Association between single nucleotide polymorphisms in the CXCR1 gene and somatic cell score in Holstein dairy cattle

In addition to its position in a quantitative trait locus for somatic cell score (SCS) and its function in the immune response, the CXCR1 chemokine receptor gene located on Bos taurus autosome 2 is an auspicious candidate gene for udder health in dairy cattle. An association analysis was conducted in the German Holstein-Friesian population to test the association between the single nucleotide polymorphism (SNP) at position +777 within the CXCR1 gene and the SNP at position −1768 in the 5′ upstream region of this gene (rs41255711) and the indicator trait SCS by using a granddaughter design. Data were analyzed for 3 families, with a total of 749 genotyped bulls and an extended pedigree of 8,071 animals from the national German bovine genome mapping project. Variance component estimation was used to determine the source of phenotypic variation in the chromosomal area of interest. A 20-cM window surrounding the 2 SNP in the CXCR1 gene was examined. Although the percentage of variance caused by the putative quantitative trait locus in the area studied was relatively large (12 and 11%, respectively), no statistically significant association of the SNP CXCR1+777 or CXCR1−1768 with SCS was found. These results contradict previously published studies.     

Association of three single nucleotide polymorphisms of the E-cadherin gene with endometriosis in a Chinese population

Endometriosis, one of the most frequent diseases in gynecology, is a benign but invasive and metastatic disease. The altered expression of E-cadherin may play an important role in developing endometriosis. In this paper, we discuss the association of three single nucleotide polymorphisms (SNPs) on the E-cadherin gene and risk of endometriosis. We examined the genotype frequency of three polymorphisms in 152 endometriosis patients and 189 control women. There was a significant difference in the frequency of the E-cadherin 3'-UTR C --> T genotypes between endometriosis and controls (P = 0.01). The frequency of the C allele in patients (71.1%) was significantly higher than in the controls (63.8%; P = 0.04). When compared with the T/T + T/C genotypes, the C/C genotype had a significantly increased susceptibility to endometriosis, with an adjusted odds ratio of 1.79 (95% confidence interval = 1.17-2.76). No significant difference was found between endometriosis and control women on two polymorphisms (-160 C --> A, -347 G --> GA) at the gene promoter region of E-cadherin. The -160 C --> A and -347 G --> GA polymorphisms displayed linkage disequilibrium (D' = 0.999). The -160 A/-347 GA haplotype was only detected in endometriosis patients (2%). These data show a relation between the E-cadherin 3'-UTR C --> T polymorphism, the -160 A/-347 GA haplotype of two promoter polymorphisms and risk of endometriosis, suggesting a potential role in endometriosis development, at least in North Chinese women.     

The relationship between smoking cessation and mouth ulcers.

Patients who stop smoking often complain of aphthous (mouth) ulcers. This symptom is sometimes attributed to the use of smoking cessation medications, but little is known about it. We investigated the incidence, severity, and time course of mouth ulcers in abstaining smokers and the effect of different smoking cessation medications on the symptom. The sample consisted of 1234 smokers who sought treatment at a large smoking cessation clinic, maintained at least 1 week of continuous biochemically validated abstinence, and provided usable data. Participants assessed their mouth ulcers by rating a mouth ulcer item added to the Mood and Physical Symptoms Scale. Subjects made ratings weekly on three occasions while still smoking and over 4 weeks following smoking cessation. After stopping smoking, some 40% of patients developed mouth ulcers, mostly in the first 2 weeks. The problem was generally mild, but 8% reported severe ulceration. The ulcers resolved within 4 weeks in 60% of patients affected. The ulcer ratings in patients using oral nicotine replacement products were higher than in those using patch, nasal spray or bupropion in the first week of abstinence but not afterward. Mouth ulcers were more prevalent in more dependent smokers, and the occurrence of ulcers correlated with other tobacco withdrawal symptoms. Our results confirm that mouth ulcers are a common result of stopping smoking, affecting two in five quitters. Patients should be reassured that the lesions are a result of stopping smoking and not a side-effect of smoking cessation medication.     

Association study of single nucleotide polymorphisms in IL-10 and IL-17 genes with the severity of microbial keratitis

PurposeExploratory analysis to assess the association of single nucleotide polymorphisms (SNPs) in the interleukin (IL) 10 and IL-17 genes with severity of contact lens keratitis.MethodsThis was a retrospective case control study of 88 contact lens keratitis cases (25 severe) and 185 healthy contact lens wearers recruited from studies conducted at Moorfields Eye Hospital and in Australia-wide during 2003–2005. Buccal swab samples were collected on Whatman FTA cards and mailed by post for DNA extraction and SNP genotyping. IL-10 (rs1800871; rs1800896; rs1800872) and IL-17 (rs1800871; rs1800896; rs1800872) SNPs were screened by pyrosequencing. Genetic association analyses were performed via Cochran-Armitage trend tests and logistic regression models using PLINK software.ResultsNone of the SNPs tested showed evidence of association with severity of contact lens keratitis at P < 0.05. Nevertheless, minor allele G in SNP rs2397084 of the IL-17F gene was associated with increased risk of severe MK, with OR=2.1 (95% CI=0.9-4.8, P = 0.066).ConclusionOur study cannot exclude with confidence that genetic variation in the IL-17 F proinflammatory cytokine is associated with more severe outcomes of MK. However, there is general body of information that the IL-17 pathway is important in the mechanisms of MK. Studies with larger power and the expanded array of laboratory tools will elucidate the exact role of IL-17 in MK.     

Association of acyl-CoA-binding protein (ACBP) single nucleotide polymorphisms and type 2 diabetes in two German study populations

The human acyl-CoA-binding protein (ACBP) is a potential candidate gene of type 2 diabetes (T2D), since it plays a central role in determining the intracellular concentration of activated fatty acids which contribute to insulin resistance. The aim of our study was to evaluate whether single nucleotide polymorphisms (SNPs) of the ACBP gene are associated with risk of T2D. Genotyping of eight SNPs (rs2084202, rs3731607, rs8192501, rs8192504, rs2244135, rs2276596, rs8192506, rs2289948) was performed in 192 incident T2D subjects and 384 matched controls of the European Prospective Investigation into Cancer and Nutrition-Potsdam cohort. A putative promoter SNP (rs2084202) of splice variant ACBP 1c showed decreased risk of T2D (odds ratio (OR) 0.63, 95% CI 0.41-0.96). The haplotype, that contained the mutant base of rs2084202 showed similar evidence for the association with disease risk as single SNP rs2084202. In a second population-based study, Cooperative Health Research in the Augsburg Region of 226 individuals with T2D and 863 control subjects a borderline significant association between rs2084202 and T2D (OR 0.72, 95% CI 0.51-1.01) was observed. In summary, we obtained evidence from two Caucasian study populations that the minor allele of ACBP rs2084202 might be associated with reduced risk of T2D.     

Association of post-treatment smoking change with future smoking and cessation efforts among adolescents with psychiatric comorbidity.

Little is known about how initial change following a smoking intervention relates to longer-term smoking outcomes among adolescent smokers with psychiatric comorbidity. The present study investigated this relationship among psychiatrically hospitalized adolescents (N = 183) who participated in a controlled trial comparing motivational interviewing to brief advice. Quit attempters (n = 37), reducers (n = 45), and maintainers (n = 101) were assembled based on, respectively, having made a quit attempt, having reduced smoking by at least 50%, and having reduced smoking by less than 50% in the first week after hospital discharge. Hierarchical linear models and generalized estimating equations were conducted to test group differences in average number of cigarettes per smoking day and odds of making a quit attempt during subsequent weeks of a 12-month continuous follow-up, and in cotinine-verified abstinence rates at 1, 6, and 12 months posthospitalization. Baseline smoking levels and presence of a substance use disorder or anxiety disorder were predictive of outcomes. After controlling for covariates, we found that quit attempters smoked less during follow-up than did the other change groups and that reducers smoked less than maintainers. Quit attempters evidenced a higher percentage of quit attempts during follow-up than did the other change groups. Reducers had a greater average percentage of quit attempts during follow-up than did maintainers. However, groups did not differ on cotinine-verified abstinence rates across the follow-up period. Findings have implications for initial post-treatment change as it relates to subsequent smoking and cessation outcomes among adolescent smokers at especially high risk for smoking persistence.     

单核苷酸多态性在多倍体作物油菜中的研究进展

单核苷酸多态性（single nucleotide polymorphism,SNP）是新型分子标记,广泛存在于生物基因组中,在人类及动物的许多研究领域得到了应用,但是在油菜等一些重要的多倍体植物中应用较少。本文以油菜为例,对作物中常用的SNP开发及检测方法作了概述,其中包括第二代测序方法和SNP芯片等快速发展的新技术;综述了SNP在油菜基因定位、遗传多样性研究、全基因组关联分析等研究中的应用进展;讨论了作物SNP研究的发展趋势;以期为SNP在油菜等重要多倍体作物中广泛应用提供参考。     

Associations between phenylthiocarbamide gene polymorphisms and cigarette smoking.

Phenotypic evidence indicates that the ability to taste the bitter compounds phenylthiocarbamide (PTC) and 6-n-propylthiouracil (PROP) may protect against cigarette smoking. In this study, PTC gene haplotypes were found to be associated with both the odds of being a smoker and the importance of cigarette taste as a smoking motive. Smokers (n = 384) and nonsmokers (n = 183) were genotyped for polymorphisms that affect taste sensitivity to PTC and PROP. The "taster" PAV haplotype, relative to the "nontaster" AVI haplotype, was predicted to be associated with reduced odds of being a smoker and lower taste motivation as measured by the Wisconsin Inventory of Smoking Dependence Motives-68 taste/sensory processes scale. The results did not support the predicted association between the PAV and AVI haplotypes and smoker odds, but the AAV haplotype, which confers intermediate PTC/PROP taste sensitivity, was associated with reduced smoker prevalence (49% vs. 70%), chi(2)(1, N = 567) = 10.392, p = .001. The predicted relationship between PAV and AVI and taste motivation was found, F(2, 348) = 3.303, p = .038. The results encourage further exploration of the role of taste/sensory processes in tobacco dependence.     

A review of the associations between single nucleotide polymorphisms in taste receptors,eating behaviors,and health

Food preferences and dietary habits are heavily influenced by taste perception. There is growing interest in characterizing taste preferences based on genetic variation. Genetic differences in the ability to perceive key tastes may impact eating behavior and nutritional intake. Therefore, increased understanding of taste biology and genetics may lead to new personalized strategies, which may prevent or influence the trajectory of chronic disease risk. Recent advances show that single nucleotide polymorphisms (SNPs) in the CD36 fat taste receptor are linked to differences in fat perception, fat preference, and chronic-disease biomarkers. Genetic variation in the sweet taste receptor T1R2 has been shown to alter sweet taste preferences, eating behaviors, and risk of dental caries. Polymorphisms in the bitter taste receptor T2R38 have been shown to influence taste for brassica vegetables. Individuals that intensely taste the bitterness of brassica vegetables (“supertasters”) may avoid vegetable consumption and compensate by increasing their consumption of sweet and fatty foods, which may increase risk for chronic disease. Emerging evidence also suggests that the role of genetics in taste perception may be more impactful in children due to the lack of cultural influence compared to adults. This review examines the current knowledge of SNPs in taste receptors associated with fat, sweet, bitter, umami, and salt taste modalities and their contributions to food preferences, and chronic disease. Overall, these SNPs demonstrate the potential to influence food preferences and consequently health.     

Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population

The aim of this study was to evaluate the effects of 28 single nucleotide polymorphisms (SNP) in 10 candidate genes previously shown to be associated with quality traits in pigs and cattle. The data set comprised 28 traits recorded on a commercial population of 536 Aberdeen Angus-cross beef cattle. Among the traits, 20 were carcass and sirloin quality related, one mechanical measure of tenderness, and the remaining seven were taste panel assessed sensory traits. The candidate genes studied included growth hormone (GH) and pro-opiomelanocortin (POMC). Association analysis showed that 13 of the 28 SNPs were significantly associated with at least one of the traits. Some of these were novel (POMC and mechanical tenderness), whilst others confirmed previous results (GH and eye muscle length).     

Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle

Growth hormone, produced in the anterior pituitary gland, stimulates the release of insulin-like growth factor-I from the liver and is of critical importance in the control of nutrient utilization and partitioning for lactogenesis, fertility, growth, and development in cattle. The aim of this study was to discover novel polymorphisms in the bovine growth hormone gene (GH1) and to quantify their association with performance using estimates of genetic merit on 848 Holstein-Friesian AI (artificial insemination) dairy sires. Associations with previously reported polymorphisms in the bovine GH1 gene were also undertaken. A total of 38 novel single nucleotide polymorphisms (SNP) were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, exonic, and 3′ regulatory regions, encompassing approximately 7 kb of the GH1 gene. Following multiple regression analysis on all SNP, associations were identified between 11 SNP (2 novel and 9 previously identified) and milk fat and protein yield, milk composition, somatic cell score, survival, body condition score, and body size. The G allele of a previously identified SNP in exon 5 at position 2141 of the GH1 sequence, resulting in a nonsynonymous substitution, was associated with decreased milk protein yield. The C allele of a novel SNP, GH32, was associated with inferior carcass conformation. In addition, the T allele of a previously characterized SNP, GH35, was associated with decreased survival. Both GH24 (novel) and GH35 were independently associated with somatic cell count, and 3 SNP, GH21, 2291, and GH35, were independently associated with body depth. Furthermore, 2 SNP, GH24 and GH63, were independently associated with carcass fat. Results of this study further demonstrate the multifaceted influences of GH1 on milk production, fertility, and growth-related traits in cattle.     

单核苷酸多态性在茶树中应用的研究进展

茶树原产于中国西南地区,是一种重要的经济作物。茶叶作为中国的传统饮品,是世界上三大无酒精饮料之一。长期的自然演化及自交不亲和使得茶树的种质资源极其丰富。单核苷酸多态性(single nucleotide polymorphism,SNP)是基因组水平上单核苷酸突变引起的基因序列多样性,是继限制性酶切片段多态性(restriction fragment length polymorphism,RFLP)和简单序列重复(simple sequence repeat,SSR)的第3代分子标记,广泛存在于生物基因组中。SNP分子标记作为最重要的分子标记技术对遗传学研究有极其重要的作用。本文介绍了SNP分子标记的特征,综述了SNP在茶树中的开发检测方法,研究应用于分子标记、基因定位、关联分析等,旨在为理解和研究SNP分子标记在茶树中的研究应用提供参考。     

Artificial neural network predictive model for allergic disease using single nucleotide polymorphisms data

The purpose of this study was to develop a novel diagnostic prediction method for allergic diseases from the data of single nucleotide polymorphisms (SNPs) using an artificial neural network (ANN). We applied the prediction method to four allergic diseases, such as atopic dermatitis (AD), allergic conjunctivitis (AC), allergic rhinitis (AR) and bronchial asthma (BA), and verified its predictive ability. Almost all the learning data were precisely predicted. Regarding the evaluation data, the learned ANN model could correctly predict a diagnosis with more than 78% accuracy. We also analyzed the SNP data using multiple regression analysis (MRA). Using the MRA model, less than 10% of patients with the above allergic diseases were correctly diagnosed, while this figure was more than 75% for persons without allergic diseases. From these results, it was shown that the ANN model was superior to the MRA model with respect to predictive ability of allergic diseases. Moreover, we used two different methods to convert the genetic polymorphism data into numerical data. Using both methods, diagnostic predictions were quite precise and almost the same predictive abilities were observed. This is the first study showing the application and usefulness of an ANN for the prediction of allergic diseases based on SNP data.     

Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle

Single nucleotide polymorphism (SNP) associations with milk production traits found to be significant in different screening experiments, including SNP in genes hypothesized to be in gene pathways affecting milk production, were tested in a validation population to confirm their association. In total, 423 SNP were genotyped across 411 Holstein bulls, and their association with 6 milk production traits--Australian Selection Index (indicating the profitability of an animal's milk production), protein, fat, and milk yields, and protein and fat composition--were tested using single SNP regressions. Seventy-two SNP were significantly associated with one or more of the traits; their effects were in the same direction as in the screening experiment and therefore their association was considered validated. An over-representation of SNP (43 of the 423) on chromosome 20 was observed, including a SNP in the growth hormone receptor gene previously published as having an association with protein composition and protein and milk yields. The association with protein composition was confirmed in this experiment, but not the association with protein and milk yields. A multiple SNP regression analysis for all SNP on chromosome 20 was performed for all 6 traits, which revealed that this mutation was not significantly associated with any of the milk production traits and that at least 2 other quantitative trait loci were present on chromosome 20.     

Association analyses of single nucleotide polymorphisms in the LEP and SCD1 genes on the fatty acid profile of muscle fat in Simmental bulls

The aim was to investigate the effect of the genetic polymorphisms of leptin (LEP) and stearoyl-CoA desaturase (SCD1) genes on the fatty acid (FA) composition of the muscle of 103 Simmental bulls. Ten single nucleotide polymorphisms (SNP) were detected in exons 2 and 3 of the LEP gene, two of them encoding non-synonymous mutations. Allelic substitution effects of all the SNP on 28 single fatty acids, monounsaturated (MUFA) and polyunsaturated (PUFA) and desaturation indexes were estimated. Both the SCD1 SNP, as well as three SNP of the leptin gene, affected, to different extents, the desaturation of FA into MUFA. Because it was previously proposed that leptin's metabolic action involves down-regulation of SCD1, it is possible that, beyond the mere additive effect of SCD1 gene on FA desaturation, the non-synonymous mutations in the leptin gene also contribute to the variability of FA composition in muscle fat.     

Dimensions of depressive symptoms and smoking cessation.

Because different psychopathologic components of depressive symptoms may have distinct etiologies, examining their differential effects on smoking cessation may elucidate mechanisms underlying the smoking-depression relationship. Negative affect (NA), somatic features (SF), low positive affect/anhedonia (PA), and interpersonal disturbance (IP) have been identified as unique dimensions of depression that can be measured using the Center for Epidemiologic Studies Depression Scale (CESD). This study examined common and unique associations between CESD subscales and baseline smoking characteristics, nicotine withdrawal, and relapse in 157 participants enrolled in a smoking cessation trial for heavy social drinkers. Each dimension was univariately associated with negative and positive reinforcement smoking motives. Only SF had unique relations with tolerance smoking motives and univariate associations with nicotine dependence severity. Only PA predicted cessation-related changes in withdrawal symptoms on quit day. Analyses predicting abstinence at 8, 16, and 26 weeks post quit date showed that NA, SF, and PA each univariately predicted relapse, ps< or =.0083. Only low PA predicted poorer outcomes incrementally to the other dimensions, even when controlling for level of nicotine dependence, smoking frequency, and history of major depression, p = .0018. Interventions targeting anhedonia and low positive affect may be useful for smokers trying to quit.     

Parental smoking cessation and children's smoking: mediation by antismoking actions.

The present study investigated whether parents' antismoking actions mediated the prospective relationship between parental smoking cessation and children's smoking. Smoking status of parents (predictor) was assessed when their children were in 3rd grade, parental antismoking actions (mediators) were assessed when their children were in 11th grade, and children's smoking status (outcome) was assessed when they were in 12th grade. In 20 Washington state school districts, data were collected from 1,600 children (49% female, 91% White) and from their parents. Results showed that children's odds of daily smoking were reduced by 39% (95% CI = 24%-51%) for those whose parents had quit smoking, compared with those whose parents were current smokers. Asking to sit in nonsmoking sections of public establishments was a significant (p<.01) mediator that explained 64% of the association between parental smoking cessation and children's smoking. However, not allowing smoking in the home and asking others not to smoke around them were not significant mediators (p = .10, and p = .06, respectively). In conclusion, asking to sit in a nonsmoking section of a public establishment substantially mediates the relationship between parental smoking cessation and children's smoking.     

Multi-locus genotyping of bottom fermenting yeasts by single nucleotide polymorphisms indicative of brewing characteristics

Yeast plays a capital role in brewing fermentation and has a direct impact on flavor and aroma. For the evaluation of competent brewing strains during quality control or development of novel strains it is standard practice to perform fermentation tests, which are costly and time-consuming. Here, we have categorized DNA markers which enable to distinguish and to screen brewing strains more efficiently than ever before. Sequence analysis at 289 loci in the genomes of six bottom fermenting Saccharomyces pastorianus strains revealed that 30 loci contained single nucleotide polymorphisms (SNPs). By determining the nucleotide sequences at the SNP-loci in 26 other S. pastorianus strains and 20 strains of the top fermenting yeast Saccharomyces cerevisiae, almost all these strains could be discriminated solely on the basis of the SNPs. By comparing the fermentative phenotypes of these strains we found that some DNA markers showed a strong association with brewing characteristics, such as the production of ethyl acetate and hydrogen sulphide (H2S). Therefore, the DNA markers we identified will facilitate quality control and the efficient development of brewing yeast strains.     

Social class, education, and smoking cessation: Long-term follow-up of patients treated at a smoking cessation unit.

Our objective was to examine social class and educational differences in long-term smoking cessation success among a cohort of smokers attending a specialized smoking clinic. We studied sustained abstinence after cessation among 1,516 smokers (895 men and 621 women) treated for smoking cessation between 1995 and 2001 at a university teaching hospital in the metropolitan area of Barcelona, Spain. We calculated 1-year and long-term (up to 8-year) abstinence probabilities by means of Kaplan-Meier curves and the hazard ratio of relapse by means of Cox regression, after adjusting for other predictors of relapse. Overall abstinence probability was .277 (95% CI = .254-.301). Men and women in social classes IV-V had significant hazard ratios of relapse after long-term follow-up (men: 1.36, 95% CI = 1.07-1.72; women: 1.60, 95% CI = 1.24-2.06), as compared with patients in social classes I-II. The same independent effect was observed for education: Men and women with primary or less than primary studies had higher hazard ratios of relapse (men: 1.75, 95% CI = 1.35-2.25; women: 1.92, 95% CI = 1.51-2.46), as compared with patients with a university degree. Similar estimates were obtained after adjustment for stage of change, Fagerstr?m score for nicotine dependence, and type of treatment. Patients of lower socioeconomic status are at higher risk of relapse, and this association is independent of other well-known predictors of relapse. Social differences have to be taken into account in the clinical setting when tailoring specific actions to treat smoking dependence.