| 1. |
- Groenen, M. A., et al.
(författare)
-
Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
-
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.
|
|
| 2. |
- Crous, P. W., et al.
(författare)
-
Fusarium : more than a node or a foot-shaped basal cell
- 2021
-
Ingår i: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
-
Tidskriftsartikel (refereegranskat)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
|
|
| 3. |
- George, T. S., et al.
(författare)
-
Organic phosphorus in the terrestrial environment : a perspective on the state of the art and future priorities
- 2018
-
Ingår i: Plant and Soil. - : Springer Netherlands. - 0032-079X .- 1573-5036. ; 427:1-2, s. 191-208
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (P-o) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction.Scope: We asked a group of experts to consider the global issues associated with P-o in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the P-o cycle, and to set priorities for P-o research.Conclusions: We identified seven key opportunities for P-o research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of P-o in natural and managed systems; the role of microorganisms in controlling P-o cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the P-o research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.
|
|
| 4. |
- Yun, H. B., et al.
(författare)
-
Warming, permafrost thaw and increased nitrogen availability as drivers for plant composition and growth across the Tibetan Plateau
- 2023
-
Ingår i: Soil Biology and Biochemistry. - 0038-0717 .- 1879-3428. ; 182
-
Tidskriftsartikel (refereegranskat)abstract
- Permafrost-affected ecosystems are subject to warming and thawing, which can increase the availability of subsurface nitrogen (N) with consequences in otherwise N-limited tundra and alpine vegetation. Here, we quantify the extent of warming and permafrost thawing and the corresponding effects on nitrogen availability and plant growth based on a 20-year survey across 14 sites on the Tibetan Plateau. The survey showed that most sites have been subject to warming and thawing and that the upper permafrost zone across all sites was rich in inorganic N, mainly as ammonium. We further explore the efficiency of plants to utilize 15N-labelled inorganic N over five years following 15N addition at the permafrost table far below the main root zone. The 15N experiment showed that deep-rooted plant species were able to utilize the labelled N. A SEM model suggests that changes in vegetation can be explained by both active layer warming and permafrost thawing and the associated changes in inorganic nitrogen availability. Our results highlight a feedback mechanism of climate warming, in which released plant-available N may favour deep-rooted plants. This can explain important changes in plant composition and growth across the sites on the Tibetan Plateau.
|
|
| 5. |
- Mardinoglu, Adil, 1982, et al.
(författare)
-
An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans
- 2018
-
Ingår i: Cell Metabolism. - : Elsevier BV. - 1550-4131 .- 1932-7420. ; 27:3
-
Tidskriftsartikel (refereegranskat)abstract
- A carbohydrate-restricted diet is a widely recommended intervention for non-alcoholic fatty liver disease (NAFLD), but a systematic perspective on the multiple benefits of this diet is lacking. Here, we performed a short-term intervention with an isocaloric low-carbohydrate diet with increased protein content in obese subjects with NAFLD and characterized the resulting alterations in metabolism and the gut microbiota using a multi-omics approach. We observed rapid and dramatic reductions of liver fat and other cardiometabolic risk factors paralleled by (1) marked decreases in hepatic de novo lipogenesis; (2) large increases in serum beta-hydroxybutyrate concentrations, reflecting increased mitochondrial beta-oxidation; and (3) rapid increases in folate-producing Streptococcus and serum folate concentrations. Liver transcriptomic analysis on biopsy samples from a second cohort revealed downregulation of the fatty acid synthesis pathway and upregulation of folate-mediated one-carbon metabolism and fatty acid oxidation pathways. Our results highlight the potential of exploring diet-microbiota interactions for treating NAFLD.
|
|
| 6. |
- Qin, Ning, 1990, et al.
(författare)
-
Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast
- 2023
-
Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 186:4, s. 748-763.e15
-
Tidskriftsartikel (refereegranskat)abstract
- Although many prokaryotes have glycolysis alternatives, it's considered as the only energy-generating glucose catabolic pathway in eukaryotes. Here, we managed to create a hybrid-glycolysis yeast. Subsequently, we identified an inositol pyrophosphatase encoded by OCA5 that could regulate glycolysis and respiration by adjusting 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7) levels. 5-InsP7 levels could regulate the expression of genes involved in glycolysis and respiration, representing a global mechanism that could sense ATP levels and regulate central carbon metabolism. The hybrid-glycolysis yeast did not produce ethanol during growth under excess glucose and could produce 2.68 g/L free fatty acids, which is the highest reported production in shake flask of Saccharomyces cerevisiae. This study demonstrated the significance of hybrid-glycolysis yeast and determined Oca5 as an inositol pyrophosphatase controlling the balance between glycolysis and respiration, which may shed light on the role of inositol pyrophosphates in regulating eukaryotic metabolism.
|
|
| 7. |
- Rasmussen, L. H., et al.
(författare)
-
Nitrogen transport in a tundra landscape : the effects of early and late growing season lateral N inputs on arctic soil and plant N pools and N2O fluxes
- 2022
-
Ingår i: Biogeochemistry. - : Springer Nature. - 0168-2563 .- 1573-515X. ; 157:1, s. 69-84
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding N budgets of tundra ecosystems is crucial for projecting future changes in plant community composition, greenhouse gas balances and soil N stocks. Winter warming can lead to higher tundra winter nitrogen (N) mineralization rates, while summer warming may increase both growing season N mineralization and plant N demand. The undulating tundra landscape is inter-connected through water and solute movement on top of and within near-surface soil, but the importance of lateral N fluxes for tundra N budgets is not well known. We studied the size of lateral N fluxes and the fate of lateral N input in the snowmelt period with a shallow thaw layer, and in the late growing season with a deeper thaw layer. We used 15N to trace inorganic lateral N movement in a Low-arctic mesic tundra heath slope in West Greenland and to quantify the fate of N in the receiving area. We found that half of the early-season lateral N input was retained by the receiving ecosystem, whereas half was transported downslope. Plants appear as poor utilizers of early-season N, indicating that higher winter N mineralization may influence plant growth and carbon (C) sequestration less than expected. Still, evergreen plants were better at utilizing early-season N, highlighting how changes in N availability may impact plant community composition. In contrast, later growing season lateral N input was deeper and offered an advantage to deeper-rooted deciduous plants. The measurements suggest that N input driven by future warming at the study site will have no significant impact on the overall N2O emissions. Our work underlines how tundra ecosystem N allocation, C budgets and plant community composition vary in their response to lateral N inputs, which may help us understand future responses in a warmer Arctic.
|
|
| 8. |
- Senapathi, Deepa, et al.
(författare)
-
Wild insect diversity increases inter-annual stability in global crop pollinator communities
- 2021
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954 .- 0962-8452. ; 288:1947
-
Tidskriftsartikel (refereegranskat)abstract
- While an increasing number of studies indicate that the range, diversity and abundance of many wild pollinators has declined, the global area of pollinator-dependent crops has significantly increased over the last few decades. Crop pollination studies to date have mainly focused on either identifying different guilds pollinating various crops, or on factors driving spatial changes and turnover observed in these communities. The mechanisms driving temporal stability for ecosystem functioning and services, however, remain poorly understood. Our study quantifies temporal variability observed in crop pollinators in 21 different crops across multiple years at a global scale. Using data from 43 studies from six continents, we show that (i) higher pollinator diversity confers greater inter-annual stability in pollinator communities, (ii) temporal variation observed in pollinator abundance is primarily driven by the three-most dominant species, and (iii) crops in tropical regions demonstrate higher inter-annual variability in pollinator species richness than crops in temperate regions. We highlight the importance of recognizing wild pollinator diversity in agricultural landscapes to stabilize pollinator persistence across years to protect both biodiversity and crop pollination services. Short-term agricultural management practices aimed at dominant species for stabilizing pollination services need to be considered alongside longer term conservation goals focussed on maintaining and facilitating biodiversity to confer ecological stability.
|
|
| 9. |
- Ge, Yaxin, 1992, et al.
(författare)
-
Impacts of fresh bed materials on alkali release and fuel conversion rate during wood pyrolysis and char gasification
- 2023
-
Ingår i: Fuel. - : Elsevier BV. - 0016-2361 .- 1873-7153. ; 353
-
Tidskriftsartikel (refereegranskat)abstract
- Bed materials provide efficient heat transfer and catalytic function in the thermochemical conversion of biomass, but their interactions with the fuel remain incompletely understood. In this study, the effects of bed materials on alkali release and fuel conversion during wood pyrolysis and CO2 gasification are investigated by online alkali detection combined with thermogravimetric analysis. The investigated bed materials include silica, sea sand, alumina and the natural ores olivine, ilmenite and dolomite. Only dolomite has a significant effect on fuel mass loss and alkali release during wood pyrolysis, while all bed materials influence char reactivity and alkali release during gasification. Sea sand, alumina and dolomite enhance the char gasification during the whole or most of the gasification process, which is related to alkali migration from the bed materials. All bed materials affect char reactivity and alkali release when the conversion approaches completion, and small amounts of some bed materials reduce the alkali release by an order of magnitude. The findings can be understood based on the chemical composition of the different materials. Silicon-rich materials reduce the levels of catalytically active alkali by formation of stable alkali silicates, and a similar explanation applies for ilmenite that captures alkali efficiently. Magnesium and calcium in contrast promote alkali release through their influence on alkali silicate chemistry. Analysis of char surfaces using scanning electron microscopy with energy dispersive spectroscopy indicates that low amounts of several elements are transferred from the bed material to the char where they may be directly involved in the char conversion process. The transferred elements are specific for each bed material and relates to their chemical composition. Mechanisms for material exchange between bed material and char are discussed.
|
|
| 10. |
|
|
