AG Allele Research Articles

HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys

In barley, three genes are responsible for the vernalization requirement: VrnH1, VrnH2 and VrnH3. The winter growth habit of barley requires the presence of a recessive VrnH1 allele, together with an active VrnH2 allele. The candidate for VrnH3 (HvFT1) has been recently identified, with evidences pointing at a central role in the integration of the vernalization and photoperiod pathways. Functional polymorphisms have been proposed, but experimental evidence of their role on agronomic performance and adaptation is needed. We examined allelic variation at the promoter and intron 1 of the HvFT1 gene in a landrace collection of barley, finding a high diversity level, with its geographic distribution correlated with latitude. Focusing on genotypes with winter alleles in VrnH1 and VrnH2, an association analysis of the four main HvFT1 haplotypes found in the landrace collection detected differences in time to flowering. Landraces with the intron 1 TC allele, prevalent in the south, flowered 6-7days earlier than those with the AG allele, under natural conditions. These results were validated in an independent F(2) population. In both data sets, the effect found was similar, but in opposite direction to that described in literature. The polymorphism reported at intron 1 contributes to variation in flowering time under field conditions. We have found that polymorphisms at the promoter also contribute to the effect of the gene on flowering time under field and controlled conditions. The variety of HvFT1 alleles described constitutes an allelic series that may have been a factor in agro-ecological adaptation of barley.

Glutathione S-Transferase P1 (GSTP1) gene polymorphism increases age-related susceptibility to hepatocellular carcinoma

BackgroundHepatocellular carcinoma (HCC) is one of the most frequent malignant neoplasms in the world. Genetic polymorphism has been reported to be a factor increasing the risk of HCC. Phase II enzymes such as glutathione s-transferases (GSTP1, GSTA1) play important roles in protecting cells against damage induced by carcinogens. The aim of this study was to estimate the relationship of the GSTP1 and GSTA1 gene polymorphisms to HCC risk and clinico-pathological status.MethodsPolymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to measure GSTP1 (A→G) and GSTA1 (C→T) gene polymorphisms in 386 healthy controls and 177 patients with HCC.ResultsNeither gene polymorphism was associated with the clinico-pathological status of HCC and serum expression of liver-related clinico-pathological markers. No association between the GSTA1 gene polymorphism and HCC susceptibility was found. However, in the younger group, aged ≤ 57 years, individuals with AG or GG alleles of GSTP1 had a 2.18-fold (95%CI = 1.09-4.36; p = 0.02) and 5.64-fold (95%CI = 1.02-31.18; p = 0.04) risk, respectively, of developing HCC compared to individuals with AA alleles, after adjusting for other confounders.ConclusionAG and GG alleles of GSTP1 gene polymorphisms may be considered as factors increasing the susceptibility to and risk of HCC in Taiwanese aged ≤ 57 years.

The COMT Val158 Met polymorphism as an associated risk factor for Alzheimer disease and mild cognitive impairment in APOE 4 carriers

BackgroundThe aim of this study is to examine the influence of the catechol-O-methyltranferase (COMT) gene (polymorphism Val158 Met) as a risk factor for Alzheimer's disease (AD) and mild cognitive impairment of amnesic type (MCI), and its synergistic effect with the apolipoprotein E gene (APOE).A total of 223 MCI patients, 345 AD and 253 healthy controls were analyzed. Clinical criteria and neuropsychological tests were used to establish diagnostic groups.The DNA Bank of the University of the Basque Country (UPV-EHU) (Spain) determined COMT Val158 Met and APOE genotypes using real time polymerase chain reaction (rtPCR) and polymerase chain reaction (PCR), and restriction fragment length polymorphism (RFLPs), respectively. Multinomial logistic regression models were used to determine the risk of AD and MCI.ResultsNeither COMT alleles nor genotypes were independent risk factors for AD or MCI. The high activity genotypes (GG and AG) showed a synergistic effect with APOE ε4 allele, increasing the risk of AD (OR = 5.96, 95%CI 2.74-12.94, p < 0.001 and OR = 6.71, 95%CI 3.36-13.41, p < 0.001 respectivily). In AD patients this effect was greater in women.In MCI patients such as synergistic effect was only found between AG and APOE ε4 allele (OR = 3.21 95%CI 1.56-6.63, p = 0.02) and was greater in men (OR = 5.88 95%CI 1.69-20.42, p < 0.01).ConclusionCOMT (Val158 Met) polymorphism is not an independent risk factor for AD or MCI, but shows a synergistic effect with APOE ε4 allele that proves greater in women with AD.

De novo mutation in POLG leads to haplotype insufficiency and Alpers syndrome

Mutations in POLG are a major contributor to pediatric and adult mitochondrial diseases. However, the consequences of many POLG mutations are not well understood. We investigated the molecular cause of Alpers syndome in a patient harboring the POLG mutations A467T in trans with c.2157+5_+6 gc→ag in intron 12. Analysis of transcripts arising from the c.2157+5_+6 gc→ag allele revealed alternative splicing with an insertion of 30 intronic nucleotides leading to a premature termination codon. These transcripts were subsequently removed through nonsense-mediated decay, leading to haplotype insufficiency due to expression of the A467T allele and decreased expression of the c.2157+5_+6 gc→ag allele, which is likely responsible for the Alpers syndrome phenotype.

MMP‐13 promoter polymorphisms in patients with chronic periodontitis: effects on GCF MMP‐13 levels and outcome of periodontal therapy

The aims of this study were to investigate (a) the matrix metalloproteinase-13 (MMP-13) promoter polymorphisms in severe, generalized chronic periodontitis (CP), (b) the relationship of periodontal therapy outcome with these genotypes and (c) gingival crevicular fluid (GCF) MMP-13 level-MMP-13 genotype correlation. Genomic DNA was obtained from peripheral blood of 102 patients with severe, generalized CP, and 98 periodontally healthy subjects. MMP-13 -77A/G and 11A/12A polymorphisms were determined by the polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods, respectively. Fifty-eight CP patients received non-surgical periodontal therapy and were followed for 6 months. Clinical periodontal parameters and GCF samples were collected at baseline and at 6 months. GCF MMP-13 levels were analysed by an enzyme-linked immunosorbent assay. The distribution of MMP-13 -77AG genotypes and allele frequencies did not differ significantly between study groups (p>0.05). Study subjects, except 3, had the 11A/11A genotype. MMP-13 -77G allele carriers had similar GCF MMP-13 levels and clinical periodontal parameters compared with AA genotypes after non-surgical periodontal therapy (p<0.05). These data suggest that the -77A/G and 11A/12A polymorphisms of MMP-13 gene are not associated with susceptibility to severe, generalized CP in a Turkish population. It seems that -77G allele carriage may not influence the outcome of periodontal therapy.

Abstract 6074: Vitamin K Epoxide Reductase Genotype Alters Warfarin Dose Requirements in Pediatric Patients

Warfarin is an oral anticoagulant used for prevention of thromboembolism in children. Its dosing is difficult due to the narrow therapeutic index &amp; individual variability in effective dosage. Genetic polymorphism in 2 enzymes involved in warfarin metabolism, vitamin K epoxide reductase (VKORC) &amp; cytochrome P450 isoenzyme 2C9 (CYP2C9), have been associated with lower dose requirements in adults. Testing for these polymorphisms is now recommended and being performed to guide dosing in adult patients(pts). Currently there is no information available on these polymorphisms &amp; warfarin dosing in children. To examine the relationship between warfarin dosing &amp; polymorphisms of CYP2C9 &amp; VKORC1 in pediatric patients. Pts 0 –18 years old on warfarin for minimum 2 weeks were included. Data included ethnicity, age, weight, body surface area, gender, indication, dose, INR, target INR, medical illness or medications &amp; adverse effects. Blood sample tested for CYP2C9 &amp; VKORC1 genotypes &amp; correlated with above variables. Dose at time of stable INR was compared to genetic alleles. Multivariate linear regression analysis was performed to identify factors associated with warfarin dosing. 29 pts were studied(62% males). There were 18 Hispanics, 7 Caucasian, 2 African Americans &amp; 2 Mixed ethnicities. Indication for warfarin included Congenital heart disease(CHD) 45% &amp; non CHD 55%. Mean age 5yrs 2mo(6mo-18yrs) &amp; wt 22kg(6.9 – 84). For VKORC1, there were 13 AA(44%), 9 GA(31%), &amp; 7 GG (24%) alleles. For CYP29, 4/23 were *2(17%) &amp; 0 *3 alleles. There was no relationship between ethnicity &amp; VKORC1 alleles. Pts with VKORC1 AA + AG allele required a significantly lower dose/kg(0.10mg/kg) compared to GG allele(0.19mg/kg)(p &lt;0.001) even after adjusting for target INR. In this study, pts with VKORC1 AA + AG alleles require a 47% lower dose/kg compared to pts with GG alleles. This preliminary data suggest that VKORC1 status is an important factor in dosing requirements in pediatric pts. A study using a larger pediatric population is necessary to construct a dosing nomogram based on presence of genetic polymorphism.

Family‐based association study between NOS‐I and ‐IIA polymorphisms and autism spectrum disorders in Korean trios

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a strong genetic component and environmental risk factors. Nitric oxide (NO), which is produced by nitric oxide synthase (NOS), may play a role in the development of ASD. We genotyped nine single nucleotide polymorphisms (SNPs) in the NOS-I gene and nine SNPs in the NOS-IIA gene and carried out the transmission disequilibrium test (TDT) and haplotype analysis in 151 Korean ASD trios. We found preferential transmission of the A allele of rs8068149 (P = 0.039) and G allele of rs1060826 (P = 0.035) of NOS-IIA in ASD and the haplotype analysis revealed that the two haplotypes had significant associations (P = 0.014 and 0.031, respectively). The behavioral subdomain score of failure to use nonverbal behaviors to regulate social interaction in Autism Diagnostic Interview-Revised (ADI-R) was significantly higher in subjects with the GG or AG allele in rs1060826 of NOS-IIA compared to those who had the AA allele (P = 0.027). These results provide significant but weak evidence for an association between NOS-IIA and ASD in the Korean population.

Serotonin Receptor 2A Gene Polymorphism (–1438A/G) and Short-Term Treatment Response to Citalopram

The 5-HTR2A gene is a candidate gene for influencing the clinical response to antidepressant treatment. The purpose of this study was to determine the relationship between the –1438A/G polymorphism in the 5-HTR2A gene and the response to citalopram in a Korean population with major depressive disorder (MDD). Citalopram was administered for 4 weeks to the 71 patients who completed this study. We found significant differences in genotype, allele, and carrier distribution between the normal group and MDD patients (genotypes: χ² = 6.473, d.f. = 2, p = 0.039; alleles: χ² = 5.589, d.f. = 1, p = 0.018; OR = 0.618, 95% CI = 0.414–0.922; allele carriers: χ² = 5.383, d.f. = 1, p = 0.020; OR = 0.473, 95% CI = 0.249–0.879). The frequency of the –1438G allele was much higher in MDD patients than in the normal group (allele carriers: χ² = 5.383, d.f. = 1, p = 0.020; OR = 0.473, 95% CI = 0.249–0.879). There were also significant differences in response to citalopram according to the –1438A/G variation of 5-HTR2A in MDD patients. The group of remitters carried a higher frequency of the GG allele than of the AA and AG alleles. More of nonremitters carried the A allele than were without it (genotype: χ² = 8.016, p = 0.018; allele carrier: χ² = 4.512, p = 0.034; OR = 0.324, 95% CI = 0.112–0.936). The response to citalopram differed with the –1438A/G polymorphism genotype and allele carriers. The –1438G/–1438G genotype appeared to be associated with a better response to citalopram, with especially the G allele being related to core depressive symptoms and psychic anxiety improvement (p<0.05). These results suggest that the G allele of the –1438A/G polymorphism in the 5-HTR2A gene is associated with MDD, and that patients with –1438G/–1438G have a better response to citalopram treatment than patients with –1438A/–1438A or –1438A/–1438G.

Polymorphisms in the TNFA gene promoter region show evidence of strong linkage disequilibrium with HLA and are associated with delayed neutrophil engraftment in unrelated donor hematopoietic stem cell transplantation.

Sustained myeloid engraftment is an important determinant of outcome in hematopoietic stem cell transplantation (HSCT). Human tumor necrosis factor (TNF)-alpha is encoded by a gene, TNFA, located in the class III region of the major histocompatibility complex on chromosome 6, flanked by the human leukocyte antigen (HLA) class I and II regions. A number of polymorphisms in the promoter region of the TNFA gene have been associated with increased production of TNF-alphain vivo. Additionally, raised TNF-alpha levels have been reported to have a detrimental effect on the outcome in HSCT, in particular on early complications such as acute graft vs host disease, failure to engraft, and transplant-related mortality. There is evidence of linkage disequilibrium (LD) between TNFA promoter polymorphisms and extended HLA haplotypes. We have genotyped 73 cell lines and 189 donor/recipient pairs (undergoing HSCT) for their TNFA polymorphism, all of which had been well characterized with respect to their HLA genes. We found evidence of strong LD between HLA genes and TNFA; however, there was also evidence for recombination events having taken place, as we found that a number of transplant pairs who were matched for their HLA haplotypes were not matched for their TNFA alleles. We analyzed early outcomes in the transplant recipients and found a significant delay in engraftment in those pairs where both donor and recipients possessed an AG allele (associated with higher TNF-alpha levels). Our results suggest a functional effect of TNFA polymorphisms on myeloid engraftment in unrelated HSCT.

HUA1 and HUA2 Are Two Members of the Floral Homeotic AGAMOUS Pathway

The identities of the four floral organ types in an Arabidopsis flower are specified by the combinatorial activities of the floral homeotic A, B, and C function genes; AGAMOUS is the only known C function gene. We have identified two genes that interact with AG in the specification of floral structure, HUA1 and HUA2, from a screen for enhancers of a weak ag allele, ag-4. HUA1 and HUA2 are involved in all aspects of AG function. HUA2 encodes a novel protein that contains nuclear localization signals and signature motifs that suggest HUA2, like AG, may be a transcription factor. Molecular analyses suggest that HUA2 (and possibly HUA1) acts to facilitate AG action at the same hierarchical level as AG.

The binding epitopes of human CD16 (Fc gamma RIII) monoclonal antibodies. Implications for ligand binding.

Numerous mAbs have been generated against Fc gamma RIII (CD16), the low-affinity receptor for the Fc part of IgG. Most of the mAbs recognize both the receptor isoforms, transmembranous Fc gamma RIIIA, and glycosylphosphatidylinositol-linked Fc gamma RIIIB. Binding epitopes of some of the mAbs that differentiate between the two neutrophil Ag (NA) alleles of Fc gamma RIIIB (CLB-Gran11 against NA1; GRM1, BL-LGL/1 against NA2 allele) have been mapped on the first, membrane-distal domain of CD16. We demonstrate that mAbs 3G8, B88-9, CLB-Gran1, MEM-154, and LNK16 almost completely block the receptor's interaction with IgG. Using chimeric Fc gamma RIIIB/Fc epsilon RI receptors and molecular modeling, we localized the epitopes of 3G8 and B88-9 on the putative FG loop of the membrane-proximal Ig-like domain, which we have previously identified as the major binding site for IgG. The epitopes of CLB-Gran1 and MEM-154 are shown to reside in proximity to the FG loop (probably BC or C'E loop). The blocking mAb LNK16 was detected to be directed against the putative C' beta-sheet of the membrane-proximal domain, suggesting that additional residues may be involved in IgG binding of Fc gamma RIII.

Genetic separation of third and fourth whorl functions of AGAMOUS.

AGAMOUS (AG) is an Arabidopsis MADS box gene required for normal development of the third and fourth whorls of the flower. In previously described ag mutants, the third whorl stamens are replaced by petals, and the fourth whorl is replaced by another (mutant) flower. We describe two new ag alleles, ag-4 and AG-Met205, retaining partial AG activity. Both produce flowers with stamens in the third whorl and indeterminate floral meristems; however, ag-4 flowers contain sepals in the fourth whorl, and AG-Met205 produces carpels. The ag-4 mutation results in partial loss of the C terminus of the K domain, a putative coiled coil, and AG-Met205 contains a site-directed mutation that causes a single amino acid change in this same region of the K box. Two models that might explain how these changes in AG result in the separation of different AG activities are discussed.

Apolipoprotein B polymorphism and altered apolipoprotein B concentrations in Congolese blacks

The immunoreactivity of apolipoprotein B (apo B) in plasma obtained from 238 unrelated black African male subjects from the People's Republic of Congo was analysed by non-competitive Enzyme Linked-Immunosorbent Assay (ELISA) with monoclonal BIP 45 anti-LDL antibody. The polymorphism detected by BIP 45 monoclonal antibody is identical to the Ag(c,g) polymorphism. Antibody BIP 45 distinguishes three apo B allotypes (immunophenotypes) encoded by the two allelic genes apo B Ag(c) and apo B Ag(g). Because of co-dominant transmission, genotypes may be inferred from allotypes, and it has been shown that BIP 45 binds strongly to the Ag(c) factor and only weakly to the allelic Ag(g) factor. Analysis of the Congolese plasma samples indicated that 67.65% of them bound BIP 45 with low affinity (Ag(c-,g+) genotype), 28.15% with intermediate affinity (Ag(c+,g+) genotype) and 4.20% with high affinity (Ag(c+,g-) genotype). According to the Hardy-Weinberg equilibrium, this corresponds to gene frequencies of 0.817 and 0.183 for the type Ag(g)/Ag(c) alleles, respectively. After adjustment for age and body-mass index, it was found that the Ag(c) allele decreases the apo B level by 9.62 mg/dl and that the Ag(g) allele increases apo B by 0.43 mg/dl. Therefore, as much as 4.30% of the genetic variance for apo B level could be accounted for by the Ag(c,g) gene locus.

Association of a genetic polymorphism in human apolipoprotein B‐100 with intermediate density lipoprotein concentrations

Immunochemical techniques have been used to identify five antigenic (Ag) sites on apolipoprotein B-100 (apoB), the major protein constituent of very low density (VLDL), intermediate density (IDL), and low density lipoproteins (LDL). Each Ag site results from allelic variation at a specific locus of the apoB gene. In the present study, we assessed whether variations in the five Ag loci were associated with concentrations of plasma lipids or lipoprotein fractions measured by analytical ultracentrifugation in a group of 44 healthy men. Pair-wise analyses of the Ag markers revealed that Ag(a1/d), in association with either Ag(x/y) or Ag(t/z), is significantly related to plasma IDL-mass concentrations. In this cohort we detected no significant associations of the Ag alleles (singly or in combination) with plasma total cholesterol, triglycerides, LDL-cholesterol, HDL-cholesterol, or mass of total VLDL or LDL. These results suggest that genetic variations in the apoB molecule may predispose to variations in concentrations of IDL that could have consequences for atherosclerotic risk.

Genetic linkage between the antigenic group (Ag) variation and the apolipoprotein B gene: assignment of the Ag locus.

The antigenic group (Ag) system of homospecific human serum antigens of low density lipoprotein is detected by antiserum from multiply transfused patients. A complex series of common Ag alleles has been described, but the biochemical nature of this polymorphism is uncertain. Here we report that DNA polymorphisms at the human apolipoprotein B (apoB) locus are very closely linked to alleles of the Ag system. We also show a strong association between Ag(x) and a polymorphism detected with the restriction endonuclease Xba I. We conclude that the immunologically determined Ag system represents protein polymorphism of apoB rather than primary genetic differences in posttranslational processing or lipid binding. These studies therefore demonstrate that the Ag locus is located on the short arm of human chromosome 2 in the region p23-p24 to which the apoB gene has been assigned. Since the Ag(x) antigen is associated with altered plasma lipid levels, this determinant may indicate a functionally important domain of apoB.