| 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. |
- Kim, Dae-Kyum, et al.
(författare)
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EVpedia: A Community Web Portal for Extracellular Vesicles Research
- 2015
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 31:6, s. 933-939
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. Results: We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research.
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| 3. |
- Lee, Alpha A., et al.
(författare)
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Fluctuation spectra and force generation in nonequilibrium systems
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:35, s. 9255-9260
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Tidskriftsartikel (refereegranskat)abstract
- Many biological systems are appropriately viewed as passive inclusions immersed in an active bath: from proteins on active membranes to microscopic swimmers confined by boundaries. The nonequilibrium forces exerted by the active bath on the inclusions or boundaries often regulate function, and such forces may also be exploited in artificial active materials. Nonetheless, the general phenomenology of these active forces remains elusive. We show that the fluctuation spectrum of the active medium, the partitioning of energy as a function of wavenumber, controls the phenomenology of force generation. We find that, for a narrow, unimodal spectrum, the force exerted by a nonequilibrium system on two embedded walls depends on the width and the position of the peak in the fluctuation spectrum, and oscillates between repulsion and attraction as a function of wall separation. We examine two apparently disparate examples: the Maritime Casimir effect and recent simulations of active Brownian particles. A key implication of our work is that important nonequilibrium interactions are encoded within the fluctuation spectrum. In this sense, the noise becomes the signal.
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| 4. |
- Suñé, Marc, et al.
(författare)
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Wrinkling composite sheets
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We examine the buckling shape and critical compression of confined inhomogeneous composite sheets lying on a liquid foundation. The buckling modes are controlled by the bending stiffness of the sheet, the density of the substrate, and the size and the spatially dependent elastic coefficients of the sheet. We solve the (linearized) Föppl–von Kármán equations describing the mechanical equilibrium of a sheet when its bending stiffness varies parallel to the direction of confinement. The case of a homogeneous bending stiffness exhibits a degeneracy of wrinkled states for certain sizes of the confined sheet. This degeneracy disappears for spatially dependent elastic coefficients. Medium length sheets buckle similarly to their homogeneous counterparts, whereas the wrinkled states in large length sheets localize the bending energy towards the soft regions of the sheet.
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| 5. |
- Sune, Marc, et al.
(författare)
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Wrinkling composite sheets
- 2023
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Ingår i: Soft Matter. - 1744-683X .- 1744-6848. ; 19:45, s. 8729-8743
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Tidskriftsartikel (refereegranskat)abstract
- We examine the buckling shape and critical compression of confined inhomogeneous composite sheets lying on a liquid foundation. The buckling modes are controlled by the bending stiffness of the sheet, the density of the substrate, and the size and the spatially dependent elastic coefficients of the sheet. We solve the beam equation describing the mechanical equilibrium of a sheet when its bending stiffness varies parallel to the direction of confinement. The case of a homogeneous bending stiffness exhibits a degeneracy of wrinkled states for certain lengths of the confined sheet; we explain this degeneracy using an asymptotic analysis valid for long sheets, and show that it corresponds to the switching of the sheet between symmetric and antisymmetric buckling modes. This degeneracy disappears for spatially dependent elastic coefficients. Medium length sheets buckle similarly to their homogeneous counterparts, whereas the wrinkled states in large length sheets concentrate the bending energy towards the soft regions of the sheet. We examine the buckling shape and critical compression of confined inhomogeneous composite sheets lying on a liquid foundation.
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| 6. |
- Suñé, Marc, et al.
(författare)
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Wrinkling composite sheets
- 2023
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 19:45, s. 8729-8743
-
Tidskriftsartikel (refereegranskat)abstract
- We examine the buckling shape and critical compression of confined inhomogeneous composite sheets lying on a liquid foundation. The buckling modes are controlled by the bending stiffness of the sheet, the density of the substrate, and the size and the spatially dependent elastic coefficients of the sheet. We solve the beam equation describing the mechanical equilibrium of a sheet when its bending stiffness varies parallel to the direction of confinement. The case of a homogeneous bending stiffness exhibits a degeneracy of wrinkled states for certain lengths of the confined sheet; we explain this degeneracy using an asymptotic analysis valid for long sheets, and show that it corresponds to the switching of the sheet between symmetric and antisymmetric buckling modes. This degeneracy disappears for spatially dependent elastic coefficients. Medium length sheets buckle similarly to their homogeneous counterparts, whereas the wrinkled states in large length sheets concentrate the bending energy towards the soft regions of the sheet.
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