The CALERIE™ Genomic Data Resource.

Caloric restriction (CR) slows biological aging and prolongs healthy lifespan in model organisms. Findings from CALERIE-2™ - the first ever randomized, controlled trial of long-term CR in healthy, non-obese humans - broadly supports a similar pattern of effects in humans. To expand our understanding of the molecular pathways and biological processes underpinning CR effects in humans, we generated a series of genomic datasets from stored biospecimens collected from n=218 participants during the trial. These data constitute the first publicly-accessible genomic data resource for a randomized controlled trial of an intervention targeting the biology of aging. Datasets include whole-genome SNP genotypes, and three-timepoint-longitudinal DNA methylation, mRNA, and small RNA datasets generated from blood, skeletal muscle, and adipose tissue samples (total sample n=2327). The CALERIE Genomic Data Resource described in this article is available from the Aging Research Biobank. This mult-itissue, multi-omic, longitudinal data resource has great potential to advance translational geroscience.

Adiposity associated DNA methylation signatures in adolescents are related to leptin and perinatal factors.

Epigenetics links perinatal influences with later obesity. We identifed differentially methylated CpG (dmCpG) loci measured at 17 years associated with concurrent adiposity measures and examined whether these were associated with hsCRP, adipokines, and early life environmental factors. Genome-wide DNA methylation from 1192 Raine Study participants at 17 years, identified 29 dmCpGs (Bonferroni corrected p < 1.06E-07) associated with body mass index (BMI), 10 with waist circumference (WC) and 9 with subcutaneous fat thickness. DmCpGs within Ras Association (RalGDS/AF-6), Pleckstrin Homology Domains 1 (RAPH1), Musashi RNA-Binding Protein 2 (MSI2), and solute carrier family 25 member 10 (SLC25A10) are associated with both BMI and WC. Validation by pyrosequencing confirmed these associations and showed that MSI2 , SLC25A10 , and RAPH1 methylation was positively associated with serum leptin. These were  also associated with the early environment; MSI2 methylation (ß = 0.81, p = 0.0004) was associated with pregnancy maternal smoking, SLC25A10 (CpG2 ß = 0.12, p = 0.002) with pre- and early pregnancy BMI, and RAPH1 (ß = -1.49, p = 0.036) with gestational weight gain. Adjusting for perinatal factors, methylation of the dmCpGs within MSI2, RAPH1, and SLC25A10 independently predicted BMI, accounting for 24% of variance. MSI2 methylation was additionally associated with BMI over time (17 years old ß = 0.026, p = 0.0025; 20 years old ß = 0.027, p = 0.0029) and between generations (mother ß = 0.044, p = 7.5e-04). Overall findings suggest that DNA methylation in MSI2, RAPH1, and SLC25A10 in blood may be robust markers, mediating through early life factors.

Use of a maltodextrin-based feed with a lysozyme product to alter bacterial in the ileum of market-aged broilers.

Poultry meats can become contaminated with pathogenic bacteria through digesta leakage during processing. Reducing the bacteria load in digesta of market-aged broilers prior to processing reduces the incidence of fecal contamination at the processing plant. A lysozyme product was incorporated in a maltodextrin-based feed offered during the pre-shipping feed withdrawal period to reduce bacteria in ileal contents of market-aged broilers. Twenty 36-day-old broilers were randomly allocated to each of 16 pens. For a 9 h period each pen was randomly assigned to one of the following treatments: no feed, maltodextrin-based feed with a lysozyme product (Inovapure) added at 0, 10, or 20 g per kg of feed. Feed consumption was determined and a minimum of 3 birds were randomly selected from each pen and euthanized. The ileal contents were removed and weighed. Samples were analyzed for Clostridium perfringens, aerobic bacteria, Enterobacteriaceae, E. coli, and coliform numbers using standard culturing techniques and next generation sequencing was performed to determine population shifts. Bacteria counts were transformed to log10 colony forming units (cfu) and analyzed as a completely randomized design. The data from next generation sequencing was analyzed as a 3 × 5 factorial design using Proc Mixed of SAS. Lysozyme did not affect feed consumption nor were the weight of ileal contents different for birds fed maltodextrin-based feeds compared to birds on traditional feed withdrawal. E. coli/coliforms and Enterobacteriaceae plates had no signs of bacterial growth. The number of Clostridium perfringens and aerobic bacteria in the ileal contents of market-aged broilers was not different between treatments using the traditional culturing techniques. Next generation sequencing was a useful alternative to traditional culture techniques as results revealed that bacilli were reduced and clostridia increased for the 20 g lysozyme treatment. Addition of lysozyme to a maltodextrin based feed did not change overall numbers of bacteria but was effective in altering the participants in the bacteria community in ileal contents of market-aged broilers.

Blood and nasal epigenetics correlate with allergic rhinitis symptom development in the environmental exposure unit.

BACKGROUND: Epigenetic alterations may represent new therapeutic targets and/or biomarkers of allergic rhinitis (AR). Our aim was to examine genome-wide epigenetic changes induced by controlled pollen exposure in the environmental exposure unit (EEU). METHODS: 38 AR sufferers and eight nonallergic controls were exposed to grass pollen for 3 hours on two consecutive days. We interrogated DNA methylation at baseline and 3 hours in peripheral blood mononuclear cells (PBMCs) using the Infinium Methylation 450K array. We corrected for demographics, cell composition, and multiple testing (Benjamini-Hochberg) and verified hits using bisulfite PCR pyrosequencing and qPCR. To extend these findings to a clinically relevant tissue, we investigated DNA methylation and gene expression of mucin 4 (MUC4), in nasal brushings from a separate validation cohort exposed to birch pollen. RESULTS: In PBMCs of allergic rhinitis participants, 42 sites showed significant DNA methylation changes of 2% or greater. DNA methylation changes in tryptase gamma 1 (TPSG1), schlafen 12 (SLFN12), and MUC4 in response to exposure were validated by pyrosequencing. SLFN12 DNA methylation significantly correlated with symptoms (P < 0.05), and baseline DNA methylation pattern was found to be predictive of symptom severity upon grass allergen exposure (P = 0.029). Changes in MUC4 DNA methylation in nasal brushings in the validation cohort correlated with drop in peak nasal inspiratory flow (Spearman's r = 0.314, P = 0.034), and MUC4 gene expression was significantly increased (P < 0.0001). CONCLUSION: This study revealed novel and rapid epigenetic changes upon exposure in a controlled allergen challenge facility, and identified baseline epigenetic status as a predictor of symptom severity.

Accelerated DNA methylation age in adolescent girls: associations with elevated diurnal cortisol and reduced hippocampal volume.

Numerous studies have linked exposure to stress to adverse health outcomes through the effects of cortisol, a product of the stress response system, on cellular aging processes. Accelerated DNA methylation age is a promising epigenetic marker associated with stress and disease risk that may constitute a link from stress response to changes in neural structures. Specifically, elevated glucocorticoid signaling likely contributes to accelerating DNA methylation age, which may signify a maladaptive stress-related cascade that leads to hippocampal atrophy. We examined the relations among diurnal cortisol levels, DNA methylation age and hippocampal volume in a longitudinal study of 46 adolescent girls. We computed area under the curve from two daily cortisol collection periods, and calculated DNA methylation age using previously established methods based on a set of CpG sites associated with chronological age. We computed a residual score by partialling out chronological age; higher discrepancies reflect relatively accelerated DNA methylation age. We assessed hippocampal volume via T1-weighted images and automated volumetric segmentation. We found that greater diurnal cortisol production was associated with accelerated DNA methylation age, which in turn was associated with reduced left hippocampal volume. Finally, accelerated DNA methylation age significantly mediated the association between diurnal cortisol and left hippocampal volume. Thus, accelerated DNA methylation age may be an epigenetic marker linking hypothalamic-pituitary-adrenal axis dysregulation with neural structure. If these findings are replicated, the current study provides a method for advancing our understanding of mechanisms by which glucocorticoid signaling is associated with cellular aging and brain development.

The Added Value of Exercise Variables in Heart Failure Prognosis.

INTRODUCTION: Diminished exercise capacity is a key symptom in heart failure (HF). Exercise predictors (peak VO2, VE/VCO2 slope, and oxygen uptake efficiency slope [OUES]) are prognostic markers but studied in isolation. We evaluated if these exercise variables offer additional prognostic value to clinical predictors in HF. METHODS AND RESULTS: This was a single-institution retrospective cohort study of 517 consecutive HF patients. We used Cox proportional hazards modeling to determine the additional prognostic value of exercise variables on mortality, HF hospital admissions, and a composite outcome of ventricular assistance device (VAD) implantation, heart transplantation (HT), and death. During a mean follow-up of 2.7 years, 52 deaths, 47 HTs, and 19 VAD implantations occurred. After adjusting for age, New York Heart Association functional class, ejection fraction, body mass index, creatinine, and B-type natriuretic peptide, peak VO2 (hazard ratio [HR] 0.91, 95% confidence interval [CI] 0.85-0.96), OUES (HR 0.92, 95% CI 0.87-0.97), and VE/VCO2 (HR 1.03, 95% CI 1.01-1.05) were independent predictors of the composite outcome. Similar discriminatory capacity existed between the exercise variables (c-statistics 0.77, 0.78, and 0.78, respectively). Only VE/VCO2 was an independent predictor of admissions (HR 1.04, 95% CI 1.01-1.07), and only peak VO2 was an independent predictor of mortality (HR 0.90, 95% CI 0.84-0.98). CONCLUSIONS: Peak VO2, OUES, and VE/VCO2 are independent predictors of HF prognosis over recognized clinical variables. However, no single exercise variable was superior.

Low birth weight associates with hippocampal gene expression.

Birth weight predicts the lifetime risk for psychopathology suggesting that the quality of fetal development influences the predisposition for mental disorders. The connectivity and synaptic network of the hippocampus are implicated in depression, schizophrenia and anxiety. We thus examined the underlying molecular adaptations in the hippocampus as a function of the fetal conditions associated with low birth weight. We used tissues from the non-human primate, Macaca fascicularis, to identify changes in hippocampal gene expression early in postnatal development associated with naturally occurring low compared with normal birth weight. Microarrays were used to analyze gene expression and DNA methylation in the hippocampus of five low- and five normal-birth weight neonates. Real-time PCR was employed to validate differentially expressed genes. Birth weight associated with altered global transcription in the hippocampus. Hierarchical clustering of gene expression profiles from 24,154 probe sets grouped all samples except one by their birth weight status. Differentially expressed genes were enriched in biological processes associated with neuronal projection, positive regulation of transcription and apoptosis. About 4% of the genes with differential expression co-varied with DNA methylation levels. The data suggest that low birth weight is closely associated with hippocampal gene expression with a small epigenetic underpinning by DNA methylation in neonates. The data also provide a potential molecular basis for the developmental origin of an enhanced risk for mental disorders.

Evaluating by-products of the Atlantic shellfish industry as alternative feed ingredients for laying hens.

A full-cycle laying hen study was conducted to evaluate crab meal (CM) and lobster meal (LM) as feed ingredients for laying hens by assigning four hundred thirty-two 35-wk-old White Leghorns to 1 of 6 diets [control, 2.5% CM, 2.5% LM, 5% CM, 5% LM, and 2.5% CM + 2.5% LM (blend)]. Productive performance and egg parameters were evaluated every 28-d period. Eggs were collected at 67 wk of age from the 5% CM, 5% LM, and blend treatments for analysis of yolk fatty acid composition. At 55 and 67 wk of age, ulnas were collected to determine breaking strength, percent ash, and calcium. Body weights, feed consumption, hen-day production, feed efficiency, and egg quality were not affected (P > 0.05) by treatment. The L* scores of eggs from 5% CM, 5% LM, and blend were lower (P < 0.05) than eggs from the control by the end of the second 28-d period. The a* score of the eggs from 5% CM, 5% LM, and blend was higher (P < 0.05) than the control by the end of the first 28-d period. The content of docosahexaenoic acid (DHA) in egg yolks was different (P < 0.05) among the control (0.17 g/100 g), 5% CM (0.46 g/100 g), 5% LM (0.32 g/100 g), and blend (0.38 g/100 g) treatments. Treatment did not affect (P > 0.05) any of the bone parameters measured at 55 and 67 wk of age. CM and LM supported similar egg production, feed efficiency, egg yolk color, adequate bone strength, and the incorporation of DHA into egg yolks.

Color and fatty acid profile of abdominal fat pads from broiler chickens fed lobster meal.

Consumer demands for food products enriched with healthful n-3 fatty acids are steadily increasing. Feeding marine byproducts may provide an economical means of increasing the long-chain n-3 content of broiler tissues. A study was conducted to evaluate the effect of dietary lobster meal (LM) on the color and fatty acid profile of broiler chicken fatty tissue. Broilers were fed increasing levels (0, 2, 4, 6, 8, and 10%) of LM for 35 d. Fat pad samples were collected at slaughter and color and fatty acid concentrations were determined. A linear effect was found of LM on red coloration (P < 0.05) as dietary LM increased. Fat pad eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) levels also increased (P < 0.0001) in a linear fashion. The essential long-chain fatty acids were lower for the 10% LM diet (0.37 mg of EPA/g; 0.16 mg of DHA/g) compared with the 8% LM diet (0.51 mg of EPA/g; 0.27 mg of DHA/g). Using lobster meal as a feed ingredient resulted in broiler abdominal fat pads with a favorable increase in n-3 fatty acids.

The effect of calcium source and particle size on the production performance and bone quality of laying hens.

The efficacy of 3 local limestone sources as potential Ca sources for laying hens was studied. Limestone sources were assessed for in vitro solubility. Four Ca sources (control, A, B, or C) and 2 particle size combinations (ground, 100% ground; or mixed, 67% ground+33% large particle) was used. The control consisted of a commercial ground limestone for the ground Ca source and oyster shell of the large particle Ca source. DeKalb laying hens were randomly placed in 32 battery cage units (n=12/cage). At 19 wk of age, hens received 1 of 8 Ca source and particle size treatments (4 replicates/treatment) until 74 wk. Egg production, feed consumption, BW, and egg quality were measured throughout. Bone mineral density (by quantitative computed tomography), breaking strength, ash, and Ca were assessed at the end of lay. In vitro solubility was dependent upon Ca source and particle size (P<0.0001) with oyster shell generally having a greater in vitro solubility than test limestone sources A, B, and C of similar particle sizes. Feed consumption (100 to 117 g/bird per day), BW (1,500 to 1,800 g), egg production (92% peak egg production), egg weight (55 to 67 g), and egg specific gravity (1.090 to 1.078) did not differ among hens fed the different Ca sources (P>0.05). Tibia bone mineral density indicated the oyster shell treatment had a lower trabecular density than Ca source A; however, all other Ca sources had similar bone mineral density for all measures (P>0.05). Hens fed the mixed Ca particle treatments consistently had greater feed consumption from 27 to 70 wk than those fed the 100% ground Ca source (P<0.05). Bone mineralization was enhanced in hens that received the mixed Ca particle treatments (P<0.05). Overall, the results of this study indicate that the local limestone sources A, B, and C would be suitable alternatives to current commercial sources of Ca for laying hens. In addition, large particle Ca did improve bone quality.

The stress and fear levels of microwave toe-treated broiler chickens grown with two photoperiod programs.

The current study was conducted to investigate the influence of microwave toe treatment and an increasing photoperiod on stress and fear levels in broiler chickens. Upon delivery from the hatchery, the toe tips of 364 male and 364 female broilers were exposed to microwave energy to restrict claw growth, whereas the same numbers of birds retained intact toes. Birds from each sex and toe treatment were grown under 23 h of light or increasing photoperiods, with 4 replicates of each treatment combination. Elevated activity of plasma creatine kinase (CK) and increased heterophil to lymphocyte (H/L) ratios were employed as indicators of stress. Tonic immobility (TI) was conducted on d 10, 22, and 36 and used as an index of fear response. Males had lower plasma CK activity and H/L ratios (P < 0.05). Birds on 23 h of light had a higher activity of plasma CK (P < 0.05) but similar H/L ratios compared with birds on the increasing photoperiod. Microwave toe treatment did not affect the activity of plasma CK or H/L ratios. Photoperiod, microwave toe treatment, or sex did not affect the number of attempts required to induce TI. The increasing lighting program decreased the duration of TI on d 10 (P < 0.05), had no effect on d 22, and increased duration of TI on d 36 (P < 0.05). There was no microwave toe treatment or sex effect on the duration of TI at any ages tested.

Feeding turkeys a highly digestible supplement during preslaughter feed withdrawal.

Standard commercial practice is to deny poultry access to feed 8 to 12 h prior to slaughter. Occasionally a flock of turkeys is marketed at several ages, and starvation can occur for birds that are not shipped. For this project multiple marketed female turkeys were fed a special diet (nutritive supplement) during the preslaughter feed withdrawal period to reduce live weight loss, bird stress, and grazing on manure. Three trials were conducted at the Nova Scotia Agricultural College using 60 female turkey poults for each of 8 pens for each trial. The birds were separated into 8 pens with 20 birds from half of the pens shipped at 63 d of age and all remaining birds shipped 1 wk later. Prior to shipping, feed was withdrawn, with half the pens receiving the supplement. The pens that had received supplement at 63 d of age received it again a week later along with half the pens not previously marketed. The supplement was only consumed in a significant quantity when it was new to the birds (~10 g/kg of bird). The carcass yield, based on the live weight before the conventional feed withdrawal period, was improved for birds that consumed the supplement. Microbiological profiles of the crops revealed that although the total number aerobic bacteria was not affected, birds ingesting the supplement had fewer Escherichia coli and coliforms present. Breast meat samples collected at 15 min postmortem and 24 h postmortem and measured for pH were not found to be different between the treatments. Because birds would only consume the supplement on the first exposure, this supplement is only effective for reducing live weight loss and microbial load of the crop in an all-in all-out management situation.