-
1.
Postprandial Gastrointestinal Function Differs after Acute Administration of Sourdough Compared with Brewer's Yeast Bakery Products in Healthy Adults.
Polese, B, Nicolai, E, Genovese, D, Verlezza, V, La Sala, CN, Aiello, M, Inglese, M, Incoronato, M, Sarnelli, G, De Rosa, T, et al
The Journal of nutrition. 2018;(2):202-208
-
-
Free full text
-
Abstract
BACKGROUND Europeans consume large quantities of bakery products, although these are known as one of the food categories that potentially leads to postprandial symptoms (such as fullness and bloating). OBJECTIVE The aim of this study was to evaluate the effects of sourdough baked goods on gastric emptying and gastrointestinal fermentation and symptoms in healthy people. METHODS In a double-blind, randomized crossover study, 2 sourdough croissants (SCs) or 2 brewer's yeast croissants (BCs) were served as single meals to 17 healthy adults [9 women; age range: 18-40 y; body mass index range (in kg/m2): 18-24]. Gastric volume (GV) was evaluated by magnetic resonance to calculate gastric-emptying rate in the 3-h interval after croissant ingestion. A hydrogen breath test was performed to measure hydrogen production after SC and BC ingestion. Palatability and postprandial gastrointestinal symptoms (discomfort, nausea, fullness, and bloating) over a 4-h period after the meal were evaluated. The area under the curve (AUC) was used to evaluate the overall effects on all variables tested. RESULTS The total GV AUC was reduced by 11% during the 3 h after the consumption of SCs compared with BCs (P = 0.02). Hydrogen production during the 4-h interval after ingestion of SCs was 30% lower than after BCs (P = 0.03). SCs were rated as being >2 times as palatable as BCs (P < 0.001). The overall severity of postprandial symptoms was 36% lower during the 4 h after intake of SCs compared with BCs (P = 0.05). CONCLUSION Sourdough bakery products could promote better postprandial gastrointestinal function in healthy adults and be more acceptable than those prepared with brewer's yeast. This trial was registered at www.clinicaltrials.gov as NCT03207516.
-
2.
Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.
Acton, E, Lee, AH, Zhao, PJ, Flibotte, S, Neira, M, Sinha, S, Chiang, J, Flaherty, P, Nislow, C, Giaever, G
Open biology. 2017;(6)
Abstract
The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, 'prototrophic' versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PBprot) or by backcrossing (Backcrossed, BCprot) to a wild-type strain. To systematically assess the impact of the auxotrophies, genome-wide fitness profiles of prototrophic and auxotrophic collections were compared across diverse drug and environmental conditions in 250 experiments. Our quantitative profiles uncovered broad impacts of genotype on phenotype for three deletion collections, and revealed genotypic and strain-construction-specific phenotypes. The PBprot collection exhibited fitness defects associated with plasmid maintenance, while BCprot fitness profiles were compromised due to strain loss from nutrient selection steps during strain construction. The repaired prototrophic versions of the YKO collection did not restore wild-type behaviour nor did they clarify gaps in gene annotation resulting from the auxotrophic background. To remove marker bias and expand the experimental scope of deletion libraries, construction of a bona fide prototrophic collection from a wild-type strain will be required.
-
3.
Calcium homeostasis and signaling in yeast cells and cardiac myocytes.
Cui, J, Kaandorp, JA, Sloot, PM, Lloyd, CM, Filatov, MV
FEMS yeast research. 2009;(8):1137-47
Abstract
Calcium ions are the most ubiquitous and versatile signaling molecules in eukaryotic cells. Calcium homeostasis and signaling systems are crucial for both the normal growth of the budding yeast Saccharomyces cerevisiae and the intricate working of the mammalian heart. In this paper, we make a detailed comparison between the calcium homeostasis/signaling networks in yeast cells and those in mammalian cardiac myocytes. This comparison covers not only the components, structure and function of the networks but also includes existing knowledge on the measured and simulated network dynamics using mathematical models. Surprisingly, most of the factors known in the yeast calcium homeostasis/signaling network are conserved and operate similarly in mammalian cells, including cardiac myocytes. Moreover, the budding yeast S. cerevisiae is a simple organism that affords powerful genetic and genomic tools. Thus, exploring and understanding the calcium homeostasis/signaling system in yeast can provide a shortcut to help understand calcium homeostasis/signaling systems in mammalian cardiac myocytes. In turn, this knowledge can be used to help treat relevant human diseases such as pathological cardiac hypertrophy and heart failure.
-
4.
Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation.
Mendes-Ferreira, A, del Olmo, M, García-Martínez, J, Jiménez-Martí, E, Mendes-Faia, A, Pérez-Ortín, JE, Leão, C
Applied and environmental microbiology. 2007;(9):3049-60
-
-
Free full text
-
Abstract
Gene expression profiles of a wine strain of Saccharomyces cerevisiae PYCC4072 were monitored during alcoholic fermentations with three different nitrogen supplies: (i) control fermentation (with enough nitrogen to complete sugar fermentation), (ii) nitrogen-limiting fermentation, and (iii) the addition of nitrogen to the nitrogen-limiting fermentation (refed fermentation). Approximately 70% of the yeast transcriptome was altered in at least one of the fermentation stages studied, revealing the continuous adjustment of yeast cells to stressful conditions. Nitrogen concentration had a decisive effect on gene expression during fermentation. The largest changes in transcription profiles were observed when the early time points of the N-limiting and control fermentations were compared. Despite the high levels of glucose present in the media, the early responses of yeast cells to low nitrogen were characterized by the induction of genes involved in oxidative glucose metabolism, including a significant number of mitochondrial associated genes resembling the yeast cell response to glucose starvation. As the N-limiting fermentation progressed, a general downregulation of genes associated with catabolism was observed. Surprisingly, genes encoding ribosomal proteins and involved in ribosome biogenesis showed a slight increase during N starvation; besides, genes that comprise the RiBi regulon behaved distinctively under the different experimental conditions. Here, for the first time, the global response of nitrogen-depleted cells to nitrogen addition under enological conditions is described. An important gene expression reprogramming occurred after nitrogen addition; this reprogramming affected genes involved in glycolysis, thiamine metabolism, and energy pathways, which enabled the yeast strain to overcome the previous nitrogen starvation stress and restart alcoholic fermentation.
-
5.
High degree of correlation between molecular polymorphism and geographic origin of wine yeast strains.
Martínez, C, Cosgaya, P, Vásquez, C, Gac, S, Ganga, A
Journal of applied microbiology. 2007;(6):2185-95
-
-
Free full text
-
Abstract
AIMS: To guarantee the endemic genetic background of the isolates obtained in yeast isolation programs, it is necessary to differentiate between endemic and commercial strains because the progressive use of commercial yeast in wine areas around the world would affect the autochthonous yeast populations. METHODS AND RESULTS Mitochondrial DNA restriction analysis, electrophoretic karyotyping and random amplification of polymorphic DNA (RAPD) were evaluated as experimental approaches to correlate genomic polymorphism and geographic origin of native wine yeast strains. The three molecular methods were capable of detecting a European commercial strain among native Chilean strains; however, RAPD proved to have the best performance. CONCLUSIONS The molecular polymorphism analysis is useful to evaluate the geographical origin of native yeast isolates and confirms or refutes the genetic background of currently marketed strains. SIGNIFICANCE AND IMPACT OF THE STUDY This study permits a genetic characterization of native yeast populations and confirms its utility as a tool for evaluating if a native isolate derives from the region where it was collected, permitting, furthermore, to develop studies on the evolution of native yeast populations and to evaluate the effect of introduced yeasts on these populations.
-
6.
Yeast as a biosensor for antioxidants: simple growth tests employing a Saccharomyces cerevisiae mutant defective in superoxide dismutase.
Zyracka, E, Zadrag, R, Kozioł, S, Krzepiłko, A, Bartosz, G, Biliński, T
Acta biochimica Polonica. 2005;(3):679-84
Abstract
Mutants of Saccharomyces cerevisiae devoid of Cu,Zn-superoxide dismutase are hypersensitive to a range of oxidants, hyperbaric oxygen and hyperosmotic media, show lysine and methionine auxotrophy when grown under the atmosphere of air and have a shortened replicative life span when compared to the wild-type strain. Ascorbate and other antioxidants can ameliorate these defects, which may be a basis of simple tests sensing the presence of antioxidants. In particular, tests of growth on solid medium (colony formation) in the absence of methionine and/or lysine, or in the presence of 0.8 M NaCl can be useful for detection and semiquantitative estimation of compounds of antioxidant properties. Hypoxic atmosphere was found to increase the sensitivity of detection of antioxidants. The test of abolishment of lysine auxotrophy showed a concentration dependence of the antioxidant effects of cysteine and N-acetylcysteine which, however, lost their protective action at high concentration, in contrast to glutathione which was effective also at higher concentrations.
-
7.
Effects of pressure on deuterium isotope effects of yeast alcohol dehydrogenase using alternative substrates.
Park, H, Kidman, G, Northrop, DB
Archives of biochemistry and biophysics. 2005;(1):335-40
Abstract
Hydrostatic pressure causes biphasic effects on the oxidation of alcohols by yeast alcohol dehydrogenase as expressed on the kinetic parameter V/K which measures substrate capture. Moderate pressure increases capture by activating hydride transfer, whose transition-state must therefore have a smaller volume than the free alcohol plus the capturing form of enzyme, with DeltaV(double dagger)=-30 mL mol(-1) for isopropanol. A comparison of these effects with those on the oxidation of deutero-isopropanol generates a monophasic decrease in the intrinsic isotope effect; therefore, the volume of activation for the transition-state of deuteride transfer must be even more negative, by 7.6 mL mol(-1). The pressure data extrapolate and factor the kinetic isotope effect into a semi-classical reactant-state component, with a null value of k(H)/k(D)=1, and a transition-state component of Q(H)/Q(D)=4, suggestive of hydrogen tunneling. Pressures above 1.5 kbar decrease capture by favoring a minor conformation of enzyme which binds nicotinamide adenine dinucleotide (NAD(+)) less tightly. This inactive conformation has a smaller volume than active E-NAD(+), with a difference of 74 mL mol(-1) and an equilibrium constant of 93 between them, at one atmosphere of pressure. These results are virtually identical to those obtained with benzyl alcohol and give credence to this method of analysis. Moreover, qualitatively similar results with greater pressure sensitivity but less precision are obtained using ethanol as a substrate, only with pressure driving the value of the isotope effect to a value less than (D)k=1.03 directly, without extrapolation. The ethanol data verify the most surprising finding of these studies, namely that the entire kinetic isotope effect arises from a transition-state phenomenon.
-
8.
Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling.
Kolkman, A, Dirksen, EH, Slijper, M, Heck, AJ
Molecular & cellular proteomics : MCP. 2005;(3):255-66
Abstract
Quantitative protein expression profiling is a crucial part of proteomics and requires methods that are able to efficiently provide accurate and reproducible differential expression values for proteins in two or more biological samples. In this report we evaluate in a direct comparative assessment two state-of-the-art quantitative proteomic approaches, namely difference in gel electrophoresis (DiGE) and metabolic stable isotope labeling. Therefore, Saccharomyces cerevisiae was grown under well defined experimental conditions in chemostats under two single nutrient-limited growth conditions using (14)N- or (15)N-labeled ammonium sulfate as the single nitrogen source. Following lysis and protein extraction from the two yeast samples, the proteins were fluorescently labeled using different fluorescent CyDyes. Subsequently, the yeast samples were mixed, and the proteins were separated by two-dimensional gel electrophoresis. Following in-gel digestion, the resulting peptides were analyzed by mass spectrometry using a MALDI-TOF mass spectrometer. Relative ratios in protein expression between these two yeast samples were determined using both DiGE and metabolic stable isotope labeling. Focusing on a small, albeit representative, set of proteins covering the whole gel range, including some protein isoforms and ranging from low to high abundance, we observe that the correlation between these two methods of quantification is good with the differential ratios determined following the equation R(Met.Lab.) = 0.98R(DiGE) with r(2) = 0.89. Although the correlation between DiGE and metabolic stable isotope labeling is exceptionally good, we do observe and discuss (dis)advantages of both methods as well as in relation to other (quantitative) approaches.
-
9.
Integrative model of the response of yeast to osmotic shock.
Klipp, E, Nordlander, B, Krüger, R, Gennemark, P, Hohmann, S
Nature biotechnology. 2005;(8):975-82
Abstract
Integration of experimental studies with mathematical modeling allows insight into systems properties, prediction of perturbation effects and generation of hypotheses for further research. We present a comprehensive mathematical description of the cellular response of yeast to hyperosmotic shock. The model integrates a biochemical reaction network comprising receptor stimulation, mitogen-activated protein kinase cascade dynamics, activation of gene expression and adaptation of cellular metabolism with a thermodynamic description of volume regulation and osmotic pressure. Simulations agree well with experimental results obtained under different stress conditions or with specific mutants. The model is predictive since it suggests previously unrecognized features of the system with respect to osmolyte accumulation and feedback control, as confirmed with experiments. The mathematical description presented is a valuable tool for future studies on osmoregulation in yeast and-with appropriate modifications-other organisms. It also serves as a starting point for a comprehensive description of cellular signaling.
-
10.
Enzymatic saccharification and fermentation of xylose-optimized dilute acid-treated lignocellulosics.
Chung, YC, Bakalinsky, A, Penner, MH
Applied biochemistry and biotechnology. 2005;:947-61
Abstract
The cellulose reactivity of two lignocellulosic feedstocks, switchgrass and poplar, was evaluated under straight saccharification (SS) and simultaneous saccharification and fermentation (SSF) conditions following dilute sulfuric acid pretreatments designed for optimum xylose yields. The optimum pretreatment conditions, within the constraints of the experimental system (Parr batch reactor), were 1.2% acid, 180 degrees C, and 0.5 min for switchgrass and 1% acid, 180 degrees C, and 0.56 min for poplar. The cellulase enzyme preparation was from Trichoderma reesei and fermentations were done with Saccharomyces cerevisiae. Time courses for SS were monitored as the sum of glucose and cellobiose; those for SSF as the sum of glucose, cellobiose, and ethanol. Percentage conversions under SS conditions were 79.1% and 91.4% for the pretreated poplar and switchgrass feedstocks, respectively. Analogous values under SSF conditions were 73.0% and 90.3% for pretreated poplar and switchgrass, respectively.