1-0 alleles differ from Glb1-S by the presence of small nucleotide insertions which are imperfect or perfect duplications, respectively, of adjacent sequences. In the case of Glb1-L, the insertion is in-frame and results in a protein larger than that encoded by Glb1-S, whereas in Glb1-0 the insertion causes a translational frameshift which introduces a premature termination codon. Although steady-state levels of Glb1-0 transcripts are extremely low in Glb1-0/0 embryos, nuclear transcription assays indicate that the Glb1-0 gene is transcribed at a level comparable to that of Glb1-L. This suggests that the low amounts of Glb1-0 transcripts in the cytoplasm may be due to mRNA instability.

Alleles↗

PubMed1993

Molecular analysis of allelic polymorphism at the AAT2 locus of alfalfa.

Aspartate aminotransferase (AAT) plays a key enzymatic role in the assimilation of symbiotically fixed nitrogen in legume root nodules. In alfalfa, two distinct genetic loci encode dimeric AAT enzymes: AAT1, which predominates in roots, and AAT2, which is expressed at high levels in nodules. Three allozymes of AAT2 (AAT2a, -2b and -2c), differing in net charge, result from the expression of two alleles, AAT2A and AAT2C, at this locus. Utilizing antiserum to alfalfa AAT2, we have previously isolated from an expression library one AAT2 cDNA clone. This clone was used as a hybridization probe to screen cDNA libraries for additional AAT2 cDNAs. Four different clones were obtained, two each that encode the AAT2a and AAT2c enzyme subunits. These two sets of cDNAs encode polypeptides that differ in net charge depending upon the amino acid at position 296 (valine or glutamic acid). Within each set of alleles, the two members differ from each other by the presence or absence of a 30 bp (ten amino acid) sequence. The presence or absence of this ten amino acid sequence has no effect on the size or charge of the mature AAT2 protein because it is located within the region encoding the protein's transit peptide, which is proteolytically removed upon transport into plastids. The data suggest that a deletion event has occurred independently in two AAT2 progenitor alleles, resulting in the four allelic cDNA variants observed. The deletion of this ten amino acid sequence does not appear to impair the normal maturation of the enzyme.

Alleles↗

PubMed2006

Direct molecular haplotyping of multiple polymorphisms within exon 4 of the human catechol-O-methyltransferase gene by liquid chromatography-electrospray ionization time-of-flight mass spectrometry.

The applicability of ion-pair reversed-phase high-performance liquid chromatography hyphenated to electrospray ionization time-of-flight mass spectrometry (ICEMS) for the haplotyping of five SNPs (rs769223, rs4818, rs4986871, rs8192488, rs4680) located within exon 4 of the human catechol-O-methyltransferase (COMT, EC 2.1.1.6) gene is demonstrated. Two differently sized products of polymerase chain reaction--a 71-bp amplicon partially covering the sequence of a 124-bp amplicon--were used to determine unequivocally the allelic states of the single nucleotide polymorphisms linked on both chromosomes. The two amplicons were co-loaded onto the chromatographic column and simultaneously analyzed within a single gradient run. Using the described strategy, 101 individuals representing an Austrian population sample were typed. The obtained haplotype frequencies will serve as reference values in future association studies to examine the impact of the COMT gene on neuropsychiatric disorders. Additionally, two newly discovered polymorphic sites within the sequence of the COMT gene are described (a synonymous C>T mutation at the third position of the amino acid codon 99 in the soluble COMT protein or 149 in the membrane-bound COMT protein; a non-synonymous G>A substitution at the second position of the amino acid codon 95 in the soluble COMT protein or 145 in the membrane-bound-COMT protein).

Base Sequence↗

PubMed1983

Molecular basis of length polymorphism in the human zeta-globin gene complex.

The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies.

Base Composition↗

PubMed2005

Evaluation of tRNA intergenic spacer length polymorphism analysis as a molecular method for species identification of streptococcal isolates from bovine mastitis.

Sixty-nine bovine mastitis streptococci belonging to the species Str. agalactiae (n = 13), Str. dysgalactiae (n = 16), Str. canis (n = 22), Str. uberis (n = 20) and Str. parauberis (n = 4) and six reference strains of the five streptococcal species were examined for their tRNA gene intergenic length polymorphism (tDNA-ILP) fingerprint pattern. Epidemiologically unrelated isolates from bovine mastitis cases were selected by macrorestriction analysis with pulsed-field gel electrophoresis (PFGE). Their results were compared with those obtained from biochemical and serological studies and with those obtained by PCR-mediated identification amplifying species-specific gene segments of the five streptococcal species. According to the present results tDNA-ILP allowed a correct identification of all Str. agalactiae, Str. uberis and Str. parauberis strains investigated also including the reference strains of each species showing species-specific banding pattern. However, all Str. dysgalactiae ssp. dysgalactiae and all Str. canis strains appeared with an undistinguishable pattern which did not allow an identification of the species.

Animals↗

PubMed1995

The molecular basis for genetic polymorphism of human deoxyribonuclease I: identification of the nucleotide substitution that generates the fourth allele.

In addition to the three alleles commonly responsible for the protein polymorphism of human deoxyribonuclease I, a mutation encoded by a fourth allele, DNASE1*4, was detected by isoelectric focusing. All 8 exons covering the entire open reading frame of the human DNase I gene were amplified by the polymerase chain reaction and subjected to direct sequencing. Only one nucleotide substitution, a C-to-G transition (CAG-->GAG), in the codon for amino acid 9 of the mature enzyme was found. This substitution resulted in the replacement of Gln with Glu (Q9E).

Alleles↗

PubMed1994

Molecular genetics of human polymorphic N-acetyltransferase: enzymatic analysis of 15 recombinant wild-type, mutant, and chimeric NAT2 allozymes.

Human polymorphic N-acetyltransferase (NAT2) catalyzes the N-acetylation of arylamine drugs and carcinogens. Human acetylator phenotype is regulated at the NAT2 locus and has been associated with differential risk to certain drug toxicities or cancer. We examined arylamine substrate and acetyl coenzyme A cofactor affinities, and the N-acetyltransferase catalytic activities of the wild-type and 14 different mutant or chimeric human NAT2 alleles expressed in an Escherichia coli JM105 expression system. NAT2 alleles contained nucleic acid substitutions at positions 191(G-->A; Arg64-->Gln), 282(C-->T; silent), 341(T-->C; Ile114-->Thr), 481(C-->T; silent), 590(G-->A; Arg197-->Gln), 803(A-->G; Lys268-->Arg), 857(G-->A; Gly286-->Glu) and various combinations (282/590; 282/803; 282/857; 341/481; 341/803; 341/481/803; 481/803) of the 870 base pair NAT2 coding region. Expression of all 15 NAT2 alleles produced immunoreactive NAT2 protein with N-acetylation activity. NAT2 proteins encoded by alleles with nucleic acid substitutions at positions 191, 341, 590, 282/590, 341/481, 341/803, and 341/481/803 exhibited arylamine N-acetyltransferase maximum velocities significantly (P < 0.001) lower than the wildtype NAT2. Thus, nucleic acid substitutions at positions 191, 341, and 590 either alone or in combination with other silent or conservative amino acid substitutions were sufficient to result in NAT2 proteins with significant reductions in N-acetylation activities. The recombinant NAT2 proteins also showed relative differences in intrinsic stability following incubation at 37 degrees C and 50 degrees C. NAT2 encoded by alleles with nucleotide substitutions at positions 191 and 857 were particularly unstable relative to the wild type.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetyl Coenzyme A↗

PubMed1996

Molecular characterization of antigenic polymorphisms (Ond(a) and Mart(a)) of the beta 2 family recognized by human leukocyte alloantisera.

We show that the previously described alloantisera Ond and Mart, which recognize the alloantigens Ond(a) and Mart(a), react with polymorphic variants of alpha L and alpha M subunits of the beta 2 integrin family (CD11a and CD11b molecules). This was shown by testing the alloantisera in a monoclonal antibody-specific immobilization of leukocyte antigens, immunoprecipitation, and immunofluorescence assay against cells from normal donors and from patients with leukocyte adhesion deficiency (beta 2 intergrin deficient). To elucidate the molecular basis of the Ond(a) and Mart(a) alloantigens, RNA was isolated from mononuclear leukocytes derived from individuals of known serologic phenotype. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to amplify the entire coding region of the alpha L and alpha M mRNAs. The Ond(a) antigen was found to be due to a G2466C substitution in the DNA coding for the alpha L subunit, which predicts an Arg766Thr amino-acid polymorphism. The Mart(a) antigen was also found to be due to a single nucleotide substitution (G302A) in the DNA coding for the alpha M subunit, which predicts an Arg61His amino acid polymorphism. Using allele-specific restriction enzyme analysis, the association between point mutations and phenotypes was confirmed. The localization of these alloantigens on integrin molecules further illustrates the polymorphic nature of this class of proteins. Whether the polymorphisms influence the adhesive capacity of the leukocyte integrins remains to be investigated.

Alleles↗

PubMed2002

[The relationship of beta-fibrinogen gene polymorphisms and ischaemic cardiocerebral vascular disease].

OBJECTIVE: To analyze the frequency of beta-fibrinogen (beta-Fg) gene -455G/A, -148C/T and 448G/A polymorphism, fibrinogen molecular reactivity and their association with plasma fibrinogen levels in health adults, myocardial infarction and cerebral infarction disease. METHODS: The beta-Fg gene -455G/A, -148C/T and 448G/A polymorphisms were analyzed by restriction fragment length polymorphism (RFLP). Fibrinogen molecular reactivity was analyzed for the conversion kinetics of fibrinogen into fibrin by a computer assistant procedure. Plasma fibrinogen levels were determined by Clauss method. RESULTS: The frequencies of -455A, -148T, 448A allele in health adults were 0.185, 0.194 and 0.192, in myocardial infarction disease 0.295, 0.318 and 0.307, in cerebral infarction disease 0.177, 0.193 and 0.182, respectively. The frequencies of -455A, -148T, 448A alleles in myocardial infarction disease were apparently higher than that of health adults. There were close linkage between -455G, -148C and 448G or -455A, -148T and 448A, the correspondence was over 98%. There are no differences in the plasma fibrinogen levels of the three polymorphisms in two genotype groups. The fibrinogen molecular reactivity was significantly increased in cardiocerebral vascular disease and related with plasma fibrinogen level. CONCLUSION: The three polymorphisms loci are strong linkage disequilibrium. There are no significant differences in the plasma fibrinogen levels of the three polymorphisms in two genotype groups. The frequencies of -455A, -148T, 448A alleles in myocardial infarction disease were apparently higher than that of health adults. It suggest that there was no association between beta-Fg gene -455G/A, -148C/T and 448G/A polymorphisms and plasma fibrinogen levels, but did in myocardial infarction disease. The fibrinogen molecular reactivity was significantly increased in cardiocerebral vascular disease and related with plasma fibrinogen level.

Adult↗

PubMed1987

Molecular analysis of a polymorphic domain of alpha satellite from the human X chromosome.

Alpha satellite DNA, a diverse family of tandemly repeated DNA sequences located at the centromeric region of each human chromosome, is organized in a highly chromosome-specific manner and is characterized by a high frequency of restriction-fragment-length polymorphism. To examine events underlying the formation and spread of these polymorphisms within a tandem array, we have cloned and sequenced a representative copy of a polymorphic array from the X chromosome and compared this polymorphic copy with the predominant higher-order repeat form of X-linked alpha satellite. Sequence data indicate that the polymorphism arose by a single base mutation that created a new restriction site (for HindIII) in the sequence of the predominant repeat unit. This variant repeat unit, marked by the new HindIII site, was subsequently amplified in copy number to create a polymorphic domain consisting of approximately 500 copies of the variant repeat unit within the X-linked array of alpha satellite. We propose that a series of intrachromosomal recombination events between misaligned tandem arrays, involving multiple rounds of either unequal crossing-over or sequence conversion, facilitated the spread and fixation of this variant HindIII repeat unit.

Chromosome Mapping↗

PubMed2006

NADPH-diaphorase histochemical changes in the hippocampus, cerebellum and striatum are correlated with different modalities of exercise and watermaze performances.

Nitric oxide is involved in memory and motor learning. We investigated possible influences of exercise on spatial memory and NADPH-diaphorase (NADPH-d) histochemical activity in the hippocampus, striatum and cerebellum. Fifteen albino Swiss mice between the 22nd and 55th post-natal days were exercised in the following modalities: voluntary (V), acrobatic (A), acrobatic/voluntary (AV) and forced (F) and compared to inactive group (I). After the exercise period, all subjects were tested in the water maze for 3 days. Animal brains were processed for NADPH-d histochemistry. Densitometry of the neuropil of the hippocampus, striatum and cerebellum and morphometric analysis of NADPHd+ type I neurons of the striatum were done. Exercise groups presented higher levels of NADPH-d activity in the molecular and polymorphic layers of dentate gyrus and lacunosum molecular layer of CA1. The A group presented higher NADPH-d activity in the cerebellar granular layer than all other groups. Branching points and dendritic segment densities of NADPH-d type I neurons were higher in V, A and AV than in F and I groups. Exercise groups revealed best performances on water maze tests. Thus, different modalities of exercise increases in different proportions for the nitrergic activity in the hippocampus, striatum and cerebellum, and these changes seem to be beneficial to spatial memory.

Analysis of Variance↗

PubMed2003

Molecular characterization of new polymorphisms at the beta2, alpha1, gamma2 GABA(A) receptor subunit genes associated to a rat nonpreferring ethanol phenotype.

Recent preclinical and clinical studies have indicated a possible involvement of the genes encoding for the GABA(A) receptor subunits alpha6, beta2, alpha1 and gamma2 in the genetic susceptibility to alcohol abuse. We have recently found an (R) to (Q) mutation in codon 100 of the alpha6 GABA(A) subunit, that segregated in a rat line selectively bred for its voluntary ethanol aversion, Sardinian alcohol nonpreferring (sNP), but not in their Sardinian alcohol preferring (sP) counterpart, selected for its ethanol preference. In the present study the molecular composition of other GABA(A) subunits (beta2, alpha1 and gamma2) were analyzed in order to further investigate the involvement of the GABA(A) receptors in the genetic predisposition to voluntary alcohol intake. Automated sequencing analysis indicated the presence of six new silent substitutions (289 T-->C in the beta2 gene; 115 G-->A in the alpha1 gene; 157 G-->A, 174 C-->T, 347 A-->G and 385 A-->T in the gamma2 gene), in sNP but not in sP rats. These polymorphisms were linked to the alpha6 R100Q mutation previously described in sNP rats. The strict association between the alpha6 point mutation and the new polymorphisms found in the beta2, alpha1 and gamma2 genes, demonstrate that such genes belong to the same cluster and are inherited together in the rat. These results sustain the synteny for these clusters between the rodent and human genomes, and suggest that mutated GABA(A) beta2, alpha6, alpha1 and gamma2 subunit genes might contribute to the expression of an ethanol nonpreferring phenotype in a rat line that voluntarily avoids alcoholic solutions.

Alcohol-Induced Disorders, Nervous System↗

PubMed2000

Molecular genetics of granulocyte polymorphisms.

BACKGROUND AND OBJECTIVES: Granulocyte (neutrophil) antibodies have been implicated in transfusion-related acute lung injury (TRALI) and immune neutropenias. In the last decade enormous efforts have been made to characterize the involved alloantigens. MATERIALS AND METHODS: Review of the literature. RESULTS: The NA1, NA2, and SH antigens have been identified as polymorphic forms of the neutrophil Fc gamma receptor IIIb encoded by three alleles. The antigens MART and OND have been located on leucocyte adhesion molecules (beta 2 integrins) and were found to be due to single nucleotide mutations in the alpha M (CD11b) and alpha L (CD11a) subunits. Recently, we succeeded in throwing light on the primary structure of the NB1 antigen. On the basis of these findings a new nomenclature has been introduced for human neutrophil alloantigens (HNA nomenclature). Glycoprotein location has made the development of antigen-specific immunoassays possible and antigen characterization on the molecular level now allows genotyping by DNA techniques. CONCLUSION: Considerable progress has been made in the characterization of granulocyte antigens. Further studies will improve our diagnostic tools and will facilitate the prevention and management of transfusion reactions and immune neutropenias.

Gene Frequency↗

PubMed1980

Characterization, evolution, and molecular basis of a polymorphic antigenic determinant shared by HLA-A and B products.

In our search for monoclonal antibodies defining specific HLA-A,B antigens we have found a significant number of antibodies with polymorphic reactions that are not explicable with our current picture of HLA-A,B interrelationships. Analysis of one antibody (MB40.1) in some detail shows that it recognizes subsets of both A and B antigens and that it is able to split highly cross-reactive pairs of A or B antigens. These results address an outstanding difference in the serological interpretation of H-2, where these types of public reactions have been well established, from HLA, where they have been poorly characterized. Comparison of these types of serological reactions with amino acid sequence data and the apparent evolutionary stability of these broad cross-reacting determinants suggests a simple model for the molecular nature based upon limited amino acid variability and convergent evolution.

Amino Acid Sequence↗

PubMed1994

Molecular genotyping for N-acetylation polymorphism in Japanese patients with colorectal cancer.

BACKGROUND: N-acetylation polymorphism has been documented as a representative pharmacogenetic trait, and also has been implicated ecogenetically in an individual's susceptibility to cancer. However, there still remains controversy concerning the association between colorectal cancer and N-acetylation polymorphism. METHODS: A newly established molecular genotyping method using polymerase chain reaction-based restriction fragment length polymorphism to analyze the distribution of polymorphism in a large group of Japanese patients with colorectal cancer was used. RESULTS: Based on an analysis of 234 Japanese patient with colorectal cancer and 329 healthy control subjects, no significant difference was observed in either the distribution of acetylator phenotypes or of allele frequencies between the two groups. In addition, no significant difference in their distribution was found based on the age at which cancer was first detected, the location of tumors, or the histopathologic features. CONCLUSIONS: N-acetylation polymorphism does not appear to be implicated crucially as a genetic trait affecting an individual's susceptibility to colorectal cancer.

Acetylation↗