Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “yeast model”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed1996

Control of frequency and amplitudes is shared by all enzymes in three models for yeast glycolytic oscillations.

The three main existing models for glycolytic oscillations in yeast were re-examined to investigate how these oscillations are controlled. We implemented the operational definitions provided by metabolic control analysis to quantify the control properties of enzymes with regard to glycolytic oscillations. In all three models, the control of the frequency and that of the amplitudes of the metabolites were distributed among the enzymes. There was no obvious correlation between the control of the average flax and the control of the frequency. Most importantly, the so-called 'oscillophore' of the system, traditionally the enzyme primarily held responsible for the generation of the oscillation, was not the only controlling step. We conclude that just like steady-state flux control is not necessarily limited to a rate-limiting step, oscillations are not dictated by a single 'oscillophore'.

Glycolysis↗
PubMed1989

[Inhibition of porphyrin synthesis by isonicotinic acid hydrazide in models simulating porphyria].

Increased activity of haem synthesis key enzyme is a common phenomenon in hepatic porphyrias. Synthase activity of delta-aminolevulinic acid is extensively increased in acute hepatic porphyrias or it can be by means of feedback moderately secondarily increased in their chronic forms. Isonicotinic acid hydrazide (INH) is a competitive inhibitor of delta-aminolevulinic acid synthase as it combines with enzyme co-factor, pyridoxalphosphate (PDX) to form hydrazone. The INH porphyrinstatic effects were verified by testing two experimental models. The yeast model exhibited 5-fold inhibition at 10 mM INH concentration in medium. The chicken germ model after a 10 microM INH dose exhibited 82% inhibition. This inhibition can be eliminated by PDX administration to reach the original porphyrin synthesis at equimolar INH and PDX concentrations. Histological study of transversal chicken liver sections proved that 1 microM INH administration does not result in disturbance of chicken hepatocyte integration. The suggested preparation has the advantage of being commonly manufactured and approved to be used in human medicine.

Animals↗
PubMed1989

Crystallographic characterization and three-dimensional model of yeast Cu,Zn superoxide dismutase.

The Cu,Zn superoxide dismutase from yeast was crystallized in the orthorhombic space group P21212 with unit cell dimension a = 105.1 A,b = 142.2 A, c = 62.1 A. The crystals grow in 25 mM citrate, 10 mM phosphate buffer pH 6.5, and 6% (W/V) polyethylene glycol, with a Vm of 3,4 A3/dalton, for two dimers/asymmetric unit. The crystals were unstable in the mother liquor, but were stabilized by transfer to a 35% polyethylene glycol solution. This crystalline form diffracts at high resolution and is suitable for determination of the atomic structure. The three dimensional structure of the yeast enzyme could be model-built by computer graphics techniques using the bovine enzyme atomic coordinates as template. The proposed model requires removal of some salt bridges and non equivalence of the metal-binding sites in the subunits, in line with reported functional properties of the yeast enzyme.

Amino Acid Sequence↗
PubMed2005

A regulatory network analysis of phenotypic plasticity in yeast.

Models for the evolution of phenotypic plasticity suggest when and why plasticity might evolve. However, relatively little is known about the genetic basis of plasticity. Molecular studies have recently demonstrated that gene networks can provide a powerful way to infer phenotype from genotype. Information on the structure of the yeast gene regulatory network was combined with data on variation in gene expression in yeast across multiple environments in order to explore the genetic basis of phenotypic plasticity. The phenotypic plasticity of a gene was positively correlated with the number of transcription factors regulating that gene and was significantly lower for transcription factors than for downstream, nonregulatory genes. Plasticity of a gene was also affected by the local substructure of the network in which it was found and by the gene's function. These results illustrate how network analyses can be used to understand the complex genetic architecture of quantitative traits.

Gene Expression Regulation, Fungal↗
PubMedDate not supplied

Efficacy of denture cleansing agents in an in vitro bacteria-yeast colonization model.

The purpose of this investigation was to develop a new, in vitro bacteria-yeast denture colonization model. Candida albicans and Streptococcus mutans, organisms associated with denture stomatitis, reproducibly colonized denture blanks in high numbers. Both Efferdent and Super-Strength Polident were able to substantially reduce or eliminate colonizing S mutans. In sharp contrast, however, no significant decreases in adherent C albicans were observed with either denture soaking agent.

Candida albicans↗
PubMed2004

Cycling without the cyclosome: modeling a yeast strain lacking the APC.

The construction of viable Saccharomyces cerevisiae strains that lack the anaphase promoting complex (APC) was recently reported. The normally lethal deletions of APC genes were suppressed by the double deletion of the PDS1 and CLB5 genes in conjunction with the insertion of multiple copies of the SIC1 gene controlled by its endogenous promoter. It was proposed that cyclic expression and degradation of Sic1 results in oscillations of Clb/CDK activity necessary for the cell cycle. We have used an updated version of a mathematical model of the yeast cell cycle to model strains that lack the APC. With a few modifications, the model accurately simulates the viability of Apc- strains, as well as the phenotypes of 27 other previously characterized strains. We discuss a few minor inconsistencies between the model and experiment, and how these may inform future revisions to the model.

Anaphase-Promoting Complex-Cyclosome↗
PubMed1998

Modeling brewers' yeast flocculation

Flocculation of yeast cells occurs during the fermentation of beer. Partway through the fermentation the cells become flocculent and start to form flocs. If the environmental conditions, such as medium composition and fluid velocities in the tank, are optimal, the flocs will grow in size large enough to settle. After settling of the main part of the yeast the green beer is left, containing only a small amount of yeast necessary for rest conversions during the next process step, the lagering. The physical process of flocculation is a dynamic equilibrium of floc formation and floc breakup resulting in a bimodal size distribution containing single cells and flocs. The floc size distribution and the single cell amount were measured under the different conditions that occur during full scale fermentation. Influences on flocculation such as floc strength, specific power input, and total number of yeast cells in suspension were studied. A flocculation model was developed, and the measured data used for validation. Yeast floc formation can be described with the collision theory assuming a constant collision efficiency. The breakup of flocs appears to occur mainly via two mechanisms, the splitting of flocs and the erosion of yeast cells from the floc surface. The splitting rate determines the average floc size and the erosion rate determines the number of single cells. Regarding the size of the flocs with respect to the scale of turbulence, only the viscous subrange needs to be considered. With the model, the floc size distribution and the number of single cells can be predicted at a certain point during the fermentation. For this, the bond strength between the cells, the fractal dimension of the yeast, the specific power input in the tank and the number of yeast cells that are in suspension in the tank have to be known. Copyright 1998 John Wiley & Sons, Inc.

Journal Article↗
PubMed2005

Exploratory modeling of yeast stress response and its regulation with gCCA and associative clustering.

We model dependencies between m multivariate continuous-valued information sources by a combination of (i) a generalized canonical correlations analysis (gCCA) to reduce dimensionality while preserving dependencies in m - 1 of them, and (ii) summarizing dependencies with the remaining one by associative clustering. This new combination of methods avoids multiway associative clustering which would require a multiway contingency table and hence suffer from curse of dimensionality of the table. The method is applied to summarizing properties of yeast stress by searching for dependencies (commonalities) between expression of genes of baker's yeast Saccharomyces cerevisiae in various stressful treatments, and summarizing stress regulation by finally adding data about transcription factor binding sites.

Animals↗
PubMed2003

Yeast, a model organism for iron and copper metabolism studies.

Virtually all organisms on earth depend on transition metals for survival. Iron and copper are particularly important because they participate in vital electron transfer reactions, and are thus cofactors of many metabolic enzymes. Their ability to transfer electrons also render them toxic when present in excess. Disturbances of iron and copper steady-state levels can have profound effects on cellular metabolism, growth and development. It is critical to maintain these metals in a narrow range between utility and toxicity. Organisms ranging from bacteria and plants to mammals have developed sophisticated mechanisms to control metal homeostasis. In this review, we will present an overview of the current understanding of iron and copper metabolism in yeast, and the utility of yeast as a model organism to investigate iron and copper metabolism in mammals and plants.

Copper↗
PubMed2005

One-dimensional model of yeast prion aggregation.

Mammalian prion proteins (PrP) are of significant public health interest. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP, without posing a threat to the organism. These yeast "prions," such as SUP35, are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein found long aggregates, pure exponential growth of the misfolded form, and a lag time which depended weakly on the monomer concentration. To explain this data, we have extended a previous model of aggregation kinetics along with a stochastic approach. We assume reconformation only upon aggregation and include aggregate fissioning and an initial nucleation barrier. We find that for sufficiently small nucleation rates or seeding by a small number of preformed nuclei, the models achieve the requisite exponential growth, long aggregates, and a lag time which depends weakly on monomer concentration. The spread in aggregate sizes is well described by the Weibull distribution. All these properties point to the preeminent role of fissioning in the growth of misfolded proteins.

Computer Simulation↗
PubMed1994

A general model of yeast energy metabolism in aerobic chemostat culture.

The pattern of energy metabolism of different types of yeasts (obligate aerobes and facultative anaerobes) in aerobic chemostat cultures has been evaluated and interpreted on the basis of a coupling of metabolic fluxes between glycolytic and oxidative components. A model has been formulated which defines glycolytic and oxidative subunits through which the substrate C-flux (gram-atom g-1 h-1) is calculated, stating that a relative imbalance between glycolytic flux and subsequent oxidative steps alone is sufficient to account for the onset of oxidoreductive metabolism in any type of yeast, irrespective of the maximum respiratory capacity. The model is able to reproduce the patterns of behaviour reported for the different types of yeasts, and the individual features of each strain are explained on the basis of metabolic differences which are defined by a set of normalized parameters. The model can be applied to different substrates and conditions, providing a methodological basis for more detailed studies of the steps controlling yeast energy metabolism.

Aerobiosis↗
PubMed2005

Oregano and clove essential oils induce surface alteration of Saccharomyces cerevisiae.

The antimicrobial properties of volatile aromatic oils have been recognized since antiquity. Oregano and clove oils have been shown to possess a broad spectrum of antimicrobial activity. In this paper, the fungicidal action of these two essential oils was studied on the yeast model Saccharomyces cerevisiae. Yeast cell lysis was shown by the release of substances absorbing at 260 nm. In addition, scanning electron microscopy analyses revealed that the surface of treated cells by oregano and clove oils was significantly damaged.

Antifungal Agents↗
PubMed2005

Reverse engineering galactose regulation in yeast through model selection.

We examine the application of statistical model selection methods to reverse-engineering the control of galactose utilization in yeast from DNA microarray experiment data. In these experiments, relationships among gene expression values are revealed through modifications of galactose sugar level and genetic perturbations through knockouts. For each gene variable, we select predictors using a variety of methods, taking into account the variance in each measurement. These methods include maximization of log-likelihood with Cp, AIC, and BIC penalties, bootstrap and cross-validation error estimation, and coefficient shrinkage via the Lasso.

Journal Article↗
PubMed2003

Modeling of yeast metabolism and process dynamics in batch fermentation.

Much is known about yeast metabolism and the kinetics of industrial batch fermentation processes. In this study, however, we provide the first tool to evaluate the dynamic interaction that exists between them. A stoichiometric model, using wine fermentation as a case study, was constructed to simulate batch cultures of Saccharomyces cerevisiae. Five differential equations describe the evolution of the main metabolites and biomass in the fermentation tank, while a set of underdetermined linear algebraic equations models the pseudo-steady-state microbial metabolism. Specific links between process variables and the reaction rates of metabolic pathways represent microorganism adaptation to environmental changes in the culture. Adaptation requirements to changes in the environment, optimal growth, and homeostasis were set as the physiological objectives. A linear programming routine was used to define optimal metabolic mass flux distribution at each instant throughout the process. The kinetics of the process arise from the dynamic interaction between the environment and metabolic flux distribution. The model assessed the effect of nitrogen starvation and ethanol toxicity in wine fermentation and it was able to simulate fermentation profiles qualitatively, while experimental fermentation yields were reproduced successfully as well.

Adaptation, Physiological↗
PubMed1993

Three-dimensional model of yeast RNA polymerase I determined by electron microscopy of two-dimensional crystals.

Two-dimensional crystals of yeast RNA polymerase I dimers were obtained upon interaction with positively charged lipid layers. A three-dimensional surface model of the enzyme was determined by analyzing tilted crystalline areas and by taking advantage of the non-crystallographic internal symmetry of the dimer to correct for the missing viewing directions. The structure shows, at approximately 3 nm resolution, an irregularly shaped molecule 11 nm x 11 nm x 15 nm in size characterized by a 3 nm wide and 10 nm long groove which constitutes a putative DNA binding site. The overall structure is similar to the Escherichia coli holo enzyme and the yeast RNA polymerase II delta 4/7 structures. The most remarkable structural feature is a finger-shaped stalk which partially occludes the entrance of the groove and forms a 2.5 nm wide channel. We discuss the possible location of the catalytic centre and of the carboxy-terminal region of the beta-like subunit in the channel. The interference of different DNA fragments with RNA polymerase dimerization and crystallization indicates the orientation of the template in the putative DNA binding groove.

Amino Acid Sequence↗
PubMed2001

Bakers' yeast, a model for fungal biofilm formation.

Biofilms are formed by the aggregation of microorganisms into multicellular structures that adhere to surfaces. Here we show that bakers' yeast Saccharomyces cerevisiae can initiate biofilm formation. When grown in low-glucose medium, the yeast cells adhered avidly to a number of plastic surfaces. On semi-solid (0.3% agar) medium they formed "mats": complex multicellular structures composed of yeast-form cells. Both attachment to plastic and mat formation require Flo11p, a member of a large family of fungal cell surface glycoproteins involved in adherence. The ability to study biofilm formation in a tractable genetic system may facilitate the identification of new targets for antifungal therapy.

Agar↗
PubMed2000

Functional interaction of human Cdc37 with the androgen receptor but not with the glucocorticoid receptor.

Cdc37 is a molecular chaperone closely associated with the folding of protein kinases. Results from studies using a yeast model system showed that it was also important for activation of the human androgen receptor (AR). Based on results from the yeast model system (Fliss, A. E., Fang, Y., Boschelli, F., and Caplan, A. J. (1997) Mol. Biol. Cell 8, 2501-2509), we initiated studies to address whether AR and Cdc37 interact with each other in animal cell systems. Our results show that Cdc37 binds to AR but not to glucocorticoid receptors (GR) synthesized in rabbit reticulocyte lysates. This binding occurs via the ligand-binding domain of the AR in a manner that is partially dependent on Hsp90 and the presence of hormone. Further studies using the yeast system showed that Cdc37 is not interchangeable with Hsp90, suggesting that it functions at a distinct step in the activation pathway. Expression of a dominant negative form of Cdc37 in animal cells down-regulates full-length AR but has very little effect on an AR truncation lacking the ligand-binding domain or full-length GR. These results reveal differences in the mechanisms by which AR and GR become active transcription factors and strengthen the notion that Cdc37 has a wider range of polypeptide clients than was realized previously.

Binding Sites↗
PubMed2001

L1-like non-LTR retrotransposons in the yeast Candida albicans.

Non-LTR retrotransposons (also known as LINEs) have had a major influence on the structure of many eukaryote genomes. They are abundant in many multicellular eukaryotes, including mammals, but appear to be absent from the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. This absence has, to date, precluded the development of a yeast model system for the study of non-LTR retrotransposons. In this report we describe several families of non-LTR retrotransposons from the yeast Candida albicans. These elements, which we call Zorro elements, are all members of the L1 clade of non-LTR retrotransposons. Some are intact, transcriptionally active and have transposed recently. This finding should allow the development of a yeast model system.

Amino Acid Sequence↗