Targeted bisulfite sequencing of Scots pine adaptation-related genes

Abstract During environmental changes, epigenetic processes can enable adaptive responses faster than natural selection. In plants, very little is known about the role of DNA methylation during long-term adaptation. Scots pine is a widely distributed coniferous species which must adapt to different environmental conditions throughout its long lifespan. Thus, epigenetic modifications may contribute towards this direction. We provide bisulfite next-generation sequencing data from the putative promoters and exons of eight adaptation-related genes (A3IP2, CCA1, COL1, COL2, FTL2, MFT1, PHYO, and ZTL) in three Scots pine populations located in northern and southern parts of Finland. DNA methylation levels were studied in the two seed tissues: the maternal megagametophyte which contributes to embryo viability, and the biparental embryo which represents the next generation. In most genes, differentially methylated cytosines (DMCs) were in line with our previously demonstrated gene expression differences found in the same Scots pine populations. In addition, we found a strong correlation of total methylation levels between the embryo and megagametophyte tissues of a given individual tree, which indicates that DNA methylation can be inherited from the maternal parent. In conclusion, our results imply that DNA methylation differences may contribute to the adaptation of Scots pine populations in different climatic conditions.Abstract During environmental changes, epigenetic processes can enable adaptive responses faster than natural selection. In plants, very little is known about the role of DNA methylation during long-term adaptation. Scots pine is a widely distributed coniferous species which must adapt to different environmental conditions throughout its long lifespan. Thus, epigenetic modifications may contribute towards this direction. We provide bisulfite next-generation sequencing data from the putative promoters and exons of eight adaptation-related genes (A3IP2, CCA1, COL1, COL2, FTL2, MFT1, PHYO, and ZTL) in three Scots pine populations located in northern and southern parts of Finland. DNA methylation levels were studied in the two seed tissues: the maternal megagametophyte which contributes to embryo viability, and the biparental embryo which represents the next generation. In most genes, differentially methylated cytosines (DMCs) were in line with our previously demonstrated gene expression differences found in the same Scots pine populations. In addition, we found a strong correlation of total methylation levels between the embryo and megagametophyte tissues of a given individual tree, which indicates that DNA methylation can be inherited from the maternal parent. In conclusion, our results imply that DNA methylation differences may contribute to the adaptation of Scots pine populations in different climatic conditions

Differentiating Non-Motor Symptoms in Parkinson's Disease from Controls and Hemifacial Spasm

10.1371/journal.pone.0049596PLoS ONE82

The ongoing pursuit of neuroprotective therapies in Parkinson disease

Many agents developed for neuroprotective treatment of Parkinson disease (PD) have shown great promise in the laboratory, but none have translated to positive results in patients with PD. Potential neuroprotective drugs, such as ubiquinone, creatine and PYM50028, have failed to show any clinical benefits in recent high-profile clinical trials. This 'failure to translate' is likely to be related primarily to our incomplete understanding of the pathogenic mechanisms underlying PD, and excessive reliance on data from toxin-based animal models to judge which agents should be selected for clinical trials. Restricted resources inevitably mean that difficult compromises must be made in terms of trial design, and reliable estimation of efficacy is further hampered by the absence of validated biomarkers of disease progression. Drug development in PD dementia has been mostly unsuccessful; however, emerging biochemical, genetic and pathological evidence suggests a link between tau and amyloid-β deposition and cognitive decline in PD, potentially opening up new possibilities for therapeutic intervention. This Review discusses the most important 'druggable' disease mechanisms in PD, as well as the most-promising drugs that are being evaluated for their potential efficiency in treatment of motor and cognitive impairments in PD

Estimating the environmental impact of dairy cattle breeding programs through emission intensity.

A recently developed methodological approach for determining the greenhouse gas emissions impact of national breeding programs was applied to measure the effects of current and future breeding goals on the emission intensity (EI) of the Canadian dairy industry. Emission intensity is the ratio of greenhouse gas outputted in comparison to the product generated. Traits under investigation affected EI by either decreasing the direct emissions yield (i.e. increasing feed performance), changing herd structure (i.e. prolonging herd life) or through the dilution effect of increased production (i.e. increasing fat yield). The intensity value (IV) of each trait, defined as the change in emissions' intensity per unit change in each trait, was calculated for each of the investigated traits. The IV trend of these traits was compared for the current and prospective selection index, as well as for a system with and without quota (the supply management policy designed to prevent overproduction). The overall EI of the average genetic merit Canadian dairy herd per breeding female was 5.07 kg CO2eq/kg protein equivalent output. The annual reduction in EI due to the improvement of production traits was -0.027, -0.018 and -0.006 for fat, protein and milk other solids, respectively. The functional traits, herd life and mastitis resistance, had more modest effects (-0.008 and -0.001, respectively). These results are consistent with international studies that identified traits related to production, survival, health and fertility as having the largest impact on the environmental footprint of dairy cattle. Overall, the dairy industry is becoming more efficient by reducing its EI through selection of environmentally favorable traits, with a 1% annual reduction of EI in Canada

DNA extraction optimization and authentication of Vaccinium berries and their products by high-resolution DNA melting analysis

Abstract Food adulteration has been an issue in the food industry for many decades. The market for natural and healthy products has been expanding and therefore the value of raw ingredients harvested from natural sources has increased, and, in some cases, it has led to adulteration of such high-valued products. Berry fruits and products from different species of the genus Vaccinium have been gaining worldwide popularity because of their nutraceutical benefits. However, there are increasing reports of adulteration or misidentification of high-value wild berries with their cultivated counterparts. During recent years, DNA-based methods for the authentication of commercial products have gained popularity, especially regarding species identification. Based on the availability of their chloroplast genome information, we developed DNA markers to differentiate lingonberry from cranberry as well as to discriminate European bilberry from North American blueberry. By using Bar-HRM analysis (DNA barcoding combined with High Resolution Melting), the markers were tested on plant DNA as well as DNA extracted from diverse berry products. The developed markers were able to discriminate between species and, moreover, detect potential adulteration in products made from these berry species. Subsequently, the Bar-HRM result was verified by amplicon sequencing. To conclude, the developed molecular markers represent a valuable tool for the berry food industry.Abstract Food adulteration has been an issue in the food industry for many decades. The market for natural and healthy products has been expanding and therefore the value of raw ingredients harvested from natural sources has increased, and, in some cases, it has led to adulteration of such high-valued products. Berry fruits and products from different species of the genus Vaccinium have been gaining worldwide popularity because of their nutraceutical benefits. However, there are increasing reports of adulteration or misidentification of high-value wild berries with their cultivated counterparts. During recent years, DNA-based methods for the authentication of commercial products have gained popularity, especially regarding species identification. Based on the availability of their chloroplast genome information, we developed DNA markers to differentiate lingonberry from cranberry as well as to discriminate European bilberry from North American blueberry. By using Bar-HRM analysis (DNA barcoding combined with High Resolution Melting), the markers were tested on plant DNA as well as DNA extracted from diverse berry products. The developed markers were able to discriminate between species and, moreover, detect potential adulteration in products made from these berry species. Subsequently, the Bar-HRM result was verified by amplicon sequencing. To conclude, the developed molecular markers represent a valuable tool for the berry food industry

Protocol for a home-based integrated physical therapy program to reduce falls and improve mobility in people with Parkinson’s disease

Background The high incidence of falls associated with Parkinson’s disease (PD) increases the risk of injuries and immobility and compromises quality of life. Although falls education and strengthening programs have shown some benefit in healthy older people, the ability of physical therapy interventions in home settings to reduce falls and improve mobility in people with Parkinson’s has not been convincingly demonstrated.Methods/design 180 community living people with PD will be randomly allocated to receive either a home-based integrated rehabilitation program (progressive resistance strength training, movement strategy training and falls education) or a home-based life skills program (control intervention). Both programs comprise one hour of treatment and one hour of structured homework per week over six weeks of home therapy. Blinded assessments occurring before therapy commences, the week after completion of therapy and 12 months following intervention will establish both the immediate and long-term benefits of home-based rehabilitation. The number of falls, number of repeat falls, falls rate and time to first fall will be the primary measures used to quantify outcome. The economic costs associated with injurious falls, and the costs of running the integrated rehabilitation program from a health system perspective will be established. The effects of intervention on motor and global disability and on quality of life will also be examined. Discussion This study will provide new evidence on the outcomes and cost effectiveness of home-based movement rehabilitation programs for people living with PD

Genetic and economic benefits of foreign sire contributions to a domestic sheep industry; including an Ireland-New Zealand case study

peer-reviewedBackground Importation of foreign genetics is a widely used genetic improvement strategy. However, even if the foreign genetic merit is currently greater than the domestic genetic merit, differences in foreign and domestic trends mean that the long-term competitiveness of an importation strategy cannot be guaranteed. Gene flow models are used to quantify the impact that a specific subpopulation, such as foreign genetics, can have over time on the genetic or economic benefit of a domestic industry. Methods We used a deterministic recursive gene flow model to predict the commercial performance of lambs born across various subpopulations. Numerous breeding strategies were evaluated by varying market share, proportions of rams selected for mating, genetic trend, superiority of foreign genetics over domestic genetics and frequency of importation. Specifically, an Ireland-New Zealand case study was simulated to quantify the potential gain that could be made by using foreign sire contributions (New Zealand) in a domestic sheep industry (Ireland). Results Genetic and economic gains were generated from alternative breeding strategies. The ‘base scenario’ (i.e. representing the current industry) predicted an average genetic merit value of €2.51 for lambs born and an annualised cumulative benefit of €45 million (m) after 20 years. Maximum genetic (€9.45 for lambs born) and economic (annualised cumulative benefit of €180 m after 20 years) benefits were achieved by implementing the ‘PRO-intense-market scenario’ which involved shifting market share away from conservative domestic breeders and reducing the proportion of rams that were selected for mating by progressive domestic breeders from the top 40% to the top 20%, without the use of any foreign genetics. The ‘PROFOR scenario’, which considered the use of foreign and progressive domestic genetics, predicted an average genetic merit value of €7.37 for lambs born and an annualised cumulative benefit of €144 m, after 20 years. Conclusions Our results demonstrate that there is opportunity for a domestic industry to increase industry benefits without the use of foreign genetics but through an attempt to shift the market share away from conservative domestic breeders towards progressive domestic breeders. However, the importation and use of progressive foreign genetics may be an effective method to trigger a change in behaviour of conservative domestic breeders towards the use of progressive genetics

Genetic and Environmental Influences on Sweet Taste Liking and Related Traits: New Insights from Twin Cohorts

Reducing sugar intake is a key component of global health policies and dietary guidelines. However, individuals vary substantially in sweet-liking, commonly characterized by sweet-liking status (extreme sweet-likers, moderate sweet-likers, and sweet-dislikers), yet the heritability of these categories remains unexplored. Monozygotic and dizygotic twins from Finland (FinnTwin12; n = 468; 60% female, aged 21–24) and the UK (TwinsUK; n = 967; 90% female, aged 18–81) rated their liking and perceived intensity of a 20% (w/v) sucrose solution, reported their liking and consumption-frequency of food and beverages and completed additional behavioral, eating and personality measures. We estimated the contribution of additive genetic (A), nonadditive genetic (D), shared (C), and unshared environmental factors (E) in the variance and covariance of sweet-liking (defined ordinally through sweet-liking status and continuously) with related traits to see if they share similar proportions of genetic and environmental factors. Model-fitting indicated 30–48% of the variability in sweet-liking was attributed to (A) additive genetic factors and 52–70% to (E) environmental exposures not shared by siblings. Importantly, such AE models consistently fit best, regardless of sex, cohort, or sweet-liking assessment method. Broadly, correlations between sweet-liking and behavioral, eating, and personality measures were modest (–0.19 to 0.21), mostly positive and largely driven by shared genetic rather than environmental factors, with the strongest relationship seen for reported liking, consumption-frequency and craving for sweet foods. We demonstrate that unshared environment modulates individual differences in sweet-liking alongside a substantial genetic component that is partly shared with reported liking, consumption-frequency and craving for sweet foods

Usability of therapy controllers in elderly patients with deep brain stimulation

<p>Abstract</p> <p>Background</p> <p>Technical devices are becoming more prevalent in society and also in medical care. Older adults need more support to learn new technologies than younger subjects. So far, no research has been done on the usability of patient controllers in deep brain stimulation in an elderly population. The aim of the study was to investigate the factors influencing the performance of elderly DBS patients with respect to usability aspects of Medtronic Access therapy controllers.</p> <p>Methods</p> <p>Time, mistakes and frequency of use of the controller were compared in 41 elderly DBS patients who prior to the study had already owned a therapy controller for more than six years. One group (n = 20, mean age = 66.4 years) was watching an instructional video and then completed practical assignments on a model implantable pulse generator (IPG). The other group (n = 21, mean age = 65.9 years) completed the tasks without having seen the video before. Any errors that patients made were documented and also corrected so that all of them received hands-on training. After six months all patients were re-evaluated on the dummy IPG in order to compare the effects of hands-on alone vs. video-based training combined with hands-on.</p> <p>Results</p> <p>The group that had seen the video before significantly outperformed the control group at both assessments with respect to number of errors. Both groups performed faster after six months compared to baseline and tend to use the controller more often than at baseline.</p> <p>Conclusion</p> <p>Our results indicate that elderly DBS patients who have been using the controller for several years still have various difficulties in operating the device. However, we also showed that age-specific training may improve the performance in older adults. In general, the design of DBS patient controllers should focus on the specific needs of the end-users. But as changes to medical devices take a long time to be implemented, video instructions with age-specific content plus hands-on training may improve learning for older adults.</p