A novel efficient method to identify beta-glucuronidase activity in rat small intestine

BACKGROUND: Recent epidemiologic studies promote the notion that high intake of food rich in phytochemicals protects against degenerative diseases such as coronary heart diseases and cancer. Phytochemicals are detoxified in mammalian tissues by conjugation with glucuronic acid yielding less active glucuronide conjugates. However, in several tissues glucuronide conjugates are reactivated by the cleaving enzyme beta-glucuronidase. The aim of the present study was to develop a routinely manageable, rapid technique to localize the beta-glucuronidase activity in the small intestinal tissue. METHODS: Histologic slices of rat duodenum, jejunum, and ileum were incubated with a specific chromogenic beta-glucuronidase substrate, 5-bromo-4-chloro-3-indolyl-beta-D-glucuronide (X-GlcU). After enzymatic cleavage, X-GlcU yields 5-bromo-4-chloro-3-indol, a dark blue crystalline precipitate easily monitored by light microscopic technique. RESULTS: The number and intensity of the crystals were highest in the jejunum and lowest in the ileum. In all three sections of the small intestine, the highest activity was observed at the villar tip and in the tela submucosa and only moderate activity in other layers of the intestinal tissue. CONCLUSIONS: By using the X-GlcU-technique, it could be demonstrated convincingly that beta-glucuronidase exists in all three segments of the rat small intestine. The proposed method is an efficient, simple, and convenient method to visualize beta-glucuronidase activity.     

Genotype-based association test for general pedigrees: the genotype-PDT

Many family-based tests of linkage disequilibrium (LD) are based on counts of alleles rather than genotypes. However, allele-based tests may not detect interactions among alleles at a single locus that are apparent when examining associations with genotypes. Family-based tests of LD based on genotypes have been developed, but they are typically valid as tests of association only in families with a single affected individual. To take advantage of families with multiple affected individuals, we propose the genotype-pedigree disequilibrium test (geno-PDT) to test for LD between marker locus genotypes and disease. Unlike previous tests for genotypic association, the geno-PDT is valid in general pedigrees. Simulations to compare the power of the allele-based PDT and geno-PDT reveal that under an additive model, the allele-based PDT is more powerful, but that the geno-PDT can have greater power when the genetic model is recessive or dominant. Perhaps the most important property of the geno-PDT is the ability to test for association with particular genotypes, which can reveal underlying patterns of association at the genotypic level. These genotype-specific tests can be used to suggest possible underlying genetic models that are consistent with the pattern of genotypic association. This is illustrated through an application to a candidate gene analysis of the MLLT3 gene in families with Alzheimer disease. The geno-PDT approach for testing genotypes in general family data provides a useful tool for identifying genes in complex disease, and partitioning individual genotype contributions will help to dissect the influence of genotype on risk.     

A Bayesian approach to multipoint mapping in nuclear families

We describe the application of a Markov Chain Monte Carlo approach for multipoint mapping of a quantitative trait locus to the Nuclear Families simulated data. The method involves repeated sampling of genotype vectors for each nuclear family from their conditional distributions, given phenotypes, markers, and model parameters, using peeling and gene dropping, followed by random sampling of each model parameter given genotypes and the other parameters. Reversible jump methods are used to sample the number of trait loci. © 1997 Wiley-Liss, Inc     

Biology‐Driven Gene‐Gene Interaction Analysis of Age‐Related Cataract in the eMERGE Network

Bioinformatics approaches to examine gene‐gene models provide a means to discover interactions between multiple genes that underlie complex disease. Extensive computational demands and adjusting for multiple testing make uncovering genetic interactions a challenge. Here, we address these issues using our knowledge‐driven filtering method, Biofilter, to identify putative single nucleotide polymorphism (SNP) interaction models for cataract susceptibility, thereby reducing the number of models for analysis. Models were evaluated in 3,377 European Americans (1,185 controls, 2,192 cases) from the Marshfield Clinic, a study site of the Electronic Medical Records and Genomics (eMERGE) Network, using logistic regression. All statistically significant models from the Marshfield Clinic were then evaluated in an independent dataset of 4,311 individuals (742 controls, 3,569 cases), using independent samples from additional study sites in the eMERGE Network: Mayo Clinic, Group Health/University of Washington, Vanderbilt University Medical Center, and Geisinger Health System. Eighty‐three SNP‐SNP models replicated in the independent dataset at likelihood ratio test P < 0.05. Among the most significant replicating models was rs12597188 (intron of CDH1)–rs11564445 (intron of CTNNB1). These genes are known to be involved in processes that include: cell‐to‐cell adhesion signaling, cell‐cell junction organization, and cell‐cell communication. Further Biofilter analysis of all replicating models revealed a number of common functions among the genes harboring the 83 replicating SNP‐SNP models, which included signal transduction and PI3K‐Akt signaling pathway. These findings demonstrate the utility of Biofilter as a biology‐driven method, applicable for any genome‐wide association study dataset.     

GAB2 gene does not modify the risk of Alzheimer’s disease in Spanish APOE 4 carriers

Objectives  The genetic basis of Alzheimer’s disease (AD) is being analyzed in multiple whole genome association studies (WGAS). The GAB2 gene has been proposed as a modifying factor of APOE ε4 allele in a recent case-control WGAS conducted in the US. Given the potential application of these novel results in AD diagnostics, we decided to make an independent replication to examine the GAB2 gene effect in our series. Design  We are conducting a multicenter population-based study of AD in Spain. Participants  We analyzed a total of 1116 Spanish individuals. Specifically, 521 AD patients, 475 controls from the general population and 120 neurologically-normal elderly controls (NNE controls). Methods  We have genotyped GAB2 (rs2373115 G/T) and APOE rs429358 (SNP112)/rs7412 (SNP158) polymorphisms using real time-PCR technologies. Results  As previously reported in Spain, APOE ε4 allele was strongly associated with AD in our series (OR=2.88 [95% C.I. 2.16–3.84], p=7.38E-11). Moreover, a large effect for ε4/ ε4 genotype was also observed (OR=14.45 [95% C.I., 3.34–125.2], p=1.8E-6). No difference between the general population and the NNE controls series were observed for APOE genotypes (P>0.61). Next, we explored GAB2 rs2373115 SNP single-locus association using different genetic models and comparing AD versus controls or NNE controls. No evidence of association with AD was observed for this GAB2 marker (p>0.17). To evaluate GAB2-APOE gene-gene interactions, we stratified our series according to APOE genotype and case-control status, in accordance with the original studies. Again, no evidence of genetic association with AD was observed in any strata of GAB2-APOE loci pair (p>0.34). Conclusion  GAB2 rs2373115 marker does not modify the risk of Alzheimer’s disease in Spanish APOE ε4 carriers.     

The longitudinal nonparametric test as a new tool to explore gene‐gene and gene‐time effects in cohorts

Current approaches for analysis of longitudinal genetic epidemiological data of quantitative traits are typically restricted to normality assumptions of the trait. We introduce the longitudinal nonparametric test (LNPT) for cohorts with quantitative follow‐up data to test for overall main effects of genes and for gene‐gene and gene‐time interactions. The LNPT is a rank procedure and does not depend on normality assumptions of the trait. We demonstrate by simulations that the LNPT is powerful, keeps the type‐1 error level, and has very good small sample size behavior. For phenotypes with normal residuals, loss of power compared to parametric approaches (linear mixed models) was small for the quite general scenarios, which we simulated. For phenotypes with non‐normal residuals, gain in power by the LNPT can be substantial. In contrast to parametric approaches, the LNPT is invariant with respect to monotone transformations of the trait. It is mathematically valid for arbitrary trait distribution. Genet. Epidemiol. 34: 469?478, 2010. © 2010 Wiley‐Liss, Inc.     

Body-Mass Index and Mortality in Incident Dementia: A Cohort Study on 11,398 Patients From SveDem,the Swedish Dementia Registry

BackgroundBody mass index (BMI) is used worldwide as an indirect measure of nutritional status and has been shown to be associated with mortality. Controversy exists over the cut points associated with lowest mortality, particularly in older populations. In patients suffering from dementia, information on BMI and mortality could improve decisions about patient care.ObjectivesThe objective was to explore the association between BMI and mortality risk in an incident dementia cohort.DesignCohort study based on SveDem, the Swedish Quality Dementia Registry; 2008–2011.SettingSpecialist memory clinics, Sweden.ParticipantsA total of 11,398 patients with incident dementia with data on BMI (28,190 person-years at risk for death).Main outcome measuresHazard ratios and 95% confidence intervals for mortality associated with BMI were calculated, controlling for age, sex, dementia type, results from Mini-Mental State Examination, and number of medications. BMI categories and linear splines were used.ResultsHigher BMI was associated with decreased mortality risk, with all higher BMI categories showing reduced risk relative to patients with BMI of 18.5 to 22.9 kg/m², whereas underweight patients (BMI <18.5 kg/m²) displayed excess risk. When explored as splines, increasing BMI was associated with decreased mortality risk up to BMI of 30.0 kg/m². Each point increase in BMI resulted in an 11% mortality risk reduction in patients with BMI less than 22.0 kg/m², 5% reduction when BMI was 22.0 to 24.9 kg/m², and 3% risk reduction among overweight patients. Results were not significant in the obese weight range. Separate examination by sex revealed a reduction in mortality with increased BMI up to BMI 29.9 kg/m² for men and 24.9 kg/m² for women.ConclusionHigher BMI at the time of dementia diagnosis was associated with a reduction in mortality risk up to and including the overweight category for the whole cohort and for men, and up to the normal weight category for women.     

吸烟校正因素间接调整法在职业流行病学队列研究中的应用

目的介绍一种新的吸烟校正因素间接调整法在职业流行病学队列研究中的应用。方法以1981—1999年香港男性矽肺回顾性队列研究人群纯石英暴露组作为研究实例,用吸烟组[1/((1-PAR%)×RR)]与非吸烟组(1/(1-PAR%))各自的吸烟校正因素校正原始的标准化死亡比(SMR),用暴露超相对危险度和增效指数作为指标来判断吸烟与暴露对肺癌死亡的危险有无偏离乘法和相加模型。结果非吸烟和吸烟组矽肺队列人群的吸烟校正因素分别为1/0.33和1/1.62,校正吸烟后矽肺队列肺癌的SMR由原来的1.61(95%CI:1.22～2.10)显著地下降到1.08(95%CI:0.81～1.41),结果与Axelson方法完全一致。矽肺超相对危险度和增效指数分别为0.63(95%CI:0.08～0.79)和0.90(95%CI:0.42～1.94),提示吸烟与矽肺对肺癌死亡的危险呈明显的负相乘交互作用。结论吸烟校正因素间接调整法的优势是能定量分析和评估吸烟的混杂和交互作用的影响,但也有局限性。     

Confronting complexity in late-onset Alzheimer disease: application of two-stage analysis approach addressing heterogeneity and epistasis

Common diseases with a genetic basis are likely to have a very complex etiology, in which the mapping between genotype and phenotype is far from straightforward. A new comprehensive statistical and computational strategy for identifying the missing link between genotype and phenotype has been proposed, which emphasizes the need to address heterogeneity in the first stage of any analysis and gene-gene interactions in the second stage. We applied this two-stage analysis strategy to late-onset Alzheimer disease (LOAD) data, which included functional and positional candidate genes and markers in a region of interest on chromosome 10. Bayesian classification found statistically significant clusterings for independent family-based and case-control datasets, which used the same five markers in leucine-rich repeat transmembrane neuronal 3 (LRRTM3) as the most influential in determining cluster assignment. In subsequent analyses to detect main effects and gene-gene interactions, markers in three genes--urokinase-type plasminogen activator (PLAU), angiotensin 1 converting enzyme (ACE) and cell division cycle 2 (CDC2)--were found to be associated with LOAD in particular subsets of the data based on their LRRTM3 multilocus genotype. All of these genes are viable candidates for LOAD based on their known biological function, even though PLAU, CDC2 and LRRTM3 were initially identified as positional candidates. Further studies are needed to replicate these statistical findings and to elucidate possible biological interaction mechanisms between LRRTM3 and these genes.     

复杂疾病病因研究中基因问交互作用分析:基于基因型传递不平衡的多因子降维法

介绍复杂疾病病因研究中分析基因-基因交互作用的一种新方法：基于基因型传递不平衡的多因子降维法（MDR-PDT）。文中简述MDR-PDT的基本原理、步骤及特点，并结合研究实例说明其应用过程。MDR-PDT是原始MDR的扩展，可用于多种结构类型的核心家系资料分析基因-基因交互作用。结论MDR-PDT具有非参数、无需遗传模式的特点，并能充分利用家系中多个家庭成员的信息，在复杂疾病病因研究中分析基因-基因交互作用具有良好的效能。     

Nutritional Strategies in the Management of Alzheimer Disease: Systematic Review With Network Meta-Analysis

Background

Alzheimer disease (AD) is the major cause of dependency and disability in the elderly. Numerous studies have sought to achieve its prevention and/or management examining a role for modifiable risk factors, such as nutrition. This work aims to investigate the effects of food and/or nutrients in the management of AD at different stages.

The Broken Lens of BPSD: Why We Need to Rethink the Way We Label the Behavior of People Who Live With Alzheimer Disease

For the past 20 years, the behaviors of people who live with dementia (PLWD) that others find challenging or problematic have primarily been ascribed to Alzheimer disease and related dementias and have been assessed through the biomedical lens of Behavioral and Psychological Symptoms of Dementia (BPSD). This has led to the root causes of these behaviors being overlooked, which in turn leaves them unaddressed. Further, using the artificial construct of BPSD has led to many PLWD being inappropriately prescribed (off-label) medications that are largely ineffective in resolving the behaviors because they do nothing to remedy the underlying psychosocial and environmental causes. The fact that many of the behaviors we call BPSD are normal human responses to particular sets of circumstances can be relatively easily demonstrated by directly observing the individual behaviors of PWLD, and putting them in context, as well as by asking ourselves how we would respond under similar conditions. Re-evaluating the use of the construct of BPSD, and replacing it with a person-centered rather than disease-focused approach will result in better care as well as healthier and happier long-term care residents and staff.     

南昌市社区老年人轻度认知功能障碍向阿尔茨海默病转归研究

目的  探讨南昌市社区老年人轻度认知功能障碍(mild cognitive impairment, MCI)向阿尔茨海默病(Alzheimer disease, AD)的转归率, 并分析其影响因素。 方法  采用分层整群抽样方法选取南昌市10个社区作为研究现场, 从抽取年龄≥60岁的1 942名老年人中筛查出361名MCI患者, 采用问卷调查和实验室检测收集研究对象一般人口学特征、生活习惯信息、疾病既往史、阿尔茨海默病相关神经丝蛋白(Alzheimer-associated neuronal thread protein, AD7c-NTP)、β淀粉样蛋白42(amyloidβ-protein 42, Aβ42)、β淀粉样蛋白40(amyloidβ-protein 40, Aβ40)等信息, 对MCI患者随访三年判断是否进展为AD。 结果  361例MCI患者共有121例转归为AD, 年均转归率为9.49%, Logistic回归分析模型分析结果显示, 高龄(80~98岁)(OR=3.651, 95%CI:1.295~10.297, P < 0.001)、女性(OR=2.603, 95%CI:1.136~5.966, P < 0.001)、大量饮酒(OR=1.479, 95%CI:1.343~1.627, P < 0.001)、ADL分值升高(OR=1.790, 95%CI:1.443~2.220, P=0.031)、吸烟(OR=1.157, 95%CI:1.091~1.224, P < 0.001)是危险因素, 而Moca分值升高(OR=0.766, 95%CI:0.681~0.861, P < 0.001)则是保护因素。 结论  加强对高龄女性的MCI患者监控, 并提倡老年人拥有健康生活方式, 积极参加体育锻炼、多读书和看报, 以延缓MCI患者向AD转归。     

α-Lipoic acid,functional fatty acid,as a novel therapeutic alternative for central nervous system diseases: A review

Objectives: α-lipoic acid (ALA) is a natural antioxidant which acts as a cofactor of bioenergetic mitochondrial enzymes. Along with its mitochondrial action, ALA and its reduced form have many biological functions resulting in a wide variety of actions such as anti-inflammation and antioxidant protection, scavenging reactive oxygen species, regenerating other antioxidant agents, such as vitamins C and E, and cytosolic glutathione, chelating the transitional metal ions (e.g. iron and copper), and modulating the signal transduction of nuclear factor.

Methods: By selecting papers from PubMed, Science Direct, EBSCO, and databases, this review discusses the biochemical properties of LA, its mechanism of action, pharmacokinetics, and its possible therapeutic role in central nervous system diseases, such as Alzheimer’s disease, Parkinson’s disease, Multiple sclerosis, stroke, and spinal cord injury.

Results: ALA as an antioxidant and anti-inflammation agent has therapeutical effects on central nervous system diseases, especially multiple sclerosis and PD.

Discussion: ALA can be considered as a potentially useful treatment in central nervous disorders.     

Centralizing the non-central chi-square: A new method to correct for population stratification in genetic case-control association studies

We present a new method, the delta-centralization (DC) method, to correct for population stratification (PS) in case-control association studies. DC works well even when there is a lot of confounding due to PS. The latter causes overdispersion in the usual chi-square statistics which then have non-central chi-square distributions. Other methods approach the noncentrality indirectly, but we deal with it directly, by estimating the non-centrality parameter tau itself. Specifically: (1) We define a quantity delta, a function of the relevant subpopulation parameters. We show that, for relatively large samples, delta exactly predicts the elevation of the false positive rate due to PS, when there is no true association between marker genotype and disease. (This quantity delta is quite different from Wright's F(ST) and can be large even when F(ST) is small.) (2) We show how to estimate delta, using a panel of unlinked "neutral" loci. (3) We then show that delta2 corresponds to tau the noncentrality parameter of the chi-square distribution. Thus, we can centralize the chi-square using our estimate of 6; this is the DC method. (4) We demonstrate, via computer simulations, that DC works well with as few as 25-30 unlinked markers, where the markers are chosen to have allele frequencies reasonably close (within +/- .1) to those at the test locus. (5) We compare DC with genomic control and show that where as the latter becomes overconservative when there is considerable confounding due to PS (i.e. when delta is large), DC performs well for all values of delta.     

A statistical method for scanning the genome for regions with rare disease alleles

Studying the role of rare alleles in common disease has been prevented by the impractical task of determining the DNA sequence of large numbers of individuals. Next‐generation DNA sequencing technologies are being developed that will make it possible for genetic studies of common disease to study the full frequency spectrum of genetic variation, including rare alleles. This report describes a method for scanning the genome for disease susceptibility regions that show an increased number of rare alleles among a sample of disease cases versus an ethnically matched sample of controls. The method was based on a hidden Markov model and the statistical support for a disease susceptibility region characterized by rare alleles was measured by a likelihood ratio statistic. Due to the lack of empirical data, the method was evaluated through simulation. The performance of the method was tested under the null and alternative hypotheses under a range of sequence generating and hidden Markov models parameters. The results showed that the statistical method performs well at identifying true disease susceptibility regions and that performance was primarily affected by the amount of variation in the neutral sequence and the number of rare disease alleles found in the disease susceptibility region. Genet. Epidemiol. 34: 386–395, 2010. © 2010 Wiley‐Liss, Inc.     

Linkage analysis in familial Alzheimer disease: Description of the Duke and Boston data sets

Familial Alzheimer disease is a neurological disorder of adult onset. Three research centers have each contributed their families and genetic linkage data for combined analyses. The data from the Duke and Boston centers, comprising 73 pedigrees for whom numerous markers on chromosomes 19 and 21 were typed, are described. © 1993 Wiley-Liss, Inc.     

Gender-specific nonrandom association between the α1-antichymotrypsin and apolipoprotein E polymorphisms in the general population and its implication for the risk of Alzheimer's disease

A common polymorphism in the α1-antichymotrypsin (ACT) gene has been found to modify the APOE*4-associated risk of Alzheimer's disease due to an apparent interaction between the two loci. This study was undertaken to determine the gender- and age-related distributions of these two polymorphisms in two large population-based samples of Caucasians (n = 803) and Nigerian Blacks (n = 730). Significantly higher frequencies of the ACT*A (78.6% vs. 48.4%; P < 0.001) and APOE*4 (25.6% vs. 15.6%; P < 0.001) alleles were observed in Nigerian Blacks than in Caucasians. In Caucasian women but not in men, the frequency of the APOE*4 allele was significantly lower in the ACT/AA genotype as compared to the ACT/AT and ACT/TT genotypes, while a reverse trend was seen for the APOE*3 allele frequency among the ACT genotypes. The distribution of the ACT*A allele between the APOE*4 carriers and non-APOE*4 carriers was also different in Caucasian women but not in men. A similar gender-specific nonrandom association between the two polymorphisms was observed in Black women but this was not as strong as observed in Caucasian women. When the two samples were stratified by age group, an association or trend of association was observed in all age groups in women only. These data indicate the existence of a nonrandom association between the APOE and ACT loci in women which may have an important implication for the higher prevalence of Alzheimer's disease in women. Genet. Epidemiol. 14:169–180,1997. © 1997 Wiley-Liss. Inc.     

Analytical strategies to include the X-chromosome in variance heterogeneity analyses: Evidence for trait-specific polygenic variance structure

Genotype-stratified variance of a quantitative trait could differ in the presence of gene–gene or gene–environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from “whole-genome” scans due to analytical challenges. Specifically, as males carry only one copy of the X-chromosome, the inherent sex-genotype dependency could bias the trait-genotype association, through sexual dimorphism in quantitative traits with sex-specific means or variances. Here we investigate phenotypic variance heterogeneity associated with X-chromosome single nucleotide polymorphisms (SNPs) and propose valid and powerful strategies. Among those, a generalized Levene's test has adequate power and remains robust to sexual dimorphism. An alternative approach is a sex-stratified analysis but at the cost of slightly reduced power and modeling flexibility. We applied both methods to an Estonian study of gene expression quantitative trait loci (eQTL; n = 841), and two complex trait studies of height, hip, and waist circumferences, and body mass index from Multi-Ethnic Study of Atherosclerosis (MESA; n = 2,073) and UK Biobank (UKB; n = 327,393). Consistent with previous eQTL findings on mean, we found some but no conclusive evidence for cis regulators being enriched for variance association. SNP rs2681646 is associated with variance of waist circumference (p = 9.5E-07) at X-chromosome-wide significance in UKB, with a suggestive female-specific effect in MESA (p = 0.048). Collectively, an enrichment analysis using permutated UKB (p < 0.1) and MESA (p < 0.01) datasets, suggests a possible polygenic structure for the variance of human height.