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| 2. |
- 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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| 3. |
- Kristan, Matej, et al.
(författare)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Sun, M. D., et al.
(författare)
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New short-lived isotope 223Np and the absence of the Z = 92 subshell closure near N = 126
- 2017
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Ingår i: Physics Letters B. - : Elsevier. - 0370-2693 .- 1873-2445. ; 771, s. 303-308
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Tidskriftsartikel (refereegranskat)abstract
- The N=130 short-lived isotope 223Np was produced as evaporation residue (ER) in the fusion reaction 40Ar + 187Re at the gas-filled recoil separator Spectrometer for Heavy Atom and Nuclear Structure (SHANS). It was identified through temporal and spatial correlations with α decays of 215Ac and/or 211Fr, the third and fourth members of the α-decay chain starting from 223Np. The pileup signals of ER(223Np)–α(223Np)–α(219Pa) were resolved by using the digital pulse processing technique. An α decay with half-life of T1/2=2.15(52100) μs and energy of Eα=9477(44) keV was attributed to 223Np. Spin and parity of 9/2− were tentatively proposed for the ground state of 223Np by combining the reduced α-decay width and large-scale shell-model calculations. This assignment together with the proton separation energy disprove the existence of a Z=92 subshell closure.
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| 8. |
- Bard-Chapeau, Emilie A, et al.
(författare)
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Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:1
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Tidskriftsartikel (refereegranskat)abstract
- The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC, we performed a near-saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers and a very large number (2,860) of candidate later stage drivers that were enriched for genes that are mutated, deregulated or functioning in signaling pathways important for human HCC, with a striking 1,199 genes being linked to cellular metabolic processes. Our study provides a comprehensive overview of the genetic landscape of HCC.
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| 9. |
- Bonzom, Cyrielle, 1987, et al.
(författare)
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Feruloyl esterases, effects of glycosylation on activity, stability and immobilization
- 2017
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Feruloyl esterases (FAE; EC 3.1.1.73) are a subclass of carboxylic ester hydrolases. They catalyze the hydrolysis of ester linkages in plant cell walls materials releasing ferulic acid and other hydroxycinnamic acids and therefore have been classified in the CAZy database [1] in the carbohydrate esterase (CE) family. Currently, all FAEs in the CAZY database belong to the CE1 family. Immobilization is a powerful tool to allow enzyme reuse and therefore decrease their cost in the overall process. Immobilization on solid carriers can be achieved by different approaches, one of them is by physical adsorption. This technique relies mainly on the surface charges of the support and enzyme. Mesoporous silica particles (MPS) are porous supports made of silica which pore size can be tuned from 2 to 50 nm depending on the synthesis conditions [2]. Because they are negatively charged, silica particles allow for rapid enzyme immobilization by physical adsorption. Furthermore, the diameter of their pore size can be tuned to match the one of the enzyme used and greatly reduces leaching after immobilization.Depending on the production host of the enzyme, the glycosylation extent and/or pattern can vary from none in Escherichia coli to hyper-glycosylation in Pichia pastoris. Glycosylation has been shown to alter activity and stability of enzymes [3]. Our hypothesis was that glycosylation would influence the immobilization behavior of the studied FAE in MPS as well as its activity.In this study, the same enzyme MtFae1a from the fungus Myceliophtora thermophila has been expressed in three different host organisms: E. coli, M. thermophila and P. pastoris to achieve different degrees of glycosylation. The proteins were then purified and biochemically characterized. Different behaviors were observed depending on the production host of the enzymes, for instance in terms of specific activity and temperature optima. Furthermore, glycosylation affected the immobilization capacity of the enzymes on MPS, as well as the activity of immobilized FAEs.[1]B.L. Cantarel, P.M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, B. Henrissat, The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Res. 37 (2009) D233–238. doi:10.1093/nar/gkn663.[2]D. Zhao, J. Feng, Q. Huo, N. Melosh, G.H. Fredrickson, B.F. Chmelka, G.D. Stucky, Triblock Copolymer Syntheses of Mesoporous Silica with Periodic 50 to 300 Angstrom Pores, Science. 279 (1998) 548–552. doi:10.1126/science.279.5350.548.[3]A. Basso, P. Braiuca, S. Cantone, C. Ebert, P. Linda, P. Spizzo, P. Caimi, U. Hanefeld, G. Degrassi, L. Gardossi, In Silico Analysis of Enzyme Surface and Glycosylation Effect as a Tool for Efficient Covalent Immobilisation of CalB and PGA on Sepabeads®, Adv. Synth. Catal. 349 (2007) 877–886. doi:10.1002/adsc.200600337.
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| 10. |
- Bonzom, Cyrielle, 1987, et al.
(författare)
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Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila
- 2019
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Ingår i: AMB Express. - : Springer Science and Business Media LLC. - 2191-0855. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Heterologous protein production is widely used in industrial biotechnology. However, using non-native production hosts can lead to enzymes with altered post-translational modifications, such as glycosylation. We have investigated how production in a non-native host affects the physicochemical properties and enzymatic activity of a feruloyl esterase from Myceliophthora thermophila, MtFae1a. The enzyme was produced in two microorganisms that introduce glycosylation (M. thermophila and Pichia pastoris) and in Escherichia coli (non-glycosylated). Mass spectrometric analysis confirmed the presence of glycosylation and revealed differences in the lengths of glycan chains between the enzymes produced in M. thermophila and P. pastoris. The melting temperature and the optimal temperature for activity of the non-glycosylated enzyme were considerably lower than those of the glycosylated enzymes. The three MtFae1a versions also exhibited differences in specific activity and specificity. The catalytic efficiency of the glycosylated enzymes were more than 10 times higher than that of the non-glycosylated one. In biotechnology, immobilization is often used to allow reusing enzyme and was investigated on mesoporous silica particles. We found the binding kinetics and immobilization yield differed between the enzyme versions. The largest differences were observed when comparing enzymes with and without glycosylation, but significant variations were also observed between the two differently glycosylated enzymes. We conclude that the biotechnological value of an enzyme can be optimized for a specific application by carefully selecting the production host.
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