New & Noteworthy

A Nobel Prize for Work in Yeast. Again!

October 03, 2016

Dr. Yoshinori Ohsumi has won the 2016 Nobel Prize in Physiology or Medicine for his groundbreaking work on autophagy in yeast. Image from

Dr. Yoshinori Ohsumi has won the 2016 Nobel Prize in Physiology or Medicine for his groundbreaking work on autophagy in yeast. This is the process whereby cells recycle their worn out parts or where a cell, like Mobius, the snake eating its own tail, eats less essential bits of itself to stay alive during times of starvation. Think Scarlett O’Hara using her drapes as a dress in Gone With the Wind (or Carol Burnett’s hilarious parody).

Like many, many Nobel Prizes in the past, Ohsumi’s work uncovered basic biological properties using a model organism. In this case he used our favorite lab workhorse, the yeast Saccharomyces cerevisiae, to piece together the steps involved in the recycling of a cell’s own internal structures.

And like many other basic biological studies, this one has important medical applications. In this case the two most obvious are chemotherapy resistance and amyloid-β aggregation in Alzheimer’s disease, but it isn’t restricted to just these two. For example, a specialized form of autophagy that targets damaged mitochondria, mitophagy, may not be working well in people with Parkinson’s disease.

The key to Ohsumi’s work was finding a way to disrupt this process in yeast so that he could find the important genes underlying autophagy using the awesome power of yeast genetics (#APOYG!). It turns out that this is trickier than it might seem because yeast and their autophagosomes, the little vesicles that surround and encase the bits to be degraded, are very small and so hard to see. In fact, they are so small that there was some question about whether yeast even had this process!

If yeast did, then it would take place in the vacuole, the recycling center in yeast. The equivalent organelle in people is the lysosome.

To see if autophagy happens in yeast, Ohsumi starved yeast that had vacuoles but couldn’t digest anything. The idea was that there would be a buildup of autophagosomes in the vacuole because the yeast would be desperately trying to eat itself but had no way to digest what it ate. He indeed saw that these poor yeast developed huge vacuoles bloated with autophagosomes.

Dr. Yoshinori Ohsumi now had the makings of a yeast screen! “All” he had to do was to look for mutants that didn’t form giant vacuoles under these conditions with the logic being that if you knocked out autophagy, you wouldn’t get a buildup of autophagosomes.

The rest, as they say, is history. Ohsumi and his lab managed to tease out the subtleties of this vital cellular process using good old baker’s yeast. What other nuggets of knowledge about ourselves will we pry out of this most useful of eukaryotes? I can’t wait to see what it reveals about us next!

Other Nobel Prizes have been awarded in recent years for work in yeast:

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Yeast and Human Disease News and Views

Support Model Organism Databases!

June 22, 2016

Model Organisms such as yeast, worm, fly, fish, and mouse are key drivers of biological research, providing experimental systems that yield insights into human biology and health. Model Organism Databases (MODs) enable researchers all over the world to uncover basic, conserved biological mechanisms relevant to new medical therapies. These discoveries have been recognized by many Nobel Prizes over the last decades.

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While integration presents advantages, the funding cut will cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs.

Leaders of several Model Organism communities, working with the Genetics Society of America (GSA), have come together to write a Statement of Support for the MODs, and to urge the NIH to revise its proposal. We ask all scientists who value the community-specific nature of the MODs to sign this ‘open letter’. The letter, along with all signatures, will be presented to NIH Director Francis Collins at a GSA-organized meeting on July 14, 2016 during The Allied Genetics Conference in Orlando. We urge you to add your name, and to spread the word to all researchers who value the MODs.

In other words, sign this letter!

Categories: Announcements Yeast and Human Disease News and Views

Help SGD by Taking a Brief Survey

October 21, 2014

If you could wave a magic wand and change something about SGD, what would it be? We want to know!

We need your feedback to make SGD even more useful to the biomedical research community. Which features are most important to you and how could they be improved? Which new data, tools, or resources will you need from SGD over the next few years as your research evolves?

We would greatly appreciate your thoughts on how we can serve you better. It will take just a few minutes to take our survey. Click the button below, or access the survey from the button in our website header. Thank you in advance for your time.

Categories: News and Views

Look for SGD at the Yeast Genetics Meeting in Seattle!

July 23, 2014

SGD staff will be attending the GSA Yeast Genetics Meeting in Seattle, July 29 – August 2, 2014 en force! We will be hosting a Workshop, Posters, and an Exhibit Table. The Workshop, “Computational Tools at SGD,” is on Thursday, July 31 at 1:30 PM in Kane Hall, Room 220. We will be discussing our powerful search tool, YeastMine, what’s new in the realm of Strains and Sequences, and new displays in SGD. Bring your questions and comments – we love feedback!

Follow @yeastgenome and #YEAST14 on Twitter for the latest research being presented at YGM.

Find these SGD staff members, as well as those presenting posters, at the Workshop and the Exhibit table:</p?

Maria Costanzo
Workshop Speaker
Rob Nash
Rob Nash
Workshop Speaker
Ben Hitz
Ben Hitz

Workshop: “Computational Tools at SGD”

Thursday, July 31, 1:30 – 3:00 PM
Kane Hall, Room 220
Featured topics: YeastMine (our powerful search tool), Sequences and Strains update, New data displays at SGD


In addition to the Workshop, SGD curators will present 4 posters – please stop by and chat with us.

Poster Date & Time Poster Title Presenter
318C Friday, August 1
7:30 – 8:30 PM
HUB Grand Ballroom
Defining the transcriptome of Saccharomyces cerevisiae Edith Wong
Edith Wong
387C Friday, August 1
8:30 – 9:30 PM
HUB Grand Ballroom
Yeast – it simply has a lot to say about human disease Selina Dwight
Selina Dwight
411C Friday, August 1
8:30 – 9:30 PM
HUB Grand Ballroom
Transcriptional regulation and protein complexes in budding yeast Stacia Engel
Stacia Engel
459C Friday, August 1
8:30 – 9:30 PM
HUB Grand Ballroom
Staying current and modern: Overhauling an actively-used model organism database website Kelley Paskov
Kelley Paskov

Exhibit Table

SGD will also have an exhibit table at the YGM. Come by to take a spin on our site, receive a prize for taking a survey, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD. Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!

Categories: News and Views Conferences

Professor Jure Piskur, Ph.D. (1960 &#8211; 2014)

June 04, 2014

Jure Piskur, 1960-2014

Dr. Jure Piskur, Professor and Carlsberg Foundation Chair in Molecular Food Microbiology at Lund University, sadly passed away on May 18, 2014. Dr. Piskur worked on yeast early in his scientific career, including postdoctoral research in yeast molecular biology at Carlsberg Brewery. From there, he studied Drosophila genes involved in the metabolism of nucleic acid precursors as well as yeast biodiversity and mitochondrial genetics. Most recently, his research focused on genes involved in the metabolism of nucleic acid precursors and “the evolution and molecular mechanisms which reshaped the modern enzymes and yeast genomes.” Dr. Piskur published many scientific papers, many of them represented in SGD. He was also a FEMS Microbiology Reviews Editor and Yeast Research Editorial Board Member. For more information on Dr. Piskur, please view his Lund University profile page.

Categories: News and Views

Yeast Researchers Take the Lion’s Share of GSA 2014 Awards

February 03, 2014

Congratulations to fellow yeasties Angelika Amon, Charlie Boone, and Robin Wright for winning three of the five annual Genetics Society of America awards for 2014! Just another confirmation that the awesome power of yeast genetics attracts excellent researchers…

Angelika Amon, of MIT and the Howard Hughes Medical Institute, has been awarded the Genetics Society of America Medal for outstanding contributions to the field of genetics during the past 15 years. Charlie Boone, of the University of Toronto and a longstanding member of SGD’s Scientific Advisory Board, received the Edward Novitski Prize for his extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. Robin Wright, of the University of Minnesota, has been awarded the Elizabeth W. Jones Award for Excellence in Education, which recognizes significant and sustained impact in genetics education. Find full details about the awards and recipients at the GSA website.

Categories: News and Views

Web Primer Redesign Survey

January 27, 2014

Have you used SGD’s Web Primer tool? This tool allows you to enter the name of a yeast gene, or any DNA sequence, and design primers for sequencing or PCR. We are planning to redesign this tool and we need to hear from you to make sure that the next version meets your needs. Please let us know how you use the tool and which features are most useful by filling out the Web Primer Survey. We appreciate your feedback!

Categories: News and Views

GOing Deeper into the Gene Ontology

December 12, 2013

The most interesting board games can’t be played right out of the box. You can admire the board and the game pieces, but before the fun can begin you need to spend some time reading the instructions and understanding the strategy.

A little effort put into learning the game allows you to not only play it, but master it. The same can be said for Gene Ontology! Image by Arbitrarily0 from Wikimedia Commons

Gene Ontology (GO) annotations are a little bit like that. You can get interesting information very quickly by just reading the GO terms on the Locus Summary page of your favorite yeast protein in SGD. But if you look deeper and learn just a little bit more about GO, you’ll find that you can get so much more out of it.

A new article by Judith Blake in PLoS Computational Biology is intended to help you do just that. Dr. Blake very succinctly summarizes the most important points in her article, “Ten Quick Tips for Using the Gene Ontology”.

If you’re a molecular or cell biologist, a geneticist, or a computational biologist (or are studying one of those fields), you’re probably already aware of GO. But still, you may be wondering, “Where did these annotations come from? What do those three-letter acronyms mean? How can this help me in my research?” This short and sweet article is a great place to start getting answers to these questions.

We recommend that everyone devote a few minutes to reading this brief article, even if you think you already understand GO.  Based on the most frequent questions that we get from researchers who use GO annotations at SGD, we can distill it even further into these top three points as seen from an SGD perspective.

There are people behind these annotations. GO terms are assigned either by real, live humans called biocurators, or computationally using automated methods (each annotation is marked, so you can easily see which is which). At SGD, biocurators are Ph.D. biologists who read the yeast literature and capture experimental results as GO annotations; SGD biocurators are also involved in developing the structure of the GO. We try our best, but like all human beings, we are not infallible. So if you see an annotation that looks wrong or confusing, or if you think an area of the GO could better represent the biology, please contact us ( to talk about it. The more expert help we can get, the better the GO and our GO annotations will be.

The details matter.  Those three-letter codes that accompany each annotation mean something. Imagine you are deciding how to allocate your lab’s resources and a critical experiment will be based on a particular protein having a particular function. You see a GO annotation for that function and that protein, so you’re good to go! But wait a minute…

Those codes tell you the experimental evidence behind the assignment of a GO term to a gene product. If that annotation has an IDA (Inferred from Direct Assay) evidence code, then the function was shown in an actual experiment, so you probably are good to go. On the other hand, if the annotation has an ISS (Inferred from Sequence Similarity) evidence code, then it was made solely based on resemblance to another protein. This is still valuable information, but you might not want to bet the farm (or the lab) on it.

Dates are very important too. Both the annotations and the GO itself are constantly updated to keep up with new biological knowledge. Because of this, everything related to GO – from a single annotation shown on an SGD GO Details page, to the downloadable files that contain all GO annotations or the ontology itself – is associated with the date it was created. So if you do any analysis using GO annotations it’s important to note the dates of both the annotation and ontology files that you used. This is especially important if you repeat a GO term enrichment for a gene set over time.  The results will definitely change, as significant enrichments become more strongly supported while marginally significant enrichments may not be reproduced.

Go deeper. GO is not just a list of terms. GO terms have defined relationships to each other, with some being broader (parent terms) and some more specific (child terms). If you really understand the structure of GO, you’ll be able to make much better use of the annotations.

For example, if you look for gene products in SGD annotated to the GO term “mitochondrion,” you’ll currently find 1055 of them1. Does that mean that there are exactly 1055 proteins or noncoding RNAs known to be in yeast mitochondria? Noooo!

There are more than that, because the term “mitochondrion” has more specific child terms such as “mitochondrial matrix”; some proteins are annotated directly to those terms and not to the parent term. If you had used the original list of proteins annotated to “mitochondrion”, you’d be missing 92 gene products2 that are so well-studied that their precise locations in the organelle are known! The structure of the GO allows you to gather all the gene products annotated to a term and to all its child terms (YeastMine has a template tailored to this kind of query).

As you can tell, there is a lot more to GO annotations than a lot of people think.  And as you dig deeper, you begin to be able to use them in ever more sophisticated ways.  Sort of like the natural progression with a strategy board game like Settlers of Catan.  At first, even after reading the instructions, you are just trying to work through the game.  But as you play more and more, you quickly learn where to build your roads, which islands to colonize and so much more.  So get out there and master GO.  You’ll be glad you did.

1As of December 2013, using YeastMine template “GO Term -> All genes” (includes Manually curated and High-throughput annotation types).

 2As of December 2013, using YeastMine template “GO Term Name [and children of this term] -> All genes” (filtered to exclude Computational annotation type so that only Manually curated and High-throughput annotation types are included).

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: News and Views

Tags: GO , Gene Ontology

A Hands-On Class That Shows Undergraduates the Power of Yeast

November 25, 2013

Stanford offers an innovative class, targeted at sophomore undergraduates, where students use yeast to determine how a mutation in the p53 gene affects the activity of the resulting p53 protein. What makes this class even cooler is that the p53 mutants come from actual human tumors—the undergraduates are figuring out what actual cancer mutations are doing! And the class uses what we think is the most important organism in the world, S. cerevisiae.

To learn more about the course, we decided to interview Jamie Imam, one of the instructors. After reading the interview, you will almost certainly be as excited about this class as we were and it may even get you to wishing that you could teach the class at your institution. With a little help, you can.

The creators of the course, Tim Stearns and Martha Cyert, really want as many people as possible to use this class to teach undergraduates about what real science is and how fun and exciting it can be. To that end, they are happy to help you replicate the course wherever you are. If you are interested, please contact Tim and/or Martha. You’ll be happy you did. Their contact information can be found at the Stearns lab and Cyert lab websites.

Here now is the interview with Jamie. What a great way to get undergraduates excited about the scientific process.

Dr. Jamie Imam

Can you describe the class?

Sure. Bio44X is designed to be similar to an authentic research experience or as close to one as you can replicate in the classroom. During the quarter, students study mutant versions of a gene called p53, a tumor suppressor that is frequently mutated in cancer. Each partner pair in a classroom gets one p53 mutant that has been identified in a human tumor to study in our yeast system. Throughout the course of the 10 weeks, the students study the transactivation ability of their mutant compared to the wild-type version, and then work to figure out what exactly is wrong with the mutant (Can it bind DNA?, Does it localize to the nucleus properly?, etc.). Multiple sections of this course are taught during the Fall and Winter quarters, so several pairs end up studying the same mutant. We bring these students together to discuss and combine their data throughout the quarter, so there is a lot of collaboration involved. I think the students really enjoy having one topic to study in depth over the quarter rather than short individual modules, and the fact that we are studying a gene so important in cancer makes it easier to get them to care about the work they are doing.

Tell me a little bit about how this class was started.

Previously, Bio44X at Stanford was the more traditional “cookbook” type lab course. Every 2 weeks, the topic would change and students would work through set protocols that had a known correct answer. In 2010, Professors Martha Cyert and Tim Stearns set out to design and pilot a research-based course on a medically relevant topic (the tumor suppressor p53) in response to some national calls for biology lab course reform. Two years and many changes later, the new research-based lab course replaced the previous version and is now taken by all of the students that need an introductory lab course in Biology.

What kinds of experiments do the students get to do in the class?

Students get exposed to a variety of lab techniques that can be used beyond our classroom. We start with sterile technique and pipetting during the very first week (some students have never pipetted before!). During the first class, the students also spot out some yeast strains so they can start collecting data on the transactivation ability of their p53 mutant right away. Once they have some basic information about the function of their mutant, the students then extract protein from their yeast strains. Throughout the rest of the quarter, students use this protein to conduct a kinetic assay, Western blot, and assess DNA binding ability of their mutant p53. They also get some exposure to fluorescence microscopy when they use a GFP-tagged version of their mutant to determine whether it can localize properly to the nucleus. But the most important thing of all is that students learn how to analyze the data and think critically about it. Not only do they “crunch the numbers” but they must use that information to draw some actual conclusions about what is wrong with their mutant by the end of the quarter.

How hard is it to set up and run the class?

It takes a lot of organization because we have around 200 or more students that take this class every year! Fortunately, we have a great team to help organize the setup of the labs so that the instructors can focus on the teaching. Nicole Bradon manages a small staff that sets up the classrooms and prepares all of the reagents for the lab each week. Dr. Daria Hekmat-Scafe, who is one of the instructors, constructs many of the yeast strains that we give to the students. The team of lecturers (Dr. Shyamala Malladi, Dr. Daria Hekmat-Scafe and I) all work together on lectures and other course materials so everyone gets a similar experience. All together, it takes a lot of behind-the-scenes work, but then the students really get to focus on the experiments and their results.

Do you enjoy teaching the class? What is your favorite part? Your least favorite part?

I love teaching this class! It is so fun to go through this research experience with so many students and they all bring their unique perspectives to the course (we get engineers, psych majors, bio majors, econ majors and others). Also, each section has only 20 students so you really get the chance to get to know them over the course of the 10 weeks. Sometimes the experiments don’t work as planned (like real science) but overall it ends up being a great learning experience.

What do you hope the students will learn and get out of the class? And are they learning/getting it?

We hope that students learn to think critically and what it really means to “think like a scientist”. Too often, science is boiled down to a series of facts that students are expected to memorize and that isn’t what science really is! Science is all about finding exciting questions and constructing experiments that try and answer those questions. The beauty of a research-based lab course is that students can also feel more in charge of their own learning. We have performed assessments of the class and have found that over the course of the quarter, students develop a more sophisticated understanding of what it means to “think like a scientist” and a large portion are more interested in becoming involved in scientific research. I think this is great, as I feel that undergraduate research helped me understand science so much more deeply than many of the courses I had taken.

How would someone at another University go about replicating this course? Are there resources available to help them get started and/or keep it running?

Our group is willing to share our course materials and knowledge with others that are interested in replicating this at other institutions. Anyone who is interested should feel free to contact us! Also, there is a paper in preparation that will describe some of the key aspects of the course as well as more details about what we have learned from the assessments of the course over the past few years.

There you have it…a great class that uses the awesomeness of yeast to teach undergraduates how to think like scientists. Again, if you’re interested in learning more, please contact Tim Stearns and/or Martha Cyert at Stanford.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: News and Views

Tags: yeast model for human disease , Saccharomyces cerevisiae , undergraduate education

Follow the CSHL Cell Biology of Yeasts Meeting on Twitter!

November 03, 2013

Wish you were going to Cold Spring Harbor for the Cell Biology of Yeasts meeting this week, November 5-9?  SGD will be live tweeting from CSHL, highlighting topics from talks and posters. Keep up with events at the meeting by following @yeastgenome on Twitter or searching #YCB2013 for all tweets!

Categories: News and Views

Memorial Gathering for Dr. Fred Sherman

October 23, 2013

Fred Sherman, 1932-2013


A memorial gathering in memory of Fred Sherman will be held at 10:00 am on Friday, December 6, 2013. The gathering will be held in the Ryan Case Methods Room (Rm #1-9576) of the University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester NY 14642. This event will be a celebration of the life and science of Fred, comprised of reminiscences about Fred by some who knew him well, followed by an opportunity for any guest to say a few words about Fred. For more information, contact Mark Dumont (, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642 (Phone 585-275-2466).

Categories: News and Views

Randy Schekman and the Awesome Power of Yeast!

October 07, 2013

Congratulations to Randy Schekman, James Rothman, and Thomas Südhof, who have been awarded the 2013 Nobel Prize in Physiology or Medicine for their work in understanding how the cell organizes its transport system. Randy Schekman used the awesome power of yeast to identify and characterize genes required for vesicle traffic. James Rothman characterized these and other proteins in mammalian cells, and Thomas Südhof showed the critical role of vesicle trafficking in nerve cells. You can read summaries of their Nobel winning work at NatureThe Scientist, and The New York Times, or search SGD to see how each of these researchers has used our model organism in their research: Randy SchekmanJames RothmanThomas Südhof.

Categories: News and Views

Fred Sherman, 1932-2013

September 18, 2013

Dr. Fred Sherman

The yeast community mourns the loss of Dr. Fred Sherman, who passed away on September 16, 2013. Dr. Sherman was a member of the faculty at the University of Rochester from 1961 until his death. He served as Chair of the Department of Biochemistry and then Chair of the combined Department of Biochemistry and Biophysics from 1982-1999. He performed ground-breaking research on the structure and regulation of genes and the effects of genetic mutations on proteins and was a proponent of the use of baker’s yeast as a genetic model system – a system that is now used at virtually all research centers worldwide, largely due to Dr. Sherman’s efforts and his teaching of many leaders in the field. The importance of his work has been recognized by his appointment to the prestigious National Academy of Sciences in 1985, by his receipt of an Honorary Doctorate from the University of Minnesota in 2002, by his election as a Fellow of the American Association for the Advancement of Science in 2006, and by his receipt of both the George W. Beadle Award and the Lifetime Achievement Award from the Genetics Society of America in 2006. He was continuously funded by NIH for over 45 years.

Dr. Sherman’s family will receive friends on FRIDAY September 20, from 3-7 PM at Michael R. Yackiw Funeral Home, 1650 Empire Blvd., Webster. On SATURDAY, friends may join his family for a graveside service gathering at the Mt. Hope Ave. entrance of Mt. Hope Cemetery at 11 AM. In lieu of flowers, contributions may be directed to a fund to support an annual lecture in Fred’s memory. To donate please mail donations to: Fred Sherman Lecture of the University of Rochester, Box 712, University of Rochester Medical Center, 601 Elmwood Ave., Rochester NY, 14642.

Plans for a future memorial service will be announced at a later date.

Categories: News and Views

Carl Singer Foundation Established

April 12, 2013

Carl Singer

Carl Singer, who was an integral part of the yeast research community for many years, passed away on February 8, 2013. Throughout his career, Carl supported yeast research both with his engineering expertise and with his good cheer. In tribute to Carl, the Singer family has now set up The Carl Singer Foundation, a charitable foundation dedicated to supporting scientific education in the field of yeast genetics. Questions about the foundation may be directed to Harry Singer at

Carl’s family would be happy to receive memories of Carl’s life at

Categories: News and Views

Carl Singer, 1945 &#8211; 2013

March 25, 2013

This image, from the Singer family, exemplifies Carl’s good cheer.

It is with great sadness that we note the passing of Carl Singer on February 8, 2013. Carl was a staunch supporter of the international yeast community. His good humor, generosity and infectious enthusiasm have been bright highlights of every yeast meeting for many decades. His creativity and engineering prowess have exerted a similarly powerful impact in labs world-wide, contributing to the quality of yeast research and the ease of performing it. He will be sorely missed.

Please send memories celebrating his life to his family at A celebration of Carl’s life will be held at 2 PM on Tuesday, March 26th, at St. Michael’s Church, Minehead, UK.

Thanks to Terry Cooper for drafting this obituary.

Categories: News and Views

Symposium in remembrance of Jon Widom, 1955 &#8211; 2011

February 22, 2012

As many of you know, Jonathan Widom died suddenly last summer.  He was a Professor in the Department of Molecular Biosciences at Northwestern University.  The beauty of Jon’s scientific research was more than matched by his surpassing intellectual brilliance and personal warmth, and he is deeply missed by those who knew and loved him.  Jon’s family and colleagues have organized a symposium celebrating his life and work, which will be held at Northwestern’s Evanston campus on March 16, 2012.  Information about this gathering, called “Unraveling the Mysteries of Life:  Recognizing the Life and Work of Jon Widom”, can be found online here.  All are welcome. Additionally, tributes to Jon that will be shared at the meeting (and afterward) can be contributed here.

Categories: News and Views