Utilising surface-level data to explore surface, tooth, individual and family influence on the aetiology of hypomineralised second primary molars.

OBJECTIVES: Hypomineralised second primary molars (HSPM) are common developmental enamel defects. The aims of this study were to use surface-level data to explore the clustering of HSPM at four levels (family, child, tooth, surface). METHODS: This study of 172 twin pairs was nested within the Peri/postnatal Epigenetic Twin Study. HSPM was measured by standardised oral examinations at age 6 years. Multilevel logistic regression models were fitted to assess the correlation structure of surface level data and variation in HSPM. The associations between surface level risk factors and HSPM were then explored using the multilevel logistic regression model using the best fitting correlation structure. RESULTS: The prevalence of HSPM was 68 (19.8%) children, with a total of 141 (10.3%) teeth and 264 tooth surfaces (6.3%) affected. Multilevel models revealed that a hierarchical structure accounting for correlation at the family, child and tooth level best accounted for the variation in HSPM. The estimated variances from the best fitting model (Model 3) were largest at the family level (12.27, 95% CI 6.68, 22.51) compared with 5.23 at the child level and 1.93 at the tooth level. Application of regression analysis utilising this three-level correlation structure identified tooth/surface level factors in addition to the previously identified familial and individual risk factors for HSPM. CONCLUSION: In addition to familial (environmental and genetic) and unique child-level factors, the aetiology of HSPM is likely to be influenced by local tooth-level factors.

A twin study of body mass index and dental caries in childhood.

Sub-optimal nutrition and dental caries are both common with significant short and long-term implications for child health and development. We applied twin statistical methods to explore the relationship between body mass index (BMI) and dental caries. We measured BMI at 18 months and six years of age and cumulative dental caries experience at six years in 344 twin children. Dental caries in primary teeth was categorised into 'any' or 'advanced' and BMI was analysed as both a continuous and categorical variable. Statistical analyses included multiple logistic regression using generalized estimating equations and within/between-pair analyses. There was no association between BMI and 'any' dental caries experience at either time-point, neither overall nor in within/between pair analyses. However, 'advanced' dental caries at six years was associated with a within-pair difference in BMI of -0.55 kg/m2 (95% CI -1.00, -0.11, p = 0.015). A within-pair increase of 1 kg/m2 in BMI was associated with a lower within-pair risk of advanced dental caries (OR 0.68, 95% CI 0.52, 0.90, p = 0.007). These findings reveal a possible causal relationship between lower BMI and dental caries. As dental outcomes were only measured at one time point, the direction of this potentially causal relationship is unclear.

Etiology of Hypomineralized Second Primary Molars: A Prospective Twin Study.

The etiology of hypomineralized second primary molars (HSPM) is unclear, but genetic and environmental factors have been proposed. The aim of this study was to investigate the relative contribution of genes and environment to the etiology of HSPM and to identify potential environmental risk factors in a longitudinal twin cohort. Children from twin pregnancies ( N = 250) were recruited antenatally, and detailed demographic, health, and phenotypic data were collected at recruitment, 24- and 36-wk gestation, birth, and 18 mo of age. 25-Hydroxyvitamin D was quantified for mothers at 28-wk gestation and infants at birth. Dental examinations were conducted on the twins at 6 y of age to determine the presence, severity, and extent of HSPM per standardized criteria. To investigate associations of environmental risk factors with HSPM, multiple logistic regression models were fitted with generalized estimating equations to adjust for twin correlation. Within- and between-pair analyses were performed for unshared continuous variables: birthweight and birth 25-hydroxyvitamin D. Twin-twin concordance for monozygotic (MZ) and dizygotic (DZ) pairs was calculated and compared after adjusting for identified risk factors. A total of 344 twins underwent the 6-y-old dental assessment; HSPM occurred in 68 (19.8%). After adjusting for potential confounders, vitamin D levels at birth, infantile eczema, dizygosity, in vitro fertilization, socioeconomic position, and maternal smoking beyond the first trimester of pregnancy demonstrated the strongest associations with HSPM. Overall concordance for HSPM was 0.47 (95% CI, 0.32 to 0.62) with weak evidence ( P = 0.078) of higher concordance in MZ twins (0.63; 95% CI, 0.38 to 0.89) as compared with DZ twins (0.41; 95% CI, 0.24 to 0.58). After adjusting for known risk factors, there was no evidence ( P = 0.172) for an additive genetic influence. These findings suggest that shared and unshared environmental factors, such as maternal smoking later in pregnancy and infantile eczema, are important in the etiology of HSPM.

The Beneficial Effects of Physical Activity: Is It Down to Your Genes? A Systematic Review and Meta-Analysis of Twin and Family Studies.

BACKGROUND: There is evidence for considerable heterogeneity in the responsiveness to regular physical activity (PA) which might reflect the influence of genetic factors. The aim of this systematic review was to assess whether the response to a PA intervention for measures of body composition and cardiorespiratory fitness is (i) correlated within twin pairs and/or families and (ii) more correlated in monozygotic twins (MZ) compared to dizygotic twins (DZ), which would be consistent with genetic effects. METHODS: We performed electronic database searches, combining key words relating to "physical activity" and "genetics", in MEDLINE, CINAHL, EMBASE, SPORTS Discuss, AMED, PsycINFO, WEB OF SCIENCE, and SCOPUS from the earliest records to March 2016. Twin and family studies were included if they assessed body composition and/or cardiorespiratory fitness following a PA intervention, and provided a heritability estimate, maximal heritability estimate, or within MZ twin pair correlation (rMZ). Data on heritability (twin studies), maximal heritability (family studies), and the rMZ were extracted from included studies, although heritability estimates were not reported as small sample sizes made them uninformative. RESULTS: After screening 224 full texts, nine twin and five family studies were included in this review. The pooled rMZ in response to PA was significant for body mass index (rMZ = 0.69, n = 58), fat mass (rMZ = 0.58, n = 48), body fat percentage (rMZ = 0.55, n = 72), waist circumference (rMZ = 0.50, n = 27), and VO2max (rMZ = 0.39, n = 48), where "n" represents the total number of twin pairs from all studies. Maximal heritability estimates ranged from 0-21% for measures of body composition, and 22-57% for cardiorespiratory fitness. Twin studies differed in sample age, baseline values, and PA intervention, although the exclusion of any one study did not affect the results. CONCLUSIONS: Shared familial factors, including genetics, are likely to be a significant contributor to the response of body composition and cardiorespiratory fitness following PA. Genetic factors may explain individual variation in the response to PA. TRIAL REGISTRATIONS: PROSPERO Registration No CRD42015020056 .

The association of PTPN22 rs2476601 with juvenile idiopathic arthritis is specific to females.

A preponderance of females develop autoimmune disease, including juvenile idiopathic arthritis (JIA), yet the reason for this bias remains elusive. Evidence suggests that genetic risk of disease may be influenced by sex. PTPN22 rs2476601 is associated with JIA and numerous other autoimmune diseases, and has been reported to show female-specific association with type 1 diabetes. We performed main effect and sex-stratified association analyses to determine whether a sex-specific association exists in JIA. As expected, rs2476601 was associated with JIA in our discovery (413 cases and 690 controls) and replication (1008 cases and 9284 controls) samples. Discovery sample sex-stratified analyses demonstrated an association specifically in females (odds ratio (OR)=2.35, 95% confidence interval (CI)=1.52-3.63, P=0.00011) but not males (OR=0.91, 95% CI=0.52-1.60, P=0.75). This was similarly observed in the replication sample. There was evidence for genotype-by-sex interaction (Pinteraction=0.009). The association between rs2476601 and JIA appears restricted to females, partly accounting for the predominance of females with this disease.

Contemporary formulation and distribution practices for cold-filled acid products: Australian industry survey and modeling of published pathogen inactivation data.

A survey of 12 Australian manufacturers indicated that mild-tasting acids and preservatives are used to partially replace acetic acid in cold-filled acid dressings and sauces. In contrast to traditional ambient temperature distribution practices, some manufacturers indicated that they supply the food service sector with cold-filled acid products prechilled for incorporation into ready-to-eat foods. The Comité des Industries des Mayonnaises et Sauces Condimentaires de la Communauté Economique Européenne (CIMSCEE) Code, a formulation guideline used by the industry to predict the safety of cold-filled acid formulations with respect to Salmonella enterica and Escherichia coli, does not extend to the use of acids and preservatives other than acetic acid nor does it consider the effects of chill distribution. We found insufficient data in the published literature to comprehensively model the response of S. enterica and E. coli to all of the predictor variables (i.e., pH, acetic acid, NaCl, sugars, other acids, preservatives, and storage temperature) of relevance for contemporary cold-filled acid products in Australia. In particular, we noted a lack of inactivation data for S. enterica at aqueous-phase NaCl concentrations of >3% (wt/wt). However, our simple models clearly identified pH and 1/absolute temperature of storage as the most important variables generally determining inactivation. To develop robust models to predict the effect of contemporary formulation and storage variables on product safety, additional empirical data are required. Until such models are available, our results support challenge testing of cold-filled acid products to ascertain their safety, as suggested by the CIMSCEE, but suggest consideration of challenging with both E. coli and S. enterica at incubation temperatures relevant to intended product distribution temperatures.

Inactivation of Bacillus spores in reconstituted skim milk by combined high pressure and heat treatment.

AIMS: To determine the resistance of a variety of Bacillus species spores to a combined high pressure and heat treatment; and to determine the affect of varying sporulation and treatment conditions on the level of inactivation achieved. METHODS AND RESULTS: Spores from eight Bacillus species (40 isolates) were high pressure-heat treated at 600 MPa, 1 min, initial temperature 72 degrees C. The level of inactivation was broad (no inactivation to 6 log10 spores ml(-1) reduction) and it varied within species. Different sporulation agar, high pressure equipment and pressure-transmitting fluid significantly affected the response of some isolates. Varying the initial treatment temperature (75, 85 or 95 degrees C) shifted the relative order of isolate high pressure-heat resistance. CONCLUSIONS: The response of Bacillus spores to combined high pressure-heat treatment is variable and can be attributed to both intrinsic and extrinsic factors. The combined process resulted in a high level of spore inactivation for several Bacillus species and is a potential alternative treatment to traditional heat-only processes. SIGNIFICANCE AND IMPACT OF THE STUDY: Sporulation conditions, processing conditions and treatment temperature all affect the response of Bacillus spores to the combined treatment of high pressure and heat. High levels of spore inactivation can be achieved but the response is variable both within and between species.

Association and linkage for age at onset of a common oligogenic disease using genetic variance component models.

The aims of our analysis were: (1) to investigate association of single nucleotide polymorphisms (SNPs) and other covariates with age at onset in the simulated Genetic Analysis Workshop (GAW) 12 general population data, and (2) to use the polygenic random effects estimated during model fitting (sigma squared A random effects) as input to a Haseman-Elston linkage analysis. The association analyses used genetic variance component models in a generalized linear mixed models framework and were fitted using Gibbs sampling. This method successfully detected the only three sequenced genes that were also major genes. The single-point linkage analysis used all markers provided. Regions of linkage were found close to all four of the sites of major genes that explained a non-trivial component of the variance of age at onset. In all four cases the linkage peak fell within 5 cM of the true location. In three cases the peak significance was p < 0.01.

Genome-wide linkage analysis in a general population sample using sigma 2A random effects (SSARs) fitted by Gibbs sampling.

We used variance components analysis to investigate the underlying determinants of the quantitative phenotypes (Q1-Q5) and their interrelationships in replicate 42 of the Genetic Analysis Workshop 12 simulated general population. Variance components models were fitted using Gibbs sampling in WinBUGS v1.3. Sigma-squared-A-random-effects (SSARs) were estimated for each phenotype, and were used as derived phenotypes in subsequent linkage analyses. Whole-genome, multipoint linkage analyses were based upon a new Haseman-Elston identity-by descent sib-pair method that takes a weighted combination of the trait-sum and trait-difference. The five quantitative traits simulated were closely correlated with each other and with affection status. The whole-genome screen of quantitative traits associated with the simulated complex disease suggested that one or more major loci regulating Q1 localizes to chromosome 2p and that one or more major loci regulating Q5 may localize to chromosome 1p.

Variance components analysis for pedigree-based censored survival data using generalized linear mixed models (GLMMs) and Gibbs sampling in BUGS.

Complex human diseases are an increasingly important focus of genetic research. Many of the determinants of these diseases are unknown and there is often a strong residual covariance between relatives even when all known genetic and environmental factors have been taken into account. This must be modeled correctly whether scientific interest is focused on fixed effects, as in an association analysis, or on the covariance structure itself. Analysis is straightforward for multivariate normally distributed traits, but difficulties arise with other types of trait. Generalized linear mixed models (GLMMs) offer a potentially unifying approach to analysis for many classes of phenotype including right censored survival times. This includes age-at-onset and age-at-death data and a variety of other censored traits. Markov chain Monte Carlo (MCMC) methods, including Gibbs sampling, provide a convenient framework within which such GLMMs may be fitted. In this paper, we use BUGS ("Bayesian inference using Gibbs sampling": a readily available, generic Gibbs sampler) to fit GLMMs for right-censored survival times in nuclear and extended families. We discuss parameter interpretation and statistical inference, and show how to circumvent a number of important theoretical and practical problems. Using simulated data, we show that model parameters are consistent. We further illustrate our methods using data from an ongoing cohort study. Finally, we propose that the random effects associated with a genetic component of variance (e.g., sigma(2)(A)) in a GLMM may be regarded as an adjusted "phenotype" and used as input to a conventional model-based or model-free linkage analysis. This provides a simple way to conduct a linkage analysis for a trait reflected in a right-censored survival time while comprehensively adjusting for observed confounders at the level of the individual and latent environmental effects shared across families.

Survey for psychrotrophic bacterial pathogens in minimally processed lettuce.

A total of 120 minimally processed, cut and packaged lettuce samples were purchased from retail supermarkets or provided by a salad production facility over an 8-month period. The samples were tested for total aerobic plate counts and for the presence of potentially pathogenic species belonging to the genera of Listeria, Aeromonas and Yersinia. The aerobic plate counts ranged from 103 to 109 colony forming units (cfu) g-1. Most samples (76%) contained between 105 and 107 cfu g-1 total aerobic bacteria. Listeria monocytogenes was isolated from three samples, Aeromonas hydrophila or Aeromonas caviae from 66 samples, and Yersinia enterocolitica from 71 samples. The pathogenic potential of Y. enterocolitica isolates was determined by screening for an array of biochemical, serological and genetic traits (heat-stable enterotoxin gene, the attachment and invasion gene locus, the invasin gene locus and the virulence plasmid). The Y. enterocolitica isolates lacked many of the phenotypic and genetic markers associated with virulence in primary pathogenic strains. As the roles of the reputed virulence factors of Aeromonas spp. in human infection are uncertain, the pathogenic potential of the Aeromonas isolates in lettuce remains unclear.