New & Noteworthy

New Protein Localization Resource: YeastRGB

November 14, 2018


yeastRGB

Multiple display units in YeastRGB

YeastRGB is a new resource for exploring protein abundance and localization. Utilizing data from the classical C-terminally tagged GFP yeast library along with new-generation collections derived from SWAp Tag (SWAT) technology, YeastRGB enables simultaneous visualization of dozens of yeast strains imaged with multiple fluorescent tags.

From SGD, you can access YeastRGB through any Protein page (example: Atp12p). The YeastRGB link is located in the Resources section, under Localization. Alternatively, you can visit the YeastRGB website and search for your favorite genes or keywords.

For more information on YeastRGB, see the publication by Dubreuil et al. at Nucleic Acids Research: https://doi.org/10.1093/nar/gky941

Categories: Announcements

Registration Open for the 30th Fungal Genetics Conference

November 07, 2018


The 30th Fungal Genetics Conference takes place next year March 12-17, 2019 at Asilomar Conference Grounds in Pacific Grove, CA. The biennial Fungal Genetics Conference is a place where scientists working on any aspect of fungal genetics–such as gene regulation, evolutionary biology, cell development, fungal-host interactions and more–can come together in a common platform to share ideas and collaborate.

The schedule of events is now available. The conference features multiple workshops, Plenary Sessions with central themes on various aspects of fungal biology, and dozens of diverse Concurrent Sessions where you can attend talks on topics most relevant to your research. The 2019 Perkins/Metzenberg Lecture, which provides perspectives given by a leader in the field of fungal genetics, will be presented by John Taylor from the University of California, Berkeley.

Register soon! The abstract submission deadline and early registration deadline are both in one month, on December 5th 2018.

Categories: Announcements, Conferences

Apply Now for the 2019 Fungal Pathogen Genomics Course

October 30, 2018


Fungal Pathogen Genomics is an exciting week-long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD/CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.

Daily activities in Fungal Pathogen Genomics will include both individual and group exercises, lectures on the bioinformatics resources provided by various databases, and presentations by distinguished guest speakers. Examples of what you will learn at Fungal Pathogen Genomics include:

  • RNA-seq and SNP analysis and visualization via EuPathDB Galaxy workspace in FungiDB
  • Identification of secondary metabolite clusters in MycoCosm
  • Finding virulence genes and annotation in Ensembl
  • Accessing and analyzing genetic interactions in CGD/SGD
  • Discovering taxonomic conservation or phenotypes in PomBase

The application deadline for the Fungal Pathogen Genomics workshop to be held May 7-12, 2019 at the Wellcome Genome Campus in Hinxton, Cambridge, UK is February 7, 2019.

Don’t miss out – apply now!

Categories: Announcements

Out of China: Changing our Views on the Origins of Budding Yeast

April 17, 2018

1,011. That’s the number of different Saccharomyces cerevisiae yeast strains that were whole-genome sequenced and phenotyped by a team of researchers jointly led by Joseph Schacherer and Gianni Liti, published this week in Nature (Peter et al., 2018; data at: http://bit.ly/1011genomes-DataAtSGD).

1011genomes_FigS1bPie_chart_PaperVersion-crop

Ecological origins of the 1,011 isolates (from Peter et al., 2018; Creative Commons license)

Scrupulously gathering isolates of S. cerevisiae from as many diverse geographical locations and ecological niches as possible, the authors and their collaborators plucked yeast cells not only from the familiar wine, beer and bread sources, but also from rotting bananas, sea water, human blood, sewage, termite mounds, and more. The authors then surveyed the evolutionary relationships among the strains to describe the worldwide population distribution of this species and deduce its historical spread.

They found that the greatest amount of genome sequence diversity existed among the S. cerevisiae strains collected from Taiwan, mainland China, and other regions of East Asia. This means that in all likelihood the geographic origin of S. cerevisiae lies somewhere in East Asia. According to the authors, our budding yeast friend began spreading around the globe about 15,000 years ago, undergoing several independent domestication events during its worldwide journey. For example, it turns out that wine yeast and sake yeast were domesticated from different ancestors, thousands of years apart from each other. Whereas genomic markers of domestication appeared about 4,000 years ago in sake yeast, such markers appeared in wine yeast only 1,500 years ago.

Additionally — and similar to the situation where human interspecific hybridization with Neanderthals occurred only after humans migrated out of Africa — it appears that S. cerevisiae has inter-bred very frequently with other Saccharomyces species, especially S. paradoxus, but that most of these interspecific hybridization events occurred after the out-of-China dispersal.

There are many more gems to be found among the treasure trove of information in this paper. Some notable conclusions from the authors include: diploids are the most fit ploidy; copy number variation (CNV) is the most prevalent type of variation; most single nucleotide polymorphisms (SNPs) are very rare alleles in the population; extensive loss of heterozygosity is observed among many strains. There are also phenotype results (fitness values) for 971 strains across 36 different growth conditions.

As is often the case for yeast, the ability to sequence and analyze whole genomes at very deep coverage has yielded broad insights on eukaryotic genome evolution. The team’s work highlights this by presenting a comprehensive view of genome evolution on many different levels (e.g., differences in ploidy, aneuploidy, genetic variants, hybridization, and introgressions) that is difficult to obtain at the same scale and accuracy for other eukaryotic organisms.

SGD is happy to announce that in conjunction with the authors and publishers, we are hosting the datasets from the paper at this SGD download site. These datasets include: the actual genome sequences of the 1,011 isolates; the list of 4,940 common “core” ORFs plus 2,856 ORFs that are variable within the population (together these make up the “pangenome”); copy number variation (CNV) data; phenotyping data for 36 conditions; SNPs and indels relative to the S288C genome; and much more. We hope that the easy availability of these large datasets will be useful to many yeast (and non-yeast) researchers, and as the authors say, will help to “guide future population genomics and genotype–phenotype studies in this classic model system.”

Categories: Announcements, New Data

Tags: strains, evolution, genome wide association study, Saccharomyces cerevisiae

In Memoriam: André Goffeau

April 12, 2018

It was with great sadness that we learned that André Goffeau, renowned yeast researcher and Professor at the Université Catholique de Louvain in Belgium, passed away on April 2, 2018.

Prof. Goffeau worked on yeast transporter genes and multidrug resistance for much of his scientific career, and made many contributions to this field. But he will forever be remembered for his visionary idea to sequence the entire genome of Saccharomyces cerevisiae, ultimately leading to the coordination of a world-wide collaborative effort during the late 1980s and early 1990s by researchers from 19 countries working in 94 laboratories. The sequencing project, which represented the first completely sequenced eukaryotic genome, culminated in the landmark publication “Life with 6000 Genes” (Goffeau et al. 1996). But of course this was only the beginning of a cascading myriad of discoveries, methods, resources and careers built upon the existence of the yeast genome sequence.

AndreGoffeau

The collaborative nature of the yeast community’s effort was nicely summed up in the 1996 Goffeau et al. paper: “Whether they worked in large centers or small laboratories, most of the 600 or so scientists involved in sequencing the yeast genome share the feeling that the worldwide ties created by this venture are of inestimable value to the future of yeast research” and indeed this has proved true. Prof. Goffeau was recognized with many awards and honors over his career, including the 2002 Beadle Medal of the Genetics Society of America for his work in having “initiated and successfully led the yeast genome sequencing project”. After the completion of the S. cerevisiae genome he continued to sequence whole genomes of other microbes and also worked on novel anti-cancer agents. Prof. Goffeau was a highly praised mentor and published hundreds of scientific papers of which many resulted from large collaborations; he also served on journal editorial boards, organized meetings, and performed many other valuable services to the scientific community over his career. He was an active and treasured part of the yeast community and we will miss him greatly.

Categories: Announcements

Apply Now for the 2018 Yeast Genetics and Genomics Course

March 16, 2018

yeast_course_panorama

For almost 50 years, the legendary Yeast Genetics and Genomics course has been taught each summer at Cold Spring Harbor Laboratory.

For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists. The application deadline is April 15th, so don’t miss your chance! Find all the details and application form here. This year’s instructors – Grant Brown, Greg Lang, and Elçin Ünal – have designed a course (July 24 – August 13) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • Finding and Analyzing Yeast Information Using SGD
  • Isolation and Characterization of Mutants
  • Yeast Transformation, Gene Replacement by PCR, and Construction and Analysis of Gene Fusions
  • Tetrad Analysis
  • Genome-scale Screens Using Synthetic Genetic Array (SGA) Methodology    
  • Deep Sequencing Applied to SNP Mapping and Deep Mutational Scanning
  • Exploring Synthetic Biology with CRISPR/Cas9-directed Engineering of Biosynthetic Pathways
  • Computational Methods for Data Analysis
  • Modern Cytological Approaches Including Epitope Tagging and Imaging Yeast Cells Using Fluorescence Microscopy

Techniques have been summarized in a completely updated course manual, which was recently published by CSHL Press.

IMG_2185

There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.

Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

 

Categories: Announcements

Happy Holidays from SGD!

December 22, 2017


We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays.

Happy Holidays from SGD!

Stanford University will be closed for two weeks from December 23rd through January 7th. Regular operations will resume on Monday, January 8, 2018.

Although SGD staff members will be taking time off, please rest assured that the website will remain up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions.

Happy Holidays and best wishes for all good things in the coming New Year!

Categories: Announcements

Call for Yeast Genetics Meeting 2018 Award Nominations!

July 25, 2017


The Yeast Genetics Meeting will be held August 22-26, 2018 at Stanford University.

You are invited to submit nominations to the meeting organizers for the awards and presentations that have become a cornerstone of the meeting.

  • The Lifetime Achievement Award is given for lifetime contributions in the field of yeast genetics and outstanding community service.
  • The Ira Herskowitz Award is given for outstanding contributions in the field of yeast research in the last 20 years. This award is usually given to scientists under 50.
  • The Winge-Lindegren Address is a thought-provoking perspective given by a leader in the field of yeast genetics.
  • The Lee Hartwell Lecture is given by a noted researcher in the field who has used yeast in a way that has had an obvious impact on other fields.

Previous awardees are listed on last year’s Yeast Genetics Meeting award site.
 
The deadline for nominations is Tuesday, August 1, 2017. Nominations should include: name, affiliation, email address, and a one or two sentence overview of why you are proposing the individual. Please send nominations to mahoney@genetics-gsa.org.

Categories: Announcements

Exploring the Global Yeast Genetic Interaction Network

April 17, 2017


Global yeast genetic interaction profile similarity network. Image from TheCellMap.org.

With the construction of a global genetic interaction network in S. cerevisiae, it’s not hard to see why yeast genetic interactions remain a treasure trove for biological discovery. When combined with tools for visualization and analysis, these data can be used to draw powerful functional maps of the cell and infer potential functions for uncharacterized genes.

In a recent paper published in G3: Genes|Genomes|Genetics, Usaj et al. describe a web-based resource for exploring the global yeast genetic interaction network: TheCellMap.org. TheCellMap.org is an online database and visualization tool for quantitative yeast genetic interaction data. It provides an interactive version of the global yeast genetic interaction similarity network described by Costanzo et al., enabling users to scroll through and zoom in on different clusters of functionally related genes within the network. Users can search for specific genes or alleles, extract and re-organize sub-networks for genes of interest, functionally annotate genetic interactions, and more. Further, if more details about a gene are needed, users can even double-click on the gene to be taken to its respective locus summary page at SGD!

For more information about this resource, see http://TheCellMap.org/about/ or access the publication at https://doi.org/10.1534/g3.117.040220.

Categories: Announcements

Apply Now for the 2017 Yeast Genetics & Genomics Course

March 17, 2017


For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory.

For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.

The application deadline is April 15th, so don’t miss your chance! Find all the details and application form here.

This year’s instructors – Grant Brown, Maitreya Dunham, and Elçin Ünal – have designed a course (July 25 – August 14) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • How to Find and Analyze Yeast Information Using SGD
  • Isolation and Characterization of Mutants
  • Transformation of Plasmids & Integrating DNAs
  • Meiosis & Tetrad Dissection as well as mitotic recombination
  • Synthetic Genetic Array Analysis
  • Next-Gen. whole-genome and multiplexed DNA barcode sequencing
  • Genome-based methods of analysis
  • Visualization of yeast using light and fluorescence microscopy
  • Exploring synthetic biology with CRISPR/CAS9-directed engineering of biosynthetic pathways

Techniques have been summarized in a completely updated course manual, which was recently published by CSHL Press.

legendary plate race

There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.

Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

Categories: Announcements

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