| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Jenab, Mazda, et al.
(författare)
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Association between pre-diagnostic circulating vitamin D concentration and risk of colorectal cancer in European populations : a nested case-control study
- 2010
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Ingår i: BMJ. British Medical Journal. - : BMJ Publishing Group. - 0959-8146 .- 0959-535X. ; 340, s. b5500-
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To examine the association between pre-diagnostic circulating vitamin D concentration, dietary intake of vitamin D and calcium, and the risk of colorectal cancer in European populations. DESIGN: Nested case-control study. Setting The study was conducted within the EPIC study, a cohort of more than 520 000 participants from 10 western European countries. PARTICIPANTS: 1248 cases of incident colorectal cancer, which developed after enrolment into the cohort, were matched to 1248 controls MAIN OUTCOME MEASURES: Circulating vitamin D concentration (25-hydroxy-vitamin-D, 25-(OH)D) was measured by enzyme immunoassay. Dietary and lifestyle data were obtained from questionnaires. Incidence rate ratios and 95% confidence intervals for the risk of colorectal cancer by 25-(OH)D concentration and levels of dietary calcium and vitamin D intake were estimated from multivariate conditional logistic regression models, with adjustment for potential dietary and other confounders. RESULTS: 25-(OH)D concentration showed a strong inverse linear dose-response association with risk of colorectal cancer (P for trend <0.001). Compared with a pre-defined mid-level concentration of 25-(OH)D (50.0-75.0 nmol/l), lower levels were associated with higher colorectal cancer risk (<25.0 nmol/l: incidence rate ratio 1.32 (95% confidence interval 0.87 to 2.01); 25.0-49.9 nmol/l: 1.28 (1.05 to 1.56), and higher concentrations associated with lower risk (75.0-99.9 nmol/l: 0.88 (0.68 to 1.13); >or=100.0 nmol/l: 0.77 (0.56 to 1.06)). In analyses by quintile of 25-(OH)D concentration, patients in the highest quintile had a 40% lower risk of colorectal cancer than did those in the lowest quintile (P<0.001). Subgroup analyses showed a strong association for colon but not rectal cancer (P for heterogeneity=0.048). Greater dietary intake of calcium was associated with a lower colorectal cancer risk. Dietary vitamin D was not associated with disease risk. Findings did not vary by sex and were not altered by corrections for season or month of blood donation. CONCLUSIONS: The results of this large observational study indicate a strong inverse association between levels of pre-diagnostic 25-(OH)D concentration and risk of colorectal cancer in western European populations. Further randomised trials are needed to assess whether increases in circulating 25-(OH)D concentration can effectively decrease the risk of colorectal cancer.
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| 3. |
- Raffan, Eleanor, et al.
(författare)
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A Deletion in the Canine POMC Gene Is Associated with Weight and Appetite in Obesity-Prone Labrador Retriever Dogs
- 2016
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Ingår i: Cell Metabolism. - : Elsevier BV. - 1550-4131 .- 1932-7420. ; 23:5, s. 893-900
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Tidskriftsartikel (refereegranskat)abstract
- Sequencing of candidate genes for obesity in Labrador retriever dogs identified a 14 bp deletion in pro-opiomelanocortin (POMC) with an allele frequency of 12%. The deletion disrupts the b-MSH and beta-endorphin coding sequences and is associated with body weight (per allele effect of 0.33 SD), adiposity, and greater food motivation. Among other dog breeds, the deletion was only found in the closely related flat-coat retriever (FCR), where it is similarly associated with body weight and food motivation. The mutation is significantly more common in Labrador retrievers selected to become assistance dogs than pets. In conclusion, the deletion in POMC is a significant modifier of weight and appetite in Labrador retrievers and FCRs and may influence other behavioral traits.
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| 4. |
- Velie, Brandon, et al.
(författare)
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Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model
- 2019
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundHorses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model.ResultsPooled sequence data from three Nordic horse populations were used for F-ST analysis. After strict filtering, F-ST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n=214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL.ConclusionsNot unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development.
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| 5. |
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| 6. |
- Goodrich, H. R., et al.
(författare)
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Understanding the gastrointestinal physiology and responses to feeding in air-breathing Anabantiform fishes
- 2020
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Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 96:4, s. 986-1003
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Tidskriftsartikel (refereegranskat)abstract
- The Mekong Delta is host to a large number of freshwater species, including a unique group of facultative air-breathing Anabantiforms. Of these, the striped snakehead (Channa striata), the climbing perch (Anabas testudineus), the giant gourami (Osphronemus goramy) and the snakeskin gourami (Trichogaster pectoralis) are major contributors to aquaculture production in Vietnam. The gastrointestinal responses to feeding in these four species are detailed here. Relative intestinal length was lowest in the snakehead, indicating carnivory, and 5.5-fold greater in the snakeskin, indicating herbivory; climbing perch and giant gourami were intermediate, indicating omnivory. N-waste excretion (ammonia-N + urea-N) was greatest in the carnivorous snakehead and least in the herbivorous snakeskin, whereas the opposite trend was observed for net K+ excretion. Similarly, the more carnivorous species had a greater stomach acidity than the more herbivorous species. Measurements of acid-base flux to water indicated that the greatest postprandial alkaline tide occurred in the snakehead and a potential acidic tide in the snakeskin. Additional findings of interest were high levels of both PCO2 (up to 40 mmHg) and HCO3- (up to 33 mM) in the intestinal chyme of all four of these air-breathing species. Using in vitro gut sac preparations of the climbing perch, it was shown that the intestinal net absorption of fluid, Na+ and HCO3- was upregulated by feeding but not net Cl- uptake, glucose uptake or K+ secretion. Upregulated net absorption of HCO3- suggests that the high chyme (HCO3-) does not result from secretion by the intestinal epithelium. The possibility of ventilatory control of PCO2 to regulate postprandial acid-base balance in these air-breathing fish is discussed.
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| 7. |
- Shaheen, S. M., et al.
(författare)
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Redox chemistry of vanadium in soils and sediments : Interactions with colloidal materials, mobilization, speciation, and relevant environmental implications - A review
- 2019
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Ingår i: Advances in Colloid and Interface Science. - : Elsevier. - 0001-8686 .- 1873-3727. ; 265, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Vanadium (V), although serving as an important component of industrial activities, has bioinorganic implications to pose highly toxic hazards to humans and animals. Soils and sediments throughout the world exhibit wide ranges of vanadium concentrations. Although vanadium toxicity varies between different species, it is mainly controlled by soil redox potential (E H ). Nonetheless, knowledge of the redox geochemistry of vanadium lags in comparison to what is known about other potentially toxic elements (PTEs). In particular, the redox-induced speciation and mobilization of vanadium in soils and sediments and the associated risks to the environment have not been reviewed to date. Therefore, this review aims to address 1) the content and geochemical fate of vanadium in soils and sediments, 2) its redox-induced release dynamics, 3) redox-mediated chemical reactions between vanadium and soil organic and inorganic colloidal materials in soil solution, 4) its speciation in soil solution and soil-sediments, and 5) the use of advanced geochemical and spectroscopic techniques to investigate these complex systems. Vanadium (+5) is the most mobile and toxic form of its species while being the thermodynamically stable valence state in oxic environments, while vanadium (+3) might be expected to be predominant under euxinic (anoxic and sulfidic) conditions. Vanadium can react variably in response to changing soil E H : under anoxic conditions, the mobilization of vanadium can decrease because vanadium (+5) can be reduced to relatively less soluble vanadium (+4) via inorganic reactions such as with H 2 S and organic matter and by metal-reducing microorganisms. On the other hand, dissolved concentrations of vanadium can increase at low E H in many soils to reveal a similar pattern to that of Fe, which may be due to the reductive dissolution of Fe(hydr)oxides and the release of the associated vanadium. Those differences in vanadium release dynamics might occur as a result of the direct impact of E H on vanadium speciation in soil solution and soil sediments, and/or because of the E H -dependent changes in soil pH, chemistry of (Fe)(hydr)oxides, and complexation with soil organic carbon. Release dynamics of vanadium in soils may also be affected positively by soil pH and the release of aromatic organic compounds. X-ray absorption spectroscopy (XAS) is a powerful tool to investigate the speciation of vanadium present in soil. X-ray absorption near edge structure (XANES) is often used to constrain the average valence state of vanadium in soils and sediments, and in limited cases extended X-ray absorption fine structure (EXAFS) analysis has been used to determine the average molecular coordination environment of vanadium in soil components. In conclusion, this review presents the state of the art about the redox geochemistry of vanadium and thus contributes to a better understanding of the speciation, potential mobilization, and environmental hazards of vanadium in the near-surface environment of uplands, wetlands, and agricultural ecosystems as affected by various colloidal particles. Further research is needed to elucidate the geochemistry and speciation of vanadium in the dissolved, colloidal, and soil sediments phases, including the determination of factors that control the redox geochemistry of vanadium.
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| 8. |
- Fegraeus, Kim, et al.
(författare)
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An endothelial regulatory module links blood pressure regulation with elite athletic performance
- 2024
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 20:6
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Tidskriftsartikel (refereegranskat)abstract
- The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
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| 9. |
- Meeussen, Camille, et al.
(författare)
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Structural variation of forest edges across Europe
- 2020
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 462
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Tidskriftsartikel (refereegranskat)abstract
- Forest edges are interfaces between forest interiors and adjacent land cover types. They are important elements in the landscape with almost 20% of the global forest area located within 100 m of the edge. Edges are structurally different from forest interiors, which results in unique edge influences on microclimate, functioning and biodiversity. These edge influences have been studied for multiple decades, yet there is only limited information available on how forest edge structure varies at the continental scale, and which factors drive this potential structural diversity. Here we quantified the structural variation along 45 edge-to-interior transects situated along latitudinal, elevational and management gradients across Europe. We combined state-of-the-art terrestrial laser scanning and conventional forest inventory techniques to investigate how the forest edge structure (e.g. plant area index, stem density, canopy height and foliage height diversity) varies and which factors affect this forest edge structural variability. Macroclimate, management, distance to the forest edge and tree community composition all influenced the forest edge structural variability and interestingly we detected interactive effects of our predictors as well. We found more abrupt edge-to-interior gradients (i.e. steeper slopes) in the plant area index in regularly thinned forests. In addition, latitude, mean annual temperature and humidity all affected edge-to-interior gradients in stem density. We also detected a simultaneous impact of both humidity and management, and humidity and distance to the forest edge, on the canopy height and foliage height diversity. These results contribute to our understanding of how environmental conditions and management shape the forest edge structure. Our findings stress the need for site-specific recommendations on forest edge management instead of generalized recommendations as the macroclimate substantially influences the forest edge structure. Only then, the forest edge microclimate, functioning and biodiversity can be conserved at a local scale.
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| 10. |
- Kim, Sanghyun, et al.
(författare)
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Continuous-cover forestry maintains soil fungal communities in Norway spruce dominated boreal forests
- 2021
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Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 480
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Tidskriftsartikel (refereegranskat)abstract
- Traditional clear-fell forestry greatly alters community structure and ecosystem function within boreal forests and alternative management practices may reduce these impacts. Continuous-cover forestry can maintain similar invertebrate and plant communities to unmanaged forest, but whether this extends to soil fungal communities remains unclear. Within four sites across the mid-boreal zone of Sweden, we conducted a comprehensive study to assess the impact of continuous-cover and clear-felling on soil fungi and chemical properties within Norway spruce dominated forests, using unmanaged forest as a control. We sampled soils for chemical properties (pH, carbon, nitrogen, C/N and Organic matter) and used both surveys of fungal fruiting bodies and state of the DNA metabarcoding techniques to assess treatment effects on soil fungal communities. We found that forest management practices had significant effects soil pH, C and C/N ratio and that continuous-cover forestry had more similar soil properties to unmanaged forest. Furthermore, the biodiversity of fruiting bodies, as expressed by species richness and Shannon’s diversity index, was higher in continuous-cover forestry and unmanaged forest compared to clear-felled areas. However, the opposite was true for the diversity of soil fungal communities, which was probably due to the high level of disturbance in clear-felled areas, and thus, ample habitat for early successional colonisers and some remnants of mature forest communities. However, in agreement with predictions we found that the composition of both fruiting body and soil fungal communities broadly similar in continuous-cover and unmanaged forest, but fundamentally different to clear-felled areas. Consequently, our findings highlight that continuous-cover forestry is an alternative to conventional practise, maintaining communities associated with unmanaged forest and mimicking natural disturbance regimes.
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