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)
• Glad You Asked: We Energies' legendary cookbook; the status of the Martin Walker case; origins of the phrase 'charley horse'; What is yeast made of? Dec 22, 2006
The scientific name for one species of yeast is "Saccharomyces Cerevisiae" or "sugar eating fungus." This name is derived from the Latin word "cerevisiae," which means "brewer." This strain of yeast is very strong and capable of fermentation, the process that causes bread dough to rise. I stole this answer from the good folks at Red Star Yeast via their Web page. (Racine Journal Times, WI)
Evolution and the workaround Dec 11, 2006
The Stowers researchers used the benign budding yeast Saccharomyces cerevisiae as their model organism and deleted a key cell division gene called MYO1. Surely, eliminating this important gene would shut down cell division. (EurekAlert!)
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression Nov 5, 2006
We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. (BioMed Central)
GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima Nov 4, 2006
The resultant algorithm, GibbsST, is then validated using synthetic data and actual promoter sequences extracted from Saccharomyces cerevisiae. It is noteworthy that the marked improvement of the efficiency presented in this paper is attributable solely to the improvement of the search method. (BioMed Central)
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae Oct 29, 2006
By studying the TR network of the yeast Saccharomyces cerevisiae we show that an intermediate layer of transcription factors naturally segregates into distinct subnetworks. In these topological units transcription factors are densely interlinked in a largely hierarchical manner and respond to external signals by utilizing a fraction of these subnets. (BioMed Central)
Full 'Humanization' Of Therapeutic Proteins From Yeast Sep 12, 2006
(May 9, 2005) -- Researchers at UCSD have invented a technique that organizes the genetic information contained in the 16 chromosomes of the yeast Saccharomyces cerevisiae into a wiring diagram resembling an. . (Science Daily)
Hierarchical modularity of nested bow-ties in metabolic networks Aug 18, 2006
Network decomposition of three microbes (Escherichia coli, Aeropyrum pernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks exhibit a highly modularized bow-tie topological pattern similar to that of the global metabolic networks. Moreover, these small bow-ties are hierarchically nested into larger ones and collectively integrated into a large metabolic network, and important features of this modularity are not observed in the random shuffled network. (BioMed Central)
Genome comparison using Gene Ontology (GO) with statistical testing Aug 11, 2006
We also studied how the results vary when only subsets of the genes were used in the comparison of human vs. mouse and that of Saccharomyces cerevisiae vs. Schizosaccharomyces pombe. Conclusions. (BioMed Central)
A literature-based similarity metric for biological processes Jul 27, 2006
The method has been applied to the biological processes annotated for the Saccharomyces cerevisiae genome. We compared our results with similarities obtained with two ontology-based metrics, as well as with gene product annotation relationships. (BioMed Central)
Chromosome copies confer resistance Jul 25, 2006
J.B. Anderson et al., "Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae," Genetics, April 2003. A. Coste et al., "A mutation in Tac1p, a transcription factor regulating CDR1 and CDR2, is coupled with loss of heterozygosity at chromosome 5 to mediate antifungal resistance in Candida albicans," Genetics, April 2006. (The Scientist)
NHGRI announces latest sequencing targets Jul 20, 2006
Also selected in the latest round is a project to sequence up to 50 strains of the yeast Saccharomyces cerevisiae. The genome of Saccharomyces cerevisiae was first completed in 1996 and is a primary model for studying variations in genomes that can contribute to health and disease. (EurekAlert!)
Targeting myosin II in yeast cytokinesis Jun 28, 2006
Significant conservation between species of the components involved in cytokinesis, including those of the CR, allows the use of easily genetically manipulated organisms, such as budding yeast (Saccharomyces cerevisiae), in the study of cytokinesis. Budding yeast has a single myosin II protein, named Myo1. (BioMed Central)
DNA repair mapped, systems-wide May 20, 2006
S.A. Jelinsky, L.D. Samson, "Global response of Saccharomyces cerevisiae to an alkylating agent," PNAS, February 16, 1999. Yolanda Sanchez. (The Scientist)
Support for Golgi maturation theory May 16, 2006
The studies, published in , report observations of transitioning from early (cis) to late (trans) in the yeast Saccharomyces cerevisiae, suggesting that proteins remain within a single cisterna before being secreted. "How things move within the Golgi is one of the most contentious issues of membrane biology in the modern era," said , professor of cell biology at the University of California, Berkeley, who was not involved with the studies. (The Scientist)
Loza places first at science fair May 13, 2006
Jagadeesan earned a third-place Medicine and Health prize, worth $1,000, for her project entitled The Antimicrobial Properties of Curcuma longa and Its Growth Impediment Effects on Saccharomyces cerevisiae and Escherichia coli. . (Post-Tribune)
Motion as a phenotype: The use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics Apr 25, 2006
Recently however, actively transcribed genes have also been found localized to the nuclear periphery in the yeast Saccharomyces cerevisiae. When genes are activated, they become associated with the nuclear pore complex (NPC) at the nuclear envelope. (BioMed Central)
Malaria breakthrough raises spectre of drug resistance Apr 19, 2006
Jay Keasling at the University of California, Berkeley, and his colleagues tweaked a pathway and used three plant genes to persuade yeast (Saccharomyces cerevisiae) to produce and secrete large amounts of artemisinic acid, which is just a few chemical steps away from artemisinin. The researchers, whose paper '', hope that once the process is scaled up it will allow artemisinin to be made industrially. (Nature News Service)
Yeast cells offer last line of defense against malaria Apr 16, 2006
The researchers took a type of yeast, Saccharomyces cerevisiae, and modified its cells so they started producing a chemical called artemisininic acid. Because the drug is pushed out of the cells it makes it easy to harvest and purify into a usable drug, Keasling said. (Taipei Times)
New mechanism for essential genome-wide gene silencing identified Apr 15, 2006
In the study, conducted in a type of yeast called Saccharomyces cerevisiae, the scientists showed that a protein called SUMO binds to histones and acts to repress transcription of genes, and it does so at many different sites across the genome. While several other histone-related mechanisms have been identified for activating genes in yeast, this is the first one recognized as repressing gene transcription. (EurekAlert!)
Hopes for cheaper malaria drug Apr 13, 2006
They did this by adding two genes from A. annua to the yeast, Saccharomyces cerevisiae. Other researchers have shown that this precursor can be converted into artemisinin in a handful of chemical steps. (BBC News -- Africa)
Cyclic nucleotide specific phosphodiesterases of Leishmania major Mar 8, 2006
In contrast to other protozoa such as Dictyostelium or fungi such as Saccharomyces cerevisiae, Candida ssp or Neurospora, no genes for class II PDEs were found in the Leishmania genomes. LmjPDEA contains a class I catalytic domain at the C-terminus of the polypeptide, with no other discernible functional domains elsewhere. (BioMed Central)
Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae Feb 22, 2006
BMC Genomics 2006, 7:32 doi:10. Abstract (provisional). (BioMed Central)
Protein kinases associated with the yeast phosphoproteome Jan 31, 2006
A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned. (BioMed Central)
