| 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. |
- Abrahamsson, Oskar, 1986, et al.
(författare)
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Proof-Producing Synthesis of CakeML from Monadic HOL Functions
- 2020
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Ingår i: Journal of Automated Reasoning. - : Springer Science and Business Media LLC. - 0168-7433 .- 1573-0670. ; 64:7, s. 1287-1306
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Tidskriftsartikel (refereegranskat)abstract
- We introduce an automatic method for producing stateful ML programs together with proofs of correctness from monadic functions in HOL. Our mechanism supports references, exceptions, and I/O operations, and can generate functions manipulating local state, which can then be encapsulated for use in a pure context. We apply this approach to several non-trivial examples, including the instruction encoder and register allocator of the otherwise pure CakeML compiler, which now benefits from better runtime performance. This development has been carried out in the HOL4 theorem prover.
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| 3. |
- Ngo, Son Tung, et al.
(författare)
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Distal Hydrophobic Loop Modulates the Copper Active Site and Reaction of AA13 Polysaccharide Monooxygenases
- 2022
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:39, s. 7567-7578
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Tidskriftsartikel (refereegranskat)abstract
- Polysaccharide monooxygenases (PMOs) use a type-2 copper center to activate O2 for the selective hydroxylation of one of the two C-H bonds of glycosidic linkages. Our electron paramagnetic resonance (EPR) analysis and molecular dynamics (MD) simulations suggest the unprecedented dynamic roles of the loop containing the residue G89 (G89 loop) on the active site structure and reaction cycle of starch-active PMOs (AA13 PMOs). In the Cu(II) state, the G89 loop could switch between an open and closed conformation, which is associated with the binding and dissociation of an aqueous ligand in the distal site, respectively. The conformation of the G89 loop influences the positioning of the copper center on the preferred substrate of AA13 PMOs. The dissociation of the distal ligand results in the bending of the T-shaped core of the Cu(II) active site, which could help facilitate its reduction to the active Cu(I) state. In the Cu(I) state, the G89 loop is in the closed conformation with a confined copper center, which could allow for efficient O2 binding. In addition, the G89 loop remains in the closed conformation in the Cu(II)-superoxo intermediate, which could prevent off-pathway superoxide release via exchange with the distal aqueous ligand. Finally, at the end of the reaction cycle, aqueous ligand binding to the distal site could switch the G89 loop to the open conformation and facilitate product release.
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| 4. |
- Nguyen, Son Tien, et al.
(författare)
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Electron paramagnetic resonance and theoretical study of gallium vacancy in β-Ga2O3
- 2020
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Ingår i: Applied Physics Letters. - : AMER INST PHYSICS. - 0003-6951 .- 1077-3118. ; 117:3
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Tidskriftsartikel (refereegranskat)abstract
- Unintentionally doped n-type beta -Ga2O3 becomes highly resistive after annealing at high temperatures in oxygen ambient. The annealing process also induces an electron paramagnetic resonance (EPR) center, labeled IR1, with an electron spin of S=1/2 and principal g-values of g(xx)=2.0160, g(yy)=2.0386, and g(zz)=2.0029 with the principal axis of g(zz) being 60 degrees from the [001](*) direction and g(yy) along the b-axis. A hyperfine (hf) structure due to the hf interaction between the electron spin and nuclear spins of two equivalent Ga atoms with a hf splitting of similar to 29G (for Ga-69) has been observed. The center can also be created by electron irradiation. Comparing the Ga hf constants determined by EPR with corresponding values calculated for different Ga vacancy-related defects, the IR1 defect is assigned to the double negative charge state of either the isolated Ga vacancy at the tetrahedral site (V-Ga(I)(2-)) or the V-Ga(I)-Ga-ib-V-Ga(I) complex.
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| 5. |
- Son, Hoang Nghia, et al.
(författare)
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Effects of simulated microgravity on the morphology of mouse embryonic fibroblasts (MEFs)
- 2020
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Ingår i: Romanian Biotechnological Letters. - Bucharest : University of Bucharest. - 1224-5984 .- 2248-3942. ; 25:6, s. 2156-2160
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to assess the effects of simulated microgravity on mouse embryonic fibroblast (MEF) morphology. The results showed that the area of MEFs under simulated microgravity was 7843.39 +/- 551.31 mu m(2) which was lower than the control group (9832.72 +/- 453.86 mu m(2)) (p < 0.001). The nuclear area of MEFs under simulated microgravity (290.76 +/- 4.58 mu m(2)) and the control group (296.8 +/- 4.58 mu m(2)) did not statistically differ. In addition, the nuclear shape value of the MEFs under simulated microgravity and the control group did not statistically differ (0.86 +/- 0.006 vs. 0.87 +/- 0.003, respectively). The nuclear intensity of MEFs under simulated microgravity (19361 +/- 852) was higher than the control group (16997 +/- 285) (P <0.05). Moreover, the flow cytometry analysis indicated the reduced GO/G1 phase cell ratio and the increased S phase and G2/M phase cell ratio in MEFs under simulated microgravity. Simulated microgravity also induced a decrease in diameter of actin filament bundles of the MEFs under simulated microgravity (1.61 +/- 0.33 mu m) compared to the control group (1.79 +/- 0.32 mu m) (P <0.01). These results revealed that simulated microgravity is capable of inducing the morphological changes of mouse embryonic fibroblasts.
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