| 1. |
- Li, Cheng, et al.
(author)
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Ridge planting with transparent plastic mulching improves maize productivity by regulating the distribution and utilization of soil water, heat, and canopy radiation in arid irrigation area
- 2023
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In: Agricultural Water Management. - : Elsevier BV. - 0378-3774. ; 280
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Journal article (peer-reviewed)abstract
- Ridge-furrow mulching system is widely used for improving soil hydrothermal conditions and crop productivity in semiarid and arid rainfed areas. The response of crop productivity to resource capture and utilization is crucial for agricultural field management and sustainable development. However, few have simultaneously investigated the coupling effect of plastic film mulching (PM) types and planting patterns on root and shoot growth, photosynthesis, yield, resource capture and utilization as well as their potential links in the same experiment, especially in arid irrigation areas, limiting our understanding of PM and ridge planting application. This study conducted a two-year field experiment with four treatments: 1) flat planting with transparent plastic film mulch (FT); 2) flat planting with black plastic film mulch (FB); 3) ridge–furrow planting with transparent plastic film mulch (RT); 4) ridge–furrow planting with black plastic film mulch (RB). The results showed that RT significantly increased soil water storage and root growth at the silking and grain-filling stages in both years by enhancing soil thermal time with 151.9–176.2 °C d and the intercepted photosynthetic active radiation with 22.2–57.4 MJ m–2. In addition, RT had a significantly higher net photosynthetic rate than FT and FB at the 12-leaf and silking stages, enhancing the transportation of stem and leaf to grain. The logistic equation using growing degree days as the independent variable characterized the dynamic features of maize growth under different PM types (transparent or black) coupled with ridge–furrow planting. RT accelerated dry matter accumulation by enhancing the maximum growth rate and extending the rapid growth period, resulting in 12.9–15.2 % more dry matter accumulation and 10.0–16.7 % higher grain yields than FB. Furthermore, RT significantly increased resource use efficiencies by 10.1–17.3 % for water, 3.0–5.5 % for thermal, and 4.0–9.1 % for radiation compared with FB. Ridge planting had the highest contributor rates, with >40 % for yield and resource capture. This study suggests that RT maintains high maize productivity and resource use efficiencies in arid irrigation areas with limited water resources by regulating soil water, heat, and canopy radiation distribution and utilization.
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| 2. |
- Qin, Ning, 1990, et al.
(author)
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Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast
- 2023
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 186:4, s. 748-763.e15
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Journal article (peer-reviewed)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.
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| 3. |
- Jayasiri, Subashini C., et al.
(author)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
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Journal article (peer-reviewed)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 4. |
- Li, Meijun, et al.
(author)
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Identified temporal variation of soil hydraulic parameters under seasonal ecosystem change using the particle batch smoother
- 2024
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In: Geoderma. - 0016-7061 .- 1872-6259. ; 442
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Journal article (peer-reviewed)abstract
- Soil hydraulic parameters are influenced by various inherent soil properties, such as pore structure and organic matter content, which can vary with changes in the ecosystem. However, identifying the temporal variations of soil hydraulic parameters in a co-evolving soil-vegetation system remains a challenge. This study focused on a tropical forest with significant seasonal variations in vegetation attributes, evaporation, and carbon fluxes over a five-year monitoring period. The particle batch smoother algorithm was integrated with an unsaturated flow model to identify the seasonally varied soil hydraulic parameters through assimilation of in-situ measured soil moisture. As a benchmark, the Generalized Likelihood Uncertainty Estimation method was applied to optimize soil hydraulic parameters without considering temporal variation. The results indicated that the temporally varying soil hydraulic parameters exhibited regular seasonal patterns and outperformed the unvaried soil hydraulic parameters in terms of reducing the errors in modeling of soil moisture and evaporation. Moreover, the seasonal variations in soil hydraulic parameters were closely linked to changes in the litterfall and terrestrial carbon fluxes over time. Specifically, due to the hysteresis of the transformation from litterfall to soil organic matter, the accumulated litterfall in Hot-dry season can replenish the soil organic matter, resulting in an increase in field capacity and saturated hydraulic conductivity in the Hot-rainy season. However, the intense decomposition of soil organic matter under high temperature in Hot-dry season led to a decrease in field capacity and saturated hydraulic conductivity. This study emphasizes the value of the particle batch smoother algorithm in detecting temporal variations in soil hydraulic parameters within a coevolving soil-vegetation system, thereby contributing to a more comprehensive understanding of the intricate dynamics within the ecohydrological system under a changing environment.
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| 5. |
- Li, Wenyun, et al.
(author)
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Personalized microbial fingerprint associated with differential glycemic effects of a whole grain rye intervention on Chinese adults
- 2024
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In: Molecular Nutrition & Food Research. - : John Wiley & Sons. - 1613-4125 .- 1613-4133.
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Journal article (peer-reviewed)abstract
- Scope: This study aims to identify the gut enterotypes that explain differential responses to intervention with whole grain rye by proposing an “enterotype - metabolic” model.Methods and results: A 12-week randomized controlled trial is conducted in Chinese adults, with 79 subjects consuming whole grain products with fermented rye bran (FRB) and 77 consuming refined wheat products in this exploratory post-hoc analysis. Responders or non-responders are identified according to whether blood glucose decreased by more than 10% after rye intervention. Compared to non-responders, responders in FRB have higher baseline Bacteroides (p < 0.001), associated with reduced blood glucose (p < 0.001), increased Faecalibacterium (p = 0.020) and Erysipelotrichaceae_UCG.003 (p = 0.022), as well as deceased 7β-hydroxysteroid dehydrogenase (p = 0.033) after intervention. The differentiated gut microbiota and metabolites between responders and non-responders after intervention are enriched in aminoacyl-tRNA biosynthesis.Conclusion: The work confirms the previously suggested importance of microbial enterotypes in differential responses to whole grain interventions and supports taking enterotypes into consideration for improved efficacy of whole grain intervention for preventing type 2 diabetes. Altered short-chain fatty acids and bile acid metabolism might be a potential mediator for the beneficial effects of whole grain rye on glucose metabolism.
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| 6. |
- Shao, Wei, et al.
(author)
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Reducing uncertainties in hydromechanical modeling with a recently developed Rosetta 3 podeotransfer function
- 2023
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In: Engineering Geology. - 0013-7952 .- 1872-6917. ; 324
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Journal article (peer-reviewed)abstract
- Stability analysis of unsaturated landslide deposits requires reliable estimates of soil moisture and pore water pressure. However, modeled soil moisture and pore water pressure contain substantial uncertainties due to imperfect information on soil hydraulic properties. Due to the relatively high dimensionality, commonly used parameter optimization strategies can be significantly affected by equifinality problems. This study investigates the effectiveness of reducing parameter estimation dimensionality using soil pedo-transfer functions. Specifically, we first estimated soil hydraulic parameters using the traditional Generalized Likelihood Uncertainty Estimation (GLUE) method, with parameters randomly drawn from the entire space (refer to as GLUE-random). In a second strategy, we use the Rosetta 3 pedotransfer function to constrain soil hydraulic parameters (refer to as GLUE-Rosetta). The two methods were tested in a typical landslide deposit with in-situ measured soil moisture dynamics for inverse modeling. The GLUE-random estimated soil hydraulic parameters contained substantial uncertainties –resulting in poorly constrained soil water retention curves (SWCC) and hydraulic conductivity functions (HCF). As a result, the uncertainty bands of pore water pressure and slope stability can cross values with several orders of magnitudes. In contrast, GLUE-Rosetta provided well-constrained SWCC and HCF, which significantly reduce the uncertainties in pore water pressure and slope stability estimates. These results suggest that the Rosetta 3 pedotransfer function can significantly improve the reliability of soil hydraulic parameters by reducing the dimensionality of the optimization problem and high-quality prior information of soil hydraulic properties. In conclusion, Rosetta 3 can enhance the reliability of soil parameters estimates and the reliability of subsurface hydrology, which may benefit the development of landslide early-warning systems.
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| 7. |
- Wang, Shi Zhi, et al.
(author)
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Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds
- 2024
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7
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Journal article (peer-reviewed)abstract
- The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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| 8. |
- Wu, Tonghua, et al.
(author)
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Storage, patterns, and environmental controls of soil organic carbon stocks in the permafrost regions of the Northern Hemisphere
- 2022
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 828
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Journal article (peer-reviewed)abstract
- Large stocks of soil organic carbon (SOC) accumulated in the Northern Hemisphere permafrost regions may be vulnerable to climatic warming, but global estimates of SOC distribution and magnitude in permafrost regions still have large uncertainties. Based on multiple high-resolution environmental variables and a compiled soil sample dataset (>3000 soil profiles), we used machine-learning methods to estimate the size and spatial distribution of SOC for the top 3 m soils in the Northern Hemisphere permafrost regions. We also identified key environmental predictors of SOC. The results showed that the SOC storage for the top 3 m soil was 1079 ± 174 Pg C across the Northern Hemisphere permafrost regions (20.8 × 106 km2), including 1057 ± 167 Pg C in the northern permafrost regions and 22 ± 7 Pg C in the Third Pole permafrost regions. The mean annual air temperature and NDVI are the main controlling factors for the spatial distribution of SOC stocks in the northern and the Third Pole permafrost regions. Our estimations were more accurate than the existing global SOC stock maps. The results improve our understanding of the regional and global permafrost carbon cycle and their feedback to the climate system.
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| 9. |
- Xia, Yihan, 1990, et al.
(author)
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Large number of putative chemoreception and pheromone biosynthesis genes revealed by analyzing transcriptome from ovipositor-pheromone glands of Chilo suppressalis
- 2015
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 5
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Journal article (peer-reviewed)abstract
- The chemoreception role of moth ovipositor has long been suggested, but its molecular mechanism is mostly unknown. By transcriptomic analysis of the female ovipositor-pheromone glands (OV-PG) of Chilo suppressalis, we obtained 31 putative chemoreception genes (9 OBPs, 10 CSPs, 2 ORs, 1 SNMP, 8 CXEs and 1 AOX), in addition to 32 genes related to sex pheromone biosynthesis (1 FAS, 6 Dess, 10 FARs, 2 ACOs, 1 ACC, 4 FATPs, 3 ACBPs and 5 ELOs). Tissue expression profiles further revealed that CsupCSP2 and CsupCSP10 were OV-PG biased, while most chemoreception genes were highly and preferably expressed in antennae. This suggests that OV-PG employs mostly the same chemoreception proteins as in antennae, although the physiological roles of these proteins might be different in OV-PG. Of the 32 pheromone biosynthesis related genes, CsupDes4, CsupDes5 and CsupFAR2 are strongly OV-PG biased, and clustered with functionally validated genes from other moths, strongly indicating their involvement in specific step of the pheromone biosynthesis. Our study for the first time identified a large number of putative chemoreception genes, and provided an important basis for exploring the chemoreception mechanisms of OV-PG in C. suppressalis, as well as other moth species.
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