This study presents refined epigenetic clocks for cetaceans, building on previous research that estimated ages in several species from bottlenose dolphins to bowhead and humpback whales using cytosine methylation levels. We combined publicly available data (generated on the HorvathMammalMethylChip40 platform) from skin (n = 805) and blood (n = 286) samples across 13 cetacean species, aged 0 to 139 years. By combining methylation data from different sources, we enhanced our sample size, thereby strengthening the statistical validity of our clocks. We used elastic net regression with leave one sample out (LOO) and leave one species out (LOSO) cross validation to produce highly accurate blood only (Median Absolute Error [MAE] = 1.64 years, r = 0.96), skin only (MAE = 2.32 years, r = 0.94) and blood and skin multi-tissue (MAE = 2.24 years, r = 0.94) clocks. In addition, the LOSO blood and skin (MAE = 5.6 years, repeated measures r = 0.83), skin only (MAE = 6.22 years, repeated measures r = 0.81), and blood only (MAE = 4.11 years, repeated measures r = 0.95) clock analysis demonstrated relatively high correlation toward cetacean species not included within this current data set and provide evidence for a broader application of this model. Our results introduce a multi-species, two-tissue clock for broader applicability across cetaceans, alongside single-tissue multi-species clocks for blood and skin, which allow for more detailed aging analysis depending on the availability of samples. In addition, we developed species-specific clocks for enhanced precision, resulting in four blood-specific clocks and eight skin-specific clocks for individual species; all improving upon existing accuracy estimates for previously published species-specific clocks. By pooling methylation data from various studies, we increased our sample size, significantly enhancing the statistical power for building accurate clocks. These new epigenetic age estimators for cetaceans provide more accurate tools for aiding in conservation efforts of endangered cetaceans.

We describe a framework that addresses concern that the rate of change in any aging biomarker displays a trivial inverse relation with maximum lifespan. We apply this framework to methylation data from the Mammalian Methylation Consortium. We study the relationship of lifespan with the average rate of change in methylation (AROCM) from two datasets: one with 90 dog breeds and the other with 125 mammalian species. After examining 54 chromatin states, we conclude three key findings: First, a reciprocal relationship exists between the AROCM in bivalent promoter regions and maximum mammalian lifespan: AROCM ∝ 1/MaxLifespan. Second, the correlation between average methylation and age bears no relation to maximum lifespan, Cor(Methyl,Age) ⊥ MaxLifespan. Third, the rate of methylation change in young animals is related to that in old animals: Young animals AROCM ∝ Old AROCM. These findings critically hinge on the chromatin context, as different results emerge in other chromatin contexts.

© 2015, Shiraz University of Medical Sciences. All right reserved.Introduction: Oral intake of vitamins which present antioxidant characteristics can protect living organisms against oxidative damage caused by exposure to ionizing radiation. It was previou

DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscus clocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude in Peromyscus. The human-Peromyscus epigenetic clocks are expected to provide a significant boost to the attractiveness of Peromyscus as a biological model.

Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Although these human epigenetic clocks are not immediately applicable to all species of the animal kingdom, the principles underpinning them appear to be conserved even in animals that are evolutionarily far removed from humans. This is exemplified by recent development of epigenetic clocks for mice and other mammalian species. Here, we describe epigenetic clocks for the domestic cat (Felis catus), based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs are measured using a custom-designed Infinium array (HorvathMammalMethylChip40). From these, we present 3 epigenetic clocks for cats; of which, one applies only to blood samples from cats, while the remaining two dual-species human-cat clocks apply both to cats and humans. We demonstrate that these domestic cat clocks also lead to high age correlations in cheetahs, tigers, and lions. It is expected that these epigenetic clocks for cats possess the potential to be further developed for monitoring feline health as well as being used for identifying and validating anti-aging interventions.

Human DNA methylation data have previously been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Subsequent studies demonstrate that similar epigenetic clocks can also be developed for mice and many other mammals. Here, we describe epigenetic clocks for common marmosets (Callithrix jacchus) based on novel DNA methylation data generated from highly conserved mammalian CpGs that were profiled using a custom Infinium array (HorvathMammalMethylChip40). From these, we developed and present here two epigenetic clocks for marmosets that are applicable to whole blood samples. We find that the human-marmoset clock for relative age exhibits moderately high age correlations in two other non-human primate species: vervet monkeys and rhesus macaques. In a separate cohort of marmosets, we tested whether intervention with rapamycin, a drug shown to extend lifespan in mice, would alter the epigenetic age of marmosets, as measured by the marmoset epigenetic clocks. These clocks did not detect significant effects of rapamycin on the epigenetic age of marmoset blood. The common marmoset stands out from other mammals in that it is not possible to build accurate estimators of sex based on DNA methylation data: the accuracy of a random forest predictor of sex (66%) was substantially lower than that observed for other mammals (which is close to 100%). Overall, the epigenetic clocks developed here for the common marmoset are expected to be useful for age estimation of wild-born animals and for anti-aging studies in this species.

Age determination of wild animals, including pinnipeds, is critical for accurate population assessment and management. For most pinnipeds, current age estimation methodologies utilize tooth or bone sectioning which makes antemortem estimations problematic. We leveraged recent advances in the development of epigenetic age estimators (epigenetic clocks) to develop highly accurate pinniped epigenetic clocks. For clock development, we applied the mammalian methylation array to profile 37,492 cytosine-guanine sites (CpGs) across highly conserved stretches of DNA in blood and skin samples (n = 171) from primarily three pinniped species representing the three phylogenetic families: Otariidae, Phocidae and Odobenidae. We built an elastic net model with Leave-One-Out-Cross Validation (LOOCV) and one with a Leave-One-Species-Out-Cross-Validation (LOSOCV). After identifying the top 30 CpGs, the LOOCV produced a highly correlated (r = 0.95) and accurate (median absolute error = 1.7 years) age estimation clock. The LOSOCV elastic net results indicated that blood and skin clock (r = 0.84) and blood (r = 0.88) pinniped clocks could predict age of animals from pinniped species not used for clock development to within 3.6 and 4.4 years, respectively. These epigenetic clocks provide an improved and relatively non-invasive tool to determine age in skin or blood samples from all pinniped species.

Cytosine methylation patterns have not yet been thoroughly studied in horses. Here, we profile n = 333 samples from 42 horse tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). Using the blood and liver tissues from horses, we develop five epigenetic aging clocks: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. In addition, using blood methylation data from three additional equid species (plains zebra, Grevy's zebras and Somali asses), we develop another clock that applies across all equid species. Castration does not significantly impact the epigenetic aging rate of blood or liver samples from horses. Methylation and RNA data from the same tissues define the relationship between methylation and RNA expression across horse tissues. We expect that the multi-tissue atlas will become a valuable resource.

Introduction: Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic vegetable production. However, there is a risk of foodborne pathogen transfer to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may subsequently be transferred to the produce. Methods: To examine the effect of cover crop use and the risk of cover crop grazing on the contamination of soil and produce by foodborne pathogens in ICLS, a three-year (2019–2021) experimental study was conducted in organically managed plots, which were assigned three different treatments (fallow without cover crop or grazing, cover crop without grazing, or cover crop with grazing by sheep) in a maize/tomato rotation. During the three years of the experiment, a total of 184 pre- and post-graze fecal samples and 96 samples of tomatoes were collected to test for foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria (L.) monocytogenes). Soil samples were collected monthly until 126–171 days after grazing (824 in total) to examine the presence of foodborne pathogens, and generic E. coli (MPN/g) was quantified to compare its persistence among the three treatments. Results and Discussion: We did not detect any foodborne pathogens from harvested tomatoes in 2020 and 2021. One non-O157 STEC positive soil sample (0.1%, 1/824) was detected in the fallow treatment, and one L. monocytogenes-positive (1.1%, 1/92) was detected from the post-graze fecal samples. When assessing proportions of generic E. coli positive and counts of generic E. coli in the soil samples using mixed effect zero-inflated negative binomial models, soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61–82 days post grazing, but no difference was observed after 96–123 days, compared to the baseline of the fallow treatment. Findings from generic E. coli counts support the use of the United States Department of Agriculture (USDA) National Organic Program (NOP) 90- or 120-day interval rule between applying raw manure and harvesting in organic farming into ICLS. Additionally, we confirmed that commercial organic compost application before cover crop seeding in the winter had no significant effect on the proportions and counts of generic E. coli in the soil of the following growing seasons. This longitudinal field trial confirmed that the effect of sheep grazing on foodborne pathogen contamination in ICLS is minimal but further studies comparing the genetic associations between fecal and soil samples would be necessary to distinguish the source of foodborne pathogen contamination.