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.

The apparent quantum yield matrix (AQY-M) of CDOM photobleaching in estuarine, coastal, and oceanic surface waters.

The photochemical degradation of chromophoric dissolved organic matter (CDOM) upon solar exposure, known as photobleaching, can significantly alter the optical properties of the surface ocean. By leading to the breakdown of UV- and visible-radiation-absorbing moieties within dissolved organic matter, photobleaching regulates solar heating, the vertical distribution of photochemical processes, and UV exposure and light availability to the biota in surface waters. Despite its biogeochemical and ecological relevance, this sink of CDOM remains poorly quantified. Efforts to quantify photobleaching globally have long been hampered by the inherent challenge of determining representative apparent quantum yields (AQYs) for this process, and by the resulting lack of understanding of their variability in natural waters. Measuring photobleaching AQY is made challenging by the need to determine AQY matrices (AQY-M) that capture the dual spectral dependency of this process (i.e., magnitude varies with both excitation wavelength and response wavelength). A new experimental approach now greatly facilitates the quantification of AQY-M for natural waters, and can help address this problem. Here, we conducted controlled photochemical experiments and applied this new approach to determine the AQY-M of 27 contrasting water samples collected globally along the land-ocean aquatic continuum (i.e., rivers, estuaries, coastal ocean, and open ocean). The experiments and analyses revealed considerable variability in the magnitude and spectral characteristics of the AQY-M among samples, with strong dependencies on CDOM composition/origin (as indicated by the CDOM 275-295-nm spectral slope coefficient, S275-295), solar exposure duration, and water temperature. The experimental data facilitated the development and validation of a statistical model capable of accurately predicting the AQY-M from three simple predictor variables: 1) S275-295, 2) water temperature, and 3) a standardized measure of solar exposure. The model will help constrain the variability of the AQY-M when modeling photobleaching rates on regional and global scales.

COMT Val158Met and BDNF Val66Met Single-Nucleotide Polymorphisms Are Not Associated With Emotional Distress One Year After Moderate-Severe Traumatic Brain Injury.

Emotional distress is a common, but poorly addressed, feature of moderate-severe traumatic brain injury (TBI). Previously identified sociodemographic, psychological, and injury-related factors account for only a small proportion of the variability in emotional distress post-TBI. Genetic factors may help to further understand emotional distress in this population. The catechol-O-methyltransferase (COMT) Val158 and brain-derived neurotrophic factor (BDNF) 66Met single-nucleotide polymorphisms (SNPs) have been identified as possible contributory factors to outcomes after TBI. We investigated whether the COMT Val158 and BDNF 66Met SNPs were associated with emotional distress 1 year after moderate-severe TBI, and whether these associations were moderated by age, sex, and TBI severity (as measured by the duration of post-traumatic amnesia [PTA]). Moderate-severe TBI survivors (COMT, n = 391; BDNF, n = 311) provided saliva samples after admission to a TBI rehabilitation hospital. At a follow-up interview ∼1 year after injury, participants completed a self-report measure of emotional distress (Hospital Anxiety and Depression Scale; HADS). Multiple linear regression models were constructed for each SNP to predict total scores on the HADS. Neither COMT Val158 nor BDNF 66Met carriage status (carrier vs. non-carrier) significantly predicted emotional distress (COMT, p = 0.49; BDNF, p = 0.66). Interactions of SNP × age (COMT, p = 0.90; BDNF, p = 0.93), SNP × sex (COMT, p = 0.09; BDNF, p = 0.60), SNP × injury severity (COMT, p = 0.53; BDNF, p = 0.87), and SNP × sex × age (COMT, p = 0.08; BDNF, p = 0.76) were also non-significant. Our null findings suggest that COMT Val158 and BDNF 66Met SNPs do not aid the prediction of emotional distress 1 year after moderate-severe TBI, neither in isolation nor in interaction with age, sex and injury severity. The reporting of null findings such as ours is important to avoid publication bias and prompt researchers to consider the challenges of single-gene candidate studies in understanding post-TBI outcomes. Analyses in larger samples that incorporate multiple genetic factors and their relevant moderating factors may provide a greater understanding of the role of genetics in post-TBI emotional distress.

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.

Sensory acceptability of antioxidant-based formulations dedicated to mitigate heterocyclic aromatic amines in cooked meat.

In a previous work, we studied the inhibition of heterocyclic aromatic amine formation by natural ingredients rich in antioxidants: caper, oregano, wine and green tea. This present work aimed to assess the sensory impact of the addition of these ingredients in ground beef patties. The best liked formulations were determined by a hedonic scoring. Caper and oregano were not significantly different from the standard, the most appreciated, due to their congruency with cooked meat. Direct dissimilarity assessment was performed to evaluate the overall, gustative and odor differences between formulations. Olfactive differences were evidenced as key drivers of these differences. Standard and caper were close while oregano was found significantly different from them. A fast sensory profiling permitted to evidence that aromatic plant note was discriminant for oregano formulation. Gas chromatography-mass spectrometry/multibooth olfactometry identified the distinctive odor-active compounds of the formulations as pyrazines and sulfide for oregano formulation and ester for caper formulation.

Interaction between APOE ɛ4 and Age Is Associated with Emotional Distress One Year after Moderate-Severe Traumatic Brain Injury.

Emotional distress is common following moderate-severe traumatic brain injury (TBI) and is associated with poorer post-injury outcomes. Previously investigated sociodemographic, psychological, and injury-related factors account for only a small proportion of variance in post-TBI emotional distress, highlighting a need to consider other factors such as genetic factors. The apolipoprotein E gene (APOE) has been commonly studied in the TBI literature, with the ɛ4 allele linked to worse neuronal repair and recovery. Few studies have investigated the potential relationship between APOE ɛ4 and emotional distress after moderate-severe TBI, and results have been varied. We examined whether APOE ɛ4 was associated with emotional distress 1 year following moderate-severe TBI, and whether this relationship was moderated by age, sex, and TBI severity (as indexed by the duration of post-traumatic amnesia [PTA]). Moderate-severe TBI survivors provided saliva samples following inpatient admission to a TBI rehabilitation hospital. They completed a self-report measure of emotional distress, the Hospital Anxiety and Depression Scale (HADS), at a follow-up interview ∼1 year post-injury. Complete genetic and follow-up data were available for 441 moderate-severe TBI survivors (mean age = 39.42 years; 75% male). We constructed a linear regression model that included APOE ɛ4 carriage status (carrier vs. non-carrier) and interactions with age, sex, and TBI severity (APOE × age, APOE × sex, APOE × age × sex, and APOE × PTA duration) to predict total score on the HADS, while covarying for the main effects of age, sex, PTA duration, and previous head injury. There was a significant main effect of APOE ɛ4, whereby ɛ4 carriers reported less emotional distress than non-carriers (p = 0.04). However, we also found a significant interaction with age such that APOE ɛ4 carriers reported increasingly greater emotional distress with older age compared with non-carriers (p = 0.01). A sensitivity analysis (n = 306) suggested that the APOE × age interaction, and main effects of age and previous head injury, were not unique to individuals with pre-injury mental health problems (n = 136). However, the main effect of APOE ɛ4 was no longer significant when individuals with pre-injury mental health problems were removed. Our findings highlight the importance of considering moderation of genetic associations, suggesting that APOE ɛ4 may be a risk factor for emotional distress specifically among older survivors of moderate-severe TBI. If these findings can be independently replicated, APOE ɛ4 carriage status, interpreted in the context of age, could be incorporated into risk prediction models of emotional distress after moderate-severe TBI, enhancing targeted early detection and intervention efforts.

The Potential of a Stratified Approach to Drug Repurposing in Alzheimer's Disease.

Alzheimer's disease (AD) is a complex neurodegenerative condition that is characterized by the build-up of amyloid-beta plaques and neurofibrillary tangles. While multiple theories explaining the aetiology of the disease have been suggested, the underlying cause of the disease is still unknown. Despite this, several modifiable and non-modifiable factors that increase the risk of developing AD have been identified. To date, only eight AD drugs have ever gained regulatory approval, including six symptomatic and two disease-modifying drugs. However, not all are available in all countries and high costs associated with new disease-modifying biologics prevent large proportions of the patient population from accessing them. With the current patient population expected to triple by 2050, it is imperative that new, effective, and affordable drugs become available to patients. Traditional drug development strategies have a 99% failure rate in AD, which is far higher than in other disease areas. Even when a drug does reach the market, additional barriers such as high cost and lack of accessibility prevent patients from benefiting from them. In this review, we discuss how a stratified medicine drug repurposing approach may address some of the limitations and barriers that traditional strategies face in relation to drug development in AD. We believe that novel, stratified drug repurposing studies may expedite the discovery of alternative, effective, and more affordable treatment options for a rapidly expanding patient population in comparison with traditional drug development methods.

The contribution of water radiolysis to marine sedimentary life.

Water radiolysis continuously produces H2 and oxidized chemicals in wet sediment and rock. Radiolytic H2 has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth's surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H2 production, amplifying yields by up to 27X relative to pure water. In electron equivalents, the global rate of radiolytic H2 production in marine sediment appears to be 1-2% of the global organic flux to the seafloor. However, most organic matter is consumed at or near the seafloor, whereas radiolytic H2 is produced at all sediment depths. Comparison of radiolytic H2 consumption rates to organic oxidation rates suggests that water radiolysis is the principal source of biologically accessible energy for microbial communities in marine sediment older than a few million years. Where water permeates similarly catalytic material on other worlds, life may also be sustained by water radiolysis.

Insights into Manipulating Postprandial Energy Expenditure to Manage Weight Gain in Polycystic Ovary Syndrome.

Women with polycystic ovary syndrome (PCOS) are more likely to be obese and have difficulty in losing weight. They demonstrate an obesity-independent deficit in adaptive energy expenditure. We used a clinically realistic preclinical model to investigate the molecular basis for the reduced postprandial thermogenesis (PPT) and develop a therapeutic strategy to normalize this deficit. Sheep exposed to increased androgens before birth develop the clinical features of PCOS. In adulthood they develop obesity and demonstrate an obesity-independent reduction in PPT. This is associated with reduced adipose tissue uncoupling protein expression and adipose tissue noradrenaline concentrations. These sheep are insulin resistant with reduced insulin signaling in the brain. Increasing brain insulin concentrations using intranasal insulin administration increased PPT in PCOS sheep without any effects on blood glucose concentrations. Intranasal insulin administration with food is a potential novel strategy to improve adaptive energy expenditure and normalize the responses to weight loss strategies in women with PCOS.

Matrix Effects in Quantitative Analysis of Laser-Induced Breakdown Spectroscopy (LIBS) of Rock Powders Doped with Cr, Mn, Ni, Zn, and Co.

Obtaining quantitative chemical information using laser-induced breakdown spectroscopy is challenging due to the variability in the bulk composition of geological materials. Chemical matrix effects caused by this variability produce changes in the peak area that are not proportional to the changes in minor element concentration. Therefore the use of univariate calibrations to predict trace element concentrations in geological samples is plagued by a high degree of uncertainty. This work evaluated the accuracy of univariate minor element predictions as a function of the composition of the major element matrices of the samples and examined the factors that limit the prediction accuracy of univariate calibrations. Five different sample matrices were doped with 10-85 000 ppm Cr, Mn, Ni, Zn, and Co and then independently measured in 175 mixtures by X-ray fluorescence, inductively coupled plasma atomic emission spectrometry, and laser-induced breakdown spectroscopy, the latter at three different laser energies (1.9, 2.8, and 3.7 mJ). Univariate prediction models for minor element concentrations were created using varying combinations of dopants, matrices, normalization/no normalization, and energy density; the model accuracies were evaluated using root mean square prediction errors and leave-one-out cross-validation. The results showed the superiority of using normalization for predictions of minor elements when the predicted sample and those in the training set had matrices with similar SiO2 contents. Normalization also mitigates differences in spectra arising from laser/sample coupling effects and the use of different energy densities. Prediction of minor elements in matrices that are dissimilar to those in the training set can increase the uncertainty of prediction by an order of magnitude. Overall, the quality of a univariate calibration is primarily determined by the availability of a persistent, measurable peak with a favorable transition probability that has little to no interference from neighboring peaks in the spectra of both the unknown and those used to train it.

Hydrogen Utilization Potential in Subsurface Sediments.

Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones.

U.S. health care from a global perspective: spending, use of services, prices, and health in 13 countries.

This analysis draws upon data from the Organization for Economic Cooperation and Development and other cross-national analyses to compare health care spending, supply, utilization, prices, and health outcomes across 13 high-income countries: Australia, Canada, Denmark, France, Germany, Japan, Netherlands, New Zealand, Norway, Sweden, Switzerland, the United Kingdom, and the United States. These data predate the major insurance provisions of the Affordable Care Act. In 2013, the U.S. spent far more on health care than these other countries. Higher spending appeared to be largely driven by greater use of medical technology and higher health care prices, rather than more frequent doctor visits or hospital admissions. In contrast, U.S. spending on social services made up a relatively small share of the economy relative to other countries. Despite spending more on health care, Americans had poor health outcomes, including shorter life expectancy and greater prevalence of chronic conditions.

International survey of older adults finds shortcomings in access, coordination, and patient-centered care.

Industrialized nations face the common challenge of caring for aging populations, with rising rates of chronic disease and disability. Our 2014 computer-assisted telephone survey of the health and care experiences among 15,617 adults age sixty-five or older in Australia, Canada, France, Germany, the Netherlands, New Zealand, Norway, Sweden, Switzerland, the United Kingdom, and the United States has found that US older adults were sicker than their counterparts abroad. Out-of-pocket expenses posed greater problems in the United States than elsewhere. Accessing primary care and avoiding the emergency department tended to be more difficult in the United States, Canada, and Sweden than in other surveyed countries. One-fifth or more of older adults reported receiving uncoordinated care in all countries except France. US respondents were among the most likely to have discussed health-promoting behaviors with a clinician, to have a chronic care plan tailored to their daily life, and to have engaged in end-of-life care planning. Finally, in half of the countries, one-fifth or more of chronically ill adults were caregivers themselves.