MFS transportome of the human pathogenic yeast Candida albicans Dec 3, 2008
Family designations in C. albicans were validated by subjecting Saccharomyces cerevisiae genome to TC system. The latter also suggested putative functions and preferred substrates for all the MFS members on the basis of homology. (BioMed Central)
10 things... Nov 29, 2008
Beer is fermented with the fungus Saccharomyces cerevisiae (brewer's yeast), or Saccharomyces carlsbergensis for lager-making, developed by Danish mycologist Emil Hansen. Wine, cider and perry traditionally use naturally-occurring yeasts for fermentation. (BBC News -- UK)
How DNA Is Unwound So That Its Code Can Be Read Nov 29, 2008
Using samples from the yeast Saccharomyces cerevisiae, the scientists were able to take thousands of individual pictures of the RSC chromatin remodeling complex a large and flexible protein machine that unwinds the DNA in complex with the nucleosome, the basic organizational unit into which DNA strands are wrapped. The scientists then used mathematics and intensive digital processing to translate what were two-dimensional snapshots of single RSC molecules into a detailed picture of the... (Science Daily)
Misfolded Proteins Accelerate Yeast Evolution Nov 27, 2008
To test this hypothesis, the scientists first examined what genes might help to induce the prion state, plowing through the entire genome of Saccharomyces cerevisiae, the common baker's yeast that biologists have studied intensively for many years. Jens Tyedmers, a lead author on the paper published in PLoS Biology on November 28, tested 4700 yeast strains that each lacked one of the genes in the yeast genome, and then tested each strain's ability to create the prion. (Science Daily)
What The Social Lives Of Brewer’s Yeast Say About Evolution Nov 20, 2008
The researchers used common brewer's and baker's yeast (Saccharomyces cerevisiae) as a model for studying social behavior because yeast behavior is driven solely by genetics, without any input from cognitive learning or culture. Also, since S. cerevisiae has been widely studied and characterized, scientists are able to manipulate it with great precision. (Science Daily)
Genes That Prevent Changes In Physical Traits Due To Environmental Changes Identified Nov 6, 2008
To identify genes that buffer environmental and genetic variation, which may influence how novel traits evolve, the researchers examined Saccharomyces cerevisiae, a species of budding yeast. They investigated the molecular mechanisms that underlie its phenotypic robustness and how these mechanisms can be broken to produce differences in physical appearance within the species. (Science Daily)
Cells Coordinate Gene Activity With FM Bursts, Scientists Find Oct 3, 2008
The scientists looked specifically at the molecular changes within simple baker's yeast (Saccharomyces cerevisiae) cells after exposure to excess calcium, which increases in concentration in cells in response to stressful conditions such as high salt levels, alkaline pH, and cell wall damage ... While studying the molecular changes within simple baker's yeast (Saccharomyces cerevisiae) cells, scientists discovered that the cells tune the expression of groups of genes using discrete bursts of... (Science Daily)
SCUD: Saccharomyces Cerevisiae Ubiquitination Database Sep 24, 2008
Description SCUD is a web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's yeast). We first searched for all the known enzymes involved in the ubiquitination process in yeast, including E1, E2, E3, and deubiquitination enzymes. (BioMed Central)
Brewing A Great Beer: DNA Study Reveals Evolution Of Beer Yeasts Sep 12, 2008
One species in the group, Saccharomyces cerevisiae, commonly known as "bakers' yeast," has been used for thousands of years to make both bread and ale. S. cerevisiae grows best at temperatures between about 85 and 90 degrees Fahrenheit. (Science Daily)
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast Sep 12, 2008
In analyzing the stability of DNA replication origins in Saccharomyces cerevisiae we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a particular position weight matrix relative to another set ... SADMAMA's utility is demonstrated here by offering a plausible explanation to the differential ARS activity observed in our previous mcm1-1 mutant experiments [Donato 2006], by suggesting the relevance of multiple weak ACS... (BioMed Central)
Life Isn't 2-D, So Why Should Our Encyclopedias Be? Aug 26, 2008
21, 2007) Protein three-dimensional structures were predicted for all Saccharomyces cerevisiae domains that were found to have no sequence similarity to any proteins of known. . (Science Daily)
Integration of relational and hierarchical network information for protein function prediction Aug 23, 2008
A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard `guilt-by-association' (i. e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose `true-path' consistency. (BioMed Central)
Caltech engineers build mini drug-producing biofactories in yeast Aug 16, 2008
Christina D. Smolke, an assistant professor of chemical engineering at Caltech, along with graduate student Kristy Hawkins, genetically modified common baker's yeast (Saccharomyces cerevisiae) so that it contained the genes for several plant enzymes. The enzymes allow the yeast to produce a chemical called reticuline, which is a precursor for many different classes of benzylisoquinoline alkaloid (BIA) molecules. (EurekAlert!)
Positive-feedback System Ensures That Cells Divide Aug 12, 2008
Skotheim and his colleagues, including graduate student Stefano DiTalia, show that when budding yeast (Saccharomyces cerevisiae) cells sense that they are big enough to divide, they synthesize an activator molecule that triggers a positive feedback system in which Cln1 and Cln2 advance their own expression. So what happens is that the very rapid ramp-up of the G1 cyclins during Start lead to all those target genes getting fired synchronously, says Skotheim. (Science Daily)
New Yeast Trick For Eating Favorite Food Jul 31, 2008
This research marks the first discovery of post-transcriptional gene regulation in a key model for gene regulation in higher organisms: the galactose genetic system in the yeast Saccharomyces cerevisiae. Molecular biologists have long thought that the primary mechanism for regulating genes is through proteins called transcription factors, which can either increase or decrease the activity of a gene by binding directly to the DNA. However, a paradigm shift has occurred in recent years as... (Science Daily)
Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi Jul 2, 2008
However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. (BioMed Central)
New research on mutation in yeast can enhance understanding of human diseases Jun 20, 2008
The researchers asked a fundamental question: "What is the baseline rate and spectrum of mutation in yeast?" They found that, like the previously studied mutations in the nematode Caenorhabditis elegans, the yeast Saccharomyces cerevisiae had a very high rate of mutation from generation to generation. Its patterns of mutation, however, turned out to be unique. (EurekAlert!)
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient Jun 19, 2008
The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. (BioMed Central)
'PLoS ONE' STUDY: A Low Dose of Dietary Resveratrol Partially Mimics Caloric Restriction and Retards Aging Parameters in Mice Jun 4, 2008
Howitz KT, Bitterman KJ, Cohen HY, Lamming DW, Lavu S, et al. (2003) Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 425: 191196. (USA Today -- Tech)
DNA Defects: Vitamins And Minerals Fix? Jun 3, 2008
Electron microscope image of budding yeast, Saccharomyces cerevisiae. UC Berkeley researchers insert variants of human enzymes into yeast to see if these enzymes can be tuned up with vitamins. (Science Daily)
How Fast Does A Stressed Cell React? May 28, 2008
In the yeast Saccharomyces cerevisiae, a model eukaryotic (2) system, such a cascade has been well described. However, its dynamics remain poorly understood. (Science Daily)
Key Roadblock To Gene Expression Identified: Implications For AIDS May 10, 2008
The scientists then compared these maps to the team's earlier maps of the baker's yeast Saccharomyces cerevisiae, revealing that evolution has organized nucleosomes differently in simple life forms compared to more complex organisms like the fruit fly. In yeast, a nucleosome sits on top of the transcription start site, so RNA polymerase must contend with that nucleosome as soon as it begins to transcribe the gene. (Science Daily)
Cell biology: The cellular hullabaloo May 8, 2008
In 2006, Collins's team described engineering mutations into the control region of a gene that confers antibiotic resistance to create two strains of the yeast Saccharomyces cerevisiae , one with noisier expression of the gene, one with something more steady. Faced with a lethal antibiotic, the noisier strain survived better. (Nature News Service)
Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli Apr 16, 2008
Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions. Results. (BioMed Central)
Neonatal Diagnosis and Treatment of Menkes Disease Feb 7, 2008
Two of the 12 patients had normal neurodevelopment and brain myelination; 1 of these patients had a mutation that complemented a Saccharomyces cerevisiae copper-transport mutation, indicating partial ATPase activity, and the other had a mutation that allowed some correct ATP7A splicing. Conclusions Neonatal diagnosis of Menkes disease by plasma neurochemical measurements and early treatment with copper may improve clinical outcomes. (New England Journal of Medicine)
Efficient display of active lipase LipB52 with a Pichia pastoris cell surface display system and comparison with the LipB52 displayed on Saccharomyces cerevisiae cell surface Jan 28, 2008
The LipB52 displayed on the Pichia pastoris cell surface exhibited activity toward p-nitrophenol ester with carbon chain length ranging from C10 to C18, and the optimum substrate was p-nitrophenol-caprate (C10), which was consistent with it displayed on the Saccharomyces cerevisiae EBY100 cell surface ... The LipB52 displayed on the Pichia pastoris cell surface exhibited better stability than the lipase LipB52 displayed on Saccharomyces cerevisiae cell surface ... But the Pichia pastoris dry... (BioMed Central)
Scientists Create First Synthetic Bacterial Genome -- Largest Chemically Defined Structure Synthesized In The Lab Jan 25, 2008
After several years of work perfecting chemical assembly, the team found they could use homologous recombination (a process that cells use to repair damage to their chromosomes) in the yeast Saccharomyces cerevisiae to rapidly build the entire bacterial chromosome from large subassemblies. This extraordinary accomplishment is a technological marvel that was only made possible because of the unique and accomplished JCVI team, said J. Craig Venter, Ph. (Science Daily)
Tinkering extends life of organism Jan 15, 2008
Brewer's yeast, known formally as Saccharomyces cerevisiae, illuminated using a special technique called immunofluorescence. Scientists have recently extended the lifespan of the microscopic organism by both tinkering with aging genes and cutting the amount of calories it takes in. (MSNBC -- Technology)
Identification of cellular pathways affected by Sortin2, a synthetic compound that affects protein targeting to the vacuole in Saccharomyces cerevisiae Jan 8, 2008
Other articles by authors. Related articles/pages. (BioMed Central)
Effects of mutations in SGS1 and in genes functionally related to SGS1 on inverted repeat-stimulated spontaneous unequal sister-chromatid exchange in yeast Jan 1, 2008
The RecQ helicase Sgs1, in Saccharomyces cerevisiae, is believed to act on stalled replication forks. To determine the role of Sgs1 when the replication machinery stalls at the secondary structure, we measured the rates of IR-associated and non-IR-associated spontaneous unequal SCE events in the sgs1 mutant, and in strains bearing mutations in genes that are functionally related to SGS1. (BioMed Central)
Mutations Help Clarify Processes In Cell Division Dec 5, 2007
Pinto studies the role of chromatin in chromosome segregation in Saccharomyces cerevisiae, commonly known as baker s yeast, because yeast divides quickly, is easy to grow, amenable to molecular and genetic manipulations, and has a sequenced genome. This organism serves as a blueprint for understanding how human cells divide. (Science Daily)
Recombination rate and protein evolution in yeast Nov 28, 2007
We use a combination of polymorphism and genomic data from the yeast Saccharomyces cerevisiae to infer the relative importance of nearly-neutral (i. e. slightly deleterious) evolution in different gene categories. (BioMed Central)
Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework Oct 19, 2007
Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation in the probability of tag formation into the interpretation of SAGE data and allows us to derive exact joint and and approximate marginal posterior distributions for the mRNA frequency of genes detectable using SAGE. Our analysis of these distributions indicates that the frequency of a gene in the tag... (BioMed Central)
On the detection of functionally coherent groups of protein domains with an extension to protein annotation Oct 16, 2007
Using a new computational method, we have identified 114 groups of domains, referred to as domain assembly units (DASSEM units), in the proteome of budding yeast Saccharomyces cerevisiae ... A new computational method was developed to identify groups of domains that are linked by a common function in the proteome of Saccharomyces cerevisiae. (BioMed Central)
Sizing Cells Up: Researchers Pinpoint When A Cell Is Ready To Reproduce Oct 5, 2007
In research conducted in budding yeast (Saccharomyces cerevisiae), scientists at Rockefeller University have now identified the cellular event that marks the moment when a cell knows it is big enough to commit to cell division and spawn genetic replicas of itself. The findings provide a precise and quantitative framework for studying the possible mechanisms that allow cells to monitor and sense their size. (Science Daily)
Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome Sep 15, 2007
DNA polymerase gamma (Pol-gamma) has been shown to be essential for maintenance of the mitochondrial genome (mtDNA) in the petite-positive budding yeast Saccharomyces cerevisiae. Budding yeast cells lacking mitochondria exhibit a slow-growing or petite-colony phenotype. (BioMed Central)
Magnets Can Boost Production Of Ethanol For Fuel Sep 13, 2007
Article: "Bioreactor Coupled with Electromagnetic Field Generator: Effects of Extremely Low Frequency Electromagnetic Fields on Ethanol Production by Saccharomyces cerevisiae" ACS' Biotechnology Progress, October 5, 2007. Note: This story has been adapted from a news release issued by American Chemical Society. (Science Daily)
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks Jul 13, 2007
The algorithm is evaluated with synthetic and Saccharomyces cerevisiae expression data using the dynamic Bayesian network ... The performance of the algorithm is compared with Sparse Bayesian Learning algorithm using both synthetic and Saccharomyces cerevisiae expression data sets. (BioMed Central)
Turning Whole Plants into Fuel in Four Simple Steps Jun 24, 2007
Plus, this process, reported in Nature, works faster than the several days it takes Saccharomyces cerevisiae yeast to ferment plant sugars into ethanol, because it is chemically controlled and therefore can be completed in hours. But DMF, despite its apparent benefits, has yet to be extensively tested as a stand-alone fuel in engines. (Scientific American)
OSU to study nanotech’s safety Jun 23, 2007
Bakalinsky and collaborators from Rice University in Houston are using Saccharomyces cerevisiae the common yeast used to make wine, beer, and bread as the test subject in their research. They are focusing specifically on how the shape and tendency of nanoparticles to clump together affects yeast survival. (Corvallis Gazette Times, OR)
Fructose biofuel spells sweeter news for shift out of oil Jun 21, 2007
Most ethanol facilities harness biology, using enzymes to break down starch and cellulose to glucose, which is then fermented by a common yeast, Saccharomyces cerevisiae, to produce ethanol and carbon dioxide. But the process takes days and the fuel still has relatively high levels of oxygen, which reduces its energy density, makes it evaporate readily and leaves it liable to water contamination by absorbing atmospheric humidity. (Yahoo News -- Top Stories)
Scientists decode RNA mystery, will help aim drug therapies Jun 13, 2007
Citation: Plant EP, Nguyen P, Russ JR, Pittman YR, Nguyen T, et al (2007) Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae. PLoS ONE 2(6): e517. (EurekAlert!)
EDA methodologies aid biological research Jun 9, 2007
"We have built synthetic gene networks that implement biochemical logic circuits in a variety of cell types including Escherichia coli, Saccharomyces cerevisiae (yeast), and mammalian stem cells," Weiss said. He noted that these circuits incorporate a variety of digital and analog devices, including the AND, NOT, and IMPLIES logic gates and analog signal amplifiers. (EETimes)
Scientists Closer to Unfolding Mysteries of Prion Formation in Mad Cow Disease May 18, 2007
Biology professor Susan Lindquist and postdoctoral researcher Peter Tessier examined the behavior of prions in baker's yeast (Saccharomyces cerevisiae). (Unlike in humans or cows, these yeast prions do not negatively affect their hosts. (Scientific American)
Beer yeast used to find land mines May 8, 2007
Saccharomyces cerevisiae, a yeast used in baking as well as brewing, was engineered so that it had an "olfactory pathway" that responded to airborne molecules of DNT.. DNT chemical name 2,4-dinitrotoluene is a residue from the making of the explosive TNT. Dogs trained to sniff for explosives are believed in fact to be trained to detect DNT.. (iAfrica.com)
A search engine to identify pathway genes from expression data on multiple organisms May 4, 2007
The MSGR takes a query consisting of a list of genes that function together in a genetic pathway from one of six organisms: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana, and Helicobacter pylori. Using a probabilistic method to merge searches, the MSGR identifies genes that are significantly coregulated with the query genes in one or more of those organisms. (BioMed Central)
Deletion of the cruciform binding domain in CBP/14-3-3 displays reduced origin binding and initiation of DNA replication in budding yeast Apr 13, 2007
By expressing the human 14-3-3epsilon as the sole member of 14-3-3 proteins family in Saccharomyces cerevisiae, we show that 14-3-3epsilon complements the S. cerevisiae Bmh1/Bmh2 double knockout, conserves its cruciform binding activity, and associates in vivo with the yeast replication origins ARS307. Deletion of the alpha5-helix, the potential cruciform binding domain of 14-3-3, decreased the cruciform binding activity of the protein as well as its association with the yeast replication... (BioMed Central)
Identification and characterization of insect-specific proteins by genome data analysis Apr 4, 2007
Homologs in common to Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum, and Apis melifera were compared to the complete genomes of three non-insect eukaryotes (opisthokonts) Homo sapiens, Caenorhabditis elegans and Saccharomyces cerevisiae. This operation yielded 154 groups of orthologous proteins in Drosophila to be insect-specific homologs; 466 groups were determined to be common to eukaryotes (represented by three opisthokonts). (BioMed Central)
Protein Structures For The Entire Yeast Proteome Mar 21, 2007
These researchers divided all Saccharomyces cerevisiae proteins into nearly 15,000 distinct "domains" (regions of a protein that fold into a distinct quaternary globular structure). They then applied their own de novo structure prediction methods together with worldwide distributed computing to predict three-dimensional structures for all domains lacking sequence similarity to proteins of known structure. (Science Daily)
Super-fermenting Fungus Genome Sequenced; To Be Harnessed For Improved Biofuels Production Mar 8, 2007
"Increasing the capacity of P. stipitis to ferment xylose and using this knowledge for improving xylose metabolism in other microbes, such as Saccharomyces cerevisiae, brewer's yeast, offers a strategy for improved production of cellulosic ethanol," said Eddy Rubin, DOE JGI Director. "In addition, this strategy could enhance the productivity and sustainability of agriculture and forestry by providing new outlets for agricultural and wood harvest residues.". (Science Daily)
Pharma firms bet on healthy bacteria Jan 19, 2007
Bacterial species lactobacillus sporogenes, lactobacillus acidophillus, lactobacillus plantarum, Bifidobacterium; yeast species saccharomyces boulardii and saccharomyces cerevisiae are probiotics used for therapeutic purposes. Probiotics, which are normally associated with fermented dairy products, are used as dietary supplements in US. Refrigerated, fermented milks containing probiotic bacteria labeled as dietary supplements are currently being marketed in US.. (India Times, India -- Intl Business)
