Maize for silage II. The effect of urea and acid as preservative treament on rumen fermentations and on feeding values of silages

The rumen fermentations and N-balances of rumen fistulated sheep were studied on diets of silages treated with urea and acid preservative. The digestibilities and feeding values of the silages were also calculated. The experiment was performed according to 5 x 5 Latin-square design. The digestibilities were determined by total collection the collection period lasting seven days. The rumen samples were taken on the last two days during the collection periods before and 1.5, 3.0, 4.5 and 6.0 hours after feeding. Besides the silages the animals received mineral mixture and water ad libitum. Urea or acid treatment had no effect (P > 0.05) on the consumption of silage DM. The consumption ranged from 1.7 to 1.9 kg DM/100 kg liveweight. Urea did not have a clear effect on the VFA production in the rumen. It tended, however, to decrease the proportions of C3 and C4—C5 acids in the rumen. Acid preservative decreased the production of VFA and the proportion of C3-acid (P 0.05) were found between the energy values, which varied between 0,12—0.14 f.u./kg of silage. There were no differences in the N-balances of the animals on different diets. The balances were positive on all diets

Changes in the fine-scale genetic structure of Finland through the 20(th) century

Information about individual-level genetic ancestry is central to population genetics, forensics and genomic medicine. So far, studies have typically considered genetic ancestry on a broad continental level, and there is much less understanding of how more detailed genetic ancestry profiles can be generated and how accurate and reliable they are. Here, we assess these questions by developing a framework for individual-level ancestry estimation within a single European country, Finland, and we apply the framework to track changes in the fine-scale genetic structure throughout the 20(th) century. We estimate the genetic ancestry for 18,463 individuals from the National FINRISK Study with respect to up to 10 genetically and geographically motivated Finnish reference groups and illustrate the annual changes in the fine-scale genetic structure over the decades from 1920s to 1980s for 12 geographic regions of Finland. We detected major changes after a sudden, internal migration related to World War II from the region of ceded Karelia to the other parts of the country as well as the effect of urbanization starting from the 1950s. We also show that while the level of genetic heterogeneity in general increases towards the present day, its rate of change has considerable differences between the regions. To our knowledge, this is the first study that estimates annual changes in the fine-scale ancestry profiles within a relatively homogeneous European country and demonstrates how such information captures a detailed spatial and temporal history of a population. We provide an interactive website for the general public to examine our results. Author summary We have inherited our genomes from our parents, who, in turn, inherited their genomes from their parents, etc. Hence, a comparison between genomes of present day individuals reveals genetic population structure due to the varying levels of genetic relatedness among the individuals. We have utilized over 18,000 Finnish samples to characterize the fine-scale genetic population structure in Finland starting from a binary East-West division and ending up with 10 Finnish source populations. Furthermore, we have applied the resulting ancestry information to generate records of how the population structure has evolved each year between 1923 and 1987 in 12 geographical regions of Finland. For example, the war-related evacuation of Karelians from Southeast Finland to other parts of the country show up as a clear, sudden increase in the Evacuated ancestry elsewhere in Finland between 1939 and 1945. Additionally, different regions of Finland show very different levels of genetic mixing in 1900s, from little mixed regions like Ostrobothnia to highly mixed regions like Southwestern Finland. To distribute the results among general public, we provide an interactive website for browsing the municipality and region-level genetic ancestry profiles atPeer reviewe

Fine-Scale Genetic Structure in Finland

Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP) and FineSTRUCTURE (FS) we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Noteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.Peer reviewe

Geographic Variation and Bias in the Polygenic Scores of Complex Diseases and Traits in Finland

Polygenic scores (PSs) are becoming a useful tool to identify individuals with high genetic risk for complex diseases, and several projects are currently testing their utility for translational applications. It is also tempting to use PSs to assess whether genetic variation can explain a part of the geographic distribution of a phenotype. However, it is not well known how the population genetic properties of the training and target samples affect the geographic distribution of PSs. Here, we evaluate geographic differences, and related biases, of PSs in Finland in a geographically well-defined sample of 2,376 individuals from the National FINRISK study. First, we detect geographic differences in PSs for coronary artery disease (CAD), rheumatoid arthritis, schizophrenia, waist-hip ratio (WHR), body-mass index (BMI), and height, but not for Crohn disease or ulcerative colitis. Second, we use height as a model trait to thoroughly assess the possible population genetic biases in PSs and apply similar approaches to the other phenotypes. Most importantly, we detect suspiciously large accumulations of geographic differences for CAD, WHR, BMI, and height, suggesting bias arising from the population's genetic structure rather than from a direct genotype-phenotype association. This work demonstrates how sensitive the geographic patterns of current PSs are for small biases even within relatively homogeneous populations and provides simple tools to identify such biases. A thorough understanding of the effects of population genetic structure on PSs is essential for translational applications of PSs.Peer reviewe

Genetic risk factors have a substantial impact on healthy life years

The impact of genetic variation on overall disease burden has not been comprehensively evaluated. We introduce an approach to estimate the effect of genetic risk factors on disability-adjusted life years (DALYs; 'lost healthy life years'). We use genetic information from 735,748 individuals and consider 80 diseases. Rare variants had the highest effect on DALYs at the individual level. Among common variants, rs3798220 (LPA) had the strongest individual-level effect, with 1.18 DALYs from carrying 1 versus 0 copies. Being in the top 10% versus the bottom 90% of a polygenic score for multisite chronic pain had an effect of 3.63 DALYs. Some common variants had a population-level effect comparable to modifiable risk factors such as high sodium intake and low physical activity. Attributable DALYs vary between males and females for some genetic exposures. Genetic risk factors can explain a sizable number of healthy life years lost both at the individual and population level.Peer reviewe

100 years of atmospheric and marine observations at the Finnish Utö Island in the Baltic Sea

The Utö Atmospheric and Marine Research Station introduced in this paper is located on Utö Island (59°46.84′ N, 21°22.13′ E) at the outer edge of the Archipelago Sea, by the Baltic Sea towards the Baltic Proper. Meteorological observations at the island started in 1881 and vertical profiling of seawater temperature and salinity in 1900. Since 1980, the number of observations at Utö has rapidly increased, with a large number of new meteorological, air quality, aerosol, optical and greenhouse gas parameters, and recently, a variety of marine observations. In this study, we analyze long-term changes of atmospheric temperature, cloudiness, sea salinity, temperature and ice cover. Our main dataset consists of 248 367 atmospheric temperature observations, 1632 quality-assured vertical seawater temperature and salinity profiles and 8565 ice maps, partly digitized for this project. We also use North Atlantic Oscillation (NAO), major Baltic inflow (MBI) and Baltic Sea river runoff data from the literature as reference variables to our data. Our analysis is based on a statistical method utilizing a dynamic linear model. The results show an increase in the atmospheric temperature at Utö, but the increase is significantly smaller than on land areas and has taken place only since the early 1980s, with a rate of 0.4 °C decade−1 during the last 35 years. We also see an increase in seawater temperatures, especially on the surface, with an increase of 0.3 °C decade−1 for the last 100 years. In deeper water layers, the increase is smaller and influenced by vertical mixing, which is modulated by inflow of saline water from the North Sea and freshwater inflow from rivers and by wind-driven processes influenced by the local bathymetry. The date when air temperature in the spring exceeds +5 °C became 5 days earlier from the period 1951–1980 to the period 1981–2010 and the date when sea surface water temperature exceeds +4 °C changed to 9 days earlier. Sea ice cover duration at Utö shows a decrease of approximately 50 % during the last 35 years. Based on the combined results, it is possible that the climate at Utö has changed into a new phase, in which the sea ice no longer reduces the local temperature increase caused by the global warming.</p

FINEMAP : efficient variable selection using summary data from genome-wide association studies

Motivation: The goal of fine-mapping in genomic regions associated with complex diseases and traits is to identify causal variants that point to molecular mechanisms behind the associations. Recent fine-mapping methods using summary data from genome-wide association studies rely on exhaustive search through all possible causal configurations, which is computationally expensive. Results: We introduce FINEMAP, a software package to efficiently explore a set of the most important causal configurations of the region via a shotgun stochastic search algorithm. We show that FINEMAP produces accurate results in a fraction of processing time of existing approaches and is therefore a promising tool for analyzing growing amounts of data produced in genome-wide association studies and emerging sequencing projects.Peer reviewe

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children’s ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child’s cognitive abilities at age twelve

Tissue hyaluronan expression, as reflected in the sputum of lung cancer patients, is an indicator of malignancy

Hyaluronan (HA) shows promise for detecting cancerous change in pleural effusion and urine. However, there is uncertainty about the localization of HA in tumor tissue and its relationship with different histological types and other components of the extracellular matrix, such as angiogenesis. We evaluated the association between HA and degree of malignancy through expression in lung tumor tissue and sputum. Tumoral tissue had significantly increased HA compared to normal tissue. Strong HA staining intensity associated with cancer cells was significant in squamous cell carcinoma compared to adenocarcinoma and large cell carcinoma. A significant direct association was found between tumors with a high percentage of HA and MVD (microvessel density) in tumoral stroma. Similarly significant was the direct association between N1 tumors and high levels of HA in cancer cells. Cox multivariate analysis showed significant association between better survival and low HA. HA increased in sputum from lung cancer patients compared to cancer-free and healthy volunteers and a significant correlation was found between HA in sputum and HA in cancer tissue. Localization of HA in tumor tissue was related to malignancy and reflected in sputum, making this an emerging factor for an important diagnostic procedure in patients suspected to have lung cancer. Further study in additional patients in a randomized prospective trial is required to finalize these results and to validate our quantitative assessment of HA, as well as to couple it to gold standard sputum cytology.Research supported by FAPESP (2010/11005-5 and 2010/04462) and CNPq (#471939/2010-2 and 483005/2012-6