| 1. |
- Du, Qian, et al.
(författare)
-
Porcine circovirus type 2 infection promotes the SUMOylation of nucleophosmin-1 to facilitate the viral circular single-stranded DNA replication
- 2024
-
Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 20:2
-
Tidskriftsartikel (refereegranskat)abstract
- The mechanism of genome DNA replication in circular single-stranded DNA viruses is currently a mystery, except for the fact that it undergoes rolling-circle replication. Herein, we identified SUMOylated porcine nucleophosmin-1 (pNPM1), which is previously reported to be an interacting protein of the viral capsid protein, as a key regulator that promotes the genome DNA replication of porcine single-stranded DNA circovirus. Upon porcine circovirus type 2 (PCV2) infection, SUMO2/3 were recruited and conjugated with the K263 site of pNPM1's C-terminal domain to SUMOylate pNPM1, subsequently, the SUMOylated pNPM1 were translocated in nucleoli to promote the replication of PCV2 genome DNA. The mutation of the K263 site reduced the SUMOylation levels of pNPM1 and the nucleolar localization of pNPM1, resulting in a decrease in the level of PCV2 DNA replication. Meanwhile, the mutation of the K263 site prevented the interaction of pNPM1 with PCV2 DNA, but not the interaction of pNPM1 with PCV2 Cap. Mechanistically, PCV2 infection increased the expression levels of Ubc9, the only E2 enzyme involved in SUMOylation, through the Cap-mediated activation of ERK signaling. The upregulation of Ubc9 promoted the interaction between pNPM1 and TRIM24, a potential E3 ligase for SUMOylation, thereby facilitating the SUMOylation of pNPM1. The inhibition of ERK activation could significantly reduce the SUMOylation levels and the nucleolar localization of pNPM1, as well as the PCV2 DNA replication levels. These results provide new insights into the mechanism of circular single-stranded DNA virus replication and highlight NPM1 as a potential target for inhibiting PCV2 replication. Different types of DNA viruses employ different mechanisms to replicate their genome DNA. Porcine circovirus type 2 (PCV2) is the most representative circular single-stranded DNA virus that harms the pig industry all over the world. In this study, we found that the PCV2 Cap interacting protein pNPM1 also interacts with PCV2 DNA in a SUMOylated form to promote PCV2 DNA replication. The SUMOylation of pNPM1 at the conserved K263 site is critical for the interaction of pNPM1 with PCV2 DNA and the replication of PCV2 DNA. Furthermore, we found that PCV2 infection promotes the SUMO2/3 mediated SUMOylation of pNPM1, while does not significantly alter the expression level of pNPM1. PCV2 Cap is the major component that promotes pNPM1 SUMOylation by activating ERK/Ubc9/TRIM24 signalings. These results contribute to a better understanding of the replication mechanism of circular single-stranded DNA viruses, particularly PCV2.
|
|
| 2. |
- Ishfaq, Muhammad, et al.
(författare)
-
Improvement of nutritional quality of food crops with fertilizer : a global meta-analysis
- 2023
-
Ingår i: Agronomy for Sustainable Development. - : Springer Nature. - 1774-0746 .- 1773-0155. ; 43:6
-
Tidskriftsartikel (refereegranskat)abstract
- Providing the world’s population with sufficient and nutritious food through sustainable food systems is a major challenge of the twenty-first century. Fertilizer use is a major driver of crop yield, but a comprehensive synthesis of the effect of fertilizer on the nutritional quality of food crops is lacking. Here we performed a comprehensive global meta-analysis using 7859 data pairs from 551 field experiment-based articles published between 1972 and 2022, assessing the contribution of fertilization with a wide set of plant nutrients to the nutritional quality of food crops (i.e., fruits, vegetables, cereals, pulses/oil crops, and sugar crops). On average, fertilizer application improved crop yield by 30.9% (CI: 28.2–33.7%) and nutritional quality (referring to all nutritionally relevant components assessed; carbohydrates, proteins, oil, vitamin C, representative mineral nutrients, and total soluble solids) by 11.9% (CI: 10.7–12.1%). The improvements were largely nutrient- and crop species dependent, with vegetables being the most responsive. Potassium, magnesium, and micronutrients played important roles in promoting crop nutritional quality, whereas the combined application of inorganic and organic source(s) had the greatest impact on quality. Desirable climatic conditions and soil properties (i.e., silt loam, soil organic matter 2.5–5.0%, and pH 4.5–8.5) supported further enhancements. Considering cross-continent responsiveness, the increase in the nutritional quality of food crops with fertilizer application was greatest in Africa. In a nutshell, our findings pave the way towards a quantitative understanding of nutrient management programs and responsible plant nutrition solutions that foster the sustainable production of nutritious and healthy food crops for human consumption.
|
|
| 3. |
- Davies, Stuart J., et al.
(författare)
-
ForestGEO: Understanding forest diversity and dynamics through a global observatory network
- 2021
-
Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207. ; 253
-
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.
|
|
| 4. |
- Guo, Ying, et al.
(författare)
-
Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum
- 2023
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:12
-
Tidskriftsartikel (refereegranskat)abstract
- Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.
|
|
| 5. |
- Kumar, RM Saravana, et al.
(författare)
-
Auxin enhances grafting success in Carya cathayensis (Chinese hickory)
- 2018
-
Ingår i: Planta. - : Springer. - 0032-0935 .- 1432-2048. ; 247:3, s. 761-772
-
Tidskriftsartikel (refereegranskat)abstract
- Main conclusionApplication of auxin to root stock and scion increases the success rate of grafting in Chinese hickory.The nuts of the Chinese hickory (Carya cathayensis) tree are considered both delicious and healthy. The popularity and high demand result is that the hickory nuts are of very high economical value for horticulture. This is particularly true for the Zhejiang province in eastern China where this tree is widely cultivated. However, there are several difficulties surrounding the hickory cultivation, such as for example long vegetative growth, tall trees, labour-intensive nut picking, and slow variety improvements. These complications form a great bottleneck in the expansion of the hickory industry. The development of an efficient grafting procedure could surpass at least some of these problems. In this study, we demonstrate that application of the auxin indole-3-acetic acid promotes the grafting process in hickory, whereas application of the auxin transport inhibitor 1-N-naphthylphthalamic acid inhibits the grafting process. Furthermore, we have identified hickory genes in the PIN, ABCB, and AUX/LAX-families known to encode influx and efflux carriers in the polar transport of auxin. We show that increased expression of several of these genes, such as CcPIN1b and CcLAX3, is correlating with successful grafting.
|
|
| 6. |
- Luo, Ziteng, et al.
(författare)
-
Roots-Enhanced Preferential Flows in Deciduous and Coniferous Forest Soils Revealed by Dual-Tracer Experiments
- 2019
-
Ingår i: Journal of Environmental Quality. - : Wiley. - 0047-2425. ; 48:1, s. 136-146
-
Tidskriftsartikel (refereegranskat)abstract
- Macropores formed by roots are crucial channels for preferential flows in forest soils that are largely responsible for water percolation and solute leaching. Using dual-tracer experiments (Brilliant Blue FCF and bromide [Br]), this study investigated the preferential flows of water and solutes in a deciduous forest dominated by Bl. and a coniferous forest mainly planted with (L.) Franco. Dye-stained patterns and concentrations of Brilliant Blue and Br were obtained in vertical soil profiles (0-30 cm), whereas stained and unstained roots were collected and analyzed in horizontal soil profiles to a 30-cm soil depth. Brilliant Blue and Br were mainly accumulated in the 0- to 20-cm soil depth, which had greater total root length density than the 20- to 30-cm soil depth ( < 0.05). Only part of the roots facilitated the preferential flows, with finer roots (i.e., diameter <1 mm) contributing the most. More intriguingly, the coniferous forest soil had a greater degree of preferential flows and greater tracer concentrations at deeper soil depth than the deciduous forest soil, suggesting the importance of tree species and forest composition on water and solute transport in forest ecosystems.
|
|
| 7. |
- Manevska Tasevska, Gordana, et al.
(författare)
-
Economic outcomes from adopting cereal-legume intercropping practices in Sweden
- 2024
-
Ingår i: Agricultural Systems. - 0308-521X .- 1873-2267. ; 220
-
Tidskriftsartikel (refereegranskat)abstract
- CONTEXTThe need for sustainable and resilient farming practices is clearly communicated by the scholars and the European Union policy strategies. The low interest in adopting the practice due to the uncertainties and the variability in the economic outcomes across various intercropping types calls for research attention. In this respect, research is needed to identifying specific intercropping practices that lead to improved farm-level economic outcomes and resilience.OBJECTIVESThis study investigates consequences of intercropping adoption on the farm economic outcomes, in the context of achieving economic resilience. Specific objectives are to assess the effect of i) adopting intercropping on the economic outcomes; ii) production adjustments on the economic resilience of the intercropping practices, both in comparison to conventional mono-cropped agriculture.METHODSThe analysis is conducted by using a stochastic partial budgeting model. We use Swedish agriculture as an empirical basis for our study and model two baseline cereal monocropping scenarios and two corresponding alternative (strip and mixed) cereal-legume intercropping scenarios. This is to examine net changes and risk characteristics resulting from the adaptation from monocropping to intercropping production practices. Estimates of net changes and the respective risk characteristics are integrated in an economic resilience assessment for the intercropping practices.RESULTSResults reveal that the net economic benefit change from adopting differs across the intercropping alternatives. Prices of the monocropped and the intercropped products of both intercropping alternatives and the use of N fertilizer for the strip intercropping alternative are the most influential factors in determining the adaptability capacity.CONTRIBUTIONThis study provides a novel approach that contributes to the literature via quantifying economic resilience capacities of hypothetical technology adoption. The paper presents unique results on the economic resilience of adopting cereal-legume intercropping practices in a Nordic context, giving agriculture in Nordic regions shares common challenges such as short growing season and cold temperature. The results offer valuable insights for extension services in guiding farmers to choose appropriate intercropping practices based on the production possibilities and market needs. Policy implications targeting the adoption of cereal-legume intercropping adoption are discussed.
|
|
| 8. |
- Rahmati, Omid, et al.
(författare)
-
Contribution of physical and anthropogenic factors to gully erosion initiation
- 2022
-
Ingår i: Catena (Cremlingen. Print). - : Elsevier BV. - 0341-8162 .- 1872-6887. ; 210, s. 105925-105925
-
Tidskriftsartikel (refereegranskat)abstract
- Losses of large volumes of soil through gully formation lead to serious environmental, societal, and economic problems for human societies. This study establishes a framework based on an artificial intelligence approach to investigate the impact of geo-environmental and topo-hydrological factors on gully occurrences in the Biram region, Iran. The maximum entropy, random forest, and boosted regression trees machine-learning models were applied. The relative importance of variables (RIV) was then determined and gully erosion susceptibility maps were generated. Model results were evaluated using cutoff–dependent and –independent metrics. All models identified road construction as the main cause of gully formation in the study region (RVI ranged between 27% and 34%), and a medium contribution of distance from stream (RVI = 15–18%), lithology (RVI = 12–15%) and land use (RVI = 8–12%). Other factors such as drainage density, topographic wetness index, aspect, slope, profile curvature, elevation and plan curvature showed lower relative importance (RIV < 10%). Planners should pay attention to minimizing gully erosion along roads, so that river systems and downstream communities are adequately protected.
|
|
| 9. |
- Schoch, Conrad L., et al.
(författare)
-
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
-
Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
-
Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
|
|
| 10. |
- Shao, Wei, et al.
(författare)
-
Reduce uncertainty in soil hydrological modeling : A comparison of soil hydraulic parameters generated by random sampling and pedotransfer function
- 2023
-
Ingår i: Journal of Hydrology. - 0022-1694 .- 1879-2707. ; 623
-
Tidskriftsartikel (refereegranskat)abstract
- Numerical simulation of unsaturated soil hydrology relies on calibrated soil hydraulic parameters, which are subject to uncertainty due to imperfect information during the inverse modelling. This study investigates the effectiveness of reducing parameter uncertainty using the recently developed Rosetta 3 pedotransfer function. The GLUE method was employed for numerical modeling using the Darcy-Richards equation under two strategies for sampling Mualem-van Genuchten (MvG) parameters: the first uses conventional random generation of MvG parameters (GLUE-random), while the second adopts Rosetta 3 to transfer soil particle composition to MvG parameter (GLUE-Rosetta). Both approaches were used for inverse modeling of 9 typical soils, each with a recommended parameter set defined as true values and associated soil moisture dynamics as observations. The posterior parameters selected with both GLUE-random and GLUE-Rosetta show an equifinality phenomenon. GLUE-random fails to provide well-constrained posterior parameters to recover the pre-defined true values, and its posterior results of soil water characteristic curve (SWCC) and soil hydraulic conductivity function (HCF) are poorly constrained. In contrast, GLUE-Rosetta significantly improves the accuracy of the inversely-estimated soil hydraulic parameters, and the ensemble of posterior SWCC and HCF also encompasses the predefined true curves. The results demonstrate the effectiveness of using Rosetta 3 to reduce the dimensionality of the optimization problem, which results in reliable estimation of soil hydraulic parameters and soil particle compositions. Moreover, GLUE-Rosetta outperforms GLUE-random in predicting soil moisture dynamics under different rainfall intensities. Overall, it is recommended to integrate Rosetta 3 with existing optimization tools to reduce the uncertainty of soil parameters and support more reliable modeling of unsaturated soil hydrology.
|
|
