The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.
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Dear Tomas, The Saccharomyces Genome Database (http://genome-www.stanford.edu/Saccharomyces/) contains answers to many of your questions. You can search for all Gene Ontology terms containing the word nucleus by entering nucleus in the search box at the top of the SGD home page; the hit list will show each term, with a list of genes annotated to that term. Each gene name in the list is hyperlinked to its locus page, which contains a summary of what is known about the gene and its product, a collection of relevant literature, and links to functional genomic data about that gene. Any free text, as well as gene names, can be entered into the SGD search, so if you start with the name of your favorite gene product, you should come up with any yeast genes that have been called by that name. Good luck, and let us know (yeast-curator at genome.stanford.edu) if you have any questions about SGD. Best regards, Maria Maria C. Costanzo, Ph.D. Senior Scientific Curator Saccharomyces Genome Database ...
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Hi Eleanor, I can offer one general hint: tetraploid yeast cells are larger than diploids, and it may be possible to make cells of even higher ploidy. I did this long ago (~ 15 years!) to facilitate immunofluorescent detection of a low-abundance protein. Unfortunately I cant remember the details or references at this point (my own experiment didnt work so I never published it), but I think it was straightforward to make the polyploid cells - you just need a lot of markers to select them. Good luck! Maria Maria C. Costanzo, Ph.D. Senior Scientific Curator, Saccharomyces Genome Database Department of Genetics Stanford University School of Medicine Stanford, CA 94305-5120 Phone: 650-725-8956 Fax: 650-723-7016 http://www.yeastgenome.org/ maria at genome.stanford.edu On Thursday, November 13, 2003, at 08:14 PM, wozei wrote: , Hi all, , , does any one have an idea how I could make my yeast [S. cerevisiae] , grow to at , least 5-10 micron size or greater for an experiment I need to carry , out with , ...
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PLEASE DO NOT EDIT HERE. USE THE SECTION EDIT LINKS ON THE RIGHT MARGIN--> {{PageTop}} ,protect> {,{{Prettytable}} align = right width = 200px ,- ,valign=top nowrap bgcolor={{SGDblue}}, Systematic name ,, [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000002450 YDR043C] ,- ,valign=top nowrap bgcolor={{SGDblue}}, Gene name ,,NRG1 ,- ,valign=top nowrap bgcolor={{SGDblue}}, Aliases ,, ,- ,valign=top nowrap bgcolor={{SGDblue}}, Feature type ,, ORF, Verified[[Category:ORF]][[Category:ORF, Verified]] ,- ,valign=top nowrap bgcolor={{SGDblue}}, Coordinates ,nowrap, Chr IV:543369..542674 ,- ,valign=top nowrap bgcolor={{SGDblue}}, Primary SGDID ,, S000002450 ,} ,br> Description of YDR043C: Transcriptional repressor that recruits the Cyc8p-Tup1p complex to promoters; mediates glucose repression and negatively regulates a variety of processes including filamentous growth and alkaline pH response,ref name=S000070028>Kuchin ...
Number 10 p. 118 Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4s gene regulation was part of the cells response to a reduction in available glucose (i.e., the only available food ...
Number 10 p. 118 Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4s gene regulation was part of the cells response to a reduction in available glucose (i.e., the only available food ...
The recently sequenced genome of the filamentous fungus Ashbya gossypii revealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiae both at the level of homology and synteny (conservation of gene order). Thus, it became possible to reinvestigate the S. cerevisiae genome in the syntenic regions leading to an improved annotation. We have identified 23 novel S. cerevisiae open reading frames (ORFs) as syntenic homologs of A. gossypii genes; for all but one, homologs are present in other eukaryotes including humans. Other comparisons identified 13 overlooked introns and suggested 69 potential sequence corrections resulting in ORF extensions or ORF fusions with improved homology to the syntenic A. gossypii homologs. Of the proposed corrections, 25 were tested and confirmed by resequencing. In addition, homologs of nearly 1,000 S. cerevisiae ORFs, presently annotated as hypothetical, were found in A. gossypii at syntenic positions and can therefore be considered as authentic genes.
TY - JOUR. T1 - Functional profiling of the Saccharomyces cerevisiae genome. AU - Giaever, Guri. AU - Chu, Angela M.. AU - Ni, Li. AU - Connelly, Carla. AU - Riles, Linda. AU - Véronneau, Steeve. AU - Dow, Sally. AU - Lucau-Danila, Ankuta. AU - Anderson, Keith. AU - André, Bruno. AU - Arkin, Adam P.. AU - Astromoff, Anna. AU - El Bakkoury, Mohamed. AU - Bangham, Rhonda. AU - Benito, Rocio. AU - Brachat, Sophie. AU - Campanaro, Stefano. AU - Curtiss, Matt. AU - Davis, Karen. AU - Deutschbauer, Adam. AU - Entian, Karl Dieter. AU - Flaherty, Patrick. AU - Foury, Francoise. AU - Garfinkel, David J.. AU - Gerstein, Mark. AU - Gotte, Deanna. AU - Güldener, Ulrich. AU - Hegemann, Johannes H.. AU - Hempel, Svenja. AU - Herman, Zelek. AU - Jaramillo, Daniel F.. AU - Kelly, Diane E.. AU - Kelly, Steven L.. AU - Kötter, Peter. AU - LaBonte, Darlene. AU - Lamb, David C.. AU - Lan, Ning. AU - Liang, Hong. AU - Liao, Hong. AU - Liu, Lucy. AU - Luo, Chuanyun. AU - Lussier, Marc. AU - Mao, Rong. AU - ...
Readers are alerted that there is currently a discussion regarding the use of some of the unpublished genomic data presented in this manuscript. Appropriate editorial action will be taken once this matter is resolved. Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading
Also see the JGI Mycocosm for information on the Genomic Encyclopedia of Fungi: a range of interests into the fungal genomes that impact on mycorrhyzal symbiosis, plant pathogenicity, biocontrol as well as industrial applications such as lignocellulose degradation, sugar fermentation and other industrial applications. ...
The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.
Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression ...
The multiplexed sequencing data were then deconvoluted using the indexing barcode and aligned to the yeast genome with Novoalign (Novocraft Technologies). If a sequenced fragment did not uniquely align to the genome it was discarded. Gene promoters were defined as the 600 bp immediately upstream of the translational start site of each gene defined in the Saccharomyces Genome Database. The number of fragments that aligned to these annotated promoters was recorded for each INPUT and IP sample. This converted the data from read alignments to a table of read counts per promoter.. Transcription factor regulatory targets were determined from the wild-type ChIP-Seq experiments. Regulatory targets were determined separately for each of the biological triplicates using the MACS peak-finding algorithm (Thurman et al. 2012). MACS uses a simple sliding window strategy to compare INPUT and IP samples at each position along a chromosome. The algorithm assumes that the number of reads aligned to any particular ...
The Saccharomyces Genome Project has revealed the presence of more than 6000 open reading frames (ORFs) in the S. cerevisiae genome. Approximately one third of these ORFs currently have no known function four years after their discovery. The goal of the Saccharomyces Genome Deletion Project is to generate as complete a set as possible of yeast deletion strains with the overall goal of assigning function to the ORFs through phenotypic analysis of the mutants. The method used was a PCR-based gene deletion strategy to generate a start- to stop- codon deletion of each of the ORFs in the yeast genome. As part of the deletion process, each gene disruption was replaced with a KanMX module and uniquely tagged with one or two 20mer sequence(s) . The presence of the tags can be detected via hybridization to a high-density oligonucleotide array, enabling growth phenotypes of individual strains to be analyzed in parallel . Nearly all ORFs larger than 100 codons were disrupted; highly similar ORFs were not ...
Genome sequencing has provided a means for describing the complete genetic makeup of an organism. The application of sequencing technology to fungi has provided a wealth of data of interest to medical mycologists and to evolutionary and cellular biologists alike. The sequencing of multiple fungal genomes provides an initial view of the degree of conservation and diversity within the fungal kingdom. Furthermore, the comparison of these fungal genomes with the genomes of other eukaryotes provides a more precise view both of the scale of conservation of eukaryotic genes and of novel genes restricted to the fungi. While much research on fungi has focused on understanding conserved eukaryotic functions, the genomic sequence also will be important in characterizing fungus-specific pathways such as those involved in secondary metabolism, including antibiotics, and specialized degradation pathways, such as for cellulose. The genome sequences of related organisms provide more than just catalogs of species gene
Figure 3. Chromosomal distribution of three groups of MNase-seq reads in lengths of ,152, 147 ± 5, and ,142 bp. A, Distribution of MNase-seq reads (data from leaf tissue) along chromosome 4 of Arabidopsis. The two horizontal bars represent the positions of the pericentromeric region and a knob located in the short arm of the chromosome (both are highly heterochromatic; Fransz et al., 2000). B, Distribution of MNase-seq reads along chromosome 4 of rice. The short arm and pericentromeric region of the long arm, both highly heterochromatic (Cheng et al., 2001), are marked by two horizontal bars. The x axes show DNA positions along the chromosomes. The y axes represent the normalized DNA fragment count ratio (Materials and Methods) of a specific group within 100-kb windows. Heterochromatic regions are enriched with reads ,152 bp in both species. ...
Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Research 32(Database-Issue): 311-314 (2004 ...
To determine the fraction of the yeast Saccharomyces cerevisiae genome that is required for normal cell growth and division, we constructed diploid strains that were heterozygous for random single disruptions. We monitored the effects of approximately 200 independent disruptions by sporulating the d …
David Botstein has been one of the driving forces of modern genetics. He is a geneticist, educator and a pioneer in integrating multiple diverse disciplines into the study of biology. His work established the ground rules for human genetic mapping and laid the foundation of the human genome project. He also co-discovered transposons in bacteria. His current research activities include studies of yeast genetics and cell biology, linkage mapping of human genes predisposing to manic depressive illness, hypertension and other complex diseases and the development and maintenance of the Saccharomyces Genome Database on the World Wide Web (http://www-genome.stanford.edu). Most recently he has been involved in pioneering the application of microarray technology. Microarray studies provide a high-throughput molecular approach to simultaneously assess the behavior of many genes. This technology is being applied to understand how to better target cancer therapies based on gene profiles of the tumor cells. ...
A catalogue of known hemiascomycetous yeast splicing signals was then used as bait to screen the batch of selected coding sequences, and to validate or not the presence of an intron ...
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