Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

General calibration of microbial growth in microplate readers.

ABSTRACT: Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under different nutritional or stress environments, to characterization of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions, and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.

SUBMITTER: Stevenson K

PROVIDER: S-EPMC5153849 | biostudies-other | 2016 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

General calibration of microbial growth in microplate readers.

Stevenson Keiran K McVey Alexander F AF Clark Ivan B N IBN Swain Peter S PS Pilizota Teuta T

Scientific reports 20161213

Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under different nutritional or stress environments, to characterization of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the samp ...[more]

PMID: 27958314

Similar Datasets

A new analysis method for evaluating bacterial growth with microplate readers.

Project description:Growth curve measurements are commonly used in microbiology, while the use of microplate readers for such measurements provides better temporal resolution and higher throughput. However, evaluating bacterial growth with microplate readers has been hurdled by barriers such as multiple scattering. Here, we report our development of a method based on the time derivatives of the optical density (OD) and/or fluorescence (FL) of bacterial cultures to overcome these barriers. First, we illustrated our method using quantitative models and numerical simulations, which predicted the number of bacteria and the number of fluorescent proteins in time as well as their time derivatives. Then, we systematically investigated how the time derivatives depend on the parameters in the models/simulations, providing a framework for understanding the FL growth curves. In addition, as a demonstration, we applied our method to study the lag time elongation of bacteria subjected to treatment with silver (Ag+) ions and found that the results from our method corroborated well with that from growth curve fitting by the Gompertz model that has been commonly used in the literature. Furthermore, this method was applied to the growth of bacteria in the presence of silver nanoparticles (AgNPs) at various concentrations, where the OD curve measurements failed. We showed that our method allowed us to successfully extract the growth behavior of the bacteria from the FL measurements and understand how the growth was affected by the AgNPs.

| S-EPMC7802944 | biostudies-literature

Calibration and analysis of genome-based models for microbial ecology.

Project description:Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

| S-EPMC4608356 | biostudies-literature

Calibration and validation of an innovative approach for estimating general cognitive performance.

Project description:OBJECTIVE:To evaluate a new approach for creating a composite measure of cognitive function, we calibrated a measure of general cognitive performance from existing neuropsychological batteries. METHODS:We applied our approach in an epidemiological study and scaled the composite to a nationally representative sample of older adults. Criterion validity was evaluated against standard clinical diagnoses. Convergent validity was evaluated against the Mini-Mental State Examination (MMSE). RESULTS:The general cognitive performance factor was scaled to have a mean of 50 and standard deviation of 10 in a nationally representative sample of older adults. A cutoff point of approximately 45, corresponding to an MMSE of 23/24, optimally discriminated participants with and without dementia (sensitivity = 0.94, specificity = 0.90, area under the curve = 0.97). The general cognitive performance factor was internally consistent (Cronbach's ? = 0.91) and provided reliable measures of functional ability across a wide range of cognitive functioning. It demonstrated minimal floor and ceiling effects, which is an improvement over most individual cognitive tests. CONCLUSIONS:The cognitive composite is a highly reliable measure, with minimal floor and ceiling effects. We calibrated it using a nationally representative sample of adults over the age of 70 in the USA and established diagnostically relevant cutoff points. Our methods can be used to harmonize neuropsychological test results across diverse settings and studies.

| S-EPMC3988278 | biostudies-literature

Formulation, General Features and Global Calibration of a Bioenergetically-Constrained Fishery Model.

Project description:Human exploitation of marine resources is profoundly altering marine ecosystems, while climate change is expected to further impact commercially-harvested fish and other species. Although the global fishery is a highly complex system with many unpredictable aspects, the bioenergetic limits on fish production and the response of fishing effort to profit are both relatively tractable, and are sure to play important roles. Here we describe a generalized, coupled biological-economic model of the global marine fishery that represents both of these aspects in a unified framework, the BiOeconomic mArine Trophic Size-spectrum (BOATS) model. BOATS predicts fish production according to size spectra as a function of net primary production and temperature, and dynamically determines harvest spectra from the biomass density and interactive, prognostic fishing effort. Within this framework, the equilibrium fish biomass is determined by the economic forcings of catchability, ex-vessel price and cost per unit effort, while the peak harvest depends on the ecosystem parameters. Comparison of a large ensemble of idealized simulations with observational databases, focusing on historical biomass and peak harvests, allows us to narrow the range of several uncertain ecosystem parameters, rule out most parameter combinations, and select an optimal ensemble of model variants. Compared to the prior distributions, model variants with lower values of the mortality rate, trophic efficiency, and allometric constant agree better with observations. For most acceptable parameter combinations, natural mortality rates are more strongly affected by temperature than growth rates, suggesting different sensitivities of these processes to climate change. These results highlight the utility of adopting large-scale, aggregated data constraints to reduce model parameter uncertainties and to better predict the response of fisheries to human behaviour and climate change.

| S-EPMC5245811 | biostudies-literature

Quantitative Microplate-Based Growth Assay for Determination of Antifungal Susceptibility of Histoplasma capsulatum Yeasts.

Project description:Standardized methodologies for determining the antifungal susceptibility of fungal pathogens is central to the clinical management of invasive fungal disease. Yeast-form fungi can be tested using broth macrodilution and microdilution assays. Reference procedures exist for Candida species and Cryptococcus yeasts; however, no standardized methods have been developed for testing the antifungal susceptibility of yeast forms of the dimorphic systemic fungal pathogens. For the dimorphic fungal pathogen Histoplasma capsulatum, susceptibility to echinocandins differs for the yeast and the filamentous forms, which highlights the need to employ Histoplasma yeasts, not hyphae, in antifungal susceptibility tests. To address this, we developed and optimized methodology for the 96-well microtiter plate-based measurement of Histoplasma yeast growth in vitro. Using optical density, the assay is quantitative for fungal growth with a dynamic range greater than 30-fold. Concentration and assay reaction time parameters were also optimized for colorimetric (MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] reduction) and fluorescent (resazurin reduction) indicators of fungal vitality. We employed this microtiter-based assay to determine the antifungal susceptibility patterns of multiple clinical isolates of Histoplasma representing different phylogenetic groups. This methodology fulfills a critical need for the ability to monitor the effectiveness of antifungals on Histoplasma yeasts, the morphological form present in mammalian hosts and, thus, the form most relevant to disease.

| S-EPMC4572531 | biostudies-literature

Calibration array

Project description:Calibration array used to assess probe specific binding behaviour across eight different amounts of DNA starting material. This calibration step was performed to select one best out of three probes per gene based on probe responsiveness on increasing DNA staring material. It was further used to calibrate a subsequent microarray experiment to account for probe specific binding behaviour as part of the normalization process (see also Dennenmoser et al. 2017 Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).

2017-07-01 | GSE93063 | GEO

A Microplate Reader-Based System for Visualizing Transcriptional Activity During in vivo Microbial Interactions in Space and Time.

Project description:Here, we report the development of a microplate reader-based system for visualizing gene expression dynamics in living bacterial cells in response to a fungus in space and real-time. A bacterium expressing the red fluorescent protein mCherry fused to the promoter region of a regulator gene nunF indicating activation of an antifungal secondary metabolite gene cluster was used as a reporter system. Time-lapse image recordings of the reporter red signal and a green signal from fluorescent metabolites combined with microbial growth measurements showed that nunF-regulated gene transcription is switched on when the bacterium enters the deceleration growth phase and upon physical encounter with fungal hyphae. This novel technique enables real-time live imaging of samples by time-series multi-channel automatic recordings using a microplate reader as both an incubator and image recorder of general use to researchers. The technique can aid in deciding when to destructively sample for other methods e.g. transcriptomics and mass spectrometry imaging to study gene expression and metabolites exchanged during the interaction.

| S-EPMC5412646 | biostudies-literature

Intensive Summer Intervention Drives Linear Growth of Reading Skill in Struggling Readers.

Project description:A major achievement of reading research has been the development of effective intervention programs for struggling readers. Most intervention studies employ a pre-post design, to examine efficacy, but this precludes the study of growth curves over the course of the intervention program. Determining the time-course of improvement is essential for cost-effective, evidence-based decisions on the optimal intervention dosage. The goal of this study was to analyze reading growth curves during an intensive summer intervention program. A cohort of 31 children (6-12 years) with reading difficulties (N = 21 with dyslexia diagnosis) were enrolled in 160 h of intervention occurring over 8 weeks of summer vacation. We collected behavioral measures over 4 sessions assessing decoding, oral reading fluency, and comprehension. Mixed-effects modeling of longitudinal measurements revealed a linear dose-response relationship between hours of intervention and improvement in reading ability; there was significant linear growth on every measure of reading skill and none of the measures showed non-linear growth trajectories. Decoding skills showed substantial growth [Cohen's d = 0.85 (WJ Basic Reading Skills)], with fluency and comprehension growing more gradually [d = 0.41 (WJ Reading Fluency)]. These results highlight the opportunity to improve reading skills over an intensive, short-term summer intervention program, and the linear dose-response relationship between duration and gains enables educators to set reading level goals and design a treatment plan to achieve them.

| S-EPMC6716466 | biostudies-literature

Calibration array

Project description:Calibration array

| PRJNA359764 | ENA

Targeting chromatin readers.

Project description:Modulation of gene expression through epigenetic signaling has recently emerged as a novel approach in treating human disease. Specifically, chromatin reader proteins, which mediate protein-protein interactions via binding to modified lysine residues, are gaining traction as potential therapeutic targets. Herein, we review recent efforts to understand and modulate the activity of chromatin reader proteins with small-molecule ligands.

| S-EPMC4310568 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data