Teaching

Nature: Train students to navigate ethical swamps

Anonymous — Wed, 10 Apr 2019 06:00:00 +0000

Nature: Train students to navigate ethical swamps Anonymous (not verified) Wed, 04/10/2019 - 00:00

Mary Allen

A protocol can help with the tricky conversations essential to responsible research conduct, says Mary A. Allen.

“Either this is sloppiness or misconduct, and either way I don’t think this is a lab I want to be in anymore.” I was terrified as I spoke these words to my first graduate-school adviser in November 2004. Members of my laboratory had seen suspicious data in grant proposals, and the discovery was causing me unmanageable stress. A month later, two colleagues went to the chair of our department, and an investigation began. From the outside, deciding to have that hard conversation was a small part of a gruelling ordeal involving many people. Our lab eventually shut down, and our principal investigator was found to have falsified data on grant applications.

For me, personally, that conversation is the result of one of the most important things that I have ever done: making the decision to have a difficult discussion when something needs to change. That’s why I’ve developed a way to help others to do so.

Now I am a principal investigator co-running a lab. Our website has a light-hearted Tolkienesque map. It shows the Isle of RNA modification, the Ivory Tower, a Sea of Data — and a career track running through an ethical swamp. Many ask why this is included amid the puns and in-jokes, but I ask why it wouldn’t be. Almost every scientist I know has been through at least one ethical morass in their career.

Partly because of my past experience, I teach the responsible conduct of research (RCR) courses required of many trainees who receive government funding. Most of the mandated topics, such as responsible authorship and publication, focus on compliance — following the rules. That is necessary. But it is not sufficient. A responsible researcher needs to be able to navigate conflicts and tricky situations.

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Video: Nobel laureate Tom Cech still loves teaching

Anonymous — Mon, 15 Oct 2018 06:00:00 +0000

Video: Nobel laureate Tom Cech still loves teaching Anonymous (not verified) Mon, 10/15/2018 - 00:00

CU �鶹ӰԺ's Tom Cech won the Nobel Prize for Chemistry in 1989, but he firmly believes his place is still in the classroom teaching undergraduates. Here, he discusses how teaching adds meaning to his life and how he still works to become a better teacher.

[video:https://www.youtube.com/watch?v=k3yqYgjNBgk]

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Nobel laureate Tom Cech wins 2017 Hazel Barnes Prize

Anonymous — Fri, 24 Mar 2017 06:00:00 +0000

Nobel laureate Tom Cech wins 2017 Hazel Barnes Prize Anonymous (not verified) Fri, 03/24/2017 - 00:00

BioFrontiers

�鶹ӰԺ Distinguished Professor Tom Cech, Colorado’s first Nobel Prize winner, has been named the 2017 Hazel Barnes Prize winner – the most distinguished award a faculty member can receive from the university.

Cech, the director of the BioFrontiers Institute, shared the 1989 Nobel Prize in Chemistry for his findings that RNA in living cells is not only a molecule that encodes information but also can function as a catalyst. His discovery laid the foundation for advances in molecular genetics and gave rise to an expanding appreciation of the roles of RNA in biology.

Cech’s role in teaching is equally impressive. He has routinely taught general chemistry to freshmen, using interactive teaching methods like “clickers” and in-class demonstrations. He includes undergraduate learning assistants to help fellow students master the material as they hone their own teaching skills.

He also led the development of an innovative graduate student education program at BioFrontiers called the Interdisciplinary Quantitative Biology (IQ Biology) Ph.D certificate program. The IQ Biology program currently has 38 active doctoral students who can choose to work with many mentors in 13 departments.

“Tom Cech is one of the leading scientists in the world and has been for many years,” said Chancellor Philip P. DiStefano. “Equally important is his commitment to teaching. Over the years, he has trained and mentored thousands of undergraduates and graduate students, some of whom are now world-renowned scientists themselves. We are truly honored to have Professor Cech, one of our five Nobel Laureates, working among us.”

Since 1992 the Hazel Barnes Prize has been awarded annually to a CU �鶹ӰԺ faculty member who best exemplifies the enriching interrelationship between teaching and research, and whose work has had a significant impact on students, faculty, colleagues and the university.

The prize, which will be presented at spring commencement, includes a $20,000 cash award and an engraved university medal. Cech also will be recognized at a reception next fall that will include former Hazel Barnes Prize recipients, family members, colleagues and students. The prize was established in honor of renowned philosophy Professor Emerita Hazel Barnes, who taught at CU �鶹ӰԺ from 1943 to 1986 and who passed away in 2008.

“I love the fact that the Prize honors the synergy between research and student learning,” said Cech of chemistry and biochemistry. “For me, it’s always been a two-way street: Students contribute greatly to our biochemical discoveries and at the same time the research profoundly enriches their education.”

Cech came to CU �鶹ӰԺ as a faculty member in 1978. Over his CU �鶹ӰԺ career he has trained 54 postdoctoral scientists, 36 graduate students and countless undergraduates.

In recent years Cech has been conducting basic science research on telomerase, the replicating enzyme on chromosome ends that has implications for both cancer and aging. His current research on telomerase reverse transcriptase (TERT), building the framework for the future development of new treatments for cancer.

Cech became a Howard Hughes Medical Institute (HHMI) Investigator in 1988, then served as president of the Chevy Chase, Maryland-based HHMI – the nation’s largest science philanthropy – from 2000 to 2009 while retaining his CU �鶹ӰԺ faculty positions and lab. He is currently an HHMI Investigator and also has a faculty appointment at the University of Colorado Anschutz Medical Campus.

“One of Tom’s top priorities when he returned to the classroom was to continue to teach chemistry to CU �鶹ӰԺ undergraduates because he felt he could make the greatest impact on students if he caught them early and got them excited,” said Distinguished Professor Leslie Leinwand, the chief scientific officer of BioFrontiers.

“He also felt strongly that students should have more opportunities to interact with senior, highly accomplished scientists and was determined to serve as a role model in that regard for other faculty,” Leinwand said.

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CAREER scientist thrives at the intersection of research and teaching

Anonymous — Fri, 21 Mar 2014 06:00:00 +0000

CAREER scientist thrives at the intersection of research and teaching Anonymous (not verified) Fri, 03/21/2014 - 00:00

Meagan Taylor

Most university faculty divide their time between research activities, teaching and service to their institutions, sometimes putting in hundreds of hours weekly to accomplish the job’s demands. Being able to shine in all of these areas is a rare accomplishment, especially for newer faculty. For BioFrontiers faculty member Robin Dowell, juggling these responsibilities is somewhat second nature.

“With respect to components of academia, I firmly believe that these are difficult to separate,” she says. “The best way to deeply understand scientific concepts is to get your hands dirty— actually perform an experiment, write a program, or solve a math problem — or to teach the concepts to someone else. In the best-case scenarios, you do both.”

Her ability to apply this philosophy recently earned Dowell the National Science Foundation’s most prestigious award for junior faculty, the Faculty Early Career Development (CAREER) grant. Providing five years of support totaling more than $650,000, the grant recognizes emerging investigators who excel at combining teaching and research in ways that directly impact their institutions and the broader community. Dowell is one of only ten scientists nationwide in the field of molecular and cellular bioscience who have received the award so far this year.

The CAREER program requires scientists to complete specific aims in both teaching and research. Successful candidates have designed projects in which their research feeds into their teaching goals and vice versa, creating a long-term cycle that advances both aims. Projects are also expected to meet institutional needs, such as providing students with mentored external development opportunities or promoting interdisciplinary research.

Dowell prefers the term “antedisciplinary” in her lab’s approach, a term coined by her graduate mentor, Dr. Sean Eddy. Given her and her students’ concentrations in computer science, statistics, molecular biology and genetics, she defines the concept as “following problem wherever it leads you.”

“I have a hard time when people ask me how I integrate such diverse fields,” she says. “It isn't about integrating fields, areas or components, but rather ignoring those kinds of boundaries.”

The CAREER project embraces this philosophy by providing two unique educational activities for students while furthering the Dowell lab’s continuing research on the molecular impact of aneuploidy. Down syndrome is a well-known example of aneuploidy, which occurs when a person has more copies of a chromosome than normal.

Using computational models of biological processes and experiments on yeast cells, the Dowell lab will explore how regulators—genes that affect the function and form of other genes— affect the early processes of genetic expression, called transcription.

Dowell describes her research in musical terms. If the human genome is the score for a symphony, transcription is like the music heard from that score. In genetics, a regulator gene performs the work of the musical conductor, controlling qualities such as tempo and volume.

While regulators in the human genome number about 1,800, having too many of these conductors in a particular cell can throw off the music. Aneuploidy is an example in which the dose of regulators has altered expression of genes, causing deleterious affects for people with Down syndrome.

“We understand that transcription is affected by aneuploidy, but we don’t know how it works at the molecular level,” Dowell says.

The educational component of project contains two unique objectives that encourage students to engage in external opportunities that contribute to their education and community. The first objective is to establish a permanent iGEM team at CU. iGEM, or international Genetically Engineered Machine, is the world’s foremost synthetic biology competition for undergraduates. Last year’s CU team won the gold medal at the North American competition for their “DIY Biology” project to create a set of low-cost tools for performing synthetic biology.

The second objective is to better engage scientists in understanding Responsible Conduct of Research (RCR) by creating an interactive game. RCR encompasses professional norms and ethical principles scientists must use in the performance of their work.

“The game will not only train scientists in an engaging and interactive manner but also will enable studies into how peer pressure influences ethical behavior.” Dowell wrote in her CAREER grant application. “In the end, the long term impact of creating honest, intelligent and creative scientists is incalculable.”

More information on antedisciplinary research, iGEM and aneuploidy can be found on the Dowell Lab website.

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When the student becomes the mentor

Anonymous — Wed, 15 Aug 2012 06:00:00 +0000

When the student becomes the mentor Anonymous (not verified) Wed, 08/15/2012 - 00:00

BioFrontiers

When the student becomes the mentor

This past May, the inaugural class of IQ Biology, including myself, finished its first year of graduate study. It was an interesting year that saw different people from very different backgrounds coexist in an interdisciplinary environment where sometimes we didn’t know what each other was saying. Not a language barrier, nor a cultural shock, but a difference in perspectives and educational backgrounds. It was quite the experience seeing the first year unfold and have us all become comfortable with each other and the fact that we all have different interests.

I decided to join the MCDB department and Dr. Leslie Leinwand’s lab. I have been working on understanding the actin-myosin cross-bridge cycle kinetic model. In general, I want to understand why different myosin isoforms and mutants have different reaction rates and how they play a role in myopathy (muscle disease). Myosin, one of the main contractile proteins in muscle cells can show differences in its reaction rates depending on the muscle, the isoform and the developmental stage. Mutant forms of the protein result in muscle disease and understanding these reactions at the kinetic level can help design treatments for these myopathies. I feel very fortunate to be on this path with some great classmates and in a great lab working on a very interesting project with biotech potential.

My story in �鶹ӰԺ didn’t actually start in August 2011, but in the summer of 2005 and I attribute that summer as one of the main reasons I am in this fortunate situation. I participated in the SMART (Summer Multicultural Access to Research Training) program during that year and immediately fell in love with the �鶹ӰԺ lifestyle and was very intrigued by the research environment.

The SMART program has been going on for 24 years and its main goal is to bring minority undergraduate students from underrepresented institutions to one of the high-end CU-�鶹ӰԺ labs to do research for the summer. That summer was very meaningful for me and it was a huge factor in my decision to continue graduate studies in �鶹ӰԺ. I remained friends with Dr. Mark Hernandez and Barbara Kraus throughout the years and we were all pretty excited when I decided to join the BioFrontiers Institute.

One idea that I had of a way I could repay them for their efforts was to become a student mentor for the program. I would join some colleagues and fellow grad students in helping the intern class for this year in any way we could. But my idea was taken a few steps further, when Leslie trusted me to also mentor the student who joined the Leinwand lab for the summer.

Initially, I was confused. I had just joined the lab, what do I have to teach to a person who is probably 3-4 years younger than me and who is also joining the lab with me? Thankfully, Leslie assured me that one of the postdocs (Steve Langer) would be the one doing most of the teaching and I would help out. Then Dr. Langer told me he would be taking some much-deserved vacation time during the student’s first week, so again… confusion.

As it turned out, I actually had a lot to teach during the first two weeks. I taught the student some tissue culturing, some Q-PCR, some protein purification and some theory behind my new reason for living: myosin kinetics. Then Steve and the recently graduated John Deacon (Leinwand Lab, defended in July) helped me out for the rest of the summer.

I also had a chance to interact with the other students when I gave a workshop on how to write a research proposal. The proposal is just one of the many requirements that the SMART program has for the interns. Watching the students work on their respective proposals in the beginning of the summer was very fun because it reminded me of my proposal in 2005 and how I struggled with it.

Then, I and a fellow mentor, Joan Marcano (Batey Lab) gave a Science and Society workshop where we described to the students some ethical issues in research through a Nature article on Cohort studies. It resulted in some discussion on the future of “big data” and the responsibility of having this information. We also took some time during this workshop to talk to the students about the BioFrontiers Institute. There were also some fun times like when the group went on a rafting trip and when we went to Hartford, Connecticut for a symposium at which over 20 programs similar to the SMART program brought their groups of students to present their research for the summer.

In the end, I believe this was a very productive summer, meaningful just like the one in 2005. I joined a lab that I like, work on a project with many facets and issues, and I got a chance to give back to the people who are responsible for me being in my current situation. I was able to help train a very SMART student which was very rewarding considering he is interested in cardiac failure research. Working in a team-fashion with John (biochemist) and Steve (virologist) while training a biomedical engineering student, was just as interdisciplinary of an effort as the first year of IQ biology. I look forward to future challenges such as this one.

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Dan Knights Adventure Continues

Anonymous — Wed, 23 May 2012 06:00:00 +0000

Dan Knights Adventure Continues Anonymous (not verified) Wed, 05/23/2012 - 00:00

BioFrontiers

IQ Biology graduate's adventure continues

Dan Knights is a humble guy, with very little reason to be humble. A short list of his titles includes high school math teacher, computer scientist and the 2003 Rubik’s Cube World Champion. He has appeared on the Today Show, The Discovery Channel and as an expert on National Public Radio’s “Wait, Wait… Don’t Tell Me.” Dan has co-authored 21 journal publications, including two in Science and three in Nature.

He is interested in applying machine learning and computational statistics to challenges in biology, genomics and engineering. He is also the first student to graduate from BioFrontier’s Ph.D. certificate program in Interdisciplinary Quantitative Biology, or IQ Biology.

“The IQ Biology program encouraged me to continue to straddle the boundary between computation and biology,” said Dan “It exposed me to a new group of scientists and strengthened my foundations in the life sciences.”

Dan defended his thesis work in April 2012, which also earned him the Outstanding Dissertation Award from CU-�鶹ӰԺ’s College of Engineering and Applied Science. During his graduate studies, he spent much of his time in the lab of BioFrontiers faculty member Rob Knight, researching the microbiome.

Dan's advice for incoming graduate students is simple and effective:

Dan's advice for incoming graduate students is simple and effective: Learn programming and learn how to write code. Don't be afraid to branch out and explore other disciplines during lab rotations. You might be surprised how these connections make you better at what you do. For an impressive list of Dan's publications, visit his website.

The microbiome is the enormous collection of bacterial species that coexist in and on living organisms, including humans, and contribute substantially to our health and disease. The bacteria can be identified indirectly through their DNA genomes, but these experiments generate a vast amount of information. Making sense of all that information required Dan’s computer science expertise.

Dan recently accepted a tenure-track faulty position as an assistant professor of Computer Science at the University of Minnesota, Twin Cities Campus. Before he heads to the City of Lakes, Dan is making a year long stop at The Broad Institute of MIT and Harvard in Cambridge, Mass. to extend his research by doing post-doctoral work. His focus will be a mix of microbiome analysis, and a study of gut microbiota and the human immune response.

“It is unusual for a graduate student to jump right into a tenure-track faculty position, but Dan is unusually talented, and his accomplishments in both computer science and genomics served him well on the job market,” said Tom Cech, Director of the BioFrontiers Institute. “He sets a high standard for students in the IQ Biology program, and we wish him the very best.”

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IQ Bio Blog: Workshop on Genomics

Anonymous — Wed, 04 Apr 2012 06:00:00 +0000

IQ Bio Blog: Workshop on Genomics Anonymous (not verified) Wed, 04/04/2012 - 00:00

Daniel McDonald

This past January, I had an amazing opportunity to be an instructor at the Workshop on Genomics, and the associated advanced topic sessions, in the Czech Republic. The workshop was hosted in Cesky Krumlov, a UNESCO World Heritage site considered the best preserved medieval town in Europe. The workshop is a two week, intensive crash course on the latest and greatest tools used in genomics, with courses and lectures taught by the developers and researchers sitting at the forefront of genomics research.

For instance, a few of the sessions covered during this past workshop included lectures and tutorials on genome assembly with ALLPATHS-LG and velvet, transcriptome assembly with Trinity and variant calling with Stacks (and that's only scratching the surface). The advanced topic sessions covered R/Bioconductor and Python/BioPython. Students even got familiarity with Amazon's EC2 and cloud computing during the two weeks.

Beyond learning about tools, the workshop offered a fantastic chance to interact with peers within and across disciplines including numerous opportunities for students and invited faculty alike to interact and discuss science over meals and Budvar (the original Budweiser). Furthermore, the diversity of the workshop was immense: over 70 students ranging from graduate level to established PIs, with countless nationalities and languages represented. One of the greatest difficulties as an instructor was becoming familiar with the sheer variety of keyboards!

As an instructor for the workshop, my role was geared towards the setup and testing of tutorials and providing support during the tutorials. The majority of the students taking part did not have a computational background. Initially, many of the questions surrounded a Linux shell environment, but the students were quick to pick up on the common, and powerful, command-line-oriented tasks. During the course of the workshop, a few students began inquiring about Shell programming. We okayed it with the organizer to spawn a few impromptu three-hour practical Python programming sessions that were very well received by the students. For many, it was their first time programming which led well into the advanced topic sessions.

Genomics in the 21st century is becoming increasingly data-driven with the development of next-generation sequencing technologies. Learning how to make sense from sequence within this tsunami of data requires the development of computational skills, knowledge of the tools available and resource requirements. As a current IQ Biology student, I'm enrolled in courses teaching the theory behind many of these tools. The workshop ,in turn, offers the practical hands-on knowledge of how to use and maximize the effectiveness of the techniques; an awesome combination.

If all works out, the workshop will be coming to Biofrontiers the summer of 2013. Hope to see you there!

Daniel McDonald (below in the orange jacket) is currently completing his first year of graduate studies in the IQ Biology Interdisciplinary Quantitative Biology program.

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Multi-discipline research makes a big impact

Anonymous — Wed, 01 Feb 2012 07:00:00 +0000

Multi-discipline research makes a big impact Anonymous (not verified) Wed, 02/01/2012 - 00:00

BioFrontiers

Multi-discipline research makes a big impact

Liz Bradley is a great professor because she loved being a student. The computer science professor graduated from MIT with three degrees, a B.S., M.S., and Ph.D., in electrical engineering and computer science. And, while earning these degrees would be more than enough to earn bragging rights, Bradley earned her two graduate degrees while training as an Olympic rower. She took fifth place in the 1988 Olympic Games.

“I was lucky that I had a graduate advisor who understood that I had 11 Olympic workouts a week,” she says of her graduate experience. “But, being at MIT was a fire hose of fabulous things to think about.”

Bradley acts as an advisor on the Biofrontiers Institute’s IQ Biology Interdisciplinary Quantitative Biology graduate program because cross-discipline work is something she is passionate about. Computer science now plays a huge role in managing the massive data sets in the biosciences.

“Computers, by default, are cross-disciplinary. They are used everywhere in scientific discovery. We solve equations with computers because we can’t solve them with pencil and paper,” she says. “And it is because I am open to working across disciplines that I tend to be the home in the department for the student projects nobody else will supervise.”

Rhonda Hoenigman is pursuing a Ph.D., and with Bradley’s encouragement and advice, she has created a computer algorithm that aids in the design of efficient landscapes: those that offer the best growth, with the most shade, using the least amount of water. This “agent-based” algorithm allows the plants to move themselves in a virtual world, and find the places they would grow the best. Hoenigman has a vision for the algorithm to help building planners save water while cooling structures with shade—a necessity for water-starved areas like the American Southwest.

Caleb Phillips, another student who works with Bradley, also created a new algorithm that addresses sustainability: one that can show us how to redistribute food waste. Phillips’ algorithm takes into account how much food is being thrown away across a given region, like �鶹ӰԺ County, and also calculates the cost of rescuing it and redistributing it to organizations in need across that region.

Most food rescue organizations use a warehouse model, which usually prevents them from handling fresh produce and other perishables. In addition, transportation costs are higher when trucks are needed to deliver food from a central warehouse.

With the help of this algorithm, the organization that Phillips founded, �鶹ӰԺ Food Rescue, takes surplus foods from stores and restaurants, and delivers them immediately to organizations that will use them. The kicker: �鶹ӰԺ Food Rescue picks up and delivers food using bikes and trailers, keeping costs at their lowest.

“�鶹ӰԺ 70 or 80 pounds a day is a normal delivery, but we rescued 950 pounds the day after Thanksgiving,” says Phillips, who has to notch his belt a little tighter because of all the bike deliveries he now makes. On days where food donations are too heavy, or the snow is too deep, Phillips’ organization has access to trucks via �鶹ӰԺ’s CarShare program. “There is definitely enough food in �鶹ӰԺ County to feed everyone,” he says.

“It’s not about us faculty, it’s about them, the students,” Bradley says. “That’s what grad school is about.” And it must be that old Olympic discipline she has that allows her to mentor incredible students, while still producing amazing work of her own.

Bradley studies chaos theory and computer performance dynamics. In her work, dropping the last decimal place off of a number that has six places after the decimal may seem insignificant—not even enough to worry about in a huge data set. But those insignificant numbers can have huge impacts across a large collection of data or across a long period of time. This theory is also known as the “Butterfly Effect,” referring to the flapping of an insect’s wing that could cause enough atmospheric change, over time, to create a devastating hurricane. Bradley is using this theory to work toward learning to predict and manage how computers and data interact.

You don’t have to look too hard to see that there is another “Butterfly Effect” going on in Bradley’s world. If chaos theory is predicting how a small change can equal a large effect, you only need to look as far as Bradley’s students to see how her interactions are exactly that: the butterfly’s wing creating a hurricane of change.

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CIMB Scientist Values a Life of Learning

Anonymous — Thu, 09 Sep 2010 06:00:00 +0000

CIMB Scientist Values a Life of Learning Anonymous (not verified) Thu, 09/09/2010 - 00:00

Cynthia Pasquale

Five questions for Amy Palmer

One of Amy Palmer's life goals is to encourage everyone around her to find learning fascinating. Her passion for science is infectious, and the ways in which she explains complicated processes makes you question the wisdom of not choosing chemistry as a college major. Palmer is an assistant professor in the department of chemistry and biochemistry at the University of Colorado at �鶹ӰԺ. She recently was honored with a National Science Foundation (NSF) CAREER Award that will help support her in her attempts to unravel salmonella bacteria's unique way of invading its host.

Palmer hopes the research using a fluorescent protein will lead to the ability to block the bacteria's harmful, sometimes deadly, effects. Palmer's lab doesn't want to kill the bacteria, which she says would put a strong evolutionary pressure on it to resist antibacterial medication. Instead, she hopes to prevent the bacteria from getting inside cells and taking over the host. More frequent outbreaks of salmonella poisoning in food sources, including the most recent in eggs, make her groundbreaking research all the more important.

1. Your research on salmonella has been focused on finding ways to track the bacteria's proteins in order to understand how they create an infection. How are you doing this?

When salmonella-contaminated food gets into your small intestine, there's something about the environment that causes it to turn on a bunch of genes that make proteins. It also creates what people refer to as a needle complex or secretion system, which is a large protein complex that looks like a needle or syringe. Just like a syringe, it's hollow inside. What salmonella does is poke the host cell and injects proteins. The proteins are like a little army that bind with molecules and hijack the cells. As a consequence, the host engulfs the proteins. Salmonella continues the process over and over again, enabling it to survive and replicate inside the host but evade the immune system. Because it is inside our own cells, the immune system can't sense it.

We know the proteins go to different parts of the cell but we know almost nothing about what they are doing and how they manipulate the host. Our research is focused on how to light up the proteins so we can track them in the complex environment of the host cell. We want to label the protein but not affect its function so that we can watch the protein and monitor it over the course of a whole infection.

Over the last 10 to 15 years, cell biologists have gotten good at tracking proteins in cells. A lot of this revolution arose from the discovery and development of the green fluorescent protein. Cell biologists use this naturally occurring protein to enable them to track movements of other proteins.

2. How are you using the fluorescent protein in your research?

The problem with tracking the invasion process of salmonella is that it essentially threads its proteins through a very narrow needle. If we take this beautiful fluorescent green protein and fuse it to the bacterial protein, the space limitation prevents the injection into the host cell and we can't track the proteins. Salmonella has 60 proteins and the invasion process is a coordinated action by a lot of players. Each protein depends on the others and what they do. So we can't take the proteins out of the context of the invasion without changing the process.

It's been a struggle to track a protein while still preserving this complicated invasion process, but we've adapted two technologies. In one, we label a bacterial protein with a small molecule fluorophore. It's cell-permeable, and when it gets inside, it binds to a specific tag that we have put on the protein we are interested in studying and it causes the molecule to turn on the fluorescence. We can then watch it as it gets secreted in the host cell.

We also took the green fluorescent protein and split it into two pieces. One piece is very small; the other is big, about 95 percent of protein. When we break it apart, it is no longer fluorescent. The small fragment is put onto a protein inside the bacteria, and the large is expressed in the host. When the bacteria secrete the protein, the host then contains both pieces, which spontaneously find each other, and the fluorescence turns back on. So now we can light up the proteins and track how they move around inside the host.

3. How did you become interested in chemistry as a career?

I was an undergraduate at Dartmouth College and had an excellent professor who offered me the opportunity to do research in her lab. It really opened up an area of science that I had never seen before. I saw science as open-ended and exciting and creative. I always knew I wanted to go into academics, but I was choosing between a major in Russian and chemistry. When I was in high school, I was in a program called Peace Child, a summer theatrical exchange program between Russia and America. I had gone to the Ukraine and there was something about the culture that fascinated me, so I started taking Russian classes. I would have been in St. Petersburg had I not wound up doing research in this professor's lab. It made me want to be like her in a way, to be able to show students a side of science that we sometimes don't teach, which is the inquiry-based side of things.

I was hired through CIMB (Colorado Initiative in Molecular Biotechnology) and was able to choose my home department, chemistry. CIMB does an amazing, almost unparalleled, job of fostering connections between people in different departments and promoting collaborations and conversations. Sometimes we get so siloed in our departments that we don't talk to each other and CIMB really breaks down those barriers. It enabled me to meet people in physics and engineering and this has led to lots of collaborations. I identify as a chemist, but my research is all over the map.

4. What is one of your life goals?

When I think of myself and my trajectory of how I ended up here, I feel like I was fortunate because I interacted with people who either helped cultivate or deepened by love of learning. In the case of science, it was this one female professor who showed me a different side of science and tried to get me excited about learning and the world around me. When I think of myself both as a teacher at the university or as mentor to my students or a mom, I think my primary goal is to see if I can somehow impart or encourage people to find learning fascinating. I want them to be inquisitive, to look at the world around them and say, "Wow, this is exciting," and to not limit themselves.

5. What is your life like outside the lab? Scientists, even chemists, are sometimes stereotyped as nerdy. How do you feel about that?

I have two small kids - a 51/2-year-old son and a 3-year-old daughter - and much of my time is spent with them and my partner who also is a faculty member at CU. We go camping and we taught both kids how to ski. My 3-year-old likes to be out of control, so we keep her on a leash on the slopes to make sure she doesn't crash into everyone else. I used to do rock climbing; it was a passion through grad school, but it's harder to find time as a faculty member and your sense of safety is very different as a parent.

As far as stereotypes are concerned, I experience that all the time. If you go to a party, and people say "What do you do," and I tell them I'm a chemist, 85 percent of the time their response is, "Wow. I hated chemistry in college." I think scientists oftentimes are portrayed in the popular media as being not quite socially adept, or not being able to interact or communicate in certain situations. I don't like to think that categorizes me. I do get incredibly excited about scientific questions. Does that make me nerdy? I spent most of my childhood climbing trees and I was a competitive swimmer; I was not hidden away in my garage with a chemistry set. One of the reasons I wanted to become a professor is to show people that there's not one way to be a scientist or a professor. There are lots of ways of doing this job.

Originally published in the University of Colorado Faculty and Staff Newsletter

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Bill and Janet Freytag Make $5 Million Endowed Gift to Bolster Biotech Research, Teaching at CU

Anonymous — Mon, 24 Aug 2009 06:00:00 +0000

Bill and Janet Freytag Make $5 Million Endowed Gift to Bolster Biotech Research, Teaching at CU Anonymous (not verified) Mon, 08/24/2009 - 00:00 BioFrontiers

Bill and Janet Freytag Make $5 Million Endowed Gift to Bolster Biotech Research, Teaching at CU

October 30, 2008

The University of Colorado announced a $5 million endowment gift from former Myogen CEO and local entrepreneur Bill Freytag and his wife, Janet, in support of the Colorado Initiative in Molecular Biotechnology, or CIMB, at the University of Colorado at �鶹ӰԺ.

The endowment will support interdisciplinary research at the interface of the biomedical sciences, chemistry, physics, computer science and engineering, including collaborations between researchers at CU-�鶹ӰԺ and at the UC Denver Anschutz Medical Campus.

CIMB research teams, which pursue breakthroughs at the intersection of engineering, science, and medicine, have recently been studying melanoma cells to gain insights on the mechanism of cancer progression and exploring inhalable vaccines that allow patients greater access to lifesaving medications.

"The Freytag's generosity will help us build on the momentum of our collaborative, cross-campus efforts in biotechnology, one of CU's primary areas of research and a focus for returning Nobel Laureate Tom Cech," said CU President Bruce D. Benson. "Our scientists and researchers continue to make significant progress unlocking the mysteries of the human body and providing practical, leading-edge solutions to age-old problems."

The gift is another indicator of the rapid strengthening of biotechnology research at CU, which this year received a boost when Cech announced he would be returning to CU full time as a Distinguished Professor. Cech has been president of the Howard Hughes Medical Institute headquartered in Chevy Chase, Md., since 2000.

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