1. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)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.
|
|
2. |
- Falster, Daniel, et al.
(author)
-
AusTraits, a curated plant trait database for the Australian flora
- 2021
-
In: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
-
Journal article (peer-reviewed)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
|
|
3. |
- Pronk, Sander, 1974-, et al.
(author)
-
Copernicus : A new paradigm for parallel adaptive molecular dynamics
- 2011
-
In: Proceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis. - New York, NY, USA : ACM. - 9781450307710 ; , s. 60-
-
Conference paper (peer-reviewed)abstract
- Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6 Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h. To match Copernicus'efficiency, a classical simulation would have to exceed 50 microseconds per day, currently infeasible even with custom hardware designed for simulations.
|
|