| 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. |
- Han, Lu, et al.
(författare)
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Crystal twinning of bicontinuous cubic structures
- 2020
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Ingår i: IUCrJ. - 2052-2525. ; 7, s. 228-237
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Tidskriftsartikel (refereegranskat)abstract
- Bicontinuous cubic structures in soft matter consist of two intertwining labyrinths separated by a partitioning layer. Combining experiments, numerical modelling and techniques in differential geometry, we investigate twinning defects in bicontinuous cubic structures. We first demonstrate that a twin boundary is most likely to occur at a plane that cuts the partitioning layer almost perpendicularly, so that the perturbation caused by twinning remains minimal. This principle can be used as a criterion to identify potential twin boundaries, as demonstrated through detailed investigations of mesoporous silica crystals characterized by diamond and gyroid surfaces. We then discuss that a twin boundary can result from a stacking fault in the arrangement of inter-lamellar attachments at an early stage of structure formation. It is further shown that enhanced curvature fluctuations near the twin boundary would cost energy because of geometrical frustration, which would be eased by a crystal distortion that is experimentally observed.
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| 3. |
- Mas-Sandoval, Alex, et al.
(författare)
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ngsJulia : population genetic analysis of next-generation DNA sequencing data with Julia language
- 2022
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the estimation of population genetic parameters. Methods and implementations to estimate population genetic parameters from sequencing data available nowadays either are suitable for the analysis of genomes from model organisms only, require moderate sequencing coverage, or are not easily adaptable to specific applications. To address these issues, we introduce ngsJulia, a collection of templates and functions in Julia language to process short-read sequencing data for population genetic analysis. We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. Through simulations, we illustrate the performance of estimating various population genetic parameters using these implementations, using both established and novel statistical methods. These results inform on optimal experimental design and demonstrate the applicability of methods in ngsJulia to estimate parameters of interest even from low coverage sequencing data. ngsJulia provide users with a flexible and efficient framework for ad hoc analysis of sequencing data.ngsJulia is available from: https://github.com/mfumagalli/ngsJulia
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