ArticleBMC biotechnology2014
Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers.
Article in BMC biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Going beyond size: exploring the metabolic burden inSynthetic biology (Oxford, England) · 2026Article
- The type of carbon source not the growth rate it supports can determine diauxie in Saccharomyces cerevisiae.Communications biology · 2025Article
- Room-temperature mL-to-μL quantitative liquid concentration device for cyclone flow.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2024Article
- ACtivE: Assembly and CRISPR-TargetedACS synthetic biology · 2022Article
- Absolute protein quantification using fluorescence measurements with FPCountR.Nature communications · 2022Article
- Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity.Biophysical journal · 2022Article
- Reliable online measurement of population dynamics for filamentous co-cultures.Microbial biotechnology · 2022Article
- Tunable population dynamics in a synthetic filamentous coculture.MicrobiologyOpen · 2022Article
- SAIBR: a simple, platform-independent method for spectral autofluorescence correction.Development (Cambridge, England) · 2022Article
- Live-cell fluorescence spectral imaging as a data science challenge.Biophysical reviews · 2022Review
- Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff.PLoS computational biology · 2022Article
- Accurate characterization of dynamic microbial gene expression and growth rate profiles.Synthetic biology (Oxford, England) · 2022Article
- Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes.Trends in biotechnology · 2021Review
- FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.ACS synthetic biology · 2020Article
- A Nitrate-BlindFrontiers in bioengineering and biotechnology · 2020Article
- Fluorescent reporter plasmids for single-cell and bulk-level composition assays in E. faecalis.PloS one · 2020Article
- In vivo measurements reveal a single 5'-intron is sufficient to increase protein expression level in Caenorhabditis elegans.Scientific reports · 2019Article
- WellInverter: a web application for the analysis of fluorescent reporter gene data.BMC bioinformatics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundTo connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require specialist expertise if single cells are to be followed. Fluorescence plate readers, however, a standard in many laboratories, can in principle provide similar data, albeit at a mean, population level. Nevertheless, extracting the average fluorescence per cell is challenging because autofluorescence can be substantial.
resultsHere we propose a general method for correcting plate reader measurements of fluorescent proteins that uses spectral unmixing and determines both the fluorescence per cell and the errors on that fluorescence. Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription. We illustrate the method by following the induction of the GAL genes in Saccharomyces cerevisiae for over 20 hours in different sugars and argue that the order of appearance of the Leloir enzymes may be to reduce build-up of the toxic intermediate galactose-1-phosphate. Further, we quantify protein levels of over 40 genes, again over 20 hours, after cells experience a change in carbon source (from glycerol to glucose).
conclusionsOur methodology is sensitive, scalable, and should be applicable to other organisms. By allowing quantitative measurements on a per cell basis over tens of hours and over hundreds of genes, it should increase our understanding of the dynamic changes that drive cellular behaviour.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.