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Raas MWD, Silva TP, Freitas JCO, Campos LM, Fabri RL, Melo RCN. Whole slide imaging is a high-throughput method to assess Candida biofilm formation. Microbiol Res 2021; 250:126806. [PMID: 34157481 DOI: 10.1016/j.micres.2021.126806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 01/11/2023]
Abstract
New strategies that enable fast and accurate visualization of Candida biofilms are necessary to better study their structure and response to antifungals agents. Here, we applied whole slide imaging (WSI) to study biofilm formation of Candida species. Three relevant biofilm-forming Candida species (C. albicans ATCC 10231, C. glabrata ATCC 2001, and C. tropicalis ATCC 750) were cultivated on glass coverslips both in presence and absence of widely used antifungals. Accumulated biofilms were stained with fluorescent markers and scanned in both bright-field and fluorescence modes using a WSI digital scanner. WSI enabled clear assessment of both size and structural features of Candida biofilms. Quantitative analyses readily detected reductions in biofilm-covered surface area upon antifungal exposure. Furthermore, we show that the overall biofilm growth can be adequately assessed across both bright-field and fluorescence modes. At the single-cell level, WSI proved adequate, as morphometric parameters evaluated with WSI did not differ significantly from those obtained with scanning electron microscopy, considered as golden standard at single-cell resolution. Thus, WSI allows for reliable visualization of Candida biofilms enabling both large-scale growth assessment and morphometric characterization of single-cell features, making it an important addition to the available microscopic toolset to image and analyse fungal biofilm growth.
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Affiliation(s)
- Maximilian W D Raas
- Laboratory of Cellular Biology, Department of Biology, ICB, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil; Faculty of Medical Sciences, Radboud University, Nijmegen, the Netherlands
| | - Thiago P Silva
- Laboratory of Cellular Biology, Department of Biology, ICB, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil
| | - Jhamine C O Freitas
- Bioactive Natural Products Laboratory, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil
| | - Lara M Campos
- Bioactive Natural Products Laboratory, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil
| | - Rodrigo L Fabri
- Bioactive Natural Products Laboratory, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil
| | - Rossana C N Melo
- Laboratory of Cellular Biology, Department of Biology, ICB, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG, Brazil.
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2
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Zhao XM, Li S. HISP: a hybrid intelligent approach for identifying directed signaling pathways. J Mol Cell Biol 2018; 9:453-462. [DOI: 10.1093/jmcb/mjx054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/20/2017] [Indexed: 01/15/2023] Open
Affiliation(s)
- Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Shan Li
- Department of Mathematics, Shanghai University, Shanghai 200444, China
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3
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Hope EA, Amorosi CJ, Miller AW, Dang K, Heil CS, Dunham MJ. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast. Genetics 2017; 206:1153-1167. [PMID: 28450459 PMCID: PMC5499169 DOI: 10.1534/genetics.116.198895] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/06/2017] [Indexed: 02/02/2023] Open
Abstract
Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.
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Affiliation(s)
- Elyse A Hope
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Aaron W Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Kolena Dang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Caiti Smukowski Heil
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
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Stern DL. Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Trends Genet 2014; 30:547-54. [PMID: 25278102 DOI: 10.1016/j.tig.2014.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 12/18/2022]
Abstract
The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.
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Affiliation(s)
- David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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Rare variants in hypermutable genes underlie common morphology and growth traits in wild Saccharomyces paradoxus. Genetics 2013; 195:513-25. [PMID: 23934881 DOI: 10.1534/genetics.113.155341] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the molecular basis of common traits is a primary challenge of modern genetics. One model holds that rare mutations in many genetic backgrounds may often phenocopy one another, together explaining the prevalence of the resulting trait in the population. For the vast majority of phenotypes, the role of rare variants and the evolutionary forces that underlie them are unknown. In this work, we use a population of Saccharomyces paradoxus yeast as a model system for the study of common trait variation. We observed an unusual, flocculation and invasive-growth phenotype in one-third of S. paradoxus strains, which were otherwise unrelated. In crosses with each strain in turn, these morphologies segregated as a recessive Mendelian phenotype, mapping either to IRA1 or to IRA2, yeast homologs of the hypermutable human neurofibromatosis gene NF1. The causal IRA1 and IRA2 haplotypes were of distinct evolutionary origin and, in addition to their morphological effects, associated with hundreds of stress-resistance and growth traits, both beneficial and disadvantageous, across S. paradoxus. Single-gene molecular genetic analyses confirmed variant IRA1 and IRA2 haplotypes as causal for these growth characteristics, many of which were independent of morphology. Our data make clear that common growth and morphology traits in yeast result from a suite of variants in master regulators, which function as a mutation-driven switch between phenotypic states.
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Hsp90 regulates nongenetic variation in response to environmental stress. Mol Cell 2013; 50:82-92. [PMID: 23434373 DOI: 10.1016/j.molcel.2013.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/28/2012] [Accepted: 01/15/2013] [Indexed: 01/06/2023]
Abstract
Nongenetic cell-to-cell variability often plays an important role for the survival of a clonal population in the face of fluctuating environments. However, the underlying mechanisms regulating such nongenetic heterogeneity remain elusive in most organisms. We report here that a clonal yeast population exhibits morphological heterogeneity when the level of Hsp90, a molecular chaperone, is reduced. The morphological heterogeneity is driven by the dosage of Cdc28 and Cla4, a key regulator of septin formation. Low Hsp90 levels reduce Cla4 protein stability and cause a subpopulation of cells to switch to a filamentous form that has been previously suggested to be beneficial under certain hostile environments. Moreover, Hsp90-dependent morphological heterogeneity can be induced by environmental stress and is conserved across diverse yeast species. Our results suggest that Hsp90 provides an evolutionarily conserved mechanism that links environmental stress to the induction of morphological diversity.
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