| 1. |
- 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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| 2. |
- Michel, Maurice, et al.
(författare)
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Computational and Experimental Druggability Assessment of Human DNA Glycosylases
- 2019
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Ingår i: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 4:7, s. 11642-11656
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Tidskriftsartikel (refereegranskat)abstract
- Due to a polar or even charged binding interface, DNA-binding proteins are considered extraordinarily difficult targets for development of small-molecule ligands and only a handful of proteins have been targeted successfully to date. Recently, however, it has been shown that development of selective and efficient inhibitors of 8-oxoguanine DNA glycosylase is possible. Here, we describe the initial druggability assessment of DNA glycosylases in a computational setting and experimentally investigate several methods to target endonuclease VIII-like 1 (NEIL1) with small-molecule inhibitors. We find that DNA glycosylases exhibit good predicted druggability in both DNA-bound and -unbound states. Furthermore, we find catalytic sites to be highly flexible, allowing for a range of interactions and binding partners. One flexible catalytic site was rationalized for NEIL1 and further investigated experimentally using both a biochemical assay in the presence of DNA and a thermal shift assay in the absence of DNA.
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| 3. |
- Zhu, Bin, et al.
(författare)
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Evaluation of TMPA satellite precipitation in driving VIC hydrological model over the upper Yangtze river basin
- 2020
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- Although the Tropical Rainfall Measurement Mission (TRMM) has come to an end, the evaluation of TRMM satellite precipitation is still of great significance for the improvement of the Global Precipitation Measurement (GPM). In this paper, the hydrological utility of TRMM Multi-satellite Precipitation Analysis (TMPA) 3B42 RTV7/V7 precipitation products was evaluated using the variable infiltration capacity (VIC) hydrological model in the upper Yangtze River basin. The main results show that (1) TMPA 3B42V7 had a reliable performance in precipitation estimation compared with the gauged precipitation on both spatial and temporal scales over the upper Yangtze River basin. Although TMPA 3B42V7 slightly underestimated precipitation, TMPA 3B42RTV7 significantly overestimated precipitation at daily and monthly time scales; (2) the simulated runoff by the VIC hydrological model showed a high correlation with the gauged runoff and lower bias at daily and monthly time scales. The Nash–Sutcliffe coefficient of efficiency (NSCE) value was as high as 0.85, the relative bias (RB) was −6.36% and the correlation coefficient (CC) was 0.93 at the daily scale; (3) the accuracy of the 3B42RTV7-driven runoff simulation had been greatly improved by using the hydrological calibration parameters obtained from 3B42RTV7 compared with that of gauged precipitation. A lower RB (14.38% vs. 66.58%) and a higher CC (0.87 vs. 0.85) and NSCE (0.71 vs. −0.92) can be found at daily time scales when we use satellite data instead of gauged precipitation data to calibrate the VIC model. However, the performance of the 3B42V7-driven runoff simulation did not improve in the same operation accordingly. The cause might be that the 3B42V7 satellite products have been adjusted by gauged precipitation. This study suggests that it might be better to calibrate the parameters using satellite data in hydrological simulations, especially for unadjusted satellite data. This study is not only helpful for understanding the assessment of multi-satellite precipitation products in large-scale and complex areas in the upper reaches of the Yangtze River, but also can provide a reference for the hydrological utility of the satellite precipitation products in other river basins of the world.
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