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The distribution of cerebrovascular amyloid in Alzheimer's disease varies with ApoE genotype.

We performed a comparative study to assess cerebral amyloid angiopathy and ApoE genotype in cases of Alzheimer's disease (AD). Ten ApoE 3,3 and ten ApoE 4,4 AD brains, as well as ten normal control brains, were selected after matching for age, sex, and duration of disease. Sections of middle frontal and inferior parietal cortex including white matter sections were stained with an antibody against amyloid beta (Abeta), and extensive analysis of arteriolar Abeta deposition was performed using digital image analysis. Quantification of the staining revealed a larger cross-section of arteriolar walls occupied by Abeta in ApoE 4,4 and ApoE 3,3 AD subjects compared to controls. Our results show Abeta deposition in gray matter and white matter arterioles was predominantly found in ApoE 4,4 brains and, overall, Abeta deposition was greatest in these cases. This observation implies that there is greater vascular amyloid deposition (particularly in the white matter arterioles) in ApoE 4,4 AD individuals compared to ApoE 3,3 AD. These observations may give insight into the etiology behind the increased risk for AD associated with the ApoE-epsilon4 allele and the pathogenesis of vascular Abeta deposition.

Aged↗

Performance of TRUGENE hepatitis C virus 5' noncoding genotyping kit, a new CLIP sequencing-based assay for hepatitis C virus genotype determination.

The performance of the recently developed, standardized direct sequencing assay for hepatitis C virus (HCV) genotyping [TRUGENE HCV 5'-NC (noncoding)] was assessed in comparison with the reverse hybridization-based assay INNO-LIPA HCV II. Both assays allow HCV genotyping starting from amplification products generated by the diagnostic Roche AMPLICOR HCV test. HCV amplicons from 205 patients were used for this study: 34 were tested prospectively by both methods, while 171 had been stored at -20 degrees C for up to 2 years after LiPA genotyping. The TRUGENE procedure failed to determine a genotype in six low-titered samples (3.5 +/- 0.3 log UI/mL vs. 5.2 +/- 0.5 UI/mL for typable samples). Type and subtype could be determined by sequencing for 199 samples (97%). Among them, five were considered as coinfections by the LiPA method. Three LiPA patterns suggesting type 1 and 4 coinfection were not supported by sequence analysis while one 1a/2b and one 1a/3a coinfection was backed up by direct sequencing. For the remaining 194 samples, type assignment was concordant in 100% of the cases. LiPA subtyping was available for 162 samples (83.5%). Sub-typing results concurred in 128 cases (79%). NS5B sequencing of discrepant samples underscored the limitation of the 5'-noncoding region (NCR) in correct subtype assignment. In conclusion, the TRUGENE HCV 5'-NC genotyping kit appeared to be a specific and reliable method that can be used in the current indication of HCV genotyping.

5' Untranslated Regions↗

Relationship between ace genotype and short duration aerobic performance development.

We have previously demonstrated that, ACE D allele may be related with a better performance in short duration aerobic endurance in a homogeneous cohort with similar training backgrounds. We aimed to study the variation in the short-duration aerobic performance development amongst ACE genotypes in response to identical training programs in homogeneous populations. The study group consisted of 186 male Caucasian non-elite Turkish army recruits. All subjects had undergone an identical training program with double training session per day and 6 days a week for 6 months. Performances for middle distance runs (2,400 m) were evaluated on an athletics track before and after the training period. ACE gene polymorphisms were studied by PCR analysis. The distribution of genotypes in the whole group was 16.7% II, n=31; 46.2% ID, n=86; 37.1% DD, n=69. Subjects with ACE DD genotype had significantly higher enhancement than the ID (P<0.01) and II (P<0.05) genotype groups. Around 2,400 m performance enhancement ratios showed a linear trend as ACE DD>ACE ID>ACE II (P value for Pearson chi2=0.461 and P value for linear by linear association=0.001). ACE DD genotype seems to have an advantage in development in short-duration aerobic performance. This data in unison with the data that we have obtained from homogenous cohorts previously is considered as an existence of threshold for initiation of ACE I allele effectiveness in endurance performance. This threshold may be anywhere between 10 and 30 min with lasting maximal exercises.

Adult↗

Effect of initial breeding weight and management system using a high-producing sow genotype on resulting reproductive performance over three parities.

A study was conducted with sows of a high-producing genotype to evaluate their reproductive performance using three breeding weights over a three-parity period in two management systems. A total of 114 F1 gilts (Landrace x Yorkshire) were used in a split-plot, randomized, complete block experiment conducted as a 3 x 2 factorial arrangement of treatments in two replicates. Three gilt breeding weights of 120, 135, and 150 kg were achieved by feeding 1.8, 2.3, or 3.2 kg/d of a .73% lysine corn-soybean meal (C-SBM) diet, respectively, from 5 to 8 mo of age. Two locations, each with different management systems, were considered the main plot and consisted of 1) outside, concrete-floored gestation lots and indoor farrowing pens or 2) indoor gestation pens and farrowing crates. All sows were fed 1.8 (Parity 1) or 2.1 (Parity 2 and 3) kg/d of a .73% lysine C-SBM diet during the breeding and gestation periods, whereas a .82% lysine C-SBM diet with 5% added fat was available ad libitum during lactation. All sows lost weight during the first lactation; larger weight losses occurred as breeding weight increased (P < .01). During the second and third lactations the 135- and 150-kg sow breeding groups had less lactation weight change, whereas the 120-kg group lost more weight, resulting in a breeding weight x parity interaction (P < .01). The 120-kg breeding weight group consumed less feed (P < .05) for the three lactation periods than did the heavier weight groups. Initial breeding weight had no effect on number of pigs born (total, live) or pig and litter weights at birth. Pig mortality increased with increasing breeding weight (P < .01) and parity (P < .05), a response that was exacerbated when sows farrowed in pens vs crates. Postweaning breeding intervals and sow removal from the experiment were not significantly affected by initial breeding weight, but a numerically higher percentage of sows in the 120-kg group were anestrous or failed to conceive than the percentage of such sows in the heavier weight groups. These data suggest that an initial breeding weight of approximately 135 kg at 8 mo of age may be best when sows farrow in crates, whereas when sows farrow in pens a lower breeding weight may be more desirable.

Adipose Tissue↗

Implications of genotype and enzyme phenotype in pyridoxine response of patients with type I primary hyperoxaluria.

BACKGROUND: Marked hyperoxaluria due to liver-specific deficiency of alanine:glyoxylate aminotransferase activity (AGT) characterizes type I primary hyperoxaluria (PHI). Approximately half of PHI patients experience improvement in the degree of hyperoxaluria following pyridoxine (VB6) treatment. Recently, we showed an association between VB6 response and the commonest PHI mutation G170R, with patients possessing one or two copies showing 50% reduction or complete to near complete normalization of oxaluria, respectively. Two patients showed responses varying from this pattern. To further clarify the molecular basis of VB6 response in PHI, we performed additional genotyping. METHODS: 23 PHI patients diagnosed via hepatic enzyme analysis, hyperoxaluria and hyperglycolic aciduria or homozygosity for a known mutation, availability of pre- and post-VB6 24-hour urine oxalate and GFR >40 ml/min/1.73 m2 were included. Data was retrieved retrospectively, oxalate measured by oxalate oxidase, and genotyping performed by PCR-based methods. RESULTS: VB6 response was associated with the G170R and F152I mutations. Eight new sequence changes were detected. CONCLUSIONS: In PHI, two mutations resulting in AGT mistargeting are associated with VB6 response. Whether this favorable effect is specific to the peroxisomal-to-mitochondrial mistargeting caused by these changes or due to another mechanism remains to be determined.

Cohort Studies↗

NOD2/CARD15 variants are associated with lower weight at diagnosis in children with Crohn's disease.

OBJECTIVES: NOD2/CARD15 variants have recently been shown to be associated with Crohn's disease (CD). No analysis of NOD2/CARD15 gene variants has so far been reported in pediatric patients. Therefore, our aim was to analyze NOD2/CARD15 gene variants in children with CD and to perform genotype-phenotype analyses. METHODS: We studied 101 children with CD and 136 healthy controls. Detailed phenotypic information was obtained from each patient. Patients were genotyped for the three NOD2/CARD15 variants R702W (single nucleotide polymorphism 8 [SNP8]), G908R (SNP12), and L1007fs (SNP13), and genotype-phenotype correlations were performed. RESULTS: We found 33 NOD2/CARD15 mutations in 29 of 101 patients (29%). The frequency of NOD2 variation was 31% in white (n=87) compared with 11% in controls (chi2=14; p=0.0001; OR=3.7; 95% CI=1.7-7.8). Four white patients but not control subjects were compound heterozygotes. NOD2/CARD15 variants were significantly associated with ileal disease (chi2=4.5; p=0.03; OR=5; 95% CI=0.9-35.9). Of the children with NOD2/CARD15 variants, 44% were < or =5th percentile for weight at diagnosis, whereas only 15% of children without mutations were < or =5th percentile (chi2=8.7; p=0.003; OR=4.5; 95% CI=1.4-14.4). Similar trends were observed for height but they did not reach statistical significance. CONCLUSIONS: Our results demonstrate that: 1) the three NOD2/CARD15 variants confer risk to CD in children; 2) NOD2/CARD15 variants are associated with ileal disease in children as in adults; and 3) NOD2/CARD15 variants are associated with lower weight percentiles at diagnosis in children and a tendency toward lower height percentile, suggesting an association between growth in children with CD.

Adolescent↗

Association between vitamin D receptor polymorphism and type 2 diabetes or metabolic syndrome in community-dwelling older adults: the Rancho Bernardo Study.

Vitamin D receptor (VDR) polymorphism influences susceptibility to type 1 diabetes, but the association with type 2 diabetes is not clear. We investigated the association between VDR polymorphism and type 2 diabetes and metabolic syndrome in a community-based study of unrelated older adults without known diabetes. Oral glucose tolerance test (75 g), plasma glucose and insulin measurement, homeostasis model assessment (HOMA), and VDR genotyping were performed. The distributions of genotype frequencies of ApaI, BsmI, and TaqI polymorphism did not differ between persons with and without diabetes, but the frequency of aa genotype of ApaI polymorphism was marginally higher in persons with type 2 diabetes (P =.058). Fasting plasma glucose (P <.05) and prevalence of glucose intolerance (P <.05) were significantly higher in nondiabetic persons with aa genotype compared with those with AA genotype. The bb genotype of BsmI polymorphism was associated with insulin resistance as assessed by HOMA after adjustment for age, sex, body mass index (BMI), and calcium and vitamin D use in persons without diabetes (P <.05). Our research suggests that ApaI polymorphism may be associated with glucose intolerance independent of defective insulin secretion and BsmI polymorphism with insulin resistance in a nondiabetic Caucasian population.

Aged↗

A novel promoter polymorphism in the gene encoding complement component 5 receptor 1 on chromosome 19q13.3 is not associated with asthma and atopy in three independent populations.

BACKGROUND: The inflammatory functions of complement component 5 (C5) are mediated by its receptor, C5R1, which is expressed on bronchial, epithelial, vascular endothelial and smooth muscle cells. A susceptibility locus for murine allergen-induced airway hyper-responsiveness was identified in a region syntenic to human chromosome 19q13, where linkage to asthma has been demonstrated and where the gene encoding C5R1 is localized. OBJECTIVE: The aim of this study was to screen for novel polymorphisms in the C5R1 gene and to determine whether any identified polymorphisms are associated with asthma and/or atopy and whether they are functional. METHODS: Single-nucleotide polymorphism (SNP) detection in the gene encoding C5R1 was performed by direct sequencing. Genotyping was performed in three populations characterized for asthma and/or atopy: (1) 823 German children from The Multicenter Allergy Study; (2) 146 individuals from Tangier Island, Virginia, a Caucasian isolate; and (3) asthma case-parent trios selected from 134 families (N=783) in Barbados. Functional studies were performed to evaluate differences between the wild-type and the variant alleles. RESULTS: We identified a novel SNP in the promoter region of C5R1 at position -245 (T/C). Frequency of the -245C allele was similar in the German (31.5%) and Tangier Island (36.3%) populations, but higher in the Afro-Caribbean population (53.0%; P=0.0039 to <0.0001). We observed no significant associations between the -245 polymorphism and asthma or atopy phenotypes. Upon examination of the functional consequences of the -245T/C polymorphism, we did not observe any change in promoter activity. CONCLUSION: This new marker may provide a valuable tool to assess the risk for C5a-associated disorders, but it does not appear to be associated with asthma and/or atopy.

Asthma↗

Genome-wide linkage screen of a consanguineous multiple sclerosis kinship.

Multiple sclerosis (MS), like Alzheimer's disease (AD) and Parkinson's disease (PD), is a common neurological disorder thought to be caused by the interaction of several genes with unknown environmental factors. In both AD and PD the identification of disease forms inherited in a classic Mendelian fashion has helped investigators elucidate pathogenetic mechanisms. In this study a whole-genome screen, with an average of 608 successful genotypes per person, was performed on nine members of a consanguineous family: the index case, three of her siblings and her daughter, all of whom have been diagnosed with definite MS; as well as the parents of the index case (first cousins), one of her five healthy siblings and her husband (who is also her first cousin). Nonparametric linkage analysis was performed on genotyping data. Based on the presence of consanguinity, the a priori hypothesis was that the disease is transmitted in an autosomal recessive fashion in the pedigree. Linkage analysis revealed a suggestive logarithm of odds (LOD) score of 2.29 on the long arm of chromosome 9. Four of five affected family members were identically homozygous for a haplotype under this peak, spanning approximately 43 cM, while the fifth affected subject and all unaffected family members were heterozygous for the haplotype.

Adolescent↗

[Distribution of hepatitis B virus genotypes according to the clinical outcomes in patients with chronic hepatitis B virus infection in Jeju island].

BACKGROUND/AIMS: The genotype of hepatitis B virus (HBV) has been suggested to correlate with the clinical outcome of HBV infection. We analyzed the distribution of HBV genotypes according to the clinical outcomes of HBV infection in Jeju island. METHODS: A total of 145 HBsAg-positive samples were enrolled. To identify specific patterns of HBV genotypes, we performed restriction fragment length polymorphism (RFLP). In the case that typical restriction pattern of RFLP was not determined, phylogenetic analysis was performed. RESULTS: RFLP analysis was possible in 65 patients. Clinical diagnoses of the 65 patients with chronic liver disease were as follows: HBeAg-positive healthy carrier (HBeAg(+), anti-HBe, HBV DNA(+), transaminase normal; n=20); Inactive HBsAg carrier (n=12); chronic hepatitis B (n=14); liver cirrhosis (n=9); hepatocellular carcinoma (n=10). Sixty-two patients showed a typical restriction pattern by HinfI. However, 3 patients showed a unique restriction pattern by HinfI, which were not reported in the literature. When phylogenetic analysis was performed to classify the genotype of these 3 patients, they were also genotype C. However, all 65 patients showed typical restriction patterns by Tsp509I, which were reported in genotype C. CONCLUSIONS: All chronic HBV infections are genotype C in Jeju island regardless of clinical outcomes.

Carcinoma, Hepatocellular↗

Identification of a fourth locus (EVR4) for familial exudative vitreoretinopathy (FEVR).

PURPOSE: Familial exudative vitreoretinopathy (FEVR) is a genetically heterogeneous inherited blinding disorder of the retinal vascular system. To date three loci have been mapped: EVR1 on chromosome 11q, EVR2 on chromosome Xp, and EVR3 on chromosome 11p. The gene underlying EVR3 remains unidentified whilst the EVR2 gene, which encodes the Norrie disease protein (NDP), was identified over a decade ago. More recently, FZD4, the gene that encodes the Wnt receptor Frizzled-4, was identified as the mutated gene at the EVR1 locus. The purpose of this study was to screen FZD4 in a large family previously proven to be linked to the EVR1 locus. METHODS: PCR products were generated using genomic DNA from affected family members with primers designed to amplify the coding sequence of FZD4. The PCR products were screened for mutations by direct sequencing. Genotyping was performed in all available family members using fluorescently labeled microsatellite markers from chromosome 11q. RESULTS: Sequencing of the EVR1 gene, FZD4, in this family identified no mutation. To investigate this family further we performed high-resolution genotyping with markers spanning chromosome 11q. Haplotype analysis excluded FZD4 as the mutated gene in this family and identified a candidate region approximately 10 cM centromeric to EVR1. This new FEVR locus is flanked by markers D11S1368 (centromeric) and D11S937 (telomeric) and spans approximately 15 cM. CONCLUSIONS: High-resolution genotyping and haplotype analysis excluded FZD4 as the defective gene in a family previously linked to the EVR1 locus. The results indicate that the gene mutated in this family lies centromeric to the EVR1 gene, FZD4, and is also genetically distinct from the EVR3 locus. This new locus has been designated EVR4 and is the fourth FEVR locus to be described.

Chromosome Mapping↗

Preterm delivery and cytokine gene polymorphisms.

OBJECTIVE: To investigate the association of preterm delivery with polymorphisms of IL-6, IL-10, IFN-gamma, TGFbeta1 and TNF-alpha genes. STUDY DESIGN: The study group consisted of 45 Caucasian, 81 mixed race and 13 black women with a history of preterm labor, consecutively referred. All of them had delivered before 37 weeks' gestation. The control group was composed of 56 Caucasian, 48 mixed race and 15 black women with successful pregnancy. DNA was extracted from whole blood, and cytokine genotyping was performed using the Cytokine Genotyping Tray (One-Lambda, Canoba Park, California). The polymorphisms analyzed were: TNF-alpha (-08 G --> A), IL-10 (-1082 G --> A), IL-6 (-174 G --> C), TGFbeta1 (+10 T --> C e 25 C --> G) and IFN-gamma (+874 A --> T). RESULTS: There were no differences in genotype frequencies of IL-10, TGF-beta, TNF-alpha or IL-6 polymorphisms between the groups. In the Caucasian group there was a trend toward increased frequencies of the TT genotype of IFN-gamma in controls. CONCLUSION: Preterm delivery is not associated with TNF-alpha (-308), IL-10 (-1082), IL-6 (-174), TGFbeta1 (+10 e 25) or IFN-gamma (+874) polymorphisms.

Adolescent↗

Correlation of agar dilution and VITEK2 system for detection of resistance to macrolides, lincosamides and pristinamycin among Staphylococcus aureus and Staphylococcus epidermidis: association with genotypes.

The performance of the VITEK2 system was evaluated against the agar dilution reference procedure for testing susceptibility of Staphylococcus aureus and Staphylococcus epidermidis to macrolides, lincosamides and streptogramins (MLS). Eighty clinical isolates were selected according to their resistance phenotype and genotype. Results for erythromycin and clindamycin showed 100% agreement; results for lincomycin showed agreement of 78%, with one very major error and 17 minor errors; and results for pristinamycin showed agreement of 46%, with one major error and 43 minor errors. Most isolates resistant to lincomycin and streptogramin A (L SgAr phenotype) were falsely susceptible to lincomycin, and intermediately-resistant or resistant to pristinamycin, with the VITEK2 system. No resistance gene was detected. Most (80%) isolates resistant constitutively to MLS (MLS(r)BC phenotype) were falsely intermediately-resistant to pristinamycin with the VITEK2 system. The erm(A) gene was more common than erm(C) in MLS(r)BC strains. Resistance to pristinamycin alone (SgA SgB PTr phenotype), or associated with either lincomycin resistance (L SgA SgB PTr phenotype) or constitutive MLS(B) resistance (MLS(BC) SgA PTr phenotype), was well-characterised without discordant results. Resistance to pristinamycin was always associated with resistance to streptogramin A, encoded by the vga(A), vga(B), vgb(A) and vat(A) genes in association with the erm(A) or erm(C) genes.

Agar↗

Male mating speed in Drosophila melanogaster: differences in genetic architecture and in relative performance according to female genotype.

From a critical review of the literature on mating speed in Drosophila, the importance of fast mating in male fitness is questioned. The genetic architecture of male mating speed (MMS) has been evaluated in D. melanogaster through a populational analysis and a full 5 x 5 diallel cross between inbred lines. The results emphasize the fundamental role of the female genotype in both the absolute and the relative MMS performances. Somewhat different genetic architectures for MMS are revealed according to the female used in the tests. It is suggested that different parts of the complex genetic system involved in the male's "behavioral sexual phenotype" are relevant depending on the female's characteristics, thus causing the heterogeneity in the MMS genetic architecture. An overall picture reveals a genetic system characterized by additivity, dominance for fast mating, and no influence of the X chromosome. There results do not support strong natural selection favoring fast mating in Drosophila males.

Animals↗

Prefrontal dysfunction in schizophrenia controlling for COMT Val158Met genotype and working memory performance.

Earlier studies with functional imaging in schizophrenia have demonstrated dysfunction of the dorsolateral prefrontal cortex during working memory. Controlling for behavioral performance and for catechol-O-methyltransferase (COMT) Val158Met genotype, we here demonstrate in a functional magnetic resonance imaging paradigm that patients recruit greater neuronal resources in prefrontal cortex during working memory, suggesting that this phenotype is a core functional trait of the disease. We also replicated earlier findings that the Val allele of the COMT polymorphism is associated with greater engagement of the prefrontal cortex.

Adult↗

Characterization of equine microsatellites and microsatellite-linked repetitive elements (eMLREs) by efficient cloning and genotyping methods.

We performed efficient cloning and genotyping methods for isolation of a large number of polymorphic microsatellites. The methods contain the time-efficient cloning method of constructing microsatellite-enriched libraries and the economic genotyping method of fluorescent labeling of PCR products. Eighty novel equine microsatellites cloned were efficiently isolated from the enrichment library and analyzed for genotype polymorphism. Of these, 72 microsatellites were analyzed with a good resolution. The average heterozygosity of all loci was 0.52, and the number of alleles ranged from one to 9 with an average of 4.5 alleles. The other eight loci showed multiple bands of PCR products, suggesting the occurrence of microsatellites in a repetitive element, in which the number of microsatellite repeats varies among different members of the repetitive element. We found five homologous groups at flanking regions in comparison with the flanking regions of microsatellites from DNA databases. One of them showed homology to equine repetitive element-2. In the other four homologous groups, the two groups were named equine microsatellite-linked repetitive element-1 (eMLRE-1) and equine microsatellite-linked repetitive element-2 (eMLRE-2) as novel equine repetitive elements identified from equine genome. These data should help the analysis of equine DNA sequences and the design of equine genome markers.

Animals↗

Denaturing high-performance liquid chromatography for mutation detection and genotyping.

Denaturing high-performance liquid chromatography (DHPLC) is an accurate and efficient screening technique used for detecting deoxyribonucleic acid sequence changes by heteroduplex analysis. It can also be used for genotyping of single-nucleotide polymorphisms. The high-sensitivity of DHPLC has made this technique one of the most reliable approaches to mutation analysis and is used in various areas of genetics, both in the research and clinical arena. This chapter describes the methods used for mutation detection analysis and the genotyping of single-nucleotide polymorphisms by DHPLC on the WAVETM system from Transgenomic Inc.

Chromatography, High Pressure Liquid↗

Influence of hOGG1, XRCC1 and XRCC3 genotypes on biomarkers of genotoxicity in workers exposed to cobalt or hard metal dusts.

Identification of genetic polymorphisms responsible for reduced DNA repair capacity may allow better cancer prevention. We examined whether variations in genes involved in base-excision (hOGG1, XRCC1) and double strand break (XRCC3) DNA repair contribute to inter-individual differences in genotoxic effects induced in the lymphocytes of 21 cobalt (Co) exposed, 26 hard metal (WC-Co) exposed and 26 matched control male workers. Genotyping was performed by PCR-RFLP. DNA single strand breaks and alkali-labile sites were measured by the alkaline Comet assay. Chromosomal rearrangements resulting from chromosome loss or acentric fragments were assessed as micronucleated mononucleates (MNMC) and binucleates (MNCB) with the cytokinesis-block micronucleus test. Urinary 8-hydroxydeoxyguanosine (8-OHdG) levels were used as an indicator of systemic oxidative DNA damage. A significantly higher frequency of MNMC was observed in WC-Co exposed workers with variant hOGG1(326) genotype. Multivariate analysis performed with genotypes, age, exposure status, type of plant, smoking and their interaction terms as independent variables indicated that MNMC and Comet tail DNA (TD) were influenced by genetic polymorphisms. In the exposed and total populations, workers variant for both XRCC3 and hOGG1 had elevated MNMC frequencies. Further studies will demonstrate whether genotyping for hOGG1 and XRCC3 polymorphisms is useful for a better individual monitoring of workers.

8-Hydroxy-2'-Deoxyguanosine↗