The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.

Yeastgenome.org has Server used 44.236.125.133 IP Address with Hostname in United States. Below listing website ranking, Similar Webs, Backlinks. This domain was first 2003-03-26 (18 years, 86 days) and hosted in San Diego United States, server ping response time 79 ms. ...

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. ...

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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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SGRP, the Saccharomyces Genome Resequencing Project, is a collaboration between the Sanger Institute and Professor Ed Louis group at the Institute of Genetics, University of Nottingham. Our goal is to advance understanding of genomic variation and evolution by analysing sequences from multiple strains of the two Saccharomyces pecies, S cerevisiae and S paradoxus. We have completed ABI sequencing of haploids of 37 cerevisiae strains and 27 paradoxus strains to a depth of between 1x and 3x, yielding a total of 1.42 million reads (1,292 megabases); and Illumina GA (Solexa) sequencing of four of the 37 cerevisiae strains and an additional 10 paradoxus strains. The sequence data has been aligned to the respective reference genome sequences using SsahaSNP (for ABI) and Maq (for Illumina) followed by the application of heuristics to select the most plausible alignments. The SNPs (single-nucleotide polymorphisms) implied by these alignments have been extracted. We have also developed methods, based on ...

The BY4741 strain used in (Nagalakshmi et al. 2008) was used in this study. RNA-Seq was performed using the protocol developed in (Nagalakshmi et al. 2008), further described in (Nagalakshmi et al. 2010) and (Waern et al. 2011), and using the modifications developed by (Parkhomchuk et al. 2009) to generate strand-specific reads.. Analysis was performed on custom software developed in-house using BowTie (Langmead et al. 2009) to map reads to the S288C reference genome available on SGD, downloaded on May 17, 2010. Python, NumPy, SciPy, and matplotlib were used to further process the data. The softwares source code is available (Saccharomyces Genome Database). Of note, to maximize the information gleaned, unmappable reads were trimmed by four bases from the 3′ end and remapping was attempted; this was done iteratively until only 28 bp remained, at which point the read was considered unmappable. This end trimming typically doubled or more the number of mappable reads.. Expression levels were ...

The aim of this study was to demonstrate that good characterization of S. cerevisiae clinical isolates can be achieved by using a molecular method such as Southern blot hybridization analysis. Even though the development of a molecular typing method useful for the characterization of a yeast infection is a desirable goal for many mycologists, the number of studies in which the epidemiology of S. cerevisiae infections has been investigated is very limited (9, 17, 34). A universally accepted typing method for this organism has been not defined. This could be due in part to the low prevalence of diseases caused byS. cerevisiae, particularly of vaginal infections. However, in our investigation, these infections have been of considerable interest. As described above, of 513 women who visited our Microbiological Service in the study period, 5.8% had S. cerevisiae in their vaginal swabs. This was in agreement with the data reported by Agatensi et al. (1), by which the incidence of vaginal infections ...

Tyler, BM. 2009. Viewing the microbial world through the lens of the Gene Ontology. Trends in Microbiology. 17(7): 259-261. (July) Giglio MG, Collmer C.W. Lomax J. Ireland A. 2009. Applying the Gene Ontology in microbial annotation. Trends in Microbiology. 17(7): 262-268. (July) Hu JC. Karp PD. Keseler, IM. Krummenacker M. Siegele DA. What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology. 17(7): 269-278. (July) Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July) Christie KR, Hong EL, Cherry JM. 2009. Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends in Microbiology. 17(7): 286-294. (July) Chibucos MC, Tseng T-T, Setubal JC. 2009. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 17(7): 312-319. (July) Torto-Alalibo T, Meng S, Dean RA. 2009. Infection ...

Systematic, large-scale synthetic genetic (gene-gene or epistasis) interaction screens can be used to explore genetic redundancy and...

p53 is one of best known human proteins that induces or represses hundreds of genes and plays a pivotal role in preventing tumor development. Recent studies established unambiguously that p53 is a nucleosome-binding protein. The rotational positioning of a nucleosome is critical to determine the accessibility of a p53 site. In particular, the p53 site in a nucleosome is accessible if it is bent in the direction similar to that found in the p53-DNA co-crystals; the site becomes inaccessible if the orientation is changed by ∼180°. Importantly, we have shown that p53 response elements (REs) associated with cell cycle arrest are often exposed on the nucleosomal surface, suggesting a new role of nucleosomes in mediating the p53 binding and subsequent gene induction.. The present study aims to make a detailed analysis of nucleosome organization of all p53 functional REs in normal and cancer cells. Published genome-wide nucleosome maps from lymphoblastoid (normal) and K562 (cancer) cell lines are ...

Webpage presenting results of fungal ecology and biotechnology. At the IHI Zittau we analyze fungal genomes and use identified genes for heterologous expression. Focus is on fungal laccase, peroxidases and peroxygenase.

SANEFALCON (2016): Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles (Prenat Diagn. 2016 ...

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SAN ANTONIO-Patients with atrial fibrillation who are at high risk for stroke may benefit from continuing treatment with Coumadin (warfarin) even after sinus rhythm is restored and maintained.

Two large-scale yeast two-hybrid screens were undertaken to identify protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transfo …

Sequence alignment of Yarrowia lipolytica Pex24p with the proteins Yhr150p and Ydr479p encoded by the Saccharomyces cerevisiae genome. Amino acid sequences were

Working as part of an international research consortium, a multidisciplinary team at The Johns Hopkins University has completed the design phase for a fully synthetic yeast genome.. The details of the design concept and process will be published March 10 in Science as part of a set of seven articles; the other articles offer details of successful efforts to integrate artificial, or synthetic, yeast chromosomes into host yeast cells.. Once completed, yeast cells carrying a fully artificial genome - termed Saccharomyces cerevisiae 2.0, or Sc2.0 - will prove invaluable for both academic and industrial applications, says lead study author Joel Bader, Ph.D., professor of biomedical engineering and interim director of the High Throughput Biology Center at the Johns Hopkins University School of Medicine.. Natural yeast is a major organism for making products used in biotechnology, such as enzymes or antibiotics, but optimizing it for new products is inefficient, Bader says. Our designed synthetic ...

The sequencing of the yeast genome was a major milestone in genetics research. In 1996 Saccharomyces cerevisiae or bakers yeast was the first eukaryotic organism to have its entire nuclear genome sequenced.

Types of fruit body: There are number of fruit bodies in Ascomycota. In yeasts and related fungi the asci are not enclosed by hyphae, but in most ascomycetes they are surrounded by hyphae to form an ascocarp or ascoma. An old term for ...

The Fungal Program scales up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Encoded in the genomes of the organisms of the kingdom Fungi are biological processes with high relevance to the Department of Energy missions in bioenergy production, carbon cycling and biogeochemistry. Combining new sequencing technologies and comparative genomics analysis, we work on large and complex sequencing projects such as surveying the broad phylogenetic and ecological diversity of fungi, and capturing genomic variation in natural populations and engineered strains. This approach allows us to build a foundation for translating the genomic potential of fungi into practical applications.. Among the major initiatives of the Fungal Program are:. ...

Aflatoxin B1 (AFB1) is a fungal metabolite that contaminates the food supply in certain areas of the world. It is produced by Aspergillusflavus and related fungi that grow on improperly stored foods such as corn, rice, and ...

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Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic

Changing a single letter, or base, in an organisms genetic code impact its traits. Subtler changes can and do happen: in eukaryotes, one such modification involves adding a methyl group to base 6 of adenine (6mA). In Nature Genetics, researchers report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. This little-explored realm provides a repertoire of important and valuable gene products for DOE missions in bioenergy and environment.

چکیده علف‌کش‌ها به-طور وسیعی در مزارع مختلف مورد استفاده قرار می-گیرند اما مکانیسم فعل و انفعلات ممکن بین علف‌کش‌ها و بیمارگرهای گیاهی به‌خوبی شناخته نشده است. یکی از مهم‌ترین بیماری‌های سویا، پوسیدگی ذغالی است که عامل آن قارچ Macrophomina phaseolina ، می‌باشد. علف‌کش‌های ایمازتاپیر، تریفلورالین و متری‌بیوزین به ‌صورت -کاربرد خاکی در کشت سویا کاربرد دارند. به-منظور بررسی اثر غلظت‌های مختلف علف‌کش‌های مذکور بر سرعت رشد قارچ، آزمایشی به-صورت فاکتوریل در قالب طرح کاملاً تصادفی در شش تکرار در شرایط آزمایشگاهی انجام گردید. برای هر یک از علف‌کش‌ها، غلظت‌های