MCDB NewsletterDepartment of Molecular, Cellular, and Developmental Biology

Fall 2008, Vol 1Inaugural Issue

University of Colorado Boulder

NEWS FROM TOM BLUMENTHALCHAIR

Welcome!

CONTENT

Space and Facilities: We occupy adjacent buildings, already beau-tifully set up to be among the finest in the country. For several years now, we have been upgrading the research laboratories in the original Porter building to keep pace with modern technical advances. We have completely remod-eled numerous labs at the rate of about two per year, and a complete remodel of two labs on the first floor is currently underway. The newer MCDB building is already in excellent shape, so we have only had to make small improve-ments to accommodate new facilities, such as tissue culture rooms, our new confocal microscope and the newest fluorescence-activated cell sorter. We also have excellent classrooms and meeting rooms and we recently added an interactive classroom (described in a later feature in this newsletter). At this point we are eagerly anticipating the construction of the new building on the east campus that will house the Colorado Initiative for Molecular Biotech-nology, a group with which we are closely associated. Faculty: MCDB has had superb faculty from its inception. We boast several members of the National Academy of Sciences, Norm Pace, Bill Wood, Dick McIntosh, and Larry Gold), as well as a member of the Howard Hughes Medical Institute (HHMI), Min Han. In addition, many of our younger faculty have won prestigious national awards reserved for the top young fac-ulty nationwide, including the Searle Scholars Award, won by both Ding Xue and Gia Voeltz, the PEW Scholars Award, won by Jens Lykke-Andersen, and the Beckman Young Investigator Award, won by Greg Odorizzi and Michael Stowell. This year, Michael Stowell also won one of the very few prestigious Eureka awards from NIH, as well as a grant from the HHMI.

Let me begin by welcoming you to the MCDB Department’s new newsletter, the first in a continuing semi-annual series. Our purpose is to keep anyone who is interested, but especially our alumni and friends, in-formed about new developments in the department. It should tell you who we are and what our plans to make MCDB even better are. MCDB is a great department, one that has made enormous contributions to our understanding of how life works at the molecular level. This department has also been a fer-tile training ground for new scientists at both the graduate and post-graduate levels. Obviously, a great department is made up of strong faculty, staff and students, and a fine research and teaching space. Let me briefly summarize recent progress in each of these areas:

Front of the MCDB Building

The “BIG “Scope

Events 3New Faculty 4Faculty Research 5-6Outstanding Faculty 7-8Research News 9-10Alumni News 11-13Recent Graduates 14Outstanding Students 15Learning in MCDB 16-19New in MCDB 20MCDB Tools 21

1

Cover image shows a model of a dimeric kinesin-1 (right side) docked onto a microtubule protoflament (left part), taken in the Hoenger Lab. SeeSkiniodis et.al.,2003 EMBO J. 22:1518.

Norm Pace is the recipient of the MacArthur genius award, and over the past two years won three lifetime achievement awards from the RNA Society, the Society for Microbial Ecology and the American Society for Microbiology. Finally, Mark Winey won a prestigious Guggenheim Fellowship to pursue research in London during his sabbatical year that just ended. We recruited three new excellent faculty members this year (see feature in this newsletter), and we will continue to recruit new faculty members over the coming years. Students: MCDB has great students and post-docs, and we will continue to provide excellent education for them. Our graduate training pro-gram support comes from an NIH training grant in Cellular and Molecular Biology, which we have held since the inception of the program 35 years ago. This spring, the grant was renewed for another 5-year period. The post-docs have formed a very active postdoctoral organization that holds monthly scientific meetings and ensures an excellent environment for postdoctoral scholars. MCDB currently has about 800 undergraduate majors, and another thousand undergraduates take our courses each year. Under the leader-ship of Bill Wood and Jenny Knight, the department faculty has been heavily involved in modernizing our curriculum and switching over to new learning techniques facilitated by the Science Education Initiative. Staff: This department is held together by a truly wonderful group of staff members, who all work, mostly behind the scenes, to make the depart-ment function smoothly. More than half of our staff members have served the department admirably for more than 10 years, and six have been with us for more than 15. Finally, let me say a few words to introduce myself. I am relatively new to MCDB, having moved here only two years ago from my previous position as Chair of Biochemistry and Molecular Genetics at the CU School of Medicine, a position I held for nine years. Before that my career was mostly as a professor in the Department of Biology at Indiana University in Bloomington, where I was also Chair for 9 years. My education was at Johns Hopkins University and Harvard, where I was a post-doc in J.D. Watson’s laboratory. My research area is very basic molecular biology of gene expres-sion, using the roundworm, C. elegans, as an experimental organism. I hope you enjoy reading the first MCDB newsletter. In a depart-ment like ours, there is always a need for funds to enhance our programs. We hope that reading this newsletter will convince you that we are an orga-nization highly worthy of your support. We have provided a couple of easy ways for you to make a donation if you are so inclined. But even if you are not in a position to make a donation, we hope that reading these newsletters makes you feel like a part of the ongoing MCDB community.

MCDB Newsletter

Tom Blumenthal - Professor ChairRobert Boswell - Professor Associate Chair

Thomas Cech - Distinguished Professor, AdjunctShelley Copley - ProfessorBrian DeDecker - Research Assistant ProfessorCorella Detweiler - Assistant ProfessorJoaquin Espinosa - Assistant ProfessorLarry Gold - ProfessorNancy Guild - ProfessorMin Han - ProfessorAndy Hoenger - Associate ProfessorKevin Jones - Associate ProfessorMichael Klymkowsky - ProfessorJennifer Knight - Senior InstructorKenneth Krauter - ProfessorLeslie Leinwand - ProfessorJens Lykke-Andersen - Associate ProfessorJennifer Martin - Assistant ProfessorGreg Odorizzi - Associate ProfessorBradley Olwin - ProfessorNorman Pace - Distinguished ProfessorThomas Perkins - Assistant ProfessorRobert Poyton - ProfessorJingshi Shen - Assistant ProfessorRavinder Singh - Associate ProfessorGretchen Stein - Senior InstructorMichael Stowell - Assistant ProfessorTin Tin Su - Associate ProfessorJonathan Van Blerkom - Research ProfessorGia Voeltz - Assistant ProfessorMark Winey - ProfessorDing Xue - ProfessorRui Yi - Assistant Professor

Emeritus Faculty

Mircea Fotino - ProfessorRichard Ham - ProfessorPeter L. Kuempel - ProfessorJ. Richard McIntosh - ProfessorL. Andrew Staehelin - ProfessorWilliam Wood - Distinguished ProfessorMichael Yarus - Professor

FACULTY

2

MCDB Events2008 GRADUATE SCHOOL SYMPOSIUM

Infectious DiseasesHost-Pathogen Interactions

October 24-25, 2008

This year’s keynote speaker is Joseph B. McCormick M.D. Author of “Level 4: Virus Hunt-ers of the CDC”

Other guest speakers include:

Daniel Portnoy, Ph.D., University of CaliforniaBerkeley, Department of Molecular & Cell Biology

Britt Glaunsinger, Ph.D., University of California Berkeley, Department of Molecular Genetics & BiologyBryan Cullen, Ph.D., Duke University, Department ofMolecular Genetics & MicrobiologyAbigail A Salyers, Ph.D., University of Illinois - UrbanaChampaign, School of Molecular & Cellular BiologyCheryl A. Nickerson, Ph.D., Arizona State University,School of Life Sciences, Biodesign InstitutePeter Hudson, Ph.D., Penn State, Center forInfectious Disease Dynamics

Paul Ahlquist, Ph.D., University of Wisconsin MadisonMcArdle Laboratory for Cancer Research

2008 FALL FACULTY SEMINAR PRESENTATIONS

4 - 5 PM - MCDB A2B70

Thursday, September 11Dr. Xiang-Dong Fu

University of California San Diego

Thursday, September 18Dr. Raffi Aroian

California Institute of Technology

Thursday, September 25Dr. Andrew Staehelin

University of Colorado Boulder

Thursday, October 2Dr. Thom KaufmannIndiana University

Thursday, October 9Dr. Michel BornensInstitute Curie Paris

Thursday, October 16Dr. Michael Stowell

University of Colorado Boulder

Thursday, October 23Dr. Don Cleveland

University of California San Diego

Thursday, October 30Dr. Susan Gilbert

Rensselaer Polytechnic Institute

Thursday, November 6Dr. Kristin Artinger

University of Colorado Health Science Center

Thursday, November 13Dr. Gerard Evan

UCSF, Helen Diller Family Comprehensive Cancer Center

Thursday, November 20Dr. Janet Shaw

University of California Berkeley

Monday, December 1Dr. Larry Gold

University of Colorado Boulder

Thursday, December 4Dr. Brad Cookson

University of Washington

Thursday, December 11Dr. Bill Tsai

University of Michigan

The Graduate Symposium in October welcomes leading scientists studying Infectious Disease/Host-Pathogen Interactions. The event occurs every other year and is completely organized by the graduate students in the MCDB department. The goal of the symposium is to encourage, educate, and foster interaction between scientists, students, and the local community about mechanisms of infection and treatments of these various infectious diseases. The first day of the symposium is directed at a general audience while the second day will address more specific scientific questions and ground breaking research on diseases such as HIV and Listeriosis.

“Going where no one has gone before--and washing our hands afterward!”

Registration is required for attendance and meals are provided. For more information or to register go to: http://mcdb.colorado.edu/graduate_symposium/gss2008

3

New MCDB Faculty

BOB GARCEA, M.D. BRINGS HIS HPV RESEARCH TO MCDB

JINGSHI SHEN, PH.D IS RESEARCHING DIABETES AND DIGESTIVE KIDNEY DISEASES

RUI YI, PH.D. CONTINUES RNA-MEDIATED GENE REGULATION RESEARCH AT CU

Rui Yi, Ph.D. joined the MCDB faculty this fall. Dr. Yi was a postdoctoral research fellow at Rockefeller University, working in the lab of Elaine Fuchs. He is the recipient of a five-year K99/R00 Pathway to Independence award from the National Institutes of Health. Dr. Yi’s research focuses on the microRNA-mediated regulatory network in skin development and skin stem cells. His research has potential widespread implications for skin diseases, especially cancer.

Bob came to CU in 1993 as a Professor in the Pediatrics Depart-ment of the University of Colorado Denver and Health Sciences Center, with joint appointments in Cell and Structural Biology and Microbiology. He is also Chief of Hematology-Oncology at the Children’s Hospital. Dr. Garcea re-ceived his B.A. in Chemistry from Harvard College in 1970 and earned his M.D. from the University of California at San Francisco in 1974. Dr. Garcea studies the use of recombinant viral proteins for immunization against vari-ous diseases. Dr. Garcea recently received a Global Health Grant from the Bill and Melinda Gates Foundation to develop an inexpensive therapeutic vac-cine for human papillomavirus by training the immune system to recognize the protein marker that HPV leaves behind as it infects cells. He is working with investigators from Georgetown University, the German Cancer Research Center and the Ludwig Cancer Institute to develop this “next generation” vac-cine to treat and prevent infections by human papillomaviruses in third world countries. This work complements his continuing work on the basic cell and biology of DNA virus assembly.

MEET THE NEW FACULTY!

Jingshi Shen, Ph.D. joined the MCDB faculty this fall. Dr. Shen was a postdoctoral research fellow in the Department of Physiology & Cel-lular Biophysics at Columbia University, working in the lab of Jim Rothman. In 2007 he was awarded a five-year K99/R00 Pathway to Independence award by the National Institutes of Health. Dr. Shen studies, at the molecular level, signal transduction and membrane transport with specific emphasis on glucose homeostasis and stress responses. Imbalances in these processes may lead to major forms of disorders such as type-2 diabetes and Alzheim-er’s disease.

4

MCDB Faculty Research

I received a Laura and Arthur Colwin Endowed Summer Research Fellowship to spend part of my summer at the Marine Biological Laboratory in Woods Hole, MA. My lab at the University of Colorado in Boulder studies how cells cope with damage to DNA. We use Drosophila melanogaster (fruit fly) as a model organism for most of our work in Boulder. We also use human cells and mice to test how applicable our results in Drosophila are to mammals, because we are interested in potential clinical application of our findings. Although most people would consider fruit flies, mice and human to be quite different from each other, these organisms represent only a tiny sub-set of all the diverse life forms that exist in the animal kingdom. I wanted to know how applicable our findings in Drosophila are to other, less well-studied animal forms. This summer, I was able to work with four marine organisms that are distant from flies and mammals in terms of evolutionary descent. These are the Slipper Limpet, Sea Urchin, Ctenophore (Comb Jelly) and Hydractinia (a relative of Hydra and Sea Anemones). Most of my experiments were done with a species of Hydractinia (Photo 1) that grows on the shells of hermit crabs (Photo 2).

(Photo 3) An 8-cell stage embryo undergoing mitotic divisions. Only the top 4 cells are in focus. DNA is in red and mitotic spindles, protein structures that help divide up the DNA be-tween daughter cells, are in green.

(Photo 2) A hermit crab with a colony of Hydractinia (the orange patch) growing on the top, left part of its shell.

(Photo 1) A colony of Hydractinia. Little greenish blobs are eggs at different stages of maturation. Mature eggs are released during spawning, become fertilized, and are used in my experiments.

TIN TIN SU SHARES HER SUMMERRESEARCH FELLOWSHIP WORK

In Drosophila, cells in younger embryos are readily killed by DNA damaging agents, while cells in older embryos tend to pause and fix the damage. I found that the cells of young Hydractinia embryos pause and probably fix the damage (different from Drosophila), but that older embryos do this better than younger embryos, such that same dose of a DNA damaging chemical killed younger embryos more easily than older embryos (similar to Drosophila). The ability to respond appropriately when DNA becomes damaged is a key requirement for all cells; the failure to do so can lead to diseases such as cancer that result from loss of genetic integrity. Knowing the different responses to damaged DNA that exist across the animal kingdom could help us discover novel strategies that can help a cell deal with damage to its genetic material. I plan to incorporate what I learned about marine embryos this summer into Experimental Embryology, a critical thinking course I teach to CU undergraduates.

I spawned Hydractinia with an alternating dark/light cycle to mimic the night/day transition, collected embryos and treated them with a DNA damaging chemical (Photo 3 shows a Hydractinia embryo that was fixed and stained to visualize cell division). I was particularly interested in whether cells of the embryos ‘choose’ to pause and fix the damage or ‘choose’ to die.

Article and photos by Tin Tin Su, Ph.D.

5

MCDB Faculty Research

This past summer, Dr. Joaquin Espinosa and graduate student Na-than Gomes moved temporarily to Long Island, New York where they spent three hectic weeks teaching a course on Eukaryotic Gene Expression at the Cold Spring Harbor Laboratories. Cold Spring Harbor Laboratories, a world powerhouse in genetics and molecular biology research, offers advanced courses in diverse topics of modern biology. Instructors are selected from institutions around the globe and they are offered state-of-the-art facilities and instruments to teach on their field of expertise. Espinosa and Gomes taught sixteen scientists from thirteen different countries the latest concepts and techniques on mecha-nisms of gene expression control in animal cells. The course participants performed seventeen different experi-ments, attended lectures by fourteen international speakers and discussed their research projects at length. Despite a challenging schedule (twenty one days of fourteen hours-a-day teaching) Espinosa and Gomes did not hesitate to sign up to teach the course again in 2009.

Website: http://www.cshl.edu/

RESEARCH AT COLD SPRING HARBOR LAB

The University of Colorado at Boulder is teaming up with a Boulder biotechnology company to use pythons, which dramatically increase their heart size for a short time after swallowing prey, as models for new therapeu-tics to treat cardiac diseases. Hiberna Corp., a Boulder-based company developing drugs based on natural models of extreme metabolic regulation, has signed an exclusive agreement with the university’s Technology Transfer Office on the effort. Hi-berna licensed technology developed by CU-Boulder Professor Leslie Lein-wand based on the natural ability of pythons to increase their heart size by up to 60 percent and speed their metabolism by 40-fold after feeding episodes.The full story can be found here:http://mcdb.colorado.edu/news/cu-and-boulder-biotech-company-team-up-to-study-pythons-for-clues-to-heart-disease.html

CU & BOULDER BIOTECH COMPANY TO TEAM UP FOR RESEARCH STUDY

NEW CONFOCAL MICROSCOPE PROVIDESREAL TIME IMAGING FOR RESEARCH The MCDB department has acquired a state-of-the-art Confocal Spinning Disc Microscope for fluorescence imaging. This microscope was purchased from Solamere Technologies and AG Heinz and is ideally suited for high-resolution imaging of cells and tissues and is capable of visualizing up to 4 different colors of fluorescence at the same time. This will allow scientists in the department to image what is happening to multiple cellular components within the cell, and in synergy. The microscope can image samples live or fixed and can even acquire images in 3-dimensions by taking snapshots of multiple layers and reconstructing these layers into the final 3-D image of the biological sample. It can also image samples over time and so has 4-dimensional capabilities. This acquisition for the MCDB department will greatly improve our department’s ability to get snapshots of biological molecules and processes occurring in real-time. The quality of images obtained by this microscope system is exceptional.

These images were taken by one of our MCDB undergraduates, Brant Webster, in the Voeltz lab.

Gia Voeltz, an MCDB Assistant Professor, is profiled in a recent Journal of Cell Biology feature entitled: “Gia Voeltz: Shaping Ideas about ER Shape”. In it she discusses both personal and professional forces that have shaped her career and how her ideas are shaping the discussion about membrane topology. The Article can be found in the January issue of JCB. The link to the journal ishttp://www.jcb.org/cgi/content/full/180/1/4

GIA VOELTZ FEATURED IN A J. CELL BIOLOGY PROFILE

Leslie Leinwand holding python(Tom Cooper Lightbox Images)

6

Outstanding MCDB Faculty

With support from the Deans, Provost, Chancellor, and President, CU-Boulder is taking bold steps to build a visionary educational and research infrastructure that will prepare our students for high profile jobs, stimulate the Colorado and national economies, and add to an unprecedented tradition of excellence through the CIMB. This support includes ten new faculty lines that will attract the brightest and best to grow and build new systems biology strengths; $1M from the Butchers to support the first Genomics and Bio-technology Symposium and provide seed funding to promote interdisciplinary research; four NIH interdisciplinary training grants to educate and prepare graduate students in emerging biotechnology fields; NIH and Keck grants to build state-of-the-art equipment facilities, including proteomics, NMR, and single molecule RNA characterization tools.

Opportunities and Vision We seek to raise $200 million dollars to build on CU’s outstanding record of achievement in biotechnology and invest in people, places, and programs. Our vision is to begin with the confluence of people. To attract the world’s best investigators who integrate unparalleled scientific skills sets with the adrenalin of discovery. To expand our current infrastructure, a new build-ing is being designed with specialized equipment and a unique architecture that facilitates a “jumping together of knowledge,” to incubate the discovery process. CIMB will also develop new programs of biotechnology excellence and innovation, and support and expand the Colorado biotechnology indus-try through the education of future employees, co-operative research and educational programs, and University technology-driven start-up companies. Finally, CIMB will establish Colorado and CU as the pre-eminent leader in ‘systems’ biology by attacking the most daunting and important biomedical problems facing humankind.

Advances in biology are leading to an explosion of new informa-tion that is literally redefining our understanding of life at the molecular level. Imagine if we could harness that ultimate knowledge to diagnose, treat, and perhaps prevent disease. At CU, we have imagined those possibilities and are poised for breakthrough contributions in the field of ‘systems’ biology, by understanding the human condition from the top-down and bottom-up. At CU-Boulder, we are already leading the way in engineering tissues, such as heart valves and cartilage, that enable the body to heal itself and eliminate the need for synthetic implants; defining the genetic basis for severe heart diseases and designing new therapies based, in part, on understanding why some people are ‘protected’ from certain diseases, and discovering RNA en-zymes and aptamers that can be used to create new pharmaceuticals to treat diseases such as macular degeneration. CU-Boulder has big ideas about transforming traditional homog-enous, disciplinary, hierarchical research and education to a system that is heterogeneous, interdisciplinary, horizontal and fluid. This initiative brings together faculty and students from Molecular, Cellular, and Developmental Biology, Chemical and Biological Engineering, Chemistry and Biochemistry, Applied Math, Computer Science, Ecology and Evolutionary Biology and Physics.

PROFESSOR LESLIE LEINWAND AND THE COLORADO INITIATIVE OFMOLECULAR BIOTECHNOLOGY (CIMB)

Dr. Leslie A. Leinwand is a Professor and Director of the University of Colo-rado Colorado Systems Biotechnology Initiative

7

Outstanding MCDB Faculty

The Howard Hughes Medical Institute Presi-dent and University of Colorado at Boulder Distin-guished Professor Tom Cech announced that he will step down as the top HHMI administrator and return to CU in spring 2009 to resume his research and teaching. Cech, who shared the 1989 Nobel Prize in chemistry for his discovery that RNA in living cells is not only a molecule of heredity but also can function as a catalyst, has been president of HHMI since January 2000 and a faculty member at CU-Boulder since 1978. He will resume his position at CU as an HHMI Investigator, which he began in 1988.

TOM CECH IS RETURNING TO CU SPRING 2009

DISTINGUISHED PROFESSOR NORM PACE PULLS IN MORE ACHIEVEMENT AWARDS

MCDB’s Norm Pace continues to reap awards for his research ac-tivities. In late July of 2008 he traveled to Berlin to receive the annual Life-time Achievement in Science Award from the RNA Society, an international society devoted to the study of RNA chemistry and biology. Pace received this award in acknowledgement of his many contri-butions to RNA science, notably in RNA processing. Pace was one of the early workers in RNA processing, which has now burgeoned into a broad scientific field, with implications for fundamental biological understanding as well as health-related applications. Pace was cited for his contributions in stable RNA processing and RNA structure, particularly with ribosomal and transfer RNAs. This last August, Professor Pace attended the Cairns, Australia meeting of the International Congress on Microbial Ecology to accept the Tiedje Lifetime Achievement Award in Microbial Ecology. Here, Pace was honored for his development of methods for analysis of the makeup of natural microbial ecosystems without the traditional requirement for culture of the organisms. Since most environmental microbes defy culture, Pace’s intro-duction of molecular tools for culture-independent identifications has resulted in the discovery of many thousands of novel microbial species, and provided an entirely new window into the natural microbial world. In 2007, Norm Pace was awarded the Lifetime Achievement Award from the American Society for Microbiology for his developments and discoveries in microbiology.

You can visit his lab’s web site at: http://pacelab.colorado.edu/

Assistant professor Dr. Gia Voeltz has been named a 2007 Searle Scholar and awarded a three-year, $240,000 research grant. The Searle Scholar Award was established by the Chicago Community Trust in 1980. It is funded from the estates of Mr. and Mrs. John G. Searle. Mr. Searle was the grandson of the founder of the world-wide pharmaceutical company, G.D. Searle & Company. It was Mr. Searle’s wish that certain funds be used to support “. . . research in medicine, chemistry and the biological science.” To achieve this goal, grants are made to selected academic institutions to support the indepen-dent research of outstanding individuals who are in the first or second year of their first ap-pointment at the assistant professor level. Only 15 of these prestigious awards are made annu-ally following a national competition. The Searle Scholar award will support Voeltz’s research on organ-elle biogenesis. The Voeltz lab is studying how the shapes of membrane-bound organelles are generated by proteins. Organelles are “mini organs” within the cell which also have elaborate and highly conserved shapes. It has long been clear that a complex interplay of factors must determine organelle morphology, but how, let alone the proteins responsible, are just starting to be discovered. This award will allow the Voeltz lab to study those proteins and their mechanism for generating membrane and organelle shapes. http://www.searlescholars.net/index.html

GIA K. VOELTZ RECEIVES THE SEARLE SCHOLARS AWARD

8

Many African countries face persistent economic and social prob-lems that derive in part from diseases of people, animals, and plants that are endemic to the warm and humid climates typical for that part of the world. Cell biology is making major contributions to an understanding of diseases that plague the developed world, but less has been accomplished with the in-fections by protozoa, like Plasmodium that causes malaria and Trypanosoma that causes sleeping sickness. Nematode infections too, like onchosariasis, have taken a large toll in some areas of Africa. There are many reasons that these diseases do not get the attention they might from American scientists, funding agencies, and private sector research: the two most important are that they are not medical problems in temperate climates and that the people who suffer from them can’t afford expensive treatments. The result is “or-phaned diseases,” and with the exception of malaria, which is really a prob-lem world-wide, the under-investment in these areas poses serious problems for public health in the developing world. One approach to this thorny issue is to train indigenous scientists to tackle their own problems. Obviously, this is not a quick fix, but grow-ing numbers of American and European scientists have become interested in science education in countries that would profit greatly from an increase in their pool of well-trained biologists to approach home-grown problems. I began to think about this issue during 2002-03 when I enjoyed a Fulbright fellowship to do research on trypanosomiasis in Kampala, Uganda. The first fruits of that concern were a collaboration with my then host, George Lubega of the School of Veterinary Medicine at Makerere University and Keith Gull from Oxford University, who joined us for both an application to the Human Frontiers in Science Program and in planning and giving a course in bio-informatics and cell biology in Kampala during the summer of 2006. This course was sharply focused on the effective use of modest desktop comput-ers to use bioinformatics to organize and drive cell and molecular biological research; it seemed to do a pretty good job with this goal. It was, however, a modest effort, due to limited funds and the recognition that getting real lab work into a course like this would be a challenge. In the wake of that course, I joined forces with other members of the International Affairs Committee of the American Society for Cell Biology, chaired by Mary Beckerle and Bruce Alberts; we submitted a successful pro-posal to the Carnegie Corporation of New York for a three-year grant that would fund two courses per year, one in east and one in west Africa.

MCDB’S DICK MCINTOSH HELPS EDUCATE INDIGENOUS AFRICAN SCIENTISTS TO TACKLE THORNY PROBLEMS

MCDB Research News Thanks to a collaboration with Dr. Paul Duffy (Fig. 1) and his associates at the Seattle Biomedi-cal Research Insti-tute, we were able to put together a course in short order, pro-ducing our first teach-ing effort during July

of this past summer. Duffy has a long-standing collaboration with Dr. Paul Gwakisa (Fig. 2), Director of the Genome Science Center in the Faculty of Veterinary Medicine, Sokoine Univerity of Agriculture in Mo-rogoro, Tanzania. Together, they have built a highly effective group for the study of malaria during preg-nancy and are now funded not only by the NIH but also by a Gates Grand Challenge grant. This group had previously put on a course each year for the last six, so they were experienced in dealing with all the practicalities of making such an endeavor work. This year’s course was a collaboration with the ASCB, taking advantage of the new funding from Car-negie, but it retained some of the traditional flavor of their previous courses, including lectures, reading and discussions on vaccine development, ethics, and the organization of clinical trials. It also included a serious overture to cell biology for young African graduate students. In spite of this diversity, it seemed to work. We had about 300 applicants for 24 places, so admission was quite selective. Our students came only from Tanzania, Kenya, and Uganda, given that its focus was on East Africa; next summer’s class will be in Ghana and will serve students from that area. The faculty for the recent course included three from Seattle, led by Duffy, three from Oxford, led by Keith Gull, three Tanzanians from Sokoine, and three scientists from the ASCB, including my-self; faculty-to-student ratio was good.

9

These kinds of discus-sions were an instructive experience for all (Fig. 5). On Sunday at the mid-point of the course, we took a day off and went to visit a nearby game park, a great opportunity for the visitors though less special for the Africans. The ani-mals and birds were remarkable (Fig. 6). During the second week, the course also included sessions on the ethics of basic research and clinical experi-

mentation. Duffy and one of his colleagues, Marilyn Parsons, did an impressive role-playing job to show how stresses arise when young people have made progress and an older person wants access to the results. Our final

event was the presentation by all students of the proposals they had worked up in four tutorial sessions during the course. These were given as 10 min-ute PowerPoint shows with a timer and 5 minutes for questions, much like a professional meeting. All in all, the students did a great job, and it was clear that they had learned a lot about both science and presentation. After a clos-ing ceremony, they filled out questionnaires, which have subsequently been analyzed, providing evidence that they were pleased with the experience and the treatment they received. There are many opportunities for contributing to teaching in Africa. Few of them include resources to pay the American participants (ours includ-ed), so one must think of efforts like this as pro bono activities. However, they carry a lot of rewards for the faculty as well as the students. I hope that many American scientists will become interested in working out their own ways to engage in teaching science in Africa and other parts of the developing world, because the need is great. Guidance and financial support are available from http://www.fulbrightonline.org/ the websites of many African universities can provide information about their specific teaching needs.

MCDB Research News Our lectures were given in a very nice room (Fig. 3), and in there plus nearby rooms we had journal clubs, seminar-like dis-cussions of data, and individual tutelage on put-ting together a thesis pro-posal. Each day included tea and coffee breaks and lunch in a pleasant cafete-ria nearby (Fig. 4). In a separate building we had a hands-on lab in microscopy (conventional light microscopy, phase, and fluorescence) and one on the use of fluorescence-activated cell scanning for the study of cell cycles. We also tried a novel form of instruction which we

called “Interactive prac-ticals,” developed in the Keith Gull lab. For each of these projects a scientific question and relevant experiments were defined and car-ried out in Oxford, pro-viding data for study: gene sequences, gels,

westerns and northerns, images of growing cell populations, fluorescence images of cells stained with informative antibodies and dyes, and electron micrographs, etc. The students were divided into groups of six, then pre-sented with the question to discuss and figure out how to proceed. One such question was the relevance to trypanosome biology and treatment of a gene discovered in C. elegans, where it is essential for intraflagellar transport. Fla-gella are essential in trypanosomes, so if a homologous gene could be found in this parasite, its product might be a good drug target for the treatment of infection. The students discussed the question, used BLASTP to track the tryp gene down, and then evaluated their options for what experiment to do next. RNAi works well in tryps, and the skeleton of an RNAi vector was avail-able for them to design a perturbing agent. All the data from Oxford were then available for them to see what happened as they “carried out” various experiments and analyzed the re-sults, discussing each step and deciding what to do next.

Article and photos by Richard McIntosh, Ph.D.

10

MCDB Alumni NewsSEAN EDDY , MCDB ALUM

Sean is pictured above with fellow researcher “Muggins” whose specialty is encryption (typing random keys when Sean is not looking).

Sean Eddy is one of seventeen group leaders at Janelia Farms, part of the Howard Hughes Medical Institute (HHMI). These group leaders were selected because of their rare ability to pursue big questions with cre-ativity and focus. Sean’s current research focuses on computational genome se-quence analysis. “We use probabilistic modeling techniques to develop new algorithms to find features in DNA, RNA, and protein sequences. One of our primary interests is in identifying novel structural and catalytic RNAs, and another is to recognize remote protein sequence homologies.” Sean chose CU-Boulder for his graduate study. His choices were Harvard or CU-Boulder. Sean found that at CU, everyone was friendly and welcoming. The recruiting dinners were fun and people told jokes. It was clear that the faculty knew the students.

Working and doing research in Larry Gold’s lab had a lasting effect. Sean says, “It was a fantastic time to be in Larry’s lab.” “Larry was a great role model; I just wish I could read like him.” Sean spoke of the impression that Larry Gold’s reading habits had on him. “Larry has a mail tub at his house in which he collected Journal articles - but he actually read them!” “Larry’s depth of knowledge is staggering and he has such a memory and such quick wit.” It was a very exciting time in the lab. Larry Gold and Craig Tuerk had invented Selex. “Larry could extrapolate from one piece of data and change the world.” Sean mentioned that he has noticed that many of the scientists now involved in bioinformatics have come through CU-Boulder. Sean be-came interested in bioinformatics because he was trying to solve an intron problem and was a Ph.D. student at the time. He was trying to solve how many catalytic introns there were on T4, around 1990. He started in bioinfor-matics by creating an algorithm to solve this problem. It was a hard problem - he solved it 4 years later while he was doing his post-doctoral research in England. Sean was supposed to be doing research on something to do with worms, but became interested in bioinformatics. Bioinformatics wasn’t really new when Sean switched fields, but says “It was a time when this wave of new interest was just forming, because of the impending availability of com-plete genome sequence.” Sean said “I was really lucky being in the right place, at the right time.” In Boulder, he caught the RNA wave. When Sean was at Washington University, the wave was genomics. At Janelia, it’s neurobiology and says he is retraining himself as a neurobiologist. Sean remembers that the Wednesday night RNA club at CU-Boul-der was one of the most intellectually high-powered things, he has even done in his life. Sean also mentioned the friendly competitiveness between the MCDB and BioChem folks. Sean’s advice to undergraduates about getting into a lab is simple. “Don’t read about it – do it!” Sean stressed the importance for undergradu-ates to get in the lab and really learn about something. “Get interested in a problem and then do whatever needs to be done to solve it.”

Sean used to love playing this Empire game, check out this link http://www.the-scientist.com/article/display/54671/

Interview by Dr. Ken Krauter of MCDB, Senior Research Assistant Dan Timmons and Mary McGee, CU Foundation

11

MCDB Alumni NewsKEVIN POJASEK , MCDB ALUM

Growing up just north of Boston, Kevin chose to attend CU to broaden his horizons while having access to a top-tier academic research en-vironment. He was fortunate knowing right out of high school that he wanted to study molecular biology with an aim of heading to graduate school. This sense of direction allowed him to quickly choose MCDB as well as pursuing a minor in biochemistry. He graduated from CU in December, 1997. CU Boulder was perfect for Kevin and his learning style. He en-joyed the flexibility and the relaxed attitude of the professors. Kevin said “They were flexible – you didn’t have to attend every lecture for example.” Kevin became very good at budgeting his own time and managed to finish his BA in 3.5 years while having plenty of time to enjoy everything Boulder has to offer. Kevin’s research experience began in Min Han’s lab as a fresh-man, doing very basic tasks, such as washing pipettes, which then expanded to a small research project with a graduate student. Through this early lab exposure, Kevin learned about the “Research Experience for Undergradu-ates” Program sponsored by NSF. He applied and spent two summers (after sophomore and junior years) working in a lab at MIT. Kevin believes that undergraduate research “gives you a great edge when applying to grad school, because it shows that you are committed to that kind of work and that you have the necessary personal qualities to do the research. Graduate schools know that you aren’t coming in blind, and that you will be able to persevere when the going gets tough.“ His undergraduate research was a fantastic experience allowing Kevin to make great connections that helped him get accepted into MIT’s Biological Engineering Ph.D. program. Kevin says “UCB is great for this, because you aren’t coddled, you have to take the initiative to take advantage of the opportunities. It is a research focused department which is terrific.” As a graduate student he was attracted to the entrepreneurial nature of many of the MIT professors, and had an inclination that he wanted to go into bio-tech business. During his Ph.D. program at MIT, he worked on research that contributed to the creation of Momenta Pharmaceuticals. He also sought out a couple of internships at more established biotech companies in the Bos-ton area. These experiences taught Kevin how great biotech research was done, how to ask strategic questions, and how problems could be solved with the limited resources available at start-up biotech companies. Kevin has learned that it’s easier for a trained scientist to learn the basic business skills necessary to succeed in biotech than it is for a nontech-nical person to learn the science. Kevin also believes his Ph.D. provided the necessary tools and frameworks for solving problems in different business and scientific scenarios.

After his Ph.D., Kevin worked for 3 years at PureTech Ventures, an early stage venture capital company where he reviewed numerous bio-tech investment opportunities. While at PureTech, Kevin co-founded Solace Pharmaceuticals where he now works with seven colleagues in both the US and UK. He loves his current job and the exciting challenges that it brings. He is now running clinical development and US operations. Kevin said that “working on a project of this magnitude and responsibility early in my career is a fantastic opportunity. I’ve been fortunate to have had this chance.” In-ternational travel and the opportunity to learn different business cultures are also a wonderful part of his current work. Interestingly, Solace is discovering and developing drugs to treat chronic pain; one of which is in a similar line of research to that of Dr. Linda Watkins at CU’s Center for Neuroscience. Kevin and his wife are expecting their first child in early October and he can’t wait for the excitement and new challenges of fatherhood. Kev-in’s future is very bright and he has a lot to look forward to!

Interview by Mary McGee , CU Foundation

12

MCDB Alumni NewsJOE TURNER, MCDB ALUM

Joe Turner came to MCDB in 1973, when it was only 5 years old. At that time, Joe says, it was not at all a laid-back department. Keith Porter, the first MCDB chair, had an academic approach that was very intense. Keith had recruited a great group of young faculty, mostly from Stanford and Har-vard, who shared Keith’s intensity. Larry Gold, Mike Yarus , David Hirsch and Larry Soll were all here, so it was a very exciting and growing department. Joe, by his own admission, was as a great student, but one who lacked the skill set needed to become a creative scientist. Joe said he’s a great observer of people, but a lousy observer in the lab. Joe admits he does not have the ability to go from a known fact and move forward. “ You have to want to syn-thesize.” Joe believes that creating new knowledge is completely different from learning in a classroom. It is very important to get actual lab experience to find out whether or not it is a good match for one’s temperament and skills. Joe recalled that his lab experience at CU had an important impact on his career. He worked in Prof. Dick McIntosh’s lab and this experience convinced him that he had no talent as a researcher. Ultimately he con-cluded that he hated lab work and never did, and never would do, anything of note in the lab. “I worked very hard and hated every second of it. I don’t want this to come out sounding in any way as a reflection on Dick – it wasn’t. Dick’s personality and the stimulation he provided actually kept me plugging along despite my own limited abilities as a scientist.” It took Joe two years and Dr. McIntosh’s departure on sabbatical to accept that he did not want to get a PhD. When he left CU, he began interviewing for entry-level research and manufacturing positions with drug and chemical companies such as DuPont, but he got no offers.

Hence, Joe decided to build on his strength in academics and enrolled in an MBA program at the University of North Carolina at Chapel Hill. It was there he started to thrive. Business was the perfect fit because it played to his strengths. After his MBA, he worked for Eli Lilly in for more than 10 years. During this period, he lived in Indiana, California, Taiwan, and Switzerland. In Switzerland, he ran a $150 million trading company for Eli Lilly, and traveled a great deal. This was heavy travel to exotic and sometimes uncomfortable places like North Africa, Asia, the old Eastern bloc countries, and Iraq. Joe said, “I don’t know many people who did business in Iraq at that time – but I am one of them.” Tired of the travel and looking for a more entrepreneurial experi-ence, Joe left Eli Lilly and returned to Denver and joined Cortech as Chief Financial Officer (CFO). The company was then four years old and was fo-cused on sepsis. He was brought in to help with the IPO, and it was intense, even without the travel. Joe says, “Building companies is all-involving and draining.” He calls himself a professional manager who works well with en-trepreneurs because he employs professional managerial techniques that facilitate the entrepreneurs’ success. His talent is dealing with the biotech scientific folks who are fundamentally mavericks, and he can talk to them in ways one might not expect from a CFO. Joe is a good team builder. His understanding of the science often helps in working with investors and helps him talk with the researchers and technical managers. The 1990’s brought a great deal of optimism in biotech companies. They believed modern understanding of the molecular pathways involved in disease progression and the new technologies that came out of molecular biology, such as DNA cloning and monoclonal antibodies - techniques that only a few companies such as Amgen and Genentech were able to employ at that time - would give them more success than the traditional pharmaceutical companies. He said, “We believed in our own message of probable success, and our investors were eager to hear that message.” Joe’s experience is broad and he has worked for, or served on the boards of biotech companies who focused on drugs for septic shock, the central nervous system, stroke, cardiovascular disorders, oncology, and aes-thetic dermatology. As the CFO of several publicly traded companies, both pre- and post- IPO, his background and skills have allowed him to talk to in-vestment bankers as well as the big investing institutions. He has developed skill in answering their questions, whether financial or strategic, and can talk to the analysts on both the buying side and the selling side. Joe believes that it is essential for a company’s success for the CEO and CFO to find a business model that will work. They also must bal-ance focus and persistence in continuing to pursue a strategic direction fraught with known difficulties with a sense of when to kill a program and move on. To succeed, a biotech company needs to function as a learning organization. Key players in the company have to be very familiar with suc-cessful business models, with the competitive environment, with regulatory changes and with advances in academic research. The organization must find ways to incorporate this learning into its strategies, programs and opera-tions.

Interviewed by Dr. Tom Blumenthal, Chair and Mary McGee, CU Foundation13

Recent MCDB Graduates

Annelise Anjelica AdamsJared Tyler AhrendsenMedhat Aamer AhmedBader Hamad AlhajeriAshleigh Elizabeth AllenAllison Ross AnguianoPrasiddha AryalJennifer E BaeEmily Madeline BakerMatthew Gabriel BartleyMaximilian Magdy BekhitElizabeth Ann BemisValerie Dione BenderBryce Viktor BiefelJami BiersNicole Amber BilbroDustin Robert BergerTaylor Leigh CannizzaroLarissa CaparachiniIan Michael ConnorMoly Caitlin E. CowdreyDaniel Guillermo DavilaJeanne Mina DoyleLillian Elizabeth DurfeeAndrea Sara EadsSuzanna FialaKatherine Mary FlynnSusan Elizabeth GansterBrett Ashley GellmanRachel Megan GieslerNicholas A. GomogdaWilliam Gowen-Mac DonaldAnthony Roman Grimaldi

Jason Bruce HarrellElizabeth Ann Harvey

Hannah Allysum HathawayDavid Eliot HaukenessMichael Brent HawkinsMichael Clifford Haxby

Trista Kelly HinzAllison Rae Hoffman

Jennifer Michelle HooverSean Michael HoulihanJoedy Elizabeth Hulings

Reema A. IshteiwyBarry Lee James

Samantha Catherine JanigaJohn Peter Janson

Janna Danielle JensenShem Darius JohnsonCallan Michael Jones

Jennifer Anne KatzenbergShawn Michael Kazmieresak

Jeremiah David KeelAmanda Michelle Kelly

Caitlin Marie KettlerStephanie Gayle Koan-Irvin

Robert Michael LambkinPaul Alexander Latimer

Anh Quynh LeMatthew Kyle Leroue

Dean Marcell LockheadAnna Elizabeth LuebkeNicolette Faye Lyons

Phillip Yuen Ma

2008 UNDERGRADUATE DEGREES

Chandra Leigh Kilburn Advisor: Dr. Mark Winey “Identification and characterization of Tetrahymena and basal body components

Maengjo Kim Advisors: Dr. Roger Hajar & Dr. Ken Krauter “Resistin: A new regulator of cardiac function in diabetic cardiomyopathy”

Monica Darland Ransom Advisor: Dr. Ding Xue “The role of aminophospholipid translocases in C. elegans”

Anita Wichmann Advisor: Tin Tin Su “Cell Death and Survival after Radiation Exposure in Drosophila melanogaster”

Liang Zhang Advisor: Dr. Min Han“ Systematic analysis of C. elegans miRISC components, miRNAs and miRNA targets through their interaction with two GW182 family proteins: AIN-1 and AIN-2”

2008 DOCTORAL DEGREES

David Joseph MartinLauren Elizabeth Matelski

Veronica Joy MaytorenaRachele Lynn Mc Cawley

Samantha Jane Mc ClellanTessa Rachel Mc Spadden

Breanna Rae MillerKirsten Holliger Miller

Ashley Michelle MooreAndrew J. Clemison Moschetti

Ingrid Christine MujaJennifer Leontine Murphy

Lauren Rachael NeherLinda Tu Ngo

Vien P NgoJoshua Michael Oakes

Sean Patrick O’NeillMelissa Karen PaddockKristen Leigh Peterson

Alicia Elinor PopeStacy Lynn Romero

Patricia Lee RubiPaul Albert Shultz

Lauren Michelle SnellaAmanda Marie Travis

Livia Selina TsienMaria Elena Malone Velazquez

Zhaohui Carrie WangCaroline Elise Weller

Aleksandra Anna WolaninChung Sing Wong

Daniel Michael Yuan

Jarred Curtis Keith was an outstanding MCDB student who excelled in all of his undergraduate classes at CU. He loved biology and followed that passion by working for two years in the research laboratory of Dr. Leslie Lein-wand. He often spoke about Dr. Leinwand’s lab and the wonderful people he got the chance to work with during that time. Jarred’s achievements in the MCDB department led to his being hired as an undergraduate teaching as-sistant, a position preferentially given to graduate students or graduates from the department. He taught the laboratory portion of our introductory molecu-lar biology class and our upper division cell biology lab course. He was well liked and respected by both his fellow teaching assistants and his students. His supervisors were very impressed with his ability to assess the lab from both student and teacher perspectives. While at CU he also tutored junior and senior high school students who needed academic assistance. Later, he entered graduate school with the goal of pursuing research questions that would have an important impact on society. Jarred was compassionate, curi-ous, conscientious and kind, a student who achieved much in our department and touched many of our lives with his generous spirit. Jarred passed away in December of 2007 and in his memory his family has established the Jarred Curtis Keith Memorial Fund. This fall, the fund is awarding three undergraduate research fellowships to MCDB stu-dents. Students with advanced research skills will conduct research for the 2008-09 academic year, culminating in the presentation of their work at the Biological Sciences Initiative poster session next April.

JARRED CURTIS KEITH MEMORIAL FUNDIn May 2005 Jarred graduated with honors.

Jarred with Janice McClintock, in the Leinwand Lab.

14

Outstanding MCDB Students

The Marsico Award has again provided funding for MCDB students in the department. This award is given through an application process, based on need and academic excellence. An MCDB committee that included fac-ulty and academic advisors awarded the Marsico Scholarship this fall 2008 semester to Amy Foliano, Cara Foliano, and Whitney Hasemen. MCD Biology is grateful to Jim and Anne Hillary for their support to the undergradute students who display excellence in academics and charac-ter.

The new awardees in the CTMB program are: Brian Harry (MSTP) Joe Heimiller (MCDB) Joe Sfregola (MCDB) Tess Shideler (MCDB) Aaron Shapiro (MCDB) Pat Yannul (MCDB)

The Continuing awardees in the CTMB program are:Amber Bilak (MCDB) Dave Busha (MCDB)Chris Ebmeier (BCHM) Nicole Kennerly (MCDB)Amber Rex (MCDB) Allison Schaaf (MCDB) Jessica Stockburger (MCDB) Nesia Zurek (MCDB)

In addition (and in coordination with) the SCR Training grant gave awards to:

Jonathan Friedman (MCDB)) Timsi Rao (MCDB)Ian Ross (MCDB) Michelle Turco (BCHM)Tyson Vonderfecht (MCDB) Ryan Walters (BCHM)Lisa Warner (BCHM) Jesse Zaneveld (MCDB)

Finally (and again in coordination with) the Biophysics TG gave awards to:Robert Brown (BCHM) Allison Churnside (Physics)Julia Cope (MCDB) Cole DeForest (MCDB)Andrew Garst (BCHM) Cristina Sandoval (BCHM)

This grant is coordinated by Ken Krauter, Ph.D. , and the continued funding is provided and reviewed by the National Institute of Health.

CTMB eligible trainees are admitted from a strong national pool of over 200, most with excellent undergraduate preparation and at least a year of intensive independent research experience. The training program is rela-tively traditional with a strong emphasis on research that they begin in their first year with rotations, moving into a lab at the end of year one. Students ap-ply for a slot on the training grant at the end of year one and the top students are selected generally for two years of support. Nearly all students complete the program in 5 to 6 years and go on to postdoctoral training and careers in academia, biomedical research institutions, or the biotechnology industry. The training grant positions for this year have been awarded to 6 new and 8 current holders of slots in the CTMB program. In total, 29 places were awarded this year.

MARSICO FAMILY FOUNDATION SCHOLARSHIP

GRADUATE STUDENTS RECEIVENIH CTMB 2008-2009 TRAINING GRANT AWARDS

The Caplan-Craig Scholarship is an award available to regularly enrolled undergraduate women majoring in MCD Biology. Special consider-ation is given to returning students older than traditional 18- to 22-year-old undergraduates and is based on academic merit and/or demonstrated finan-cial eligibility. Last year the scholarship was awarded to Charlotte Black-wood, a sophomore, and Taylor Cannizzaro, a junior. This is a one thousand dollar scholarship, awarded annually and is renewable with 3.20 GPA.

CAPLAN-CRAIG SCHOLARSHIP AWARDWENT TO BLACKWOOD AND CANNIZZARO

The Creative Training in Molecular Biology program is now enter-ing its 34th year at the University of Colorado. The program has a strong tra-dition of interdisciplinary science focused in two major participating units, the Departments of Molecular, Cellular and Developmental Biology and Chem-istry and Biochemistry. The training faculty of 43 draws on a pool of over 120 Ph.D. students that matriculate in the two degree-granting programs to fill the 14 available slots. The Colorado campus is compact and there is an intimate and communicative atmosphere between the Departments that provides a broad training experience to students.

Jonathan Friedman is one of the 14 MCDB NIH grant recipients. He is currently working on research in the Voeltz Lab.

15

Learning in MCDB

The BURST (Bioscience Undergraduate Research Skills and Train-ing, formerly called URAP) program pays an hourly wage to undergraduate students with little or no research experience to work in a biology research lab on campus. BURST is completely funded and administered by BSI. As part of this program, BSI provides research-related skill seminars in topics such as how to read journal articles, how to keep a lab notebook and scientific writing, as well as training for the students’ lab mentors. Typically, BSI funds 20 to 25 students during each academic year and another 15 to 20 students during the summer. In the past few years, one-quarter to one-third of those students worked in MCDB labs. This past summer, Jill Terry has been working in the Odorizzi lab with a BURST grant, as has Katy Michaelis in the DeDecker lab (see photos). Jill, a sophomore MCDB major, is doing research to help her decide on her career path, while Katy, who will be a junior in MCDB this fall, has her sights set on graduate school and a career in research.

Getting experience in research as an undergraduate has become increasingly important as admission to graduate, medical and other profes-sional schools has become more competitive, and as more and more un-dergraduates seek a comprehensive learning experience, or seek to clarify their career goals. CU is at the forefront of this boom, due in large part to an innovative program on campus called the Biological Sciences Initiative (BSI), affiliated with MCDB, that provides grants to help students gain research experience in biology labs on campus. BSI is funded by a grant from the Howard Hughes Medical Institute (HHMI) and has been continuously funded by HHMI since BSI (formerly the Hughes Initiative) began at CU in 1989. BSI strives to increase the number of students interested in careers in the biologi-cal or medical sciences, to strengthen their biology education, and especially to encourage minority and women students entering the sciences. To this end, BSI offers a variety of programs aimed at middle and high school stu-dents and teachers, and supports undergraduate research programs. Since 1989 BSI-supported undergraduate researchers have gone on to earn 133 Science Ph.D.’s (including 65 women and 5 underrepresented minorities); 162 M.D.’s (including 84 women and 17 underrepresented minorities); and 46 M.D.-Ph.D.’s (including 9 women). BSI’s Undergraduate Research Advisor, Dr. Lynn Wolfe, provides key support for the success of CU’s undergraduate researchers. She recruits, mentors and provides training for CU undergraduates who are interested in gaining experience in a biology research laboratory, and provides information to undergraduates about funding opportunities, research-related educational opportunities, graduate schools and careers in scientific research. She may be reached by email at Lynn.Wolfe@colorado.edu. BSI funds CU undergraduates in research through three different programs: BURST, NIH/HHMI Scholars for Diversity, and Undergraduate Re-search Opportunities Program.

BSI – UNDERGRADUATE AND OUTREACH PROGRAMS

THE BURSTPROGRAM

To find out more about BSI and its undergraduate and outreach programs, please visit the BSI web site: www.colorado.edu/Outreach/BSI

Undergraduate and MCDB major Katy Michaelis is also learning the skills it will take to become a competent researcher.

MCDB major, Jill Terry, above, is learning research skills as an undergraduate.

16

Learning in MCDB

BSI provides tuition support to students accepted into the NIH/HHMI Scholars for Diversity program. This program provides research expe-rience, mentoring and training for students from groups traditionally under-represented in the biological sciences, including students of certain ethnici-ties, from disadvantaged backgrounds, or who are of the first generation in their family to go to college. This program provides an hourly wage to the students to work in research labs, plus a skills training course and a series of research related seminars. It is primarily supported by an NIH grant.

The third program that BSI supports for undergraduates is the UROP program (Undergraduate Research Opportunities Program). While UROP is a campus-wide program that supports student research in all fields at CU, BSI provides funding for the UROP HHMI Bioscience grants that are earmarked for students doing research in the biological sciences. BSI also organizes a series of workshops for these students to enhance their research experience, covering topics such as ethics in research, authorship of papers, how to get into graduate school or MD/PhD programs, and how to construct a poster. The students’ UROP experience culminates with a poster session to present the work they have done during the year. BSI’s funding typically supports 35 to 40 UROP HHMI bioscience students per year; about a third of those work in MCDB labs.

THE NIH/HHMI PROGRAM

THE UROP PROGRAM

Construction was made possible by CU’s President and Boulder Campus Chancellor as a match to BSI’s 2002 HHMI Grant. BSI’s GTP classroom can accommodate 24 students, and in-cludes both computing and wet lab capabilities that offer students hands-on experience with the study of DNA and data analysis involved in ge-nomics. The classroom is equipped with m o v e a b l e work areas to allow flexibil-ity in teaching and learning styles. The GTP is home to several undergraduate courses (e.g., “Bioinformatics and Genomics”) and BSI workshops for K-12 teach-ers. Based in part on the success of the GTP, a second interactive classroom that can accommodate 80-90 students was completed in MCDB

during 2007. Funds from BSI’s 2006 HHMI Grant equipped this new classroom, while University matching funds to the HHMI Grant supported construction. Dr. Bill Wood of MCDB was instrumental in the realization of this classroom.

INTERACTIVE CLASSROOMS IN MCDB: BSI’s GENOMICS TEACHING PLACE

Here, Dr. Nancy Guild from MCDB is discussing the bead curtain in one of BSI’s display windows. The bead curtain shows comparison of DNA sequences from the same gene in many different organisms.

The Genomics Teaching Place (GTP) is an interactive class-room and laboratory, completed in 2004, that serves CU un-dergraduates and the K-12 community.

Article and photos by Julie Anne Graf, DirectorBiological Sciences Initiative

17

Learning in MCDB FEAST YOUR EYES ON MCDB A120 A DIFFERENT KIND OF CLASSROOM Faculty who teach large core courses for MCDB majors are trans-forming the way they teach, based on educational research showing that students can learn substantially more from classes that include active learn-ing – participation in group problem solving and other activities – than from traditional lectures where students sit passively and take notes. Unfortu-nately, most university classrooms, including those in MCDB, were designed for lecturing and are poorly suited for student interaction and group work.

In 2005, Bill Wood and a few other MCDB faculty set out to create a new teaching facility that would, by the nature of the space itself, encourage more student-centered teaching. Based on the design of physicist Robert Beichner and

his “Scale-up” program at North Carolina State University, the new classroom resembles a banquet hall, with groups of nine students sitting around 7-foot diameter round tables. MCDB faculty agreed to donate A120, the attractive but little-used reading room in the MCDB building, as space for the project. Funding for remodeling was obtained from several sources, including then President Hank Brown, Dean of Arts and Sciences Todd Gleeson, the HHMI Undergraduate Initiative headed by Julie Graf, and then MCDB chair Leslie Leinwand, as well as smaller contributions from Distinguished Professors Bill Wood and Dick McIntosh of MCDB, Carl Wieman of Physics, and Dick McCray of APAS. Planning and construction of the room progressed through the spring and summer of 2007, with help from Jen Ryan, Dan Timmons, Lisa Mendoza of the HHMI program, and several interested MCDB faculty, and the room was completed in time for the start of classes in the fall. During the 2007-2008 academic year, six MCDB courses and one non-MCDB course were taught entirely in A120, with classes ranging in size from 40 to 108. Other larger courses used the room for recitation sessions with sections of the course meeting separately A few improvements were made over the summer, such as installation of microphones at each of the 12 tables so that student questions or comments coming from one side of the room could be heard on the other.

A120 has a very different feel from most classrooms of its size on campus. The room can accommodate classes of up to 108 students at 12 tables. The chairs are on wheels so that students can easily turn to face the three screens mounted on one wall, or work together at their tables in small groups of three or larger groups of nine. Although synchronized projectors allow presentation of visual materials on the three screens to the whole class, A120 is not intended for lecturing, which can be inconvenient. A standard auditorium style classroom, with students arranged in neat rows facing the lectern in front, invites the instructor to address the class with a lecture. A120, in contrast, invites everyone to get involved with the learning process, through interaction of instructor with students, and students with each other. The room does not include a podium or lectern, but encourages the instructor to circulate among the tables during class. Most users have found it admirably suited to interactive, student-centered teaching.

For CU Boulder, A120 is a unique instructional facility, which has sparked interest in other departments for the planning of new classrooms. Its design and purpose nicely complement efforts to improve the teaching of science in five different CU departments through the five-year Science Education Initiative, represented in MCDB by Science Teaching Fellows Jia Shi and Michelle Smith. They and SEI coordinator Jenny Knight have been among the most enthusiastic and creative users of the new classroom. Meanwhile, a poster on Bill Wood’s office door invites new users to the room: “Why sit and take notes in an auditorium? Come to an instructional feast in the new MCDB Banquet Hall!”

A120 the new MCDB “Banquet Hall”

Traditional university classroom at CU Boulder

Article and photos by William Wood, Ph.D.

18

Every April near the end of the spring semester, Biology of the Cancer Cell (MCDB3150) students gather for an intensive full-day Cancer Conference where the students present their research on different types of cancer. A month prior to the event, students form groups of four to investi-gate the most current research on a cancer type of their interest (e.g. breast, prostate, colon, cervix, lymphoma). Having almost completed the course, which covers the molecular and cellular biology principles of the disease, they are fully able to investigate on their own the details that make each cancer type unique. Within the groups, each student plays the role of a differ-ent professional in the war against cancer: an epidemiologist, a pathologist, a molecular biologist and a clinical oncologist. On the day of the Cancer Conference, about 150 students, their friends and relatives and interested members of the community gather to learn about this devastating disease.

CANCER SYMPOSIUM EDUCATES STUDENTSAND AUDIENCE

The conference was held on a Saturday and began with breakfast, followed by morning presentations, lunch, afternoon posters and evening talks. This activity trains students in the skills of bibliographic investigation, data presentation and discussion, and also allows them to experience the cli-mate and dynamics of a scientific conference. The students’ performance is evaluated by a panel of cancer researchers and contributes one third of their grade for the course. The Cancer Conference is organized by the course instructor, Dr. Joaquin Espinosa, the course teaching assistants and the de-partment staff member, Ms. Kathy Lozier. This event is part of a broader initiative by MCDB faculty to promote cancer research and education at CU-Boulder.

Learning in MCDB

Two samples of student presentations from the Cancer Symposium.

Dr. Joaquin Espinosa introduces the student presentations at the Spring Cancer Symposium.

Article and photos by Joaquin Espinosa, Ph.D.

19

New in MCDB

After months of anticipation, the Folsom St. Coffee has landed in the Porter 1st floor lobby. And like the mothership on the corner of Folsom and Arapahoe, the annex in the Porter lobby offers the full range of breakfast and lunch items, along with their signature coffee drinks. The design includes a great seating area, soothing lighting and the new informational kiosk makes this previously gloomy entrance to MCDB a most welcome addition to the department.

FOLSOM STREET COFFEE HAS ARRIVED

IT NEWSHAVE YOU GOOGLED US?

Here in MCDB you will find a unique website that is also a powerful tool for students, faculty, researchers and staff. This site provides a tool for faculty to download their end-note files on their own web space. Publications are now a “snap” to access. The site also provides a portal for MCDB alumni to make contact with fellow researchers and put their research and contact information on the web site. This is one of the sites newest and unique features. All of these state-of-the-art changes are being made by Dan Timmons and Matt Hynes-Grace, who are MCDB’s in-house IT professionals. MCDB is one of the very few departments on campus that has its own IT department and professional researchers. Faculty and staff now have the freedom to schedule rooms for lab meetings, to be in control of their own purchasing with the use of the interde-partmental purchasing request tool, mange their travel and many more fea-tures. A calendaring tools for events, or personal use is now just a key stroke away. MAC or PC use is a choice in the MCDB computing work area with numerous Mac and PC workstations. Department personnel and visitors will find a variety of software as readily available tools for research, teaching and presentations. The IT Resource Center is capable of versatile scanning

tasks including document scanning, transparency scanning, and gel scanning.Digital Imaging is a vital tool to everyone in academia and research and the wide format printer, and Epson 9800,

can print posters as large as 44” by 72”. Again - MAC or PC capability. Phosphorimaging is available for all researchers and a PC is attached to this unit which is equipped with the latest software from Molecular Dynamics, Image Quant TL, for use in analyzing the scans.

A new electronic Informational Kiosk has been installed in the 1st floor lobby of the Porter BioScience Building. The high-tech touch-screen adds a modern glow to the new Folsom St. Cafe that has just opened in that space. The kiosk offers MCDB visitors all sorts of information about MCDB including contacts, maps and news, all at the touch of a finger. The kiosk hardware and software is a state-of-the-art information center built on top of an interactive web development package (Plone) that also powers the MCDB web site. It leverages one of the most powerful image presentations systems (Origami Image Viewer, from Northwestern University) and the open source Staff Directory package (Penn State University) to bring about a user experience that is similar to the highly acclaimed iPhone interface. Most significantly, however, is that by using open source and off-the-shelf hardware, Dan and Matt were able to design the entire system at a cost 1/10th that of a commercial kiosk, and with far greater flexibility and capability. The faculty and staff information offered on the kiosk is gathered from each member’s web profile on the MCDB web site. Shortly there will be new capabilities and features added to the web site that will permit each person to edit their profile in new and creative ways.

THE NEW MCDB KIOSKINFORMATION AT YOUR FINGERTIPS

Subscribe to receive more MCDB News on-line. Go to

http://mcdb.colorado.edu/news/sdotnews-rss.xml

20

MCDB has purchased an electron microscope to be shared by the MCDB Electron Microscope Service overseen by Tom Giddings and the Boulder Laboratory for Three-Dimensional Electron Microscopy at MCDB di-rected by Andreas Hoenger. The new microscope is a CM-100 manufactured by FEI Company in Eindhoven, Netherlands. The scope is equipped with the latest model of a 2-K CCD camera from AMT and a computer featuring a variety of image analysis tools includ-ing calculation of Fourier transforms for image quality and column alignment checks. It has higher resolution and covers a larger field of view than the camera previously in use on the FEI CM10 microscope in the departmental EM facility. With a camera of this kind available, most users prefer to use the digital camera rather than traditional EM film for their work. Traditional film covers a wider field of view but requires chemical processing and digitizing if images will be analyzed computationally. The CM-100 complements the set of electron microscopes and advanced specimen preparation technology already available within MCDB. This microscope helps make both routine and leading edge EM applications developed by the NCRR facility and Hoenger Labs available to a broader spectrum of users within the department, and it reduces the demand for the high-end instruments in the NCRR facility which can then be better used for tomography and high-resolution cryo-applications. The new instrument is dedicated for general cell and molecular structure applications ranging from stained samples (e.g. viruses, macromolecular assemblies) to thin sections of cells. However, the new scope features a FEI CompuStage® that is com-patible with the cryo-holders available from the Boulder 3-D lab, and as such it can also be used for imaging specimens in an unstained, frozen-hydrated state. With the CM100 CompuStage® configuration, cryo-EM data can be collected for intermediate resolution, helical, 2-D crystalline and single-particle 3-D reconstruction.

In addition, all of the applications that have been supported by the CM10s in the departmental EM Service can be provided by the CM100, with a significant upgrade to the digital image quality. Having the CM100 ensures that the department has access to a modern, sophisticated 100 KV transmis-sion electron microscope. The CM 100 absorbs usage from both the sophis-ticated, higher voltage NCRR scopes (Tecnai F20 and F30) and the two 20 year old FEI CM10s in the departmental EM facility. It is located, not at the current departmental EM space, but on the ground floor of Porter Biosci-ences as part of the consolidation of EM facilities in MCDB.

Some MCDB Tools CM-100 ELECTRON MICROSCOPEKEEPING UP WITH TECHNOLOGY

The CM 100For high-resolution plastic and cryoelectron tomography currently used in the Hoenger Lab. Article and photo by Andy Hoenger.

The web site with more information about the Hoenger Lab can be found at:http://hoengerlab.colorado.edu/docs/em.html

21

ORTo give online: www.cufund.org

Select GIVE ONLINE; in the “Getting Started” section, Select University of Colorado – Boulder; in the “Colleges and Schools” sectionSelect See listing of additional in the “College of Arts & Sciences” sectionSelect See listing of additional and scroll down to “MCD Biology Fund”Then click Give Online. If you want your gift to go to a specific scholarship, please provide the scholarship name in “Comments” section.

Donor SupportThank you for your support of the Molecular, Cellular, and Developmental Biology Department Programs.I would like my gift to support

Colorado Initiative in Molecular Biotechnology (CIMB)

MCD Biology Fund

Jarred Curtis Keith Memorial Fund

Enclosed is my check made payable to:CU Foundation - Note: B2013 - MCD Biology In the amount of $ ___________OR Charge my credit card: $_______Circle one: VISA Master Card

Credit Card Number and Expiration Date

Authorized Signature

MCD Biology2008/2009

Please cut on dotted line above and send to:

MCD Biology347 UCB

Boulder, CO 80309-0347

MCD BiologyUniversity of Colorado Boulder347 UCBBoulder, CO 80309-0347

MCD BiologyGeneral Information: 492-7743Dept Fax Number: 492-7744http://mcdb.colorado.edu/