Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

YesRecently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (alpha,beta,gamma,epsilon) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level

Associations between Dietary Fiber Intake in Infancy and Cardiometabolic Health at School Age: The Generation R Study

Dietary fiber (DF) intake may be beneficial for cardiometabolic health. However, whether this already occurs in early childhood is unclear. We investigated associations between DF intake in infancy and cardiometabolic health in childhood among 2032 children participating in a population-based cohort in The Netherlands. Information on DF intake at a median age of 12.9 months was collected using a food-frequency questionnaire. DF was adjusted for energy intake using the residual method. At age 6 years, body fat percentage, high-density lipoprotein (HDL)-cholesterol, insulin, triglycerides, and blood pressure were assessed and expressed in age- and sex-specific standard deviation scores (SDS). These five factors were combined into a cardiometabolic risk factor score. In models adjusted for several parental and child cova

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea

YesAssigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies.European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (ERC funded project no. 670518 LOST FRONTIE

Neighborhood Ethnic Diversity and Behavioral and Emotional Problems in 3 Year Olds: Results from the Generation R Study

Background:Studies suggest that neighborhood ethnic diversity may be important when it comes to understanding ethnic inequalities in mental health. The primary aim of this study was to investigate whether neighborhood ethnic diversity moderated the association between the ethnic minority status and child behavioral and emotional problems.Methods:We included 3076 preschoolers participating in the Generation R Study, a birth cohort study in Rotterdam, the Netherlands. At child age 3-years, parents completed the Child Behavior Checklist (CBCL/1,5-5). Individual-level data

Correlations in Cosmic String Networks

We investigate scaling and correlations of the energy and momentum in an evolving network of cosmic strings in Minkowski space. These quantities are of great interest, as they must be understood before accurate predictions for the power spectra of the perturbations in the matter and radiation in the early Universe can be made. We argue that Minkowski space provides a reasonable approximation to a Friedmann background for string dynamics and we use our results to construct a simple model of the network, in which it is considered to consist of randomly placed segments moving with random velocities. This model works well in accounting for features of the two-time correlation functions, and even better for the power spectra.Comment: 20pp Plain LaTeX, 11 EPS figures, uses epsf.st

Diet quality in childhood: the Generation R Study

Purpose: We aimed to evaluate diet quality of 8-year-old children in the Netherlands, to identify sociodemographic and lifestyle correlates of child diet quality, and to examine tracking of diet quality from ea

Longitudinal association between preschool fussy eating and body composition at 6 years of age: The Generation R Study

Background: Children's fussy eating behavior has been related to both underweight and overweight in cross-sectional studies, but the direction of these associations and the relation with more detailed measures of body composition remains unclear. We aimed to examine whether fussy eating at age 4 years is longitudinally related to body mass index (BMI), fat mass index (FMI) and fat-free mass index (FFMI) at 6 years of age. Methods: This study was embedded in Generation R, a population-based, prospective cohort. Data were available for 4191 children. The Children's Eating Behaviour Questionnaire (CEBQ), administered at age 4 years, was used to derive a fussy eating profile. This profile is characterized by high scores on food avoidant scales and low scores on food approach scales. At age 6 years, height and weight were measured at our research center. Body fat and fat-free mass were measured using Dual-energy-X-ray absorptiometry. We used age- and sex-specific standard deviation scores (SDS) for all outcomes. Results: After adjustment for confounders, the fussy eating profile was related to lower BMI-SDS (B=-0.37, 95 % CI: -0.47;-0.26), lower FMI-SDS (B=-0.22, 95 % CI: -0.33;-0.12) and lower FFMI-SDS (B=-0.41, 95 % CI: -0.54;-0.29). When adjusting for baseline BMI at 4 years, the fussy eating profile predicted a 0.11 lower BMI-SDS at age 6 (95 % CI: -0.19;-0.04). This change in BMI was mainly due to a decrease in FFMI (B=-0.19, 95 % CI: -0.29;-0.09). Fussy eaters also had a higher risk of becoming underweight than non-fussy eaters (OR=2.28, 95 % CI: 1.34;3.87). Conclusions: Our findings suggest that young fussy eaters are at risk of having a lower fat free mass and of becoming underweight over a 2-year period. This implies that fussy eaters may benefit from careful monitoring to prevent an adverse growth development

Low serum vitamin D is associated with axial length and risk of myopia in young children

The aim of the study was to investigate the relationship between serum 25(OH)D levels and axial length (AL) and myopia in 6-year-old children. A total of 2666 children aged 6 years participating in the birth-cohort study Generation R underwent a stepwise eye examination. First, presenting visual acuity (VA) and AL were performed. Second, automated cycloplegic refraction was measured if LogMAR VA > 0.1. Serum 25-hydroxyvitamin D [25(OH)D] was determined from blood using liquid chromatography/tandem mass spectrometry. Vitamin D related SNPs were determined with a SNP array; outdoor exposure was assessed by questionnaire. The relationships between 25(OH)D and AL or myopia were investigated using linear and logistic regression analysis. Average 25(OH)D concentration was 68.8 nmol/L (SD ± 27.5; range 4–211); average AL 22.35 mm (SD ± 0.7; range 19.2–25.3); and prevalence of myopia 2.3 % (n = 62). After adjustment for covariates, 25(OH)D concentration (per 25 nmol/L) was inversely associated with AL (β −0.043; P < 0.01), and after additional adjusting for time spent outdoors (β −0.038; P < 0.01). Associations were not different between European and non-European children (β −0.037 and β −0.039 respectively). Risk of myopia (per 25 nmol/L) was OR 0.65 (95 % CI 0.46–0.92). None of the 25(OH)D related SNPs showed an association with AL or myopia. Lower 25(OH)D concentration in serum was associated with longer AL and a higher risk of myopia in these young children. This effect appeared independent of outdoor exposure and may suggest a more direct role for 25(OH)D in myopia pathogenesis

Protein intake in infancy and kidney size and function at the age of 6 years: The Generation R Study

Background: High protein intake has been linked to kidney growth and function. Whether protein intake is related to kidney outcomes in healthy children is unclear. Methods: We examined the associations between protein intake in infancy and kidney outcomes at age 6 years in 2968 children participating in a population-based cohort study. Protein intake at 1 year was assessed using a food-frequency questionnaire and was adjusted for energy intake. At age 6 years we measured the kidney volume and urinary albumin/creatinine ratio (ACR) of all participating children, and we estimated glomerular filtration rate (eGFR) using serum creatinine and cystatin C levels. Results: In models adjusted for age, sex, body surface area, and sociodemographic factors, a higher protein intake was associated with a lower ACR and a higher eGFR but was not consistently associated with kidney volume. However, after further adjustment for additional dietary and lifestyle factors, such as sodium intake, diet quality, and television watching, higher protein intake was no longer associated with kidney function. No differences in associations were observed between animal and vegetable protein intake. Conclusions: Our findings show that protein intake in early childhood is not independently associated with kidney size or function at the age of 6 years. Further study is needed on other early life predictors of kidney size and function in later life

Validation of a semi-quantitative food-frequency questionnaire for dutch pregnant women from the general population using the method or triads

Objective: We aimed to validate a food-frequency questionnaire (FFQ) for Dutch pregnant women, against three 24 h-recalls and blood concentrations of B-vitamins and fatty acids, using the method of triads. Methods: We included 83 pregnant women from the general population of Rotterdam, the Netherlands, at a median gestational age of 15.6 weeks. Participants completed three non-consecutive 24 h-recalls, and subsequently filled out the 293-item FFQ. Participants provided blood samples from which we analyzed serum folate and vitamin B12, as well as red blood cell folate, linoleic acid, and total saturated, monounsaturated, and polyunsaturated fatty acids. Results: Estimated energy intake did not differ between the FFQ and 24 h-recalls. Deattenuated Pearson’s correlation coefficients, between energy-adjusted nutrient intake estimates from the FFQ and the 24 h-recalls, ranged from 0.41 (fat) to 0.88 (fiber) for macronutrients, and were around 0.6 for most micronutrients, except for vitamin E (0.27). Using the triad method, we obtained validity coefficients of 0.86 (95% Confidence Interval (CI) 0.36, 1.00) for serum folate, 0.86 (95% CI 0.18, 1.00) for red blood cell folate, and 1.00 (95% CI 0.42, 1.00) for vitamin B12. Validity coefficients for serum fatty acids ranged from 0.22 to 0.67. Conclusion: This FFQ is a reliable tool for estimating intake of energy, macronutrients, folate and vitamin B1