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- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 8. |
- Cheung, Ho-Nam, et al.
(författare)
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Assessing the influence of sea surface temperature and arctic sea ice cover on the uncertainty in the boreal winter future climate projections
- 2022
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Ingår i: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894. ; 59:1-2, s. 433-454
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the uncertainty (i.e., inter-model spread) in future projections of the boreal winter climate, based on the forced response of ten models from the CMIP5 following the RCP8.5 scenario. The uncertainty in the forced response of sea level pressure (SLP) is large in the North Pacific, the North Atlantic, and the Arctic. A major part of these uncertainties (31%) is marked by a pattern with a center in the northeastern Pacific and a dipole over the northeastern Atlantic that we label as the Pacific–Atlantic SLP uncertainty pattern (PA∆SLP). The PA∆SLP is associated with distinct global sea surface temperature (SST) and Arctic sea ice cover (SIC) perturbation patterns. To better understand the nature of the PA∆SLP, these SST and SIC perturbation patterns are prescribed in experiments with two atmospheric models (AGCMs): CAM4 and IFS. The AGCM responses suggest that the SST uncertainty contributes to the North Pacific SLP uncertainty in CMIP5 models, through tropical–midlatitude interactions and a forced Rossby wavetrain. The North Atlantic SLP uncertainty in CMIP5 models is better explained by the combined effect of SST and SIC uncertainties, partly related to a Rossby wavetrain from the Pacific and air-sea interaction over the North Atlantic. Major discrepancies between the CMIP5 and AGCM forced responses over northern high-latitudes and continental regions are indicative of uncertainties arising from the AGCMs. We analyze the possible dynamic mechanisms of these responses, and discuss the limitations of this work.
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| 10. |
- Döscher, Ralf, et al.
(författare)
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The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6
- 2022
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 15:7, s. 2973-3020
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Tidskriftsartikel (refereegranskat)abstract
- The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.
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