ArticleApplied and environmental microbiology2015
Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.
Article in Applied and environmental microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
14 citing papers in PubMed, 25 citations in OpenAlex.
- Gellan gum-based media recover more diverse microbial communities from soil material.Archives of microbiology · 2025Article
- Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes.Molecular systems biology · 2024Article
- Development of hydrogel-based standards and phantoms for non-linear imaging at depth.Journal of biomedical optics · 2023Article
- Characterizing a Cost-Effective Hydrogel-Based Transparent Soil.Gels (Basel, Switzerland) · 2023Article
- BLINCAR: a reusable bioluminescent and Cas9-based genetic toolset for repeatedly modifying wild-typemSphere · 2023Article
- Cultivation of ammonia-oxidising archaea on solid medium.FEMS microbiology letters · 2022Article
- Advances and Challenges in FluorescenceFrontiers in microbiology · 2022Article
- Preparation of immobilized arylsulfatase on magnetic FeFood science & nutrition · 2021Article
- Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response.G3 (Bethesda, Md.) · 2020Article
- A comprehensive guide to dynamic analysis of microbial gene expression using the 3D-printed PFIbox and a fluorescent reporter library.Nature protocols · 2020Article
- Digital, Rapid, Accurate, and Label-Free Enumeration of Viable Microorganisms Enabled by Custom-Built On-Glass-Slide Culturing Device and Microscopic Scanning.Sensors (Basel, Switzerland) · 2018Article
- Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping.Molecular cell · 2018Article
- Macroscale fluorescence imaging against autofluorescence under ambient light.Light, science & applications · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition.
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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.