Increased scalability and sequencing quality of an epigenetic age prediction assay

Epigenetic ageing in a human context, has been used to better understand the relationship between age and factors such as lifestyle and genetics. In an ecological setting, it has been used to predict the age of individual animals for wildlife management. Despite the importance of epigenetic ageing in a range of research fields, the assays to measure epigenetic ageing are either expensive on a large scale or complex. In this study, we aimed to improve the efficiency and sequencing quality of an existing epigenetic ageing assay for the Australian Lungfish (Neoceratodus forsteri). We used an enzyme-based alternative to bisulfite conversion to reduce DNA fragmentation and evaluated its performance relative to bisulfite conversion. We found the sequencing quality to be 12% higher with the enzymatic alternative compared to bisulfite treatment (p-value < 0.01). This new enzymatic based approach, although currently double the cost of bisulfite treatment can increases the throughput and sequencing quality. We envisage this assay setup being adopted increasingly as the scope and scale of epigenetic ageing research continues to grow.

Calibrating epigenetic clocks with training data error

Animal age data are valuable for management of wildlife populations. Yet, for most species, there is no practical method for determining the age of unknown individuals. However, epigenetic clocks, a molecular-based method, are capable of age prediction by sampling specific tissue types and measuring DNA methylation levels at specific loci. Developing an epigenetic clock requires a large number of samples from animals of known ages. For most species, there are no individuals whose exact ages are known, making epigenetic clock calibration inaccurate or impossible. For many epigenetic clocks, calibration samples with inaccurate age estimates introduce a degree of error to epigenetic clock calibration. In this study, we investigated how much error in the training data set of an epigenetic clock can be tolerated before it resulted in an unacceptable increase in error for age prediction. Using four publicly available data sets, we artificially increased the training data age error by iterations of 1% and then tested the model against an independent set of known ages. A small effect size increase (Cohen's d >0.2) was detected when the error in age was higher than 22%. The effect size increased linearly with age error. This threshold was independent of sample size. Downstream applications for age data may have a more important role in deciding how much error can be tolerated for age prediction. If highly precise age estimates are required, then it may be futile to embark on the development of an epigenetic clock when there is no accurately aged calibration population to work with. However, for other problems, such as determining the relative age order of pairs of individuals, a lower-quality calibration data set may be adequate.

Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation

Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species' distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.

Fish species lifespan prediction from promoter cytosine-phosphate-guanine density

Lifespan is a key attribute of a species' life cycle and varies extensively among major lineages of animals. In fish, lifespan varies by several orders of magnitude, with reported values ranging from less than 1 year to approximately 400 years. Lifespan information is particularly useful for species management, as it can be used to estimate invasion potential, extinction risk and sustainable harvest rates. Despite its utility, lifespan is unknown for most fish species. This is due to the difficulties associated with accurately identifying the oldest individual(s) of a given species, and/or deriving lifespan estimates that are representative for an entire species. Recently it has been shown that CpG density in gene promoter regions can be used to predict lifespan in mammals and other vertebrates, with variable accuracy across taxa. To improve accuracy of lifespan prediction in a non-mammalian vertebrate group, here we develop a fish-specific genomic lifespan predictor. Our new model includes more than eight times the number of fish species included in the previous vertebrate model (n = 442) and uses fish-specific gene promoters as reference sequences. The model predicts fish lifespan from genomic CpG density alone (measured as CpG observed/expected ratio), explaining 64% of the variance between known and predicted lifespans. The predictions are highly robust to variation in genome quality and are applicable to all classes of fish; a taxonomically diverse and speciose group. The results demonstrate the value of promoter CpG density as a universal predictor of fish lifespan that can applied where empirical data are unavailable, or impracticable to obtain.

Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod

Age‐based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life‐history parameters such as length, maturity, mortality and fecundity. These age‐based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age‐associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochellapeelii) and Mary River cod (Maccullochellamariensis). Age estimation models were calibrated using either known‐age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.

Optimal sample size for calibrating DNA methylation age estimators

Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.

A DNA methylation age predictor for zebrafish

Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequencing method to obtain a DNA methylation level, which makes it costly to deploy as an assay to estimate age in many samples. Here, we have generated a reduced representation bisulfite sequencing data set of caudal fin tissue from a model fish species, zebrafish (Danio rerio), aged from 11.9-60.1 weeks. We identified changes in methylation at specific CpG sites that correlated strongly with increasing age. Using an optimised unique set of 26 CpG sites we developed a multiplex PCR assay that predicts age with an average median absolute error rate of 3.2 weeks in zebrafish between 10.9-78.1 weeks of age. We also demonstrate the use of multiplex PCR as an efficient quantitative approach to measure DNA methylation for the use of age estimation. This study highlights the potential further use of DNA methylation as an age estimation method in non-mammalian vertebrate species.

Lifespan estimation in marine turtles using genomic promoter CpG density

Maximum lifespan for most animal species is difficult to define. This is challenging for wildlife management as it is critical for estimating important aspects of population biology such as mortality rate, population viability, and period of reproductive potential. Recently, it has been shown cytosine-phosphate-guanine (CpG) density is predictive of maximum lifespan in vertebrates. This has made it possible to predict lifespan in long-lived species, which are generally the most intractable. In this study, we use gene promoter CpG density to predict the lifespan of five marine turtle species. Marine turtles are a particularly difficult group for lifespan estimation because of their migratory behaviour, longevity and high juvenile mortality rates, which all restrict individual tracking over their lifespan. Sanger sequencing was used to determine the CpG density in selected promoters. We predicted the lifespans for marine turtle species ranged from 50.4 years (flatback turtle, Natator depressus) to 90.4 years (leatherback turtle, Dermochelys coriacea). These lifespan predictions have broad applications in marine turtle research such as better understanding life cycles and determining population viability.

Bisphosphonates and atypical subtrochanteric fractures of the femur

OBJECTIVES

Bisphosphonates are widely used as first-line treatment for primary and secondary prevention of fragility fractures. Whilst they have proved effective in this role, there is growing concern over their long-term use, with much evidence linking bisphosphonate-related suppression of bone remodelling to an increased risk of atypical subtrochanteric fractures of the femur (AFFs). The objective of this article is to review this evidence, while presenting the current available strategies for the management of AFFs.

METHODS

We present an evaluation of current literature relating to the pathogenesis and treatment of AFFs in the context of bisphosphonate use.

RESULTS

Six broad themes relating to the pathogenesis and management of bisphosphonate-related AFFs are presented. The key themes in fracture pathogenesis are: bone microdamage accumulation; altered bone mineralisation and altered collagen formation. The key themes in fracture management are: medical therapy and surgical therapy. In addition, primary prevention strategies for AFFs are discussed.

CONCLUSIONS

This article presents current knowledge about the relationship between bisphosphonates and the development of AFFs, and highlights key areas for future research. In particular, studies aimed at identifying at-risk subpopulations and organising surveillance for those on long-term therapy will be crucial in both increasing our understanding of the condition, and improving population outcomes.Cite this article: N. Kharwadkar, B. Mayne, J. E. Lawrence, V. Khanduja. Bisphosphonates and atypical subtrochanteric fractures of the femur. Bone Joint Res 2017;6:144-153. DOI: 10.1302/2046-3758.63.BJR-2016-0125.R1.

Chloroperoxidase-catalyzed oxidation of methionine derivatives

Treatment of N-methoxycarbonyl C-carboxylate ester derivatives of L- and D-methionine and L-ethionine by chloroperoxidase–hydrogen peroxide resulted in oxidation at sulfur to produce the (RS) sulfoxide in moderate to high diastereomeric excess. The (RS) sulfoxide of methionine was also obtained in moderate to high diastereomeric excess from (±)SO-N-methoxycarbonyl-L-methionine methyl ester sulfoxide by ester hydrolysis using α-chymotrypsin, Aspergillus sp. protease or subtilisin Carlsberg. Key words: amino acid oxidation, biocatalysis, biotransformation, chloroperoxidase, enzyme catalysis, lipase, sulfoxidation.