Footprints: The Newsletter of the UC Merced School of Natural Sciences

Environmental Systems doctoral student Erin Stacy is researching fire and erosion in the mountains. Her focus? To better refine carbon models in predicting the ecosystem’s response to carbon dioxide. To do this, Stacy is studying soil samples from the Gondola fire in 2002 near South Lake Tahoe, from prescribed burns and archived samples, in an effort to assess the effects of fire and erosion in the ecosystem.

Erin Stacy. Photograph: Scott Hernandez-Jason

From an early age, Stacy has been interested in how humans affect the environment. As an undergraduate student at the University of Pittsburgh, she studied ancient horse teeth from Kazakhstan and Mongolia to learn more about the climate and environment when the animals were alive.

“I’ve always been interested in water dynamics and the ecosystem,” Stacy explained. “(California’s water system) has a pretty precarious balance and that’s what makes it interesting.”

Stacy, who is working under School of Natural Sciences professors Asmeret Asefaw Berhe and Steve Hart, was drawn to UC Merced by the opportunity to work in the Sierra Nevada Research Institute and the campus’ Critical Zone Observatory in the Sierra Nevada. She is in her second year towards pursuing a Ph.D. and would like to continue environmental research when she graduates, either by working at a nonprofit or in a research group.

“I like being at the intersection of the research and management and working with people,” Stacy said.

Undergraduate Students Participate in Department of Energy Program

The U.S. Department of Energy’s Joint Genome Institute is providing opportunities for colleges and universities across the country to “interpret” bacterial genomes for analysis. The education program makes available a selection of recently sequenced genomes for use in undergraduate courses and helps increase knowledge about microbial genome complexity. Late last year, UC Merced Professor Carolin Frank was accepted as a faculty collaborator in the “Adopt a Genome Program”, which allows students to work on an actual bacterial genome sequencing project, filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life.

Carolin Frank. Photograph: Trevor P. Hirst

Frank’s project allows students to annotate the genome of Atopobium parvulum, a bacterium commonly found in a person’s mouth.

“The students are actually looking at a gene for the first time,” Frank explained. “No one has looked at it before. It’s up to them to predict the function of the gene. It’s real.”

Over the last two semesters “the students analyzed about a third of the genome, which I think is pretty impressive - it is a lot of work,” Professor Frank concluded. “They made plenty of little discoveries, and seem to enjoy it a lot. I think it was successful and I will definitively use this format again when I teach Genomics in a year.” Professor Frank’s class is just one example of the hands-on learning experiences available to undergraduates at UC Merced.

Did you know… that dust is more than something to sneeze at? - Professor Stephen C. Hart

Most people think of dust as a health hazard that should be avoided or that requires immediate removal with the aid of a vacuum. But many terrestrial and aquatic ecosystems rely on inputs of dust transported great distances through the atmosphere to supply critical nutrients for maintaining their productivity.

For instance, dust from the Gobi desert in China helps sustain the productivity of the highly weathered soils of Kaua’i, and dust from the Sahara helps support the lush plant growth in the highly leached soils of the Amazon. However, dust transport is a two-way street; one ecosystem’s gain is another one’s loss. Furthermore, dust can dramatically increase the melting of mountain snow packs by increasing the absorption of solar energy, resulting in a shortened ski season and (more importantly) reductions in water storage for human use later in the growing season. Changes in land-use and climate over the last several decades have dramatically increased dust movement globally, and we need to better understand the importance of this little-studied movement of matter in the functioning of the biosphere.

Professor Stephen C. Hart is an ecologist that studies the factors that regulate and maintain terrestrial ecosystems. His research interests include: the impact of dust on Sierran and southwestern ecosystems; the role of fire and management on forests; how individual plant genes regulate the structure and function of associated biota; the potential effect of climate change on terrestrial ecosystems; and the processes that control one of the most limiting resources on the planet…the element nitrogen.

Student Spotlight - Cynthia Dumas

For a 14-year-old Cynthia Dumas, the only news worse than hearing she had leukemia was learning her age limited her chances of survival.

“You won’t make it through college,” she recalled the oncologist telling her. “You’ll be lucky to graduate from high school.”

Cynthia Dumas. Photograph: Veronica Adrover

Dumas, now 22, is set to graduate from UC Merced in 2011 with a degree in molecular biology. She has been in remission for eight years and off treatment for six. Because of her high-risk status, the doctors were willing to try an experimental course of treatment that ended up saving her life.

“If I hadn’t had that treatment, I wouldn’t be here. If people didn’t fundraise through the American Cancer Society (ACS), I would not be here,” said Dumas, who participated in her first Relay For Life during her second year of chemotherapy. “There is no way for me to separate myself from that. Being involved with ACS is my way of giving back.”

Three years in a row Dumas was awarded the Young Cancer Survivor Scholarship, which is given to survivors under 25 years old who are academically eligible and committed to volunteering in a leadership role. She was Survivor of the Year for the Marin County ACS unit and Volunteer of the Year in 2008.

This year, Dumas supports the event in her hometown of Los Banos as the online chair, and helps out in other communities when asked. Dumas is also the survivorship chair for the Merced Relay for Life, reaching out to cancer survivors in the Merced area. As she has done for the past seven years, Dumas is busy every spring juggling two Relay for Life teams, for both the Merced and Los Banos events. Dumas is also a local advocacy volunteer for the society’s Cancer Action Network (CAN), the sister organization that lobbies the federal government for cancer prevention and treatment-related legislation.

How can she manage so much on top of her studies? “Time management, that’s how I do everything in my life,” Dumas said. “And I’ve had to learn to say no to what drains me, so that I can say yes to what energizes, inspires and fulfills me.”

Did you know…that Elephant Seals can survive without food for several months? - Professor Rudy Ortiz

Humans wouldn’t live much longer than a month if they were deprived of food. Yet there is something that cues this behavior in seals. After nursing for approximately one month, elephant seal pups are weaned, and fast for approximately 2.5 - 3 months on land before entering the water for the first time.

While fasting, elephant seals won’t even bother to eat food put in front of them. Prolonged fasting is one of the most important survival adaptations elephant seal pups have developed through a shift in metabolized substrate from protein within the first week to fat for the remainder of the fast. Periods of food restriction and fasting induce dramatic changes in a number of different hormones that help regulate an animal’s (or human’s!) metabolic rate.

What are the physiological mechanisms that these animals employ to endure the extended fasting period? What if we could figure out that switch? Obese people could eliminate their carbohydrate intake and rely on their fat mass until they’re lean and can return to a balanced diet. However, an examination of these hormones in elephant seals is lacking. Professor Rudy Ortiz and his team have been making groundbreaking discoveries in obesity behaviors in seals and hope to eventually develop appropriate medical applications.

Student Spotlight - Juan Lopez Arriaza

Undergraduate student Juan Lopez Arriaza uses mathematical models to predict how sand and soil will be held together by the sugar naturally released by plants.

Juan Arriaza. Photograph: Veronica Adrover.

Working under the direction of physics Professor Teamrat Ghezzehei, Arriaza is studying how plants affect the soil. The research could lend insight into what could be done to create more efficient plants for biofuel production. Most plants use 50 to 90 percent of their energy on simply establishing and maintaining their root structure, Arriaza said. The only undergraduate in the lab, Arriaza creates the models of how soil will behave under certain situations. Other members on the research team then test the model with soil samples.

Arriaza, who grew up in Atwater, was accepted in the UC Leadership Excellence through Advanced Degrees program, which helped to jumpstart his research career in the summer of 2009. “The opportunities are amazing for undergraduate research,” he explained. “It’s been great. I’ve learned a lot.”

The interdisciplinary atmosphere has allowed him to interact with researchers in math, environmental science and engineering. Arriaza is scheduled to graduate in the fall of 2011 and has begun applying to graduate schools across the West Coast. He’s interested in pursuing research and teaching.

Did you know…that cholesterol is a liquid crystal? - Professor Linda Hirst

Liquid crystals open the door to a very exciting area of research because they are neither crystalline solids, nor simple liquids - they are somewhere in between! This interesting state of matter can take many forms and can be seen everywhere in the world around us. Nature uses these substances in a variety of ways. Cholesterol is a liquid crystal and so is the mucus secreted by slugs. Scientists are only beginning to understand the many ways in which liquid crystals hold promise in technological, scientific, artistic and medical applications.

Linda Hirst. Photograph: Trevor P. Hirst

Liquid crystals are formed from anisotropic molecules (i.e. not globular or spherical) that pack together to form an ordered fluid-like phase. The phases formed typically have two different refractive indices and may also respond to applied electric fields, giving rise to many technological applications. Thermotropic liquid crystals (which change their structure as a function of temperature) are now used everywhere in the form of liquid crystal displays (LCDs) but they also have many other applications including optical fiber components for telecommunications and temperature sensors. Biological liquid crystals typically change their molecular packing structure as a function of concentration in a solvent (lyotropic liquid crystals). Examples of lyotropics include the lipids of the cell membrane, or surfactant materials such as soaps and detergents.

Liquid Crystal microscope image. Photograph: Linda S. Hirst

Professor Linda Hirst’s research group works on both forms of liquid crystal material. Recently, her group has focused on an emerging field that studies nanoparticle self assembly within liquid crystal media. In recent years the dispersion and directed assembly of quantum dots (light emitting nano-particles) in liquid crystal has proved an interesting field for investigation and one that may yield new hybrid materials for optical applications and fundamental research.

UC Merced researchers in the School of Natural Sciences have brought in nearly $9 million in federal, state, and private competitive grant funding in 2010 to support the cutting-edge research being done on our campus. Research awards have come from the University of California Office of the President, National Science Foundation, the National Institutes of Health and other sources:

Biology Students Secure Prominent Postdoctoral Positions

Many UC Merced students who earned their doctoral degrees in Quantitative and Systems Biology have continued their success by securing positions at some of the leading labs in the world. Quantitative and Systems Biology (QSB) is one of the top graduate programs on campus. Of the 12 Ph.D.s awarded during May 2010 commencement, nine of them were to students in the QSB program. Some of UC Merced’s QSB graduates are in New York, Boston, Memphis, San Francisco and Germany pursuing their careers in science.

Students in the program focus on the integration of systems at molecular, cellular, organ, organismal or ecological levels to better understand the overall function of biological systems as a whole.

“The program gave me a foundation in molecular, cell and genome biology,” said Michael DeSalvo, who earned his doctoral degree in May. “With this foundation, you can study many areas of biology, from coral reefs to fruit flies. While at UC Merced, I also learned the skills necessary to be an independent scientist capable of critical thinking and troubleshooting the many obstacles that arise during a life in science.”

DeSalvo, of Novato, is working in the Department of Anesthesia at UC San Francisco’s School of Medicine. His long-term goal is to become a faculty member with a research program focused on using molecular and cellular techniques to study coral physiology.

The following is a summary of a handful of UC Merced’s recent QSB graduates and what they’re researching:

David Gravano, of Fresno, is at St. Jude Children’s Hospital in Memphis conducting research on the function of regulatory T cells.
Ali Abdul Sater, of Beirut, Lebanon, is at Columbia University working in the lab of Professor Christian Schindler on type I interferon signaling and innate immunity.
Matthew Pettengill, of Ooltewah, Tenn., is at Children’s Hospital Boston, Harvard Medical School’s primary pediatric teaching hospital. He’s determining differences in neonatal immune cell function.
Shinichi Sunagawa, of Frankurt, Germany, is working as a postdoctoral researcher in biocomputing at the European Molecular Biology Laboratory in Heidelberg, Germany.

An Unforgettable Morocco Experience With Peace Corps

Socorra Composanto (Class of 2009) is living the adventure of a lifetime as a U.S. Peace Corps Volunteer in Guefait, Morocco. Composanto and her friend, Jackie Shay (who also was sent to Morocco), are the first UC Merced graduates to sign up for the Peace Corps. Their decision to help the world reflects the university’s commitment to instilling a sense of community service in its students.

Camposanto, who had never traveled outside the country before, said that her experience at UC Merced helped her stand out to the Peace Corps representative who interviewed her. “He said he enjoyed my fresh perspective on college. I told him how being in such a new school meant that you had to start everything yourself. That really impressed him.”

Creating programs and clubs out of nothing, Camposanto told the Peace Corps representative, taught her the importance of learning how to work with other people. On a more personal level, she said that the university was a place where she was able to dabble in new arenas. “It forced me out of my comfort zone.”

UC Merced was where she sang solo for the first time. Camposanto concluded her college career performing her original song, “We Rise,” at the 2009 commencement ceremony, which she dedicated to the pioneering class of UC Merced.

Both women, who are good friends, are graduates of that class; Shay with a degree in biological sciences, and Camposanto with one in conservation biology. Although they are pleased to be based in Morocco together, their different disciplines has taken them in separate directions. Shay has been assigned to work within the rural health community program, while Camposanto’s role is centered on environmental issues.

Camposanto’s experience is definitely an adventure of a lifetime, “thus far, I’ve been in Morocco since March 2010 and I’m having a blast!”

Currently, Camposanto is spending most of her time in Youth Development. She is teaching English to Junior High Students at a local youth center and is planning to incorporate a variety of wide ranging environmental projects, including “a wastewater treatment center at one of the primary schools and a world species map mural.” The mural, Camposanto noted, “will not only help with geography of the world but also with knowledge of different ecosystems and animals that are unique in those ecosystems.”

In addition to teaching, Camposanto has been spending her time helping other volunteers with their youth development projects and is planning on creating a medicinal plant book that will help adults, tourists, and students learn about local plants and resources.

Camposanto has been busy learning Moroccan Arabic or “Darija” as well. “In the beginning I found it extremely difficult because of the pronunciation and spelling of words,” she said. “But now, little by little or in Darija ‘shwiya b shwiya’, I’m learning and developing the ability to have conversations with people in Morocco.”

Camposanto goes on to say, “It’s a definite change from America, everything from the food to the music. But I’m learning a lot from the people in my site and I’m having fun hanging out with the kids and teaching them American card games and even playing hacky sack.”

Edward and Jeanne Kashian Make Leadership Pledge to Support Stem Cell Research Facility

As respected leaders in California, the Kashians helped build the foundation of this great research university through their roles as founding UC Merced Trustee and Diplomat, respectively, and by providing critical support to develop the Library.

With their $100,000 pledge to name the Ed and Jeanne Kashian Microscopy Room, the Kashians will further assist UC Merced by providing much needed funding to enable the purchase of highly specialized instruments to be placed in the UC Merced Stem Cell Instrumentation Foundry.

The Ed and Jeanne Kashian Microscopy Room will be an auxiliary room to the UC Merced Stem Cell Instrumentation Foundry and will allow associated research to take place on site.

The gift will be directed to the UC Merced Stem Cell Fund to support UC Merced’s ability to develop an outstanding stem cell program that will have significant impact in improving our understanding of cancer, heart disease, diabetes, neural degeneration, immune rejection, and infectious diseases through stem cell biology.

Cutting-Edge Center Gets Boost from Fresno Philanthropist

Darius Assemi is supporting the future of research and medicine in the San Joaquin Valley with a $10,000 gift to the Stem Cell Instrumentation Foundry at University of California, Merced. Construction on the foundry began in January and is expected to conclude early next year. The facility, funded by $4.36 million from the California Institute for Regenerative Medicine (CIRM), will serve researchers from across the Valley.

Stem Cell Instrumentation Foundry. Photograph: Trevor P. Hirst

“We are deeply thankful for Mr. Assemi’s support of our stem cell foundry, which will greatly aid in the campus’ research mission,” said Maria Pallavicini, Dean of the School of Natural Sciences. “The foundry will not only serve the campus but the entire San Joaquin Valley.”

Mr. Assemi’s gift will be used to help outfit the facility with state-of-the-art equipment that will allow researchers to manipulate and study stem cells. The total raised so far towards the needed equipment is approximately $770,000, including an additional $600,000 grant from CIRM and individual donations.

The 3,902-square-foot facility is being constructed in the Science & Engineering I building. It will have two ultraclean rooms that prevent dust or other particles from interfering with experiments.

Valley Philanthropist Provides Ongoing Support for Research

Jane Evans Vilas. Photograph: Scott Stehle

Jane Evans Vilas has lived her life with a spirit of pioneering and a commitment to serving others – two of but many important qualities that she holds in common with students, faculty, and staff at UC Merced. For decades, Jane and her family’s altruism have helped their community prosper. Jane’s interest in the health and well-being of family, friends and community resonates with the vision of UC Merced and its’ goal to provide quality education and cutting-edge research for the San Joaquin Valley.

Vilas, who has contributed over $85,000 to the University, has recently contributed an additional $10,000 towards graduate student support in the area of stem cell and health sciences. This will provide much needed support for graduate students doing research in the exciting field of stem cell biology and health sciences at UC Merced.

$500,000 Gift Will Strengthen Research and Help Keep Top Faculty

Graduate students at any campus find tuition, the availability of affordable housing, and the cost of living to be extremely challenging. This is especially true for graduate students at UC Merced, where prestigious fellowships are still in the early stages of being funded and students have fewer opportunities for financial support.

Science & Engineering Building. Photograph: Trevor P. Hirst

If the top graduate students shun UC Merced for private schools and other campuses where fellowships are more readily obtained, research programs would not be the only ones to suffer. Recruitment and retention of the best faculty could be severely hampered, too.

“Top faculty come to UC for many reasons,” said the University of California’s President Mark Yudof. “The eminence of the department matters, but they would not come to a place without vibrant graduate programs and without outstanding graduate students.”

Over the years, graduate students have played a key role in the research success of the UC system and building California into a technology and cultural leader. UC graduate research helped spawn the biotechnology industry, and former graduate students have led the development of other industries, including electronics, pharmaceuticals, telecommunications, nanotechnology and the special effects industry, among others.

Contributions from our donors helps provide the incentive that’s needed for top graduate students and faculty alike to choose UC Merced over other top research universities. This fall, an anonymous donor contributed $500,000 towards graduate student fellowships. The donor requested that matching donations be sought to help fund an outstanding graduate program on our campus.

If you would like to know more about how to support graduate students and their research at UC Merced, please contact Marnee Chua at (209) 228-4132 or mchua@ucmerced.edu.

Message from the Dean

Support for the School of Natural Sciences

Footprints Archive

January 2011

Contents

Student Spotlight - Erin Stacy