New & Noteworthy

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.

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.

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

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

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 (Mark_Dumont@urmc.rochester.edu), 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 Nature, The 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 Schekman, James Rothman, Thomas Südhof.

Categories: News and Views

Fred Sherman, 1932-2013

September 18, 2013

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, 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 harry@thecarlsingerfoundation.org.

Carl’s family would be happy to receive memories of Carl’s life at regards@singerinstruments.com.

Categories: News and Views

Carl Singer, 1945 – 2013

March 25, 2013

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 regards@singerinstruments.com. 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 – 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

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