| 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. |
- Davies, Stuart J., et al.
(författare)
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ForestGEO: Understanding forest diversity and dynamics through a global observatory network
- 2021
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207. ; 253
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Tidskriftsartikel (refereegranskat)abstract
- ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimensions, censusing of all stems ≥1 cm in diameter, inclusion of tropical, temperate and boreal forests, and investigation of additional biotic (e.g., arthropods) and abiotic (e.g., soils) drivers, which together provide a holistic view of forest functioning. The 71 FDPs in 27 countries include approximately 7.33 million living trees and about 12,000 species, representing 20% of the world's known tree diversity. With >1300 published papers, ForestGEO researchers have made significant contributions in two fundamental areas: species coexistence and diversity, and ecosystem functioning. Specifically, defining the major biotic and abiotic controls on the distribution and coexistence of species and functional types and on variation in species' demography has led to improved understanding of how the multiple dimensions of forest diversity are structured across space and time and how this diversity relates to the processes controlling the role of forests in the Earth system. Nevertheless, knowledge gaps remain that impede our ability to predict how forest diversity and function will respond to climate change and other stressors. Meeting these global research challenges requires major advances in standardizing taxonomy of tropical species, resolving the main drivers of forest dynamics, and integrating plot-based ground and remote sensing observations to scale up estimates of forest diversity and function, coupled with improved predictive models. However, they cannot be met without greater financial commitment to sustain the long-term research of ForestGEO and other forest plot networks, greatly expanded scientific capacity across the world's forested nations, and increased collaboration and integration among research networks and disciplines addressing forest science.
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| 3. |
- Lou, H., et al.
(författare)
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The cellulose synthase-like F3 (CslF3) gene mediates cell wall polysaccharide synthesis and affects root growth and differentiation in barley
- 2022
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 110:6, s. 1681-1699
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Tidskriftsartikel (refereegranskat)abstract
- The barley cellulose synthase-like F (CslF) genes encode putative cell wall polysaccharide synthases. They are related to the cellulose synthase (CesA) genes involved in cellulose biosynthesis, and the CslD genes that influence root hair development. Although CslD genes are implicated in callose, mannan and cellulose biosynthesis, and are found in both monocots and eudicots, CslF genes are specific to the Poaceae. Recently the barley CslF3 (HvCslF3) gene was shown to be involved in the synthesis of a novel (1,4)-β-linked glucoxylan, but it remains unclear whether this gene contributes to plant growth and development. Here, expression profiling using qRT-PCR and mRNA in situ hybridization revealed that HvCslF3 accumulates in the root elongation zone. Silencing HvCslF3 by RNAi was accompanied by slower root growth, linked with a shorter elongation zone and a significant reduction in root system size. Polymer profiling of the RNAi lines revealed a significant reduction in (1,4)-β-linked glucoxylan levels. Remarkably, the heterologous expression of HvCslF3 in wild-type (Col-0) and root hair-deficient Arabidopsis mutants (csld3 and csld5) complemented the csld5 mutant phenotype, in addition to altering epidermal cell fate. Our results reveal a key role for HvCslF3 during barley root development and suggest that members of the CslD and CslF gene families have similar functions during root growth regulation.
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| 4. |
- Petersen, S. O., et al.
(författare)
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In-vitro method and model to estimate methane emissions from liquid manure management on pig and dairy farms in four countries
- 2024
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Ingår i: Journal of Environmental Management. - : Academic Press. - 0301-4797 .- 1095-8630. ; 353
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Tidskriftsartikel (refereegranskat)abstract
- Methane (CH4) emissions from manure management on livestock farms are a key source of greenhouse gas emissions in some regions and for some production systems, and the opportunities for mitigation may be significant if emissions can be adequately documented. We investigated a method for estimating CH4 emissions from liquid manure (slurry) that is based on anaerobic incubation of slurry collected from commercial farms. Methane production rates were used to derive a parameter of the Arrhenius temperature response function, lnA', representing the CH4 production potential of the slurry at the time of sampling. Results were used for parameterization of an empirical model to estimate annual emissions with daily time steps, where CH4 emissions from individual sources (barns, outside storage tanks) can be calculated separately. A monitoring program was conducted in four countries, i.e., Denmark, Sweden, Germany and the Netherlands, during a 12-month period where slurry was sampled to represent barn and outside storage on finishing pig and dairy farms. Across the four countries, lnA' was higher in pig slurry compared to cattle slurry (p < 0.01), and higher in slurry from barns compared to outside storage (p < 0.01). In a separate evaluation of the incubation method, in-vitro CH4 production rates were comparable with in-situ emissions. The results indicate that lnA' in barns increases with slurry age, probably due to growth or adaptation of the methanogenic microbial community. Using lnA' values determined experimentally, empirical models with daily time steps were constructed for finishing pig and dairy farms and used for scenario analyses. Annual emissions from pig slurry were predicted to be 2.5 times higher than those from cattle slurry. Changing the frequency of slurry export from the barn on the model pig farm from 40 to 7 d intervals reduced total annual CH4 emissions by 46 %; this effect would be much less on cattle farms with natural ventilation. In a scenario with cattle slurry, the empirical model was compared with the current IPCC methodology. The seasonal dynamics were less pronounced, and annual CH4 emissions were lower than with the current methodology, which calls for further investigations. Country-specific models for individual animal categories and point sources could be a tool for assessing CH4 emissions and mitigation potentials at farm level.
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| 5. |
- Bansal, Sheel, et al.
(författare)
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Practical Guide to Measuring Wetland Carbon Pools and Fluxes
- 2023
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Ingår i: Wetlands (Wilmington, N.C.). - : SPRINGER. - 0277-5212 .- 1943-6246. ; 43:8
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Forskningsöversikt (refereegranskat)abstract
- Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.
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| 6. |
- Schoville, Sean D., et al.
(författare)
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A model species for agricultural pest genomics : The genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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| 7. |
- Ma, S., et al.
(författare)
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Plant-soil feedbacks of forest understorey plants transplanted in nonlocal soils along a latitudinal gradient
- 2019
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Ingår i: Plant Biology. - : Wiley. - 1435-8603 .- 1438-8677. ; 21:4, s. 677-687
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is driving movements of many plants beyond, as well as within, their current distributional ranges. Even migrant plants moving within their current range may experience different plant-soil feedbacks (PSF) because of divergent nonlocal biotic soil conditions. Yet, our understanding to what extent soil biotic conditions can affect the performance of within-range migrant plants is still very limited. We assessed the emergence and growth of migrant forest herbs (Milium effusum and Stachys sylvatica) using soils and seeds collected along a 1,700 km latitudinal gradient across Europe. Soil biota were manipulated through four soil treatments, i.e. unsterilized control soil (PSFUS), sterilized soil (PSFS), sterilized soil inoculated with unsterilized home soil (PSFS+HI) and sterilized soil inoculated with unsterilized foreign soil (PSFS+FI, expected to occur when both plants and soil biota track climate change). Compared to PSFS, PSFUS had negative effects on the growth but not emergence of both species, while PSFS+FI only affected S. sylvatica across all seed provenances. When considering seed origin, seedling emergence and growth responses to nonlocal soils depended on soil biotic conditions. Specifically, the home-away distance effect on seedling emergence differed between the four treatments, and significant responses to chemistry either disappeared (M. effusum) or changed (S. sylvatica) from PSFUS to PSFS. Soil biota emerge as an important driver of the estimated plant migration success. Our results of the effects of soil microorganisms on plant establishment provide relevant information for predictions of the distribution and dynamics of plant species in a changing climate.
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| 8. |
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| 9. |
- Ramirez-Maganda, James, et al.
(författare)
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Nutritional properties and phenolic content of a bakery product substituted with a mango (Mangifera indica) 'Ataulfo' processing by-product
- 2015
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Ingår i: Food Research International. - : Elsevier BV. - 0963-9969. ; 73, s. 117-123
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Tidskriftsartikel (refereegranskat)abstract
- Wheat flour and cane sugar were partially substituted (50 and 75%) by a mango-processing by-product (MPB) as an added-value food ingredient in muffins. Their sensory analysis, chemical composition, antioxidant activity and in vitro starch hydrolysis properties were studied. Sensory analysis showed statistically significant difference (p < 0.05) between control and muffins 75% MPB substituted level (p < 0.05) with the highest score. Proximate analysis revealed that muffins substituted with MPB had significantly (p < 0.05) higher moisture, ash, soluble, insoluble and total indigestible fraction contents but lower total soluble carbohydrates and available starch contents than a non-substituted (control) muffin. Total soluble polyphenol (TSP) content increased about three times (from 1.86 to 5.36 g GAE/100 g dw) with MPB substitution. Chlorogenic, caffeic, gallic, hydroxycinnamic and ferulic acids were identified as major TSP. Muffins with MPB, exhibited better antioxidant properties (104.0 to 108.5 mu mol TE/g dw for DPPH assay and 34.1 to 19.1 mmol TE/g dw for FRAP assay) than the control formulation. The presence of high phenolic and insoluble indigestible fraction contents, which may be responsible of the lower rate of starch hydrolysis observed in muffins prepared with MPB, might modulate the postprandial glucose response in vivo. MPB may be used as an ingredient in foods with add-value with potential health-promoting features, besides providing a solution to the environmental problems associated with the disposal of mango by-products. (C) 2015 Elsevier Ltd. All rights reserved.
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| 10. |
- Van Sundert, Kevin, et al.
(författare)
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When things get MESI : The Manipulation Experiments Synthesis Initiative—A coordinated effort to synthesize terrestrial global change experiments
- 2023
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 29:7, s. 1922-1938
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Tidskriftsartikel (refereegranskat)abstract
- Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2, temperature, and nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3644 manipulation experiments at 1145 sites, simulating elevated CO2, warming, nutrient addition, and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short term (one or few growing seasons), conducted in the USA, Europe, or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.
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