A simple mathematical model that describes the growth of the area and the number of total and viable cells in yeast colonies

SNF1 plays a crucial role in the utilization of n-alkane and transcriptional regulation of the genes involved in it in the yeast Yarrowia lipolytica

Yarrowia lipolytica is an ascomycetous yeast that can assimilate hydrophobic carbon sources including oil and n-alkane. The sucrose non-fermenting 1/AMP-activated protein kinase (Snf1/AMPK) complex is involved in the assimilation of non-fermentable carbon sources in various yeasts. However, the role of the Snf1/AMPK complex in n-alkane assimilation in Y. lipolytica has not yet been elucidated. This study aimed to clarify the role of Y. lipolytica SNF1 (YlSNF1) in the utilization of n-alkane. The deletion mutant of YlSNF1 (ΔYlsnf1) exhibited substantial growth defects on n-alkanes of various lengths (C10, C12, C14, and C16), and its growth was restored through the introduction of YlSNF1. Microscopic observations revealed that YlSnf1 tagged with enhanced green fluorescence protein showed dot-like distribution patterns in some cells cultured in the medium containing n-decane, which were not observed in cells cultured in the medium containing glucose or glycerol. The RNA sequencing analysis of ΔYlsnf1 cultured in the medium containing n-decane exhibited 302 downregulated and 131 upregulated genes compared with the wild-type strain cultured in the same medium. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that a significant fraction of the downregulated genes functioned in peroxisomes or were involved in the metabolism of n-alkane and fatty acids. Quantitative real-time PCR analysis confirmed the downregulation of 12 genes involved in the metabolism of n-alkane and fatty acid, ALK1-ALK3, ALK5, ADH7, PAT1, POT1, POX2, PEX3, PEX11, YAS1, and HFD3. Furthermore, ΔYlsnf1 exhibited growth defects on the medium containing the metabolites of n-alkane (fatty alcohol and fatty aldehyde). These findings suggest that YlSNF1 plays a crucial role in the utilization of n-alkane in Y. lipolytica. This study provides important insights into the advanced biotechnological applications of this yeast, including the bioconversion of n-alkane to useful chemicals and the bioremediation of petroleum-contaminated environments.

Integrative analysis of yeast colony growth

Yeast colonies are routinely grown on agar plates in everyday experimental settings to understand basic molecular processes, produce novel drugs, improve health, and so on. Standardized conditions ensure these colonies grow in a reproducible fashion, while in nature microbes are under a constantly changing environment. Here we combine the power of computational simulations and laboratory experiments to investigate the impact of non-standard environmental factors on colony growth. We present the developement and parameterization of a quantitative agent-based model for yeast colony growth to reproduce measurements on colony size and cell number in a colony at non-standard environmental conditions. Specifically, we establish experimental conditions that mimic the effects of humidity changes and nutrient gradients. Our results show how colony growth is affected by moisture changes, nutrient availability, and initial colony inoculation conditions. We show that initial colony spread, not initial cell number have higher impact on the final size and cell number of colonies. Parameters of the model were identified by fitting these experiments and the fitted model gives guidance to establish conditions which enable unlimited growth of yeast colonies.

Modelling the In Vitro Growth of Phytopathogenic Filamentous Fungi and Oomycetes: The Gompertz Parameters as Robust Indicators of Propolis Antifungal Action

Propolis is a resinous mixture produced by honeybees, mainly from plant exudates. With a rich chemical composition including many phenolic compounds, mostly responsible for its biological properties, namely antimicrobial ones, propolis may be a promising alternative to synthetic pesticides. The study of propolis from the south of Portugal and of its potential against phytopathogenic agents are still very recent and different methodological approaches hinder a comparison of efficacies. In this context, we aimed to test the value of a mathematical model for the multiparametric characterization of propolis' antifungal action on solid medium assays. An ethanol extract (EE) of a propolis sample harvested in 2016 from Alves (A16) was characterized in terms of phenolic composition and antimicrobial potential against five phytopathogenic species. A16.EE (500-2000 µg/mL) inhibited the mycelial growth of all the species, with Phytophthora cinnamomi and Biscogniauxia mediterranea being the most susceptible and Colletotrichum acutatum being the least affected. The Gompertz mathematical model proved to be a suitable tool for quantitatively describing the growth profiles of fungi and oomycetes, and its parameters exhibit a high level of discrimination. Our results reveal that propolis extracts may have potential applications beyond traditional uses, particularly within the agri-food sector, allowing beekeepers to make their businesses more profitable and diversified.

MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission

The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.

Tools for classification of growing/non-growing bacterial colonies using laser speckle imaging

Prior research has indicated the feasibility of assessing growth-associated activity in bacterial colonies through the application of laser speckle imaging techniques. A subpixel correlation method was employed to identify variations in sequential laser speckle images, thereby facilitating the visualization of specific zones indicative of microbial growth within the colony. Such differentiation between active (growing) and inactive (non-growing) bacterial colonies holds considerable implications for medical applications, like bacterial response to certain drugs or antibiotics. The present study substantiates the capability of laser speckle imaging to categorize bacterial colonies as growing or non-growing, a parameter which nonvisible in colonies when observed under white light illumination.

Use of the speckle imaging sub-pixel correlation analysis in revealing a mechanism of microbial colony growth

The microbial colony growth is driven by the activity of the cells located on the edges of the colony. However, this process is not visible unless specific staining or cross-sectioning of the colony is done. Speckle imaging technology is a non-invasive method that allows visualization of the zones of increased microbial activity within the colony. In this study, the laser speckle imaging technique was used to record the growth of the microbial colonies. This method was tested on three different microorganisms: Vibrio natriegens, Escherichia coli, and Staphylococcus aureus. The results showed that the speckle analysis system is not only able to record the growth of the microbial colony but also to visualize the microbial growth activity in different parts of the colony. The developed speckle imaging technique visualizes the zone of "the highest microbial activity" migrating from the center to the periphery of the colony. The results confirm the accuracy of the previous models of colony growth and provide algorithms for analysis of microbial activity within the colony.

Automation of yeast spot assays using an affordable liquid handling robot

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.

Preservation of duck eggs through glycerol monolaurate nanoemulsion coating

Duck eggs have a short storage life. In this study, water-washed duck eggs and glycerol monolaurate (GML) coated duck eggs were stored at 25 °C for 70 days (away from light). The water-washed duck eggs started to lose weight from the 4th week. At the same time, Haugh unit and egg yolk index of the water-washed duck eggs started decreasing. The normal GML coating solution (NGML), the higher concentration GML diluent (HGML), and the lower concentration GML diluent (LGML) showed different preservation effects. Among them, NGML showed the strongest protection effect against spoilage of duck eggs. After 70-days storage, the weight loss rate of the NGML coated duck eggs was <6%, which was 4 times lower than that of the water-washed duck eggs; the Haugh unit and the surface morphology were also better than that of the water-washed duck eggs. Furthermore, the total colonies in NGML coated sample was >4 log CFU/g less than that was found in the water-washed samples (Control). The HGML and LGML coating agents were less effective but they might be suitable for the short storage of duck eggs due to the lower cost. Overall, this study provides a sound basis for the preparation and utilization of GML coating solution. The GML coating method is able to extend the shelf life of duck eggs by more than 6 weeks.

Laser speckle imaging for early detection of microbial colony forming units

In this study, an optical contactless laser speckle imaging technique for the early identification of bacterial colony-forming units was tested. The aim of this work is to compare the laser speckle imaging method for the early assessment of microbial activity with standard visual inspection under white light illumination. In presented research, the growth of Vibrio natriegens bacterial colonies on the solid medium was observed and analyzed. Both - visual examination under white light illumination and laser speckle correlation analysis were performed. Based on various experiments and comparisons with the theoretical Gompertz model, colony radius growth curves were obtained. It was shown that the Gompertz model can be used to describe both types of analysis. A comparison of the two methods shows that laser speckle contrast imaging, combined with signal processing, can detect colony growth earlier than standard CFU counting method under white light illumination.

A Quantitative Imaging-Based Protocol for Yeast Growth and Survival on Agar Plates

We present a detailed protocol that describes the evaluation of the growth and survival of yeast cells by quantitatively analyzing spotting assays. This simple method reproducibly detects and quantifies subtle differences in growth by measuring the density of cells within a single spot of defined size on an image of a spotting assay. Our protocol is tailored specifically for low-throughput applications, can be easily adapted for specific experimental conditions, and is accessible to yeast experts and non-experts alike.

For an example of the execution of this protocol, please refer to DiGregorio et al. (Di Gregorio et al., 2020).

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Experimental considerations for enabling spotting assay quantification

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A step-by-step procedure for spotting yeast cultures on agar plates

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Quantification and statistical analysis of spotting assay data