Growth Of Yeast Colonies Research Articles

Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis.

This study used live-cell microscopy to track changes in the level of a key enzyme in GTP nucleotide biosynthesis, inosine monophosphate dehydrogenase (IMPDH), during growth of a brewers yeast colony over 2 days in a microfluidic device. The results show that feedback regulation via transcription attenuation allows cells to adapt to nutrient limitation in the crowded environs of a yeast colony. They also identify a novel mode of regulation of IMPDH level that is not driven by guanine nucleotide availability.

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.

Влияние геотермальной воды в составе твердых сред культивирования на морфологические свойства дрожжей рода Saccharomyces

The influence of geothermal waters located on the territory of the city of Makhachkala (Republic of Dagestan), in the composition of solid cultivation media, on the cultural and morphological features of genus Saccharomyces yeast was studied. Changes in cell properties and the formation of specific parameters of giant yeast colonies S. cerevisiae Y-503, S. cerevisiae DAW-3a, S. oviformis M-12x have been established. For YPD and PD media, as a result of a series of experiments, optimal options were selected containing geothermal and distilled water in a ratio of 1:1 (well No. 36) and 2:1 (well No. 26). It was shown that the YPD medium was optimal for yeast growth, while in the population of the tetraploid Y-503 strain, the average cell size was slightly larger than cell strain M-12x and significantly exceeded the DAW-3a values. Installed that the use of diluted water from well No. 36 in the cultivation medium is most effective and leads to accelerated growth of yeast colonies. In the variant geothermal / distilled water, this indicator exceeded the control by 1.3 (Y-503, M-12x) times; in the variant with geothermal water without dilution - by 1.6 (Y-503) and 1.4 (M-12x) times. The cells of the S. cerevisiae Y-503 strain, regardless of the medium used, are characterized by the presence of various forms, including elongated ones; DAW-3a - exceptionally rounded; S. oviformis M-12x - rounded and oval shapes. A comparative analysis of the parameters of the colonies showed that all variants are characterized by a rounded shape, a radially striated surface; flat, with a convex center profile; light beige color and pasty, spreadable texture. As a result of our research, a modified nutrient medium PD has been developed - an agar for growing yeast, containing geothermal water from well No. 36 of the Makhachkala field as an additional source of mineral and organic compounds. The proposed composition of the medium is of interest for its further use in microbiological studies.

Protein-Protein Interaction via Two-Hybrid Assay in Yeast.

The yeast two-hybrid assay enables detecting interactions between proteins, which makes this tool of particular interest for plant-virus interaction studies. Basically, the reporter gene expression (HIS3) is activated by the binding of a transcription factor GAL4, which, like eukaryotic transcription factors, is modular in nature and consists of two structurally independent domains: DNA-binding (DB) and activation (AD) domains. The two proteins under investigation are expressed separately, one fused to the BD domain and the other to the AD domain. In the yeast strain AH109, activation of the reporter gene occurs only in cells that contain interacting proteins, reconstituting the transcription factor GAL4 which then binds to the responsive promoter and results in yeast colony growth.

Effects of an enzyme agent containing mutanase and dextranase for treatment of biofilms in bacteria- and yeast-infected canine otitis externa

The purpose of this study was to evaluate in detail both the in vivo and in vitro efficacy of the enzyme agents, ZYMOX® Plus Otic (ZYMOX-P), in the treatment of canine otitis externa (OE). Eight dogs with a diagnosis of non-seasonal severe chronic OE were recruited for the study. ZYMOX-P was administered for 2-4 weeks. The Otitis Index Score (OTIS3) and bacteria or yeast colony growth were measured. Also, minimum biofilm (BF) formation inhibition concentration (MBIC) and BF bactericidal concentration (BBC) were measured in vitro. OTIS3 showed a statistically significant reduction after treatment (88.2%, p⟨0.001; pre-treatment = 11.0 ± 0.9; post-treatment = 1.3 ± 0.4, mean ± SEM). The individual OTIS scores, erythema, edema, erosions/ ulcerations, exudate and pruritus showed significant reduction (85.7%, 95.7%, 83.3%, 80.0%, and 89.3%, respectively). Microscopic examination revealed the presence of BF exopolysaccharide in all 8 ear samples when stained with alcian blue. Seven of the 8 dogs (87.5%) showed a reduction in colony growth. ZYMOX-P was effective at 34-fold and 16-fold dilutions on MBIC and BBC, respectively. These findings indicate that ZYMOX-P has efficacy against BF-related infection and is beneficial when used for the management of canine OE.

Identification of Candida Species among Renal Transplanted Recipient, In Khartoum, Sudan 2021

Background: Kidney transplantation represents the optimal therapeutic tool for patients affected by end-stage renal disease (ESRD), Candidiasis is a major challenge among renal transplant recipients (RTRs) worldwide and is associated with high morbidity and mortality rates. Fluconazole is the most commonly used agent for Candida infections Aim: to identify Candida spp from renal transplanted patients. Method: cross sectional study were done, 51 Urine sample was collected on sterile urine container then cultured on Sabouraud dextrose agar, incubated at 35 °C and observed daily for 7 days. When the growth of yeast colonies was observed, the Gram stain method was done to verify the absence of bacterial contamination. The yeasts were identified via germ tube test and chromogenic media to differentiate between candida spp. Results: out of 51 patients; female were more than male wit mean age group 45 years for both male and female.The cause of ESRD was; 19 (37.3%) had DM, 12(23.5%) had hypertension, 10(19.6%) had Glomerulonephritis and 3(5.9%) had kidney stone candida species among study group as follow; c.albicans isolated from 28 (54.9%) pt., c.glabrata isolated from 11 (21.6%) pt., c.tropicalis isolated from 6 (11.8%) pt., c.krusie isolated from 3 (5.9%) of pt. and 3(5.9%) had mixed infection. C.albicans, tropicalis and C.krusie had been distributed more among DM groups and less among kidney stone groups, on the other hand C.glabrata more isolated among Glomerulonephritis groups. There was no association between candida species and ESRD. Conclusion: There was no relation between candida spp and cause of ERDS.

Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology.

Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a lattice-based framework to perform spatial-temporal Monte Carlo simulations of budding yeast colonies exposed to different nutrient and magnetic field conditions. The budding patterns of haploid and diploid yeast cells were incorporated into the framework, as well as the filamentous growth that occurs in yeast colonies under nutrient limiting conditions. Simulation of the framework predicted that magnetic fields decrease colony growth rate, solidity, and roundness. Magnetic field simulations further predicted that colony elongation and boundary fluctuations increase in a nutrient- and ploidy-dependent manner. These in-silico predictions are an important step towards understanding the effects of the physico-chemical environment on microbial colonies and for informing bioelectromagnetic experiments on yeast colony biofilms and fungal pathogens.

Modelling uniaxial non-uniform yeast colony growth: Comparing an agent-based model and continuum approximations

Biological experiments have shown that yeast can be restricted to grow in a uniaxial direction, vertically upwards from an agar plate to form a colony. The growth occurs as a consequence of cell proliferation driven by a nutrient supply at the base of the colony, and the height of the colony has been observed to increase linearly with time. Within the colony the nutrient concentration is non-constant and yeast cells throughout the colony will therefore not have equal access to nutrient, resulting in non-uniform growth. In this work, an agent based model is developed to predict the microscopic spatial distribution of labelled cells within the colony when the probability of cell proliferation can vary in space and time. We also describe a method for determining the average trajectories or pathlines of labelled cells within a colony growing in a uniaxial direction, enabling us to connect the microscopic and macroscopic behaviours of the system. We present results for six cases, which involve different assumptions for the presence or absence of a quiescent region (where no cell proliferation occurs), the size of the proliferative region, and the spatial variation of proliferation rates within the proliferative region. These six cases are designed to provide qualitative insight into likely growth scenarios whilst remaining amenable to analysis. We compare our macroscopic results to experimental observations of uniaxial colony growth for two cases where only a fixed number of cells at the base of the colony can proliferate. The model predicts that the height of the colony will increase linearly with time in both these cases, which is consistent with experimental observations. However, our model shows how different functional forms for the spatial dependence of the proliferation rate can be distinguished by tracking the pathlines of cells at different positions in the colony. More generally, our methodology can be applied to other biological systems exhibiting uniaxial growth, providing a framework for classifying or determining regions of uniform and non-uniform growth.

Network Analysis of Saccharomyces Cerevisiae Colony: Relation between Spatial Position and Generation

Yeast colony growth which can grow and produce buds can be modelled by using circular granular cells in two-dimensional form. The organizations of particles in granular materials as modelled as yeast colony growth have complex organizations on a spatial scale. Such organizations may affect how materials respond or reconfigure when exposed to external interference or loading. Particles have been studied in theoretical and require the development and application of appropriate mathematical, statistical, physical and computational frameworks. Usually, granular materials have been explored using particles or circuit models that are implicit. Today the development of network science has emerged as a powerful approach to investigate and characterize heterogeneous architecture in complex systems and diverse methods have yielded interesting insights into granular materials. In this study will learn granular materials (yeast colony growth) with the network-based approach and explore the potential of these frames to provide a useful description of yeast colony growth. This study will focus on finding the relation between the spatial position of the cells and generation that is formed.

Network Analysis of Saccharomyces cerevisiae

The pattern of yeast budding formation is essential in yeast colony expansion. By exploring how Saccharomyces cerevisiae as model cell grows, the distinction of pathological and non-pathological eukaryotic cells can be further understood. This research explores the use of FIJI software and network theory to characterize the formation pattern of Saccharomyces cerevisiae colony. By using speed distribution and degree distribution, three potential networks are compared: barbell network, relaxed caveman network, and triangular lattice network. Triangular lattice network emerges as the most suitable network to model yeast colony growth.

Isolation and identification of Autochthonous Lactic Bacteria for use in Cultures Starters in the Processing of Coastal Cheese

In this study, native lactic bacteria present in raw milk used for the elaboration of coastal cheese were isolated and identified. Aseptic milk samples were taken from three (3) companies, stored at temperatures between 0-4°C. Make dilutions were performed with peptone water and plaque (MRS agar), species were purified by morphology, reaction to oxidase case, catalase and gram staining. The Identification of the isolated species was done using the API 50 CH system (BioMerieux). The results of the first two (2) companies showed the species Lactobacillus paracasei ssp paracasei 3, with a percentage of identification above 99.5%. Third company showed growth of yeast colonies without the presence of lactic bacteria. There was no growth of other bacteria during the investigation, possibly due to the use of inhibitory substances by producers, such as hydrogen peroxide, during the transfer of milk to processing centers. It is concluded that one of the autochthonous bacteria of raw milk that affect the final characteristics of the coastal cheese is Lactobacillus paracasei ssp paracasei 3 since it showed a considerable growth rate, despite possible inhibition conditions. This species can be used in starter's cultures and inoculated in pasteurized milk, to obtain typical organoleptic characteristics of cheese made from raw milk.

Rosemary, Castor Oils, and Propolis Extract: Activity Against Candida Albicans and Alterations on Properties of Dental Acrylic Resins.

To evaluate the in vitro activity of 8% rosemary, 2% castor oils, and 12% propolis glycolic extract against Candida albicans, as well as the physical changes of properties in colorless and pink acrylic resins after immersion in these liquids. Colorimetric, roughness, and Knoop microhardness assays were evaluated in 25 specimens distributed into five groups (3 test groups and 2 control groups - distilled water and hypochlorite 1%), totaling five specimens per group for each acrylic resin (colorless and pink). The specimens were individually immersed for 30 minutes in 10mL of these liquids, washed, and dried once a week. They were maintained in distilled water at 37°C between processes during all experiments. The analyses were performed before immersion and in the 4th and/or 12thmonth. In vitro, 18 acrylic resins were exposed to C. albicans and, after a process of 30 minutes in immersion in the five groups cited and oil vehicle control of vesicle (liquid Vaseline), the specimens were washed and incubated for 24 hours in 37°C. The growth was determined by colony counting. For comparisons between the groups in each trial and the disinfection test, paired Student's t-tests and ANOVA with post hoc Tukey were performed by the SPSS program, considering α=0.05. None of the liquids altered the microhardness, but all the natural compounds and 1% sodium hypochlorite (control) altered color and roughness after the 12thmonth of immersion in these agents. In the colorless specimens, 8% rosemary oil caused a color change similar to water, and less color and roughness alterations when compared to 2% castor oil and 1% sodium hypochlorite, respectively. There was no growth of yeast colonies after immersion in rosemary oil, propolis glycolic extract, and 1% sodium hypochlorite. Eight percent rosemary oil has the potential to be used as an acrylic resin disinfectant.

Budding yeast colony growth study based on circular granular cell

Yeast colony growth can be modelled by using circular granular cells, which can grow and produce buds. The bud growth angle can be set to regulate cell budding pattern. Cohesion force, contact force and Stokes force were adopted to accommodate the behaviour and interactions among cells. Simulation steps are divided into two steps, the explicit step is due to cell growing and implicit step for the cell rearrangement. Only in explicit step that time change was performed. In this study, we examine the influence of cell diameter growth time and reproduction time combination toward the growth of cell number and colony formation. We find a commutative relation between the cell diameter growth time and reproduction time to the specific growth rate. The greater value of the multiplication of the parameters, the smaller specific growth rate is obtained. It also shows a linear correlation between the specific growth rate and colony diameter growth rate.

Hormetic Effect of H2O2 in Saccharomyces cerevisiae: Involvement of TOR and Glutathione Reductase.

In this study, we investigated the relationship between target of rapamycin (TOR) and H2O2-induced hormetic response in the budding yeast Saccharomyces cerevisiae grown on glucose or fructose. In general, our data suggest that: (1) hydrogen peroxide (H2O2) induces hormesis in a TOR-dependent manner; (2) the H2O2-induced hormetic dose–response in yeast depends on the type of carbohydrate in growth medium; (3) the concentration-dependent effect of H2O2 on yeast colony growth positively correlates with the activity of glutathione reductase that suggests the enzyme involvement in the H2O2-induced hormetic response; and (4) both TOR1 and TOR2 are involved in the reciprocal regulation of the activity of glucose-6-phosphate dehydrogenase and glyoxalase 1.

Involvement of Catalase in Saccharomyces Cerevisiae Hormetic Response to Hydrogen Peroxide

In this study, we investigated the relationship between catalase activity and H2O2-induced hormetic response in budding yeast S. cerevisiae. In general, our data suggest that: (i)hydrogen peroxide induces hormesis in a concentration- and time-dependent manner; and (ii) theeffect of hydrogen peroxide on yeast colony growth positively correlates with the activity ofcatalase that suggests the enzyme involvement in overall H2O2-induced stress response andhormetic response in yeast.

Characterisation of a Simple Non‐Thermal Atmospheric Pressure Plasma Source for Biomedical Research Applications

AbstractThe recent progress in plasma medicine as well as biomedical aspects of plasma physics over the last years have enhanced the need for experimental plasma devices which are capable of producing non‐thermal atmospheric pressure plasmas. These plasma sources are used for studying the effect of non‐thermal plasmas on biological samples of different nature. In this paper we present such an easy to build low cost apparatus that can be used for scientific as well as for educational purposes. Directions for the construction of the device are given and the basic plasma parameters are investigated. The characterisation of the experiment was done by electrical diagnostics for the measurements of the plasma potential in combination with optical emission spectroscopy. The latter is used for the determination of the excitation temperature of the plasma and the electron density. Furthermore the influence of the produced plasma on yeast cells is demonstrated. The produced plasma is characterised in different ways and it was found that the feeding gas has also a considerable impact on the radio frequency wave form of the source. It is also demonstrated that the constructed plasma source is capable of producing non‐thermal plasma that hinder cell growth of yeast colonies on a agar substrate. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Growing Yeast into Cylindrical Colonies

Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.

Growing Yeast into Cylindrical Colonies

Micro-organisms often form complex multicellular assemblies such as bio-films and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely-growing colony remains challenging. Most data available about micro-organisms are from planktonic cultures, due to the lack of experimental tools to observe multicellular assemblies. Here, we propose a method to tackle this problem by constraining the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, inexpensive, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate which is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate our approach to be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.

Hormetic Concentrations of Hydrogen Peroxide but Not Ethanol Induce Cross-Adaptation to Different Stresses in Budding Yeast

The biphasic-dose response of microorganisms to hydrogen peroxide is a phenomenon of particular interest in hormesis research. In different animal models, the dose-response curve for ethanol is also nonlinear showing an inhibitory effect at high doses but a stimulatory effect at low doses. In this study, we observed the hormetic-dose response to ethanol in budding yeast S. cerevisiae. Cross-protection is a phenomenon in which exposure to mild stress results in the acquisition of cellular resistance to lethal stress induced by different factors. Since both hydrogen peroxide and ethanol at low concentrations were found to stimulate yeast colony growth, we evaluated the role of one substance in cell cross-adaptation to the other substance as well as some weak organic acid preservatives. This study demonstrates that, unlike ethanol, hydrogen peroxide at hormetic concentrations causes cross-resistance of S. cerevisiae to different stresses. The regulatory protein Yap1 plays an important role in the hormetic effects by low concentrations of either hydrogen peroxide or ethanol, and it is involved in the yeast cross-adaptation by low sublethal doses of hydrogen peroxide.

Superoxide Triggers an Acid Burst in Saccharomyces cerevisiae to Condition the Environment of Glucose-starved Cells

Although yeast cells grown in abundant glucose tend to acidify their extracellular environment, they raise the pH of the environment when starved for glucose or when grown strictly with non-fermentable carbon sources. Following prolonged periods in this alkaline phase, Saccharomyces cerevisiae cells will switch to producing acid. The mechanisms and rationale for this "acid burst" were unknown. Herein we provide strong evidence for the role of mitochondrial superoxide in initiating the acid burst. Yeast mutants lacking the mitochondrial matrix superoxide dismutase (SOD2) enzyme, but not the cytosolic Cu,Zn-SOD1 enzyme, exhibited marked acceleration in production of acid on non-fermentable carbon sources. Acid production is also dramatically enhanced by the superoxide-producing agent, paraquat. Conversely, the acid burst is eliminated by boosting cellular levels of Mn-antioxidant mimics of SOD. We demonstrate that the acid burst is dependent on the mitochondrial aldehyde dehydrogenase Ald4p. Our data are consistent with a model in which mitochondrial superoxide damage to Fe-S enzymes in the tricarboxylic acid (TCA) cycle leads to acetate buildup by Ald4p. The resultant expulsion of acetate into the extracellular environment can provide a new carbon source to glucose-starved cells and enhance growth of yeast. By triggering production of organic acids, mitochondrial superoxide has the potential to promote cell population growth under nutrient depravation stress.