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PubMed2004

Characterization of an immunologic polymorphism (D79H) in the heavy chain of factor V.

BACKGROUND: During the study of a family with hereditary factor (F)V deficiency (FV Amersfoort, 1102 A > T in exon 7) we identified an individual with 5% FV heavy chain antigen (FV(HC)) and 50% FV light chain antigen (FV(LC)). Further testing revealed that apart from the FV Amersfoort allele a second variant FV allele was segregating in this family, which encodes for a FV molecule with a reduced affinity for mAb V-23 used in the FV heavy chain ELISA (ELISA(HC)). OBJECTIVE: Identification and characterization of the molecular basis responsible for the reduced affinity of the variant FV for mAb V-23. METHODS: Family members of the proband were screened for mutations in the exons coding for the heavy chain of FV, after which the recombinant variant FV could be generated and characterized. Next, the cases and controls of the Leiden Thrombophilia Study (LETS) were genotyped for carriership of the variant FV. RESULTS: In the variant FV allele a polymorphism in exon 3 (409G > C) was identified, which predicts the replacement of aspartic acid 79 by histidin (D79H). Introduction of this mutation in recombinant FV confirmed that it reduces the affinity for binding to mAb V-23. The substitution has no effect on FV(a) stability and Xa-cofactor activity. In Caucasians the frequency of the FV-79H allele is approximately 5%. Analysis of the LETS revealed that the FV-79H allele is not associated with FV levels (FV(LC)), activated protein C sensitivity (using an activated partial thromboplastin time-based test) or risk of venous thrombosis (OR 1.07, CI 95: 0.7-1.7). CONCLUSION: The D79H substitution in FV should be considered as a neutral polymorphism. The monoclonal antibody V-23, which has a strongly reduced affinity for FV-79H, is not suitable for application in diagnostic tests.

Activated Protein C Resistance↗
PubMed1996

Identification and characterization of AlgZ, an AlgT-dependent DNA-binding protein required for Pseudomonas aeruginosa algD transcription.

Transcriptional activation of the Pseudomonas aeruginosa algD gene results in high-level synthesis of the capsular polysaccharide alginate, an important P. aeruginosa virulence factor expressed in cystic fibrosis (CF) patients with chronic pulmonary disease. In this study, electrophoretic mobility-shift assays were used to identify a novel protein (AlgZ), which binds specifically to a sequence located 280 bp upstream of the algD promoter. While AlgZ-binding activity did not require the response regulators AlgB or AlgR, expression of AlgZ was found to be absolutely dependent on the alternative sigma factor AlgT. Electrophoretic mobility-shift assays and copper-phenanthroline footprinting localized AlgZ binding to a 36 bp algD region, which includes several helical repeats. A collection of alginate-producing (mucoid) and non-mucoid P. aeruginosa strains, derived from CF patients, was characterized for AlgZ-binding activity. In all cases, AlgZ binding to algD sequences was observed when extracts derived from mucoid P. aeruginosa CF isolates were examined. However, this binding activity was not present when extracts from non-mucoid P. aeruginosa CF isolates were tested. Oligonucleotide mutagenesis was employed to create an algD allele with a 4 bp mutation in the predicted AlgZ-binding site (algD38) and a heterologous substitution allele (algD40), in which the entire AlgZ-binding site was replaced with a non-specific DNA sequence of identical size. When the algD38 mutation was cloned into an algD-cat transcriptional fusion, this resulted in a 28-fold reduction in algD expression, whereas the algD40 mutation abolished algD transcription, indicating that AlgZ acts as an activator of algD transcription. These results support the hypothesis that activation of algD involves the formation of a high-order looped structure allowing for multivalent contacts between AlgZ, AlgR and RNA polymerase containing the alternative sigma factor AlgT. Characterization of the molecular details of algD activation will provide insights into the control of other prokaryotic and eukaryotic promoters that utilize multiple activators.

Alginates↗
PubMed2005

[Whole exon 5 and intron 5 replaced by RHD/CE in partial D phenotype DVa (Hus)].

The study was purposed to analyze DNA and allele structure of the partial D phenotypes D(Va) and D(VI) of the Rhesus blood group in Chinese. Through polymerase chain reaction (PCR) and direct genomic DNA sequencing, the RHD gene was detected in three weak D individuals identified serologically. The results showed that among the three weak D individuals, one was identified as partial D phenotype D(Va) (Hus) type and genotyped DccEe; another two were testified as D(VI) III type and genotyped DCcee. Moreover, the breakpoints of the replaced region by RHCE in D(Va) (Hus) were 5' end of the exon 5 and 3' end of the intron 5, and there were 7 novel polymorphisms in intron 5: 23-25(GCA)2, 98G>A, 168-169insG, 205-206insT, 494-495insA, 1256-1257insC, 1347G>T. In conclusion the whole exon 5 and intron 5 are replaced by RHCE in D(Va) (Hus) detected in Chinese.

China↗
PubMed1999

Molecular characterization of eutF mutants of Salmonella typhimurium LT2 identifies eutF lesions as partial-loss-of-function tonB alleles.

The eutF locus of Salmonella typhimurium LT2 was identified as a locus necessary for the utilization of ethanolamine as a sole carbon source. Initial models suggested that EutF was involved in either ethanolamine transport or was a transcriptional regulator of an ethanolamine transporter. Phenotypic characterization of eutF mutants suggested EutF was somehow involved in 1,2-propanediol, propionate, and succinate utilization. Here we provide evidence that two alleles defining the eutF locus, Delta903 and eutF1115, are partial-loss-of-function tonB alleles. Both mutations were complemented by plasmids containing a wild-type allele of the Escherichia coli tonB gene. Immunoblot analysis using TonB monoclonal antibodies detected a TonB fusion protein in strains carrying eutF alleles. Molecular analysis of the Delta903 allele identified a deletion that resulted in the fusion of the 3' end of tonB with the 3' end of trpA. In-frame translation of the tonB-trpA fusion resulted in the final 9 amino acids of TonB being replaced by a 45-amino-acid addition. We isolated a derivative of a strain carrying allele Delta903 that regained the ability to grow on ethanolamine as a carbon and energy source. The molecular characterization of the mutation that corrected the Eut- phenotype caused by allele Delta903 showed that the new mutation was a deletion of two nucleotides at the tonB-trpA fusion site. This deletion resulted in a frameshift that replaced the 45-amino-acid addition with a 5-amino-acid addition. This change resulted in a TonB protein with sufficient activity to restore growth on ethanolamine and eut operon expression to nearly wild-type levels. It was concluded that the observed EutF phenotypes were due to the partial loss of TonB function, which is proposed to result in reduced cobalamin and ferric siderophore transport in an aerobic environment; thus, the eutF locus does not exist.

Amino Acid Sequence↗
PubMed2001

Association of genetic polymorphisms in UGT1A1 with breast cancer and plasma hormone levels.

UDP-glucuronosyltransferases (UGTs) catalyze the detoxification and the elimination of a large number of endogenous and exogenous compounds in the liver and extrahepatic tissues. One of the UGT1A family members, UGT1A1, is involved in estradiol metabolism and, therefore, represents a candidate gene in breast carcinogenesis. A common insertion/deletion polymorphism in the TATA-box of the promoter region of UGT1A1 results in decreased initiation of transcription. In a previous study, we found a positive association between the UGT1A1 low-transcriptional alleles and premenopausal breast cancer risk in an African-American population. In the present study, we sought to determine whether the low-transcription UGT1A1 promoter allele, UGT1A1*28 [A(TA)(7)TAA], was associated with increased breast cancer risk among primarily Caucasian women in a nested case-control study within the Nurses' Health Study cohort. No significant association between the UGT1A1*28 [A(TA)(7)TAA] allele and breast cancer was observed. Compared with women homozygous for the UGT1A1*1 [A(TA)(6)TAA] allele, the relative risk was 0.80 (confidence interval, 0.49-1.29) for women homozygous for the UGT1A1*28 allele. The effect of the UGT1A1 genotype on plasma hormone levels in postmenopausal women not using hormone replacement was also evaluated, and overall, no significant differences in hormone levels by genotypes were observed. When restricted to women who had at least one UGT1A1*28 allele and a body mass index at blood draw of >27 kg/m(2), particularly in combination with the cytochrome p450c17alpha genotype, estrone and estradiol levels tended to vary by UGT1A1 genotypes. The results presented do not support a strong association between the UGT1A1 promoter polymorphism and the risk of breast cancer.

Adult↗
PubMed1994

Treatment of Graves' disease with the block-replace regimen of antithyroid drugs: the effect of treatment duration and immunogenetic susceptibility on relapse.

Antithyroid drugs are commonly used as first-line treatment for Graves' disease, but the optimum regimen for inducing remission remains unclear. We gave the block-replace regimen of carbimazole plus thyroxine to 100 patients for 6 or 12 months, to determine whether prolonged treatment is associated with fewer relapses. The remission rate one year after cessation of treatment was 59% with the 6 month course and 65% with 12 months; this was not significantly different. We also analysed HLA markers identified by restriction fragment length polymorphisms and could not confirm the recently reported associations of outcome with HLA-DR4 or with an HLA-DQA2 allele. These results show that six months treatment with a block-replace regimen of antithyroid drugs is probably sufficient, in the UK, to achieve maximum remission of Graves' disease and that there are no HLA markers which clearly predict outcome.

Adult↗
PubMed1997

Homeostatic regulation of copper uptake in yeast via direct binding of MAC1 protein to upstream regulatory sequences of FRE1 and CTR1.

Copper deprivation of Saccharomyces cerevisiae induces transcription of the FRE1 and CTR1 genes. FRE1 encodes a surface reductase capable of reducing and mobilizing copper chelates outside the cell, and CTR1 encodes a protein mediating copper uptake at the plasma membrane. In this paper, the protein encoded by MAC1 is identified as the factor mediating this homeostatic control. A novel dominant allele of MAC1, MAC1(up2), is mutated in a Cys-rich domain that may function in copper sensing (a G to A change of nucleotide 812 resulting in a Cys-271 to Tyr substitution). This mutant is functionally similar to the MAC1(up1) allele in which His-279 in the same domain has been replaced by Gln. Both mutations confer constitutive copper-independent expression of FRE1 and CTR1. A sequence including the palindrome TTTGCTCA ... TGAGCAAA, appearing within the 5'-flanking region of the CTR1 promoter, is necessary and sufficient for the copper- and MAC1-dependent CTR1 transcriptional regulation. An identical sequence appears as a direct repeat in the FRE1 promoter. The data indicate that the signal resulting from copper deprivation is transduced via the Cys-rich motif of MAC1 encompassing residues 264-279. MAC1 then binds directly and specifically to the CTR1 and FRE1 promoter elements, inducing transcription of those target genes. This model defines the homeostatic mechanism by which yeast regulates the cell acquisition of copper in response to copper scarcity or excess.

Alleles↗
PubMed2000

Restriction of ectopic recombination by interhomolog interactions during Saccharomyces cerevisiae meiosis.

In Saccharomyces cerevisiae meiosis, recombination occurs frequently between sequences at the same location on homologs (allelic recombination) and can take place between dispersed homologous sequences (ectopic recombination). Ectopic recombination occurs less often than does allelic, especially when homologous sequences are on heterologous chromosomes. To account for this, it has been suggested that homolog pairing (homolog colocalization and alignment) either promotes allelic recombination or restricts ectopic recombination. The latter suggestion was tested by examining ectopic recombination in two cases where normal interhomolog relationships are disrupted. In the first case, one member of a homolog pair was replaced by a homologous (related but not identical) chromosome that has diverged sufficiently to prevent allelic recombination. In the second case, ndj1 mutants were used to delay homolog pairing and synapsis. Both circumstances resulted in a substantial increase in the frequency of ectopic recombination between arg4-containing plasmid inserts located on heterologous chromosomes. These findings suggest that, during normal yeast meiosis, progressive homolog colocalization, alignment, synapsis, and allelic recombination restrict the ability of ectopically located sequences to find each other and recombine. In the absence of such restrictions, the meiotic homology search may encompass the entire genome.

Alleles↗
PubMed1996

Inducing the loss of immunoglobulin lambda light chain production and the rearrangement of a previously excluded allele in human plasma B cell lines with concanavalin A.

We investigated the expression of differential lambda light chains in human B cell lines secreting immunoglobulin (Ig). When these cell lines were cultured with concanavalin A for a long period of time, a subpopulation of some but not all of these cell lines was induced to express new lambda light chains replacing the original lambda chain (light chain shifting). Production of the new lambda chain, which replaces the original lambda chain, results from a VJ rearrangement at a previously excluded allele and a dramatic reduction of the original lambda chain transcript, although no difference was found in the level of heavy chain transcript. Recombination activating genes RAG-1 and RAG-2, which are normally expressed during specific early stages of lymphocyte development, were expressed in not only the light chain shifting-inducible lines but also in the non-inducible cells. Treatment of these Ig secreting cell lines with dibutyryl cAMP, which is known to enhance expression of the RAG genes, could not induce the creation of new lambda light chain-producing cells from the inducible lines, suggesting that the expression of the two RAG genes is not sufficient for inducing new lambda light chain production. Concanavalin A induced a gradual but significant production lost of the original lambda chain in a subpopulation of the light chain shifting-inducible cells but not in the non-inducible cells. Association of new lambda light chain production with loss of original lambda chain raises the possibility that, when the RAG genes are expressed, concanavalin A may act on a novel intracellular mechanism controlling lambda light chain allelic exclusion in these plasma cell lines.

Adenocarcinoma↗
PubMed2003

Is intestinal metaplasia of the stomach reversible?

Intestinal metaplasia (IM) of the stomach is a risk factor in developing intestinal-type gastric cancer and hence the question of reversibility is vital. There is emerging epidemiological evidence that with long term follow up, IM may be reversible although a combination of antioxidant agents and eradication of H pylori may be necessary to achieve this. The pathogenesis of IM is currently being elucidated and it is likely that a combination of bacterial, host, and environmental factors will be shown to lead to IM. In assessing gastric cancer risk, histochemical typing of IM will most probably be replaced by molecular markers.

Alleles↗
PubMedDate not supplied

Influences of common variants of apolipoprotein E on measures of lipid metabolism in a sample selected for health.

Five-hundred seventy-five white-collar workers (374 men; 99% Caucasians) aged 20-59 years were selected on the basis of their being healthy and clinically free from cardiovascular risk factors (except smoking and family history). We have observed a higher relative frequency of the epsilon 3 allele in this population, as is true of populations with a low prevalence of coronary heart disease. Each of the 11 plasma lipid and lipoprotein traits studied was adjusted for age, weight, height, body mass index, plasma glucose, and uric acid in men and women separately. The influence of each of the three common apo E alleles on each adjusted trait was evaluated by use of the average excess statistic. We established that in a population selected for health, the epsilon 2 allele is associated with lower plasma levels of total cholesterol, low density lipoprotein (LDL) cholesterol, and apolipoprotein B associated with LDL cholesterol in both men and women. Conversely, the epsilon 4 allele is associated with higher levels of these traits in women only. In contrast to the findings in populations not selected for health, the presence of the epsilon 2 allele in our subjects tended to be associated with lower and the epsilon 4 allele with higher plasma triglyceride levels. Finally and of particular note, the influence of the apolipoprotein E polymorphism on plasma measures of LDL metabolism is different in men and women. Specifically, the influence of the epsilon 4 allele is of greater magnitude in women. A part of this gender difference in allele effects on LDL metabolism in women is associated with the use of oral contraceptives and postmenopausal hormone replacement therapy.

Adult↗
PubMed1993

Gene targeting technology for creating transgenic models of lymphopoiesis.

Naturally occurring immunodeficient mouse strains express a variety of genetic defects in myeloid and/or lymphoid cell development. These strains have served as valuable animal models for studying immune cell differentiation and mechanisms of transplant rejection. Some of the most commonly used strains carry mutations at the nude, scid, beige, and/or xid loci. Gene targeting technology can now be used to directly modify endogenous alleles via homologous recombination with exogenous DNA. By performing DNA targeting in embryonic stem (ES) cells, germline transmission of these modifications can be obtained by breeding chimeras generated from cloned ES cells. This approach can be used to target the inactivation, modification, or replacement of specific genes and has been used to examine the role of several alleles in hematopoiesis. This review describes the use of this technology to generate mutations that influence the development and function of T and B lymphocytes.

Animals↗
PubMed2002

Functional comparison of the Hoxa 4, Hoxa 10, and Hoxa 11 homeoboxes.

A number of models attempt to explain the functional relationships of Hox genes. The functional equivalence model states that mammalian Hox-encoded proteins are largely functionally equivalent, and that Hox quantity is more important than Hox quality. In this report, we describe the results of two homeobox swaps. In one case, the homeobox of Hoxa 11 was replaced with that of the very closely related Hoxa 10. Developmental function was assayed by analyzing the phenotypes of all possible allele combinations, including the swapped allele, and null alleles for Hoxa 11 and Hoxd 11. This chimeric gene provided wild-type function in the development of the axial skeleton and male reproductive tract, but served as a hypomorph allele in the development of the appendicular skeleton, kidneys, and female reproductive tract. In the other case, the Hoxa 11 homeobox was replaced with that of the divergent Hoxa 4 gene. This chimeric gene provided near recessive null function in all tissues except the axial skeleton, which developed normally. These results demonstrate that even the most conserved regions of Hox genes, the homeoboxes, are not functionally interchangeable in the development of most tissues. In some cases, developmental function tracked with the homeobox, as previously seen in simpler organisms. Homeoboxes with more 5' cluster positions were generally dominant over more 3' homeoboxes, consistent with phenotypic suppression seen in Drosophila. Surprisingly, however, all Hox homeoboxes tested did appear functionally equivalent in the formation of the axial skeleton. The determination of segment identity is one of the most evolutionarily ancient functions of Hox genes. It is interesting that Hox homeoboxes are interchangeable in this process, but are functionally distinct in other aspects of development.

Alleles↗
PubMed1976

[Mutator effect of suppressed amber-alleles of early genes of bacteriophage T4].

The mutator effect of amber alleles of three early genes (43, 32, 47), which were suppressed by the bacterial suppressor gene, was studied. There are some advantages in using the suppressed amber alleles instead of ts, because in this case definite amino acid substitutions take place in the protein due to certain suppressor gene effect. For example, in Escherichia coli CR63(Su+-1) the replacement of the original amino acid by serine takes place. Studying the mutator effect of 43 alleles of DNA polymerase gene of phage T4 with tester mutant r131 showed that in condition of suppression by the gene Su+ -1 only 13,9% of alleles possessed the mutator activity. In the same experiments with mutants of genes 32 and 47 the mutator effect was not observed.

Alleles↗
PubMed1990

Class II genes of miniature swine. IV. Characterization and expression of two allelic class II DQB cDNA clones.

Two cDNA clones coding for allelic miniature swine MHC class II Ag DQB chains have been isolated, characterized, and shown to be expressed after transfection into mouse fibroblasts. The two alleles differ at the nucleotide level by an overwhelming proportion of replacement substitutions, suggesting the influence of selection for polymorphism. Most of the resulting predicted amino acid replacements are in regions commonly polymorphic in mouse Ab and human DQB sequences, corresponding to the predicted Ag recognition site. Nucleotide and amino acid sequence comparisons to homologous mouse and human sequences show more similarity between swine and man than between either swine and mouse or man and mouse. This tendency is most pronounced when comparing the 3' untranslated regions. However, an examination of unique cross-species sharing of amino acid residues suggests a closer relationship between both man and miniature swine and man and mouse than between miniature swine and mouse. The simplest explanation we can envision for these findings is that the mouse DQB gene homologue (Ab) has been subject to a higher substitution rate than either swine or human DQB genes. An additional cytoplasmic exon expressed in mouse Ab gene products and in putative human DQB2 gene products is lacking in both swine and human DQB cDNA clones. Its absence suggests either that the expression of this exon in mouse Ab genes was activated after mammalian speciation or that the expression of this exon was independently inactivated in swine DQB and human DQB1 genes. Alternatively, the mouse Ab gene may be derived from the same primordial gene as human DQB2, whereas the pig DQB gene may be derived from the same primordial gene as the human DQB1 gene.

Alleles↗
PubMed2005

On human STR sub-population structure.

This study is an investigation of genetic variation among the CODIS (combined DNA index system) STR (short tandem repeat) reference collections. The analysis was conducted in two parts. The first is an overall comparison (G-test) of allelic frequency distributions for 12 STR loci among 19 forensic databases representing various major groups and ethnic populations. In the second phase of the study, the impact of database replacement on DNA profile frequencies and inclusion probabilities is examined. The G-test results reveal clear allelic frequency differences among the major divisions, and, in some cases, among ethnically distinct subdivisions of the same major group affiliation. Other results indicate that database substitution may sometimes lead to substantial alterations in individual inclusion probabilities. Furthermore, there are numerous instances in which an allele present in some databases is missing in others. Fortunately, in most cases, these effects may not be forensically significant due to the increased discriminatory power of the STR markers employed in the CODIS system. However, differences in inclusion probabilities may become critical in situations in which DNA quantity is severely limited and/or compromised by degradation since, in these cases, the power of forensic STR analysis may be mitigated by reducing the number of informative loci.

DNA Fingerprinting↗
PubMed1997

Female gender and resistance to activated protein C (FV:Q506) as potential risk factors for thrombosis after elective hip arthroplasty.

Resistance to activated protein C (APC) caused by the R506Q mutation in factor V is the most common inherited risk factor for venous thrombosis. To elucidate whether APC-resistance is a risk factor for venous thrombosis after elective total hip replacement, the association between APC-resistance (presence of FV:Q506 allele) and postoperative thrombosis was investigated in patients (n = 198) randomised to received short (during hospitalisation, n = 100) or prolonged prophylaxis (three weeks after hospitalisation, n = 98) with low molecular weight heparin (LMWH). Among APC-resistant individuals receiving short prophylaxis, 7/10 developed thrombosis as compared to 2/12 receiving long prophylaxis (p <0.0179). Odds ratio for association between APC-resistance and thrombosis in the short prophylaxis group was 4.2 (CI 95% 1.02-17.5) (p <0.0465). Among those receiving prolonged prophylaxis, there was no increased incidence of thrombosis associated with APC-resistance. Two unexpected observations were made. One was that APC-resistance was much more common in women (19/109) than in men (3/89) (p <0.001). The other was that even women without APC-resistance were much more thrombosis-prone than men. Thus, 24/48 of women with normal FV genotype and short prophylaxis developed thrombosis vs 8/42 among men, p = 0.002. The increased risk of thrombosis associated with female gender and APC-resistance was neutralised by the prolonged treatment. In conclusion, among patients receiving short prophylaxis, female gender was found to be a strong risk factor for venous thrombosis. Even though APC-resistance appeared to be a risk factor for postoperative thrombosis, the uneven distribution of APC-resistance between men and women, taken together with the increased risk of thrombosis among women, precluded valid conclusions to be drawn about the association between APC-resistance and an increased risk of thrombosis. Our results suggest that prolonged prophylaxis with LMWH after hip surgery is more important for women than for men.

Adult↗
PubMed2006

Polymorphisms in the IL4 and IL4RA genes in Colombian patients with rheumatoid arthritis.

OBJECTIVE: Rheumatoid arthritis (RA) is considered a Th1-driven disease. Interleukin 4 (IL-4) binds to its receptor, promoting Th2 differentiation and limiting Th1 responses, but its role in the pathogenesis of RA is conflicting. We analyzed 2 polymorphisms of the IL4 gene and 4 polymorphisms of the IL4RA gene in patients with RA and in a control population, as well as rheumatoid factor (RF) seropositivity, titers of RF, and history of replacement joint surgery among patients with RA. METHODS: The study population consisted of 102 patients with RA and 102 matched healthy controls. Genotyping of IL4 -590, IL4RA +148, +1124, +1218, and +1902 was determined by restriction fragment length polymorphism-polymerase chain reaction (PCR) and sequence-specific primer-PCR. IL4 variable number tandem repeat polymorphism was determined by direct amplification. RESULTS: The IL4 -590TT genotype was significantly more frequent in patients with RA than in controls (p = 0.018, OR 3.34, 95% CI 1.08-11.04). The IL4RA +148A allele was significantly associated with the presence of RF (p = 0.0019, OR 2.55, 95% CI 1.55-4.86) and a history of articular joint replacement (p = 0.024, OR 2.08, 95% CI 1.04-4.18). The IL4RA +1902G allele was more frequently seen in patients with RA and high RF titers (p = 0.00067, OR 4, 95% CI 1.64-9.93). CONCLUSION: Highly complex pathways lead to the development of RA and may not be similar in all patients. Our findings of higher frequency of IL4 and IL4RA genotypes and alleles with RA, presence of RF, RF titers, and history of articular joint replacement support the polygenic expression of RA and the likely role of IL-4 in influencing its initiation and development.

Adult↗