Cross-disciplinary research that spans biology, chemistry, molecular biophysics, bioinformatics, and immunology is producing a wealth of information that will profoundly impact the future of personalized medicine and how it is applied.

But, when it comes to detecting and treating complex dis-eases, such as cancer, tailoring medical treatment can have adverse impacts on how the body processes medications.

“The problem is that cancer has proven to be many diseases; each of which is adaptable and difficult to treat,” begins Rice University Professor Ariel Fernandez. “There is a tremen-dous need to translate knowledge into improved therapeutic strategies that pinpoint novel drug targets with high selectiv-ity, and manipulate the cellular response so that we eliminate resistance and life-threatening side effects.”

Fernandez is the Karl F. Hasselman Professor of Bioengineer-ing. His research interests include cooperativity and many-body problems associated with biopolymer folding and inter-actions. He introduced the category of structural wrapping and established its importance in the contexts of network centrality, molecular disease, drug discovery, and the new field of molecular theranostic engineering.

In a multidisciplinary effort, two research teams from Rice University and the UT M.D. Anderson Cancer Center have used Fernan-dez’s wrapping concept to re-engineer a version of the anti-cancer drug Imatinib, the drug sold under the brand name Gleevec®.

The new version of the drug – known as WBZ-7 (pictured right) – was created, produced and tested by Fernandez and Drs. William Bornmann and Gabriel Lopez-Berestein from the UT M.D. Anderson Cancer Center.

Characterizing protein affinity

For the basis of this study, researchers targeted protein kinases, an enzyme that responds to and modifies the activity of specific proteins in cells. Because of their value as the signal transducers, kinases have become a fundamental therapeutic tool in the strug-gle against complex diseases.

Re-engineered drug tightens control of harmful side effects and resistance Large-scale effort involves researchers from Rice and M.D. Anderson

Mathematics and computers – the new virtual lens Researchers view how molecular complexes flex and bend

Advanced computational modeling and cutting-edge experi-ments by molecular biologists from the Baylor College of Medicine and Rice have discovered a new way to analyze the moving parts of large proteins – a breakthrough that

will make it easier for re-searchers to classify and scrutinize the active sites of proteins implicated in cancer and other diseases.

The research, which was led by Associate Professor Jianpeng Ma and Rice bioengineering graduate student Billy Poon (pictured left), appeared in the online Proceedings of the National Academy of Science (PNAS) in April 2007.

“To function and maintain life, certain components of proteins must move,” explains Ma, who holds joint appointments in Rice’s bioengineering department and The Verna and Mars McLean Department of Biochemistry and Molecular Biology at Baylor. “However, errors in protein movement cause even the most stable parts to misfold. When proteins misfold, something that’s known to occur in a number of diseases, they don’t function as they should.”

The recent discovery by Ma and Poon involves a new mathemati-cal algorithm that narrows all the possible ways a protein might flex and bend.

The math is used in conjunction with information captured via X-ray crystallography, a technique in which protein crystals are bombarded with X-rays, producing a diffraction pattern that re-veals the precise 3-D arrangement of every atom in the protein. When this method is applied to proteins, researchers get a snap-shot of the structure at a particular moment.

Unfortunately, proteins in the crystal are not guaranteed to orient themselves in the exact same way.

Continued on p. 3

Continued on p. 4

Message from the Chair

Bioengineering professionals today are emerging as key play-ers who work alongside medi-cal practitioners as architects of new medical techniques and devices; as researchers who are developing cutting-edge tech-nologies to detect, prevent, and treat disease; as developers of biomaterials that repair or re-place tissue damaged by injury or disease; and as engineers who produce biological substi-tutes for chemical processes that allow for greater agricul-

tural production and more efficient, safer energy production.

These are just a few examples of how bioengineers work to solve a host of life-science problems. Since the Rice University Department of Bioengineering graduate program was founded in 1996, we have worked to define this burgeoning field that encompasses many specialty areas. More than 70 students have completed our graduate program and are performing basic, applied, and translational research and development in industry or academia around the world.

The distinctive characteristics that define our graduate pro-gram have shaped undergraduate education at Rice. This year both our graduate and undergraduate programs were ranked ninth by U.S. News & World Report.

To remain competitive and position our education and re-search programs for what lies ahead in this era of technology and globalization, the department will continue to initiate multidisciplinary research and training programs with collabo-rators that boost research volume and productivity while train-ing students to become globally-minded leaders.

Currently, there are more than 120 undergraduate students, 130 graduate students, and nearly 30 postdoctoral fellows in the bioengineering program.

This fall, the university as a whole reported a four percent in-crease over last year’s incoming freshman class. Through this growth, the department hopes to expand its core of quality students interested in bioengineering.

As one of the nation’s top teaching and research bioengineer-ing programs, we offer undergraduate students amazing op-portunities and flexibility to sculpt their education through:

♦ Advantages of small classes, which include an under-graduate student-to-faculty ratio of six-to-one.

♦ Early access to cutting-edge laboratory experimentation, instruction, and research. More than 80 percent of our undergraduates participate in primary research by provid-ing contributions to faculty and graduate laboratory study

on campus through the university's Research Centers and Institutes and/or the Texas Medical Center.

♦ Innovative teaching standards and materials, based on the latest research, that provide hands-on approaches to prob-lem solving as well as foster cross-disciplinary communica-tion and teamwork skills.

♦ Opportunities to communicate research results through de-sign competitions, publication, and delivering papers at pro-fessional conferences.

Technology design challenges, design competitions, and intern-ship experiences are quickly creating new channels for educa-tion, delivering new technologies, increasing collaborations with other institutions, and expanding the university’s research profile and international orientation.

For the past three years, bioengineering faculty members have expanded the undergraduate design program to adapt and re-spond to a rapidly expanding global world. Through the BIOE 260, BIOE 301, and BIOE 451/452 design classes, student teams delve into research, invention, and design to provide practical solutions to real-world problems. The result is a proven method for engaging them in technical disciplines and global issues.

In addition, the Beyond Traditional Borders program and special laboratory research projects allow undergraduate and graduate students to participate in independent research through interna-tional internship experiences. This summer, students traveled to Mexico, Honduras, China, India, and several countries of sub-Saharan Africa and not only gained new insights into culture, research, and education at various levels, but implemented technologies of their own design. ●

Inside this issue...

Headline News……………………….pages 1,3,4,

Message from the Chair……………page 2

Department News……………………pages 5-7

Student Highlights………………….pages 8-11

Student News…………………….pages 12-14

Alumni News……………………….page 15

Events……………………….pages 16

The Rice BIOE NEWS is a biannual publication of the Department of Bioengineering, and is sent to alumni,

faculty, students, and friends of the university. Some photos and content are courtesy of Rice University

Photography Services and the Office of Public Affairs. Send comments, story ideas, and alumni news to bioeng@rice.edu

Page 2

Shaping the future of bioengineering

Since 2006, Professor Fernandez and Rice graduate students Jianping Chen and Xi Zhang have focused on the molecular basis for specificity in kinases. They found a correlation between drug-specificity and the local dehydration propensities of kinases. Recent results of their research were published in the January 25, 2007 issue of Structural Bioinformatics in a paper titled “Molecular basis for specificity in the druggable kinome: sequence-based analysis.”

“If you want to control signals that might be involved in cell fate or cell proliferation you want to control the kinases,” said Fernandez.

The problem becomes complicated, however, due to the scarcity of affinity-profiled kinases with reported structure and the simi-larity. To date, only about 20 percent of the human kinome (103 out of approximately 520 discovered protein kinases) is reported in the Protein Data Bank (PDB).

Walking a very fine line

Many diseases arise from defects in signal transduction pathways, and the cells develop mechanisms of drug resistance, mainly due to mutations, that block a drug’s ability to treat disease. The team identified differences be-tween kinases, looked at the interface between the drug and the kinases, and sought ways to redesign the drug to bind better.

“Redesigning Imatinib to target a drug-resistant mutant was like walking a very fine line. We looked at protein kinases because they are the largest group of their kind, but the process was highly complex since they evolve from the same super family and look very, very similar – almost super imposable,” added Fernandez.

The team’s most recent study, which was highlighted in as a pri-ority report in the May 1, 2007 issue of Cancer Research, differ-entiates the complex protein structure and function from previ-ous studies, and exploits its specificity to drug treatment using the C-KIT kinase. In relation to cancer, C-KIT is a proto-oncogene and an ideal therapeutic target for treating gastrointes-tinal stromal tumors.

Imatinib, one of the most effective of a new generation of cancer drugs, was designed to attack cancer cells and leave healthy cells unharmed. Imatinib targets C-KIT, which also plays a role in cell reproduction. However, to escape from Imatinib inhibition, the C-KIT kinase has developed a drug-resistant mutation that ham-pers ligand association. In healthy cells, C-KIT is active only on rare occasions, but in some cancers the protein is always "on" acting as a biochemical catalyst that spurs cancer cells to con-stantly reproduce.

To encourage a more stable bind between C-KIT and Imatinib, the team looked at the hydrogen bonds in the proteins to target

the packing defects, or dehydron. Fernandez has found that dehydrons are sticky, because the surrounding water has been removed.

“Now the new drug binds to C-KIT and to the Imatinib-resistant version of C-KIT. And finally, it binds in a way to ensure that any further version becomes resistant to WBZ-7 will no longer be effective as a catalyst for cell reproduction," said Fernandez.

To test the successful interaction of WBZ-7 and C-KIT, Rice Postdoctoral Fellow Alejandro Crespo established what was happening from a thermodynamic perspective using molecular dynamic simulations. The ligand redesign was validated through simulations, and showed theoretically

that WBZ-7 is active towards the Imatinib resistant C-KIT mutant.

Fernandez said WBZ-7 is nearly identical to Imatinib, save for the addition of four atoms – a carbon and three hydrogens – at a key point. Though the change appears to be minimal at first glance, finding a method to synthesize the compound was complex and challenging. The task fell on William Bornmann, a director of the Center for Targeted Therapy's Translational Chemistry Service, and professor of Experimen-tal Diagnostic Imaging at UT M.D. Anderson, and his colleagues Shimei Wang and Zhenghong Peng – who dubbed the com-pound WBZ-7 based on their initials and the fact that it was the seventh compound they'd made together.

Following the drug's synthesis, a second team of UT M. D. Anderson researchers, led by Lopez-

Berestein, a professor in the Department of Experimental Therapeutics, and including Angela Sanguino and Eylem Ozturk, embarked on a comprehensive testing program. In the first stage of testing, WBZ-7's effects were tested against more than 250 kinases to make sure the drug would not have unintended consequences. Finally, a range of in vitro tests were conducted. The tests confirmed that WBZ-7 was just as effective against both non-resistant and drug-resistant strains of gastrointestinal cancer cells.

WBZ-7 is not yet available for human testing, and a date for human trials has not been set. Fernandez said the research team is preparing for the next phase of testing in laboratory animals.

Fernandez’s research is supported by the National Institutes of Health, National Science Foundation, Eli Lilly and Company, and by Rice's John and Anne Doerr Fund for Computational Biomedicine. The group gratefully acknowledges Dr. J. H. Butterfield (Mayo Clinic) for the generous gift of the human mast cells. ●

Re-engineered drug tightens control (Cont.)

Headline News Page 3

“Redesigning Imatinib to

target a drug-resistant mutant was like walking

a very fine line. We looked at protein

kinases because they are the largest group

of their kind, but the process was highly

complex since they evolve from the same super family and look very, very similar – almost

super imposable.”

Ariel Fernandez

Headline News

Furthermore, due to thermal fluctuations, the configurations of the proteins also vary and are either isotropic or anisotropic.

Poon explains that for larger proteins and supramolecular com-plexes, isotropic models are standard because crystals containing large proteins yield poorer diffraction patterns, which results in a lower data-to-parameter ratio and a higher likelihood for over fitting.

"Increasingly, our discipline is faced with deciphering the structure of large, complex proteins in which some parts are constantly moving, even when the protein is locked in a crystal form," said Ma. “Producing an image from a diffraction pattern requires sophisticated pattern recognition analysis, and Billy never lost faith in the basic premise of the project.”

The main problem arises from the fact that atoms are constantly moving, and for large proteins, many of the atoms move in concert over relatively large distances. An example of this movement would be a hinge bending or a barrel stretching and twisting. These motions make the diffraction pattern less intense, which reduces the amount of data available for model building. Proteins tradi-tionally have been described by isotropic models that assume the motions of individual atoms to be independent of everything else. However, Ma and Poon found that the motions are decid-edly collective and directed. Their novel method is able to cap-ture that with much fewer parameters,

which allow researchers to build anisotropic models of large structures with greater accuracy.

Nobel laureate William Lipscomb of Harvard University, one of the founding fathers of protein crystallography in North

America, said, "This recent success in X-ray crystallographic refinement is revolutionary for the field of structure biology in terms of improving large and flexible complex structures that are becom-ing far more abundant nowadays. It is one of the largest technical leap-forwards in X-ray refinement in the last two decades. It will fundamentally change the way peo-ple do structural refinement for large and flexible complexes."

Producing the protein crystal structure was like an enormous puzzle. To study the pro-tein, optimize its parameters, and map its configuration, Ma and Poon used the Rice Terascale Cluster (RTC) in conjunction with their own Linux cluster. Then to help analyze the moving parts of large proteins and produce the atomic model pictured below, students such Xiaorui Chen, a recent graduate of Tsinghua University in China, used special goggles that allowed her to look at a computer and see 3-D rep-

resentations of both the map and protein, and to tweak the positions of the atoms so that they were more centered within the electron density map.

“The painstaking process involved a little over 16,000 atoms and she would have checked every one of them,” said Poon.

Ma will continue to use this method on many other impor-tant systems in his laboratory for advanced computational and experimental modeling to study supermolecular com-plexes across multi-length scales at multi-resolution. His state-of-the-art algorithms for computational modeling and protein structural prediction refine structures obtained from x-ray crystallography, electron cryomicroscopy (cryo-EM), fiber diffraction and small- and wide-angle x-ray scattering (SAXS/WAXS). Ma’s laboratory utilizes both structure and ligand-based approaches for computer-aided drug design. ●

The solution was tested on the protein

formiminotransferase cyclodeaminase.

The final model shows the anisotropic variability

in the atomic positions as ellipsoids.

Students such as Xiaorui Chen, a recent graduate of Tsinghua University in China, were instrumental in the new discovery that allows scientists to analyze

the moving parts of large proteins. For this study, Chen used special goggles that allow her to look at

a computer and see 3-D representations of both the map and the protein.

"This recent success in X-ray crystallographic

refinement is revolutionary for the field of structure

biology in terms of improving large and flexible complex

structures that are becoming far more abundant nowadays.

It is one of the largest technical leap-forwards in

X-ray refinement in the last two decades. It will fundamentally

change the way people do structural refinement for

large and flexible complexes."

William Lipscomb, Harvard University

Nobel Laureate

Page 4

Mathematics and computers – the new virtual lens (Cont.)

Department News Page 5

AIChE honors Professor Mikos Alpha Chi Sigma Award given for decade-long research in chemical engineering

Antonios G. Mikos received the 2007 Alpha Chi Sigma Award from the American Institute of Chemical Engineers (AIChE) for his out-standing career accomplishments over the past decade in fundamental and applied chemical engineering research, and service to the commu-nity and AIChE. The coveted award is one of the highest honors bestowed by the organization.

AIChE, the worlds leading organiza-tion for chemical engineering pro-fessionals, will formally present Mikos with the award this Novem-

ber at the institute’s annual meeting in Salt Lake City, Utah.

Mikos, the J.W. Cox Professor of Bioengineering, professor of chemical and biomolecular engineering, and director of Rice's Center for Excellence in Tissue Engineering, specializes in a broad range of research topics, including the synthesis, process-ing, and evaluation of new biomaterials for use as scaffolds for tissue engineering, carriers for controlled drug delivery, and non-viral vectors for gene therapy. His work has led to the de-velopment of novel orthopedic, dental, cardiovascular, neu-rologic, and ophthalmologic biomaterials.

Mikos joined Rice as the T.N. Law Assistant Professor of Bioen-gineering and Chemical Engineering in 1992. He was promoted to associate professor in 1996, and helped establish the Depart-ment of Bioengineering in 1997. Professor Mikos founded Rice’s Center for Excellence in Tissue Engineering in 1998. A year later, he was named the J.W. Cox Professor of Bioengineering.

While at Rice, Mikos has supervised 35 Ph.D. and 6 M.S. gradu-ate students, as well as 24 postdoctoral fellows. He holds 23 patents, has authored more than 330 publications, and is a founding editor of the journal Tissue Engineering. He serves on the editorial boards of the journals Advanced Drug Delivery Reviews, Cell Transplantation, Journal of Biomaterials Science Polymer Edition, Journal of Biomedical Materials Research (Part A and B), and Journal of Controlled Release. Mikos is a founding member of the Tissue Engineering and Regenerative Medicine International Society, a fellow of the American Institute for Medical and Biological Engineering, and president elect of the North American Tissue Engineering and Regenerative Medicine International Society. He is also active in AIChE, the Biomedical Engineering Society, Controlled Re-lease Society, and Society for Biomaterials.

In recent years, his research and service to the science commu-nity has earned numerous professional honors, including the Society for Biomaterials’ Clemson Award for Contributions to the Literature (2001), Orthopaedic Research Society's Marshall R. Urist Award for Excellence in Tissue Regeneration Research (2005), Biomedical Engineering Society’s Distinguished Lec-turer Award (2007), and the Edith and Peter O'Donnell Award in Engineering from The Academy of Medicine, Engineering and Science of Texas (2007).

Mikos is known across academia and the biomedical industry for the short course Advances in Tissue Engineering as he has organized the event since 1993. Visit http://tissue.rice.edu. Mikos received a Chemical Engineering degree from the Aris-totle University of Thessaloniki, Greece in 1983, and a doctorate in Chemical Engineering from Purdue University in 1988. From 1990-1991, he was a postdoctoral fellow at the Massachusetts Institute of Technology and Harvard Medical School. ●

Project for Deem to put new spin on predicting disease Results to aid drug/vaccine design

The adaptive immune system protects us against death by infection. By generating antibodies, or protein molecules that bind specific antigens, the human body amazingly responds to millions of different foreign antigens such as toxins, bacteria, and viruses.

“Pathogens mutate and evolve. They will continue to proliferate unless we can predict their evolution and guide them down the path to extinction,” explains Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and profes-sor of physics and astronomy.

Viruses undergo antigenic drift, which is the rapid mutation of certain proteins of pathogens that increase their ability to escape our immune system. Deem’s research at Rice employs biology, mathematics, and statistical physics to understand immune system response and vaccines, as well as the physical theories of evolution.

Through a newly awarded subcon-tract from VaxDesign related to the Defense Advanced Research Projects Agency’s (DARPA) inter-est in pathogen evolution, Deem, his students, and a team of collaborators are developing mathematical approaches to those regions of pathogens that will tend to mutate.

“Our ability to predict the type and location of amino acids is the key to unlocking major issues of antigenic variations and pathogen evolution. The results will ultimately aid drug or vaccine design, and may predict emer-gence of future epidemics,” said Deem.

Continued on p. 6

Page 6 Department News

The American Society for Engineering Education (ASEE) recog-nized two bioengineering faculty members for their excellence in instruction, research, public service, and engineering practice.

The society chose Professor Rebecca Richards-Kortum to receive this year’s Chester F. Carlson Award for innovation in engineering education and Dr. Ann Saterbak the Robert G. Quinn Award for outstanding contribu-tions in providing and promoting excellence in experimentation and laboratory instruction.

Richards-Kortum, the Stanley C. Moore Professor in Bioengineering, chair of the bioengineering department, and professor of electrical and computer engineering, was cited for her accom-plishments in boosting scientific liter-

acy while developing creative and stimulating educational mate-rials that empower students to think critically and develop prac-tical solutions to global health issues through the Beyond Traditional Borders (BTB) initiative.

The initial concept for BTB began in 2001 with the development of the course Bioengineering & World Health. This course is now offered annually at two institutions: UT at Austin and Rice to more than 100 students each year. Then through a $2.3 million grant from the Howard Hughes Medical Institute in 2006, Richards-Kortum dramatically expanded the curriculum and developed the BTB Global Health Technologies Concentration – a multi-disciplinary, four-year biomedical training and education program that unites expertise from Rice on a university-wide scale with clinicians and professors in the Texas Medical Center.

Richards-Kortum has also co-authored a new textbook with Michele Follen, director of UT M.D. Anderson’s Center for

Biomedical Engineering. Titled Bioengineering: Applications in World Health, the textbook provides an overview of the ma-jor causes of global health disparities through actual biomedi-cal case studies and insight into how society can prevent dis-ease by integrating scientific, engineering, health, policy and economic data perspectives. The textbook is scheduled for completion in 2007 and will be published by Cambridge Uni-versity Press. (To learn more, visit beyondtraditionalbor-ders.rice.edu.)

As Director of Laboratory Instruc-tion for the Department of Bioengi-neering’s undergraduate program, Saterbak’s leadership as an educa-tor and mentor has been invaluable to more than 170 students who have graduated with a Bachelor of Science degree in Bioengineering at Rice.

Since 1999, Saterbak has collabo-rated extensively with faculty to build nationally recognized, state-of-the-art undergraduate laborato-ries in experimentation and labora-tory instruction. Her passion and approach to creating innovative teaching standards and materials has positioned her as a leader in undergraduate bioengineering education.

Through a grant from the National Science Foundation, Divi-sion of Undergraduate Education, Saterbak worked with col-leagues to write Bioengineering Fundamentals. The textbook, published by Prentice Hall, provides new and unifying ap-proaches to introductory, interdisciplinary fundamentals in biomedical engineering. ●

BIOE faculty noted for excellence in engineering education and technology Richards-Kortum and Saterbak win ASEE awards

Project for Deem (Cont.) Deem and his group will use statistical mechanics to locate those amino acids in the viral proteins that are most likely to mutate. These tendencies will be tested in animal model studies by col-laborators. Preemptive vaccination against these likely future strains will then be evaluated as a viral containment strategy.

In 2006, Deem and colleagues also won a DARPA grant to iden-tify fundamental mathematical issues in biology. Some of the first results were published in the October 16, 2006 Physical Review Letters, where a new model was introduce that pre-dicted all three stages of HIV infection by incorporating a key component – competition among T-cells.

Other results, published in the February 2, 2007 issue of Physi-cal Review Letters, provided the first solution of an evolutionary model of horizontal gene transfer – a major mechanism by which pathogen resistance evolves.

The rapid evolution of pathogens to be uniformly resistant to treatment, as has occurred with multi-drug-resistant bacteria over the last couple decades, is ex-plained by these results.

A cover review article in the January 2007 issue of Phys-ics Today provided a tour of some of the challenges and opportunities in mathe-matical biology. ●

Research in the Deem laboratory has found

viruses and bacteria sped up the process of evolution by rapidly transferring DNA

from one species to another.

Department News Page 7

New findings help explain hearing loss Assistant Professor Raphael’s research supported by three new grants

Robert Raphael, the T. N. Law Assistant Professor of Bioen-gineering, investigates the intricate inner workings of the hu-man auditory system. His fundamental research into the mo-lecular biophysical-basis of hearing is producing a wave of in-sight into the causes of hearing loss and deafness.

On the whole, scientists are unclear about how auditory mem-brane cells orchestrate the detection and decoding of sounds. Raphael and his Membrane and Auditory Bioengineering Group are investigating the regulation of ion homeostasis in the inner ear by membrane transporters and the intermolecular interactions of prestin.

Prestin, a unique membrane protein found in the outer hair cells of the cochlea, transforms electrical energy into mechanical energy and powers the outer hair cells that provide cochlea amplification. Recently, Raphael demonstrated that alterations in the membrane microenvironment alter prestin’s function, which is potentially important in many diseases that cause deafness.

To function, prestin needs energy generated by a specialized tissue in the cochlea called the stria vascularis. To study this process, Raphael and graduate student Imran Quraishi constructed a mathematical model of potas-sium transport into the endolymph by the outer layer of cells of the stria vascularis. The model predicts normal tissue function and explains why several inherited forms of genetic deafness cause cochlear malfunction. The results were published in the January 2007 issue of the American Journal of Physiology.

Since then, the model was extended and now accounts for the generation of the endocochlear potential by the second layer of

cells in the stria vascularis. With a complete in silico model, the group will begin experiments to test potential drug therapies for hearing loss.

New research in Raphael’s group is supported by grants from the Deafness Research Foundation, the National Institute on Deaf-ness and Other Communication Disorders, and the National Or-ganization for Hearing Research. The funding supports a deeper understanding of the molecular basis of electromechanical trans-duction in cochlear outer-hair cells through continued research

on the characterization of prestin-prestin and prestin membrane interactions, and the effects of oxidative stress on these interactions.

To study the molecular mechanisms associated with prestin function, the potential of ototoxicity from non-steroidal anti-inflammatory agents (NSAIDs), and reactive oxygen species, Raphael uses optical imaging techniques. The group is applying fluores-cence resonance energy transfer (FRET), confocal microscopy, and other advanced optical imaging techniques. These studies also have implications for noise-induced hearing loss, and cochlea dysfunction and damage. The application of the new methods

will lay a foundation for assessing whether anti-oxidants can prevent the deleterious actions of these compounds.

“It has been known for quite some time that aspirin and other non-steroidal anti-inflammatory agents cause hearing loss and tinnitus, but we’ve discovered aspirin-like molecules alter mem-brane mechanics in model systems, and have begun to demon-strate they also change the nanoscale curvature of the outer hair cell membrane.” ●

Diehl wins Rita Schaffer Young Investigator Award BMES honor recognizes Diehl’s work in engineering motor systems

Michael R. Diehl, assistant professor of bioengineering and chemistry, was selected by the Biomedical Engineering Society (BMES) for the 2007 Rita Schaffer Young Investigator Award for his approach to engineering model systems of coupled mo-tor proteins. Diehl will receive the award at the 2007 BMES Annual Fall Meeting in Los Angeles, CA.

Detailed results of this work were published in Science on March 10, 2006 by Diehl and colleagues Kechun Zhang, Heun Jin Lee, and David A. Tirrell in a paper titled “Engineering Cooperativity in Biomotor-Protein Assemblies.”

For the study, the group synthesized a series of finite-sized assemblies of motors using newly developed protein engineer-ing techniques. A key to their assembly design is that the scaf-folds are comprised of specific protein domains that can be used to either selectively and securely anchor motors to their scaffolds, or to control the elastic interconnects between neighboring motors. With such control, their team discovered that linking motors is sufficient to introduce cooperative motor

function with respect to the rate at which motors consume their fuel and produce motion. They also demonstrated that their biosynthetic system can be used to unravel the necessary and sufficient conditions required for such cooperativity.

“Transport in cells often involves multiple motor proteins that interact to control where intracellular commodities are placed inside the cytoplasm,” explains Diehl. “However, it has been difficult to test how these interactions affect motor trans-port since the molecular-level organization of these assemblies is typically unknown. Using our methods, we can build assemblies with known structures, allowing us to probe mechanisms of col-lective motor mechanics in carefully controlled in vitro settings. This way, we hope to develop a better understanding of how in-teractions between motor molecules influence their motion, which we believe will impact our notions of how motor transport is regulated in cells.” ●

Page 8 Student Highlights

Undergrads address global health challenges

This past summer undergraduate students in the Beyond Tradi-tional Borders (BTB) program traveled to sub-Saharan Africa to work in health-care settings and test promising new technologies they developed in bioengineering classes at Rice.

The two-month internship, sponsored by the Howard Hughes Medical Institute, is part of a growing multi-disciplinary and multi-institutional global health effort at Rice. The inaugural 2007 BTB summer internship was coordinated in partnership with the Baylor International Pediatric AIDS Initiative (BIPAI), and will help promote ongoing collaborations with other institutions of the Texas Medical Center.

Working with the BIPAI clinic staff and doctors in Botswana, Lesotho, Malawi and Swaziland, students from various disciplines gained powerful insight into the considerations involved in the development and implementation of lasting health-care solutions. The experiences taught them that solutions to big problems are often found in simple, robust, cost-effective technologies that are adaptable to a country’s needs.

Rice’s Dr. Maria Oden, lecturer and laboratory coordinator for the design courses, also traveled to sub-Saharan Africa to consult with physicians on the design, building, and testing of future devices to be built in the bioengineering and BTB design courses.

“Students will use this research to develop prototypes that may help physicians in their quest to deliver quality health-care services in a challenging environment,” said Oden.

The technological challenges developing countries face are enormous. Rural clinics and some government hospitals lack consistent electrical power, clean water or climate controlled conditions. Standard medical monitoring devices such as ECG's, pulse oximeters, and apnea monitors are in short supply, and are too expensive or require too much consistent power to be used regularly. Oftentimes standard equipment from developed countries sits idle, because at the first malfunction it cannot be repaired.

Examples of a few projects slated for Rice students include: various vital-sign monitors with data storage, IV monitors, devices to assess and help adherence to medication regimen, as well as ways to improve previously deigned devices.

MEET THE STUDENT: Bioengineering’s Kim Bennett is one of seven undergraduate students who participated in the 2007 BTB summer internship. She traveled throughout Malawi with Ellie Click, M.D., Ph.D. of the Baylor Pediatric AIDS Corps.

THE PROBLEM: Malawi is at the center of the HIV/AIDS pandemic in sub-Saharan Africa. Between 19 and 30 percent

of pregnant women in country are HIV positive, and an estimated 83,000 children are living with HIV/AIDS. Of these children, 75 percent born with HIV will die by seven years of age if they do not receive treatment.

THE INTERNSHIP: The blood-spot Polymerase Chain Reaction (PCR) testing pro-gram for infant HIV diagnosis is a pilot project of the Malawi Ministry of Health. It is supported by a variety of NGOs, including BIPAI. For her internship, Bennett assisted in training health-care professionals at clinics. She also visited pharmacies and labo-ratories involved in the PCR project.

THE DESIGN PROJECT: In the BIOE 451/452 Senior Design course, Bennett and her team members: Austin Ginnings, Megan Jeans, and Brian Schwab designed a portable medication dosing system called the ABC Pump. Designed to overcome hu-man error in medicine dosing that oc-curs with the current syringe or medi-cine cup techniques, the ABC Pump accurately dispenses liquid medication according to a child’s individual needs.

THE OUTCOME: While working in Malawi, Bennett dem-onstrated the ABC Pump prototype and collected feedback from physicians and hospital/clinic pharmacies. The infor-mation will guide future improvements to the device. Visits to rural sites also helped Bennett identify new global health technology design challenges for the BTB program.

Continued on p. 9

Student Highlights Page 9

For almost two years, Rice faculty members and staff have worked with partners in the Texas Medical Center (TMC) to develop a program that targets health-related issues and empowers students to design solutions that effectively help people in countries where limited resources, minimal infrastructure, and other issues com-pound pressing health-care challenges.

This year, bioengineering faculty and staff met with communities in Honduras and sub-Saharan Africa to foster interdisciplinary endeavors that will enable the Beyond Traditional Borders (BTB) program to build on its strengths as it raises awareness about global health issues.

BTB’s goals get personal as it…

♦ Expands collaborations with research and health-care communities to generate new projects for the BIOE 260, BIOE 301, and BIOE 451/452 design classes;

♦ Expands collaborations with health-care providers and organizations to give students hands-on clinical and laboratory experience in developing countries;

♦ Provides students with opportunities to demonstrate, test, and gain valuable feedback on promising health-care technologies they developed at Rice; and

♦ Refines the curriculum and teaching material for the Global Health Technologies course of studies and com-munity outreach programs.

For Baylor Shoulder to Shoulder, a non-profit organiza-tion that addresses health care, educational, and economic issues in Santa Anna, Honduras, Rice students designed health-care technologies aimed to help physicians in underserved communities. Here is one example:

THE PROBLEM: Doctors in the developing world face the challenge of diagnosing and treating diseases in remote areas that have limited access to standard diagnostic assays and medicine.

THE DESIGN PROJECT: A diagnostic backpack containing portable test equipment and treatment materials for physicians was developed in BIOE451 by Rice undergraduate students: Jamie Lai, Junho Lee, Neel Srikishen, Nick Taboada, and Po T Wang. The backpack is equipped with a lithium-ion battery and provides power for more than 100 visits. In May 2007, it was assessed by Timothy Kirk Ruttan, a Baylor medical student who took the “lab-in-a-pack” to Santa Anna, Honduras. Ruttan’s feed-back will guide future developments of the backpack.

BTB’s outreach program rolls back borders

The BTB initiative has also designed a new science elective for middle and high school students called Bioengineering & World Health. The course has received approval from

Teaching future leaders to shoulder global health needs

the Texas State Board of Education, and is being taught in schools in Texas, Mexico and Malawi. The course materials promote global health by giving educators and stu-dents curriculum based on real global-health issues from a variety of perspectives such as psychology, sociology, philosophy, public policy, religion and culture, as well as science and engineering.

An exciting part of this curriculum is a new textbook co-authored by Professor Richards-Kortum and Michele Follen, direc-tor of UT M.D. Anderson’s Center for Biomedical Engineering. Titled Bioengineering: Applications in World Health, the textbook provides an overview of the major causes of global health dispari-ties through actual biomedical case studies and insight into how society can prevent and fight disease.

Bioengineering & World Health curriculum engages stu-dents through interactive teaching methods as they work in small groups to identify important health issues that affect a developing

country. Weekly assignments include studying a dis-ease or health issues and identifying in-country con-straints and limitations of current diagnostic and therapeutic approaches. The learning process comes alive when students design a nonfunctioning proto-type based on their research and outline a clinical trial to test the new technology.

The educational materials are disseminated to educa-tors through a four-week professional development workshop taught each summer at Rice.

Panji Chamdimba, a teacher trainer from Malawi pictured left, was one of 12 teachers and 5 high school students who participated in the workshop last June. Her passion is to educate high school teachers in her

homeland about new treatments and prevention methods for HIV/AIDS, cancer, and heart disease.

“My immediate plans are to teach what I've learned here to my student teachers as well as to science teachers who are already teaching in high schools in Malawi," Chamdimba said. "But I am also interested in seeing if we can get the University of Malawi to begin offering a degree in bioengineering with Rice's help."

To learn more, visit beyondtraditionalborders.rice.edu. ●

Page 10

Three New NSF Fellows for bioengineering

The National Science Foundation (NSF) awarded Drew McUsic (Rice B.S. ‘07), Kellie McConnell (Mercer B.S.E. ‘06), and Peter Yang (Rice B.S. ‘06) with 2007 Graduate Research Fellowships. Intended for students who are in the first- and second-year of graduate studies, NSF fellowships are substantial and provide support for three years of study.

While at Rice, McUsic (pictured right) completed independent research in Assistant Professor Michael Liebschner's Computational and Experimental Biomechanics Laboratory investi-gating the mechanically sensitive and adaptive microarchitecture of trabecular bone. Other sig-nificant awards he has received include: a Louis J. Walsh Scholarship in Engineering (2005-2006, 2006-2007); National Institutes of Health Intramural Research Training Award (2006); and Rice Univer-sity President's Honor Roll (Fall 2004, Fall 2005, and Spring 2006). Currently, McUsic is a bioengineering Ph.D. student at

the University of Washington.

This fall McConnell (pictured left) is a second-year graduate student in Assistant Professor Junghae Suh’s Nanotherapeutics Research Laboratory where she is working to pattern adeno-associated viruses (AAV) for gene delivery agents. McConnell received a Bachelor of Science in Engineering from Mercer University where she was a member of Tau Beta Pi, Phi Kappa Phi, Phi

Eta Sigma, and Gamma Sigma Epsilon honor societies; was awarded the Mercer Collegiate Fellowship Scholarship, Robert

C. Byrd Scholarship, and the Outstanding Mercer University Biomedical Engineering Graduate and Dean’s Choice Leadership awards.

NSF fellowship recipient Peter Yang (pictured below right) studied at Rice in Professor Jennifer West's group characterizing nitric oxide-releasing biomaterials to limit the effect of restenosis and de-veloping polyurethane-based biomaterials for vascu-lar grafting. His work was published in May 2007 in the Journal of Biomedical Materials Research, Part B, Applied Biomaterials in a paper tilted, “Nitric ox-ide-releasing polyurethane-PEG copolymer contain-ing the YIGSR peptide promotes endothelialization with decreased plate-

let adhesion.” Individual awards Yang received while at Rice included a Trustee Distin-guished Scholarship and Century Scholarship.

Currently, Yang is at Georgia Tech in Assistant Professor Johnna Temenoff’s group (Rice Ph.D. ‘03 and postdoctoral fellow ‘03- ‘05) where he is developing functionalized biomaterials to regenerate orthope-dic interface tissues. ●

Student Highlights

Study unveils unknown protein motifs Rice undergrad recognized for work in protein function prediction

The task of determining protein structure and function is highly complex. Proteins are made of hundreds and sometimes thou-sands of atoms strung together that take on different forms and functions, and their sheer number and random variations make experimental approaches time consuming and costly.

Drew Bryant (Rice B.S. ‘07) won the 2007 James S. Waters Creativity Award for his exceptional work in 3-D structural pattern matching for protein function prediction. His poster, Integrating Novel Protein Structure Data for Improved Func-tion Prediction Accuracy, also received 1st place honors and the 2007 Jenessa Shapiro Award at the Rice Undergraduate Research Symposium.

For the past three years, Bryant has worked in Professor Lydia Kavraki’s Physical & Biological Computing Group with Brian Y. Chen (Rice Ph.D. ‘06), Rice statistical graduate student Via-cheslav (Slava) Fofanov and his advisor Professor Marek Kimmel to develop computational techniques that compare functional information about well-studied proteins with unchar-acterized proteins of similar geometric and chemical structure.

“Drew is among the brightest and most dedicated under-graduate students I’ve ever worked with, and he has brought valuable bioengi-neering perspectives to our projects,” declares Kavraki, the Noah Harding Professor of Computer Science and Professor of Bioengineering. “He used his biological insight to suggest properties that should be incorporated in the motif design and was a key player in the development of algorithmic tools that can identify those properties in the proteins stored in the Protein Data Bank.”

To distribute the calculations and consider all proteins in the Protein Data Bank, Bryant and Chen orchestrated searches using the 600 Continued on p. 11

Student Highlights Page 11

Study unveils unknown protein motifs (Cont.)

processors of the Rice ADA cluster. Then they efficiently identi-fied matches between motifs and protein targets with high sensi-tivity and specificity. While with Kavraki’s group, Bryant also built a web server for making the protein prediction software available to the scientific community.

“We wanted to develop a rigorous computational framework that allows one to design, test, and tweak motifs quickly so that the optimal representation of the protein’s function can be found,” said Bryant. “I hope to use these statistics to understand the problem of predicting protein function more accurately.”

Bryant’s work has been part of a larger project in Professor Kavraki’s laboratory which is partially supported by an NSF

subcontract from the Baylor College of Medicine with Dr. Olivier Lichtarge serving as the principle investigator.

Initially, a pipepline called the Match Augmentation with Statistical Hypothesis Testing (MASH) was built. Once the pipeline was fully operational in 2006, it was further devel-oped and used to refine motifs provided by Dr. Lichtarge and his group. The product of this work led to the development of Geometric Sieving – a method that refines candidate motifs into optimized motifs with maximal geometric uniqueness from all known protein structures.

This year, Bryant’s accumulative work has received tremen-dous attention. He is a major contributor to two papers titled “Cavity Scaling: Automated Refinement of Cavity-Aware Mo-tifs in Protein Function and Prediction” published in August 2006 by Imperial College Press; and “The MASH Pipeline for Protein Function and Prediction and an Algorithm for the Geometric Refinement of 3-D Motifs” published by the Journal of Computational Biology.

This past summer, Bryant completed a third paper that inves-tigates different conformations of the same protein structure to define motifs while working at Genentech, Inc. in San Fran-cisco, CA. He will continue his graduate studies with Professor Kavraki. ●

This 3-D model shows an ideal motif with maximal geometric uniqueness

(highlighted in red) from functionally unrelated proteins.

This work pinpoints possible molecular targets for drug

treatment or possible side-effects with high sensitivity and specificity.

Bioengineering undergraduate student Shuai "Steve" Xu received a Barry M. Goldwater Scholarships for the 2007-2008 academic year.

Only 317 scholarships are given annually to undergraduate sophomores and juniors in the United States.

The scholarship by the Barry M. Goldwater Scholarship and Excellence in Education Foun-dation, honoring the late U.S. senator from Arizona, covers the cost of tuition, fees, books, and room and board, up to $7,500 per year.

Xu, a sophomore, is a Rice/Baylor Medical Scholar. He has guaranteed acceptance into the Baylor College of Medicine after graduating from Rice in May 2009. He plans to study clini-cal medicine at Baylor and pursue a doctorate in Bioengineering, with a focus on tissue engi-neering at Rice.

"As for a residency," Xu said, "I'm very inter-ested in cardiothoracic surgery. I hope to trans-late advances in tissue engineering research into improved treatment options for patients both as a medical scientist and a surgeon."

In the fall of 2006, Xu worked on miniaturizing collagen static-tension tissue molds. Miniaturization reduces experi-mentation costs for tissue-engineered heart valves by lowering reagent usage.

Initial results indicated that the new designs were effective replacements. Xu's faculty advisor is Jane Grande-Allen, assistant professor of bio-engineering. This past summer he was an Amgen Scholar at Columbia University, studying the bio-logical effect of biomechanical injury to tissue.

The Goldwater Scholars are selected on the basis of academic merit from a field of 1,110 mathemat-ics, science, and engineering students nominated by the faculties of colleges and universities nation-wide. In its 19 years, the Goldwater Foundation has awarded 5,202 scholarships totaling about $51 million. ●

BIOE student wins Goldwater Scholarship Steve Xu plans to study clinical medicine at Baylor

Page 12 Student News

BIOE undergrad students sweep engineering poster awards at RURS

Each year the annual Rice Undergraduate Research Symposium (RURS) features research posters, student presentations, key-note speakers, and cash prizes. RURS is open to all Rice under-graduates who are currently conducting or have conducted independent or group research.

Winners at the 6th annual engineering poster competition were selected for scientific content, quality as well as organization, appearance, and presentation of information. Bioengineering undergraduate students won the top five awards out of 48 participants from the school of engineering:

♦ 1st Place and the Jenessa Shapiro Award—Drew Bryant Poster: Integrating Novel Protein Structure Data for Improved Function Prediction Accuracy Mentor: Brian Chen Adviser: Lydia Kavraki (BIOE 400)

♦ 2nd Place—Allen Chen Poster: Nanoshell Conjugates for Targeted Lymphocyte Deletion Mentor: Felicia Tam Adviser: Naomi Halas (BIOE 400)

♦ 3rd Place—Jennifer Holm Poster: Tailoring Scaffold Morphology of PolyHIPE Tissue Engineering Scaffolds Mentor: Elizabeth Christenson Adviser: Antonios Mikos (BIOE 401)

♦ 4th Place—Dania Daye Poster: Optical Spectroscopy for the Detection of Oral Cancer Mentor: Richard Schwardz Adviser: Rebecca Richards-Kortum (BIOE 400)

♦ 5th Place—Marina Boleda Poster: Synthesis and Characterization of Injectable Thermogelling Macromers Mentor: Michael Hacker Adviser: Antonios Mikos (BIOE 401)

The department has a number of research and internship op-portunities that allow undergraduate students to sculpt their education and discovery through independent study in modern bioengineering and clinical research. In addition to gaining hands-on research experience, students co-author publications and present their research at regional and national meetings.

To learn more, visit www.bioe.rice.edu, Undergraduate Program, Research and Internship Opportunities. ●

Three students in Drezek’s lab win SPIE scholarships

SPIE (The International Society for Optical Engineering) recognized Lissett Bickford, Nastassja Lewinski, and Amneet Gulati.

Bickford is a second-year graduate student. She received the SPIE scholarship award for her research on using nanoshells and optical imaging tools to help delineate breast cancer tumor margins intraoperatively. Bickford earned an undergraduate degree in Mechanical Engineering from Texas A&M and master’s degree in Biomedical Engineering from UT at Austin.

Lewinski, also a second-year graduate student, will use the SPIE scholarship funds to investigate the use of quantum dots as an optical contrast agent for enhancing in vivo disease screening and detection.

This work compliments her undergraduate research experi-ences with Associate Professor Rebekah Drezek as it incorporates developing nanoparticles as contrast agents for diagnostic imaging and addresses public policy concerns of nanoparticle safety.

Bickford and Lewinski are also BioE Med Into Grad trainees in the Translational Bioengineering for Cancer Diagnostics and Therapeutics program at Rice and the UT M.D. Anderson Cancer Center, a program funded by the Howard Hughes Medical Institute.

Gulati, a Rice under-graduate student majoring in Chemical Physics and Biophysics, is pursuing research in dual imaging and ther-apy of cancer using gold nanoparticles. The SPIE scholarship will support her continued research in this area.

Last year, Gulati partici-pated in the Rice Undergrad Scholar’s Program (RUSP) under the mentorship of Associate Professor Drezek. She recently completed her thesis as part of RUSP, and presented her work at the SPIE Optics East confer-ence in Boston.

SPIE is the world's largest international not-for-profit society in the fields of optics, photonics, and imaging with 17,500 individ-ual members including 3,500 students. The mission of SPIE’s Scholarship and Grants Program is to recognize, assist, and encourage SPIE student members and academic organizations with outstanding potential for long-range contributions to the field of optics and photonics. ●

(Left-right) Amneet Gulati, Nastassja Lewinski, and

Lissett Bickford

Student News

International internships expand perspectives

Rice bioengineering graduate students Jim Kretlow and Jennifer Greeson are gaining new insights into research and education by working in world-class laboratories through inter-national internships in Mexico and China.

Their opportunities, which were funded by the President’s Inter-national Collaboration Travel Fund, are part of an initiative to advance Rice’s Vision for the Second Century. The program is managed by Carol Quillen, vice provost for academic affairs, and fosters new and long-term relations between the university and leading universities in Asia and Latin America.

The international internship pro-grams have been well received by bioengineering graduate students as they not only fulfill the graduate degree internship requirement, but exposes students to the leading research and academic cultures of a foreign country.

Since May 2007, Kretlow, a student in the Rice/Baylor Medical Scientist Training Program, has been working in collaboration with Professor Mikos and Dr. Yilin Cao, director of the Tissue Engineering Center at the 9th People’s Hospital in Shanghai, China. He has been investigat-ing the effect of donor animal age and cell passage on the ability of bone marrow stem cells to differentiate into fat, cartilage, and bone tissue.

Dr. Cao established the first tissue engineering center in Shanghai, which has gained an international repu-tation in the field. A major focus of the center involves the clinical application of tissue-engineered bone.

Professor Mikos and Dr. Cao and have been familiar with one another's work for some time, and both serve on the editorial board of the journal Tissue Engineering. Professor Mikos is currently editor-in-chief of the journal.

“The opportunity is showing me focus areas of the lab I’m working in,” Kretlow wrote in an e-mail. “Our lab [Mikos Re-search Group] at Rice specializes in the biomaterials aspect of tissue engineering, while the lab here specializes in the cellular aspect. Both are important, but require very different areas of expertise, so this is a pretty natural collaboration.”

Greeson, a graduate student in Assistant Professor Rob Raphael’s Membrane and Auditory Bioengineering Group, worked this past summer with Dr. Jorge Arreola at the Universidad Autonoma (UASLP), San Luis Potosi, Mexico.

Dr. Arreola, a biophysicist at UASLP’s Physics Institute and leader in the electrophysiological properties of chloride (Cl-) channels, trained Greeson in whole-cell patch-clamp

recording techniques.

While in Mexico, Greeson studied the effects of membrane-tension altering compounds on the action of volume sensitive Cl- channels. Greeson made the exciting discovery that chlorpromazine (CPZ), a lipophilic drug, specifically blocks these channels. This work opened a new line of research for Dr. Arreola’s lab that may shed light on the channel’s elusive gating mechanism.

“I feel fortunate to have had the opportunity to learn patch-clamping in Dr. Arreola's lab. Patch clamping is an essential tool for auditory research,

and his group does it very well." ●

BIOE grad student spearheads international collaborative testing effort

Mohammed Rahman is spear-heading an international collabo-rative effort to evaluate a screen-ing device for oral cancer that he helped design and submitted for patent at Rice under the supervi-sion of Professor Rebecca Richards-Kortum and Ann Gillenwater, M.D., F.A.C.S.,

associate professor and associate surgeon of the Department of Head and Neck Surgery at the UT M.D. Anderson Cancer Center.

The device, called the portable screening system (PS2), is an in-expensive, battery-operated optical instrument that utilizes prin-ciples of fluorescence imaging to differentiate between normal and pre-cancerous tissue. The PS2 uses light-emitting diodes (LED) and a miniature camera to generate and detect the auto-fluorescence signals of biomarkers present in relatively high amounts in oral cavity tissue. The PS2 can aid dentists and sur-geons in tissue biopsy as well as marginal detection of tumors.

Rahman’s nine-month research internship, which is funded by a 2007-2008 Whitaker International Fellows Grant, is part of a collaborative effort between the Rice University’s Depart-ment of Bioengineering, UT MD Anderson Cancer Center, and Tata Memorial Hospital in Mumbai, India.

“This is a very exciting opportunity in my Ph.D. pursuit. Not only did I design a biomedical instrument in the Optical Imag-ing and Spectroscopy Laboratory, but I also have the chance to test it in a real clinical setting where oral cancer is prevalent,” wrote Rahman in an e-mail from Mumbai.

Rahman, a U.S. citizen born in Bangladesh, chose to conduct the study in India because Tata Memorial Hospital is the largest cancer institution in South Asia, and India and its neighboring countries have the highest incidence rates for many acute and chronic diseases including oral cancer.

“The fellowship is ideal for my future goals to conduct research, promote technology transfer, and abridge the health disparity that exists in the region.” ●

Page 13

Page 14 Student News

Grad student recognized for service

Adrien M. Wang was presented the 2007 Sallyport Award for Community Service by the Association of Rice Alumni for his contributions and commitment to the university’s Office of International Students and Scholars (OISS).

Wang’s research in Associate Profes-sor Drezek’s laboratory focuses on the

development of novel optical spectroscopy and imaging instru-mentation for tissue diagnosis. His design of novel fiber optic probes has enhanced the "optical biopsy" of complex tissue structures layer by layer by using sensitive spectroscopic tech-niques to quantitatively assess cellular morphology and bio-chemistry. The results were published in the Journal of Bio-medical Optics (2005 and 2007). Now a postdoctoral research associate in the Drezek laboratory, Wang is working to couple fiber probe designs to nanoshells for dual cancer imaging and therapy in tissue. Wang’s research on nanoshells was published in the Journal of Nanophotonics (2007). ●

Class of 2007 Graduate Degree Recipients The Department of Bioengineering recognizes the 2007 gradu-ate degree recipients, 13 of whom obtained a doctorate degree.

Allen, Kyle Douglas, Ph.D. (May ‘07) Adviser: Dr. Kyriacos Athanasiou

Mechanical characterization, gene expression, and biosynthesis of the porcine TMJ disc for the purposes

of tissue engineering

Aufderheide, Adam, Ph.D. (May ‘07) Adviser: Dr. Kyriacos Athanasiou

Mechanical stimulation toward tissue engineering the knee meniscus

Chang, Emmanuel Yih-Herng, Ph.D. (Jan ‘07) Adviser: Dr. Rebekah A. Drezek

Biological Applications of Novel Fluorescent Nanoprobes

Gupta, Vishal, Ph.D. (May ‘07) Adviser: Dr. K. Jane Grande-Allen

Mechanical Modulation of Glycosaminoglycan and Proteoglycan Production by Vavular Interstitial Cells

Haesslein, Andrea, Ph.D. (May ‘07) Adviser: Dr. Antonios G. Mikos

Development of ocular drug delivery systems using biodegradable polymers

Lau, Ying Ka, Ph.D. (Jan ‘07) Adviser: Dr. Jennifer L. West

A Gene Therapy Approach for Tissue Engineering Applications

Lowery, Amanda, Ph.D. (May ‘07) Adviser: Dr. Jennifer L. West

Nanoshell-Assisted Cancer Therapy: Targeted Photothermal Tumor Ablation

McCurdy, Matthew, Ph.D. (May ‘07) Adviser: Dr. Frank K. Tittel

Exhaled Breath Analysis using Laser Absorption Spectroscopy

Mistry, Amit, Ph.D. (May ‘07) Adviser: Dr. Antonios G. Mikos

Development of ocular drug delivery systems using biodegradable polymers

Park, Hansoo, Ph.D. (May ‘07) Adviser: Dr. Antonios G. Mikos

Injectable Cell Hydrogel Composites for Articular Cartilage Tissue Engineering

Reddy, Gaddum, Ph.D. (May ‘07) Adviser: Dr. Peter Saggau, Baylor College of Medicine

A Multi-Photon Microscope for Three Dimensional Functional Recording of Fast Neuronal Activity

Templeton, Alistair Kiel, Ph.D. (Jan ‘07) Adviser: Dr. Michael Liebschner

Three-Dimensional Biomechanical Modeling of Vertebrae from Radiographs

Wang, Adrien, Ph.D. (May ‘07) Adviser: Dr. Rebekah A. Drezek

Spatially-Resolved Reflectance Spectroscopy with Variable Fiber Geometry

Bowden, Gregory, M.B.E. (May ‘07)

Moore, Sheila, M.S. (May ’07)

Zimmerman, Matthew, M.B.E. (May ‘07)

Grad student wins NAVBO award

Ph.D. student James J. Moon was chosen for the 2007 Outstanding Young Investigator Award at the North Ameri-can Vascular Biology Organization’s (NAVBO) annual meeting.

As a graduate research assistant in Professor West’s laboratory, Moon recently developed 3-D models to exam-ine angiogenesis in synthetic scaffold materials. He also used a co-culture model in this 3-D system to enhance angiogenesis.

A 2002 graduate from the Department of Bioengineering at the University of California-Berkeley, other awards Moon has re-cently received include a 2006 Annual Graduate Student Award in Science and Engineering from the Rice/Texas Medical Center Chapter of Sigma Xi. ●

Alumni News Page 15

Tracking BIOE alumni W T. Godbey (Rice Ph.D. '00), the Paul H. Flower Assistant Professor in Engineering at Tulane and a former graduate student of Professor Antonios Mikos, has successfully rebuilt his laboratory at Tulane's Department of Chemical and Biomolecular Engineering after hurricane Katrina struck in 2005.

Godbey and his graduate student Xiujuan Zhang evacuated New Orleans, and for four months conducted research at Rice thanks to the efforts of Professors Mikos, Richards-Kortum, and Bennett (of Biochemistry and Cell Biology).

After two years of steadfast work, Godbey writes, “Tulane is an exciting place to be...we're rebuilding the personnel roster in the Laboratory for Gene Therapy and Cellular Engineering and are once again generating some interesting data. We have projects in cancer gene therapy and circadian rhythms that should generate several papers over the coming months. Because of the kindness of Rice University, the effects of the storm's aftermath upon our laboratory were held to a minimum.” ●

Since 1996, more then 70 students have completed the bioengi-neering graduate program, and over half have tenure and tenure track positions in academia. The following alumni and postdoc-toral fellows have recently received academic appointments:

Alejandro Almarza (Ph.D. ‘05) from Professor Athanasiou’s laboratory was appointed a research assistant professor in the Musculoskeletal Research Center at the University of Pittsburgh. He is also director of the Mechanobiology Laboratory and over-sees the Intramural Internship Undergraduate Program for the bioengineering department.

Andrea S. Gobin (Ph.D. ‘03) from Professor West’s group is an assistant professor in bioengineering at the University of Louis-ville.

André M. Gobin (Ph.D. ‘07) worked as a lab manager with Professor West’s Group prior to beginning Rice’s Ph.D. program. André will be starting as an assistant professor at the University of Louisville’s Department of Bioengineering this fall.

Manuela E. Gomes (Ph.D. ‘04) from Professor Mikos’ group was appointed assistant professor at the MIT-Portugal Program in Bioengineering Systems ("Bio-MIT") at the University of Minho, Portugal.

Balaji Sitharaman (Ph.D. ‘05 and Postdoc ‘05 - ‘07) from Pro-fessor Mikos' group has accepted an assistant professor position with the Department of Biomedical Engineering at the State University of New York (SUNY) at Stony Brook.

Lakeshia Taite (Ph.D. ‘06) from Professor West’s group fin-ished a postdoctoral fellowship at the University of Washington and has accepted a faculty position as assistant professor in the School of Chemical & Biomolecular Engineering at Georgia Tech.

BIOE alumni class notes Nicole M. Bergmann, (Postdoc ‘05-‘07) from Professor West’s group was recently appointed assistant professor in Biomedical Engineering at St. Louis University.

Malavosklish “Liz” Bikram (Postdoc ‘04-‘06) from Profes-sor West’s group accepted a position as assistant professor of pharmaceutics at the University of Houston.

Elizabeth M. (Christenson) Cosgriff-Hernandez (Postdoc ‘05- ‘07) from Professor Mikos’ group is now an as-sistant professor in the Biomedical Engineering Department at Texas A&M.

Theoni K. Georgiou (Postdoc ‘06- ‘07) of Professor Mikos’ group accepted a RCUK (Research Councils UK) Academic Fellow, or assistant professor, position in the Department of Chemistry at The University of Hull, in Hull, England.

Michael Hacker (Postdoc ‘04-‘07) from Professor Mikos’ group is an assistant professor position with the Department of Pharmaceutical Technology at the University of Leipzig, Leipzig, Germany.

Mariah Hahn, (Postdoc ‘04- ‘05) from Professor West’s group is now an assistant professor in the Chemical Engineer-ing Department at Texas A&M.

Rajesh K. Uthamanthil ( ‘04-‘06) from Professor Athana-siou’s group is an assistant professor of veterinary medicine and surgery at the UT M.D. Anderson Cancer Center and an adjunct faculty member of the Rice Department of Bioengi-neering.

Mingqiang Zhu (Rice Postdoc ‘05-‘07) from Associate Pro-fessor Drezek’s group accepted a position as professor of bio-medical engineering at Funan University, Funan, China.

Rice Engineering Alumni Association recognizes BIOE undergrads

Each year, senior and junior engineering students independently compete for merit awards offered by the Engineering Alumni Association (REA). The following bioengineering undergraduates received 2007 REA awards:

♦ Stephen Wallace, Merit Scholarship ♦ Diana Daye, Outstanding Senior ♦ Austin Ginnings, Distinguished Senior

♦ Martin Bost, Merit Scholarship ♦ Brian Schwab, Bob Dickson Award

Photo by Jenny Marc, Tulane

Events Page 16

Researchers in this field are using a variety of mathematical approaches to understand

and manipulate nature.

The course will present various theoretical methods of statistical mechanics that are being

developed and applied to study the collective properties of biological systems.

More details to come at http://ctbs.rice.edu

Presented by:

The Rice University Department of Bioengineering Keck Center for Structural and Computational Biology

The University of Houston Institute for Molecular Design

Negotiating the Ideal Faculty Position

October 14 - 16, 2007 Rice University

Hosted jointly by the Rice University...

George R. Brown School of Engineering Wiess School of Natural Sciences

This workshop provides a unique opportunity for

prospective women faculty to learn how to negotiate the ideal faculty position from academic leaders across

all science and engineering disciplines.

Resource materials from the October 2006 workshop are available at http://www.advance.rice.edu/

negotiatingtheidealfacultyposition/resources.html; materials from 2007 will be posted by November 30.

Applications for the 2008 workshop may be submitted in early June 2008. To learn more or apply for the 2008 workshop,

visit: http://www.advance.rice.edu/

10th Anniversary Fall Lecture Series

Department of Bioengineering Details: visit www.bioe.rice.edu

September 6, 2007 Kimberly Hamad-Schifferli, Ph.D.

Esther and Harold E. Assistant Professor Mechanical Engineering and Biological Engineering

Massachusetts Institute of Technology (MIT)

September 11, 2007 Joel M. Schnur, Ph.D.

Director, Center for Bio/Molecular Science and Engineering Naval Research Laboratory

October 4, 2007 Jerry Pollack, Ph.D.

Professor, Molecular Bioengineering and Nanotechnology University of Washington

October 11, 2007 Jay Keasling, Ph.D.

Professor, Chemical Engineering and Bioengineering University of California, Berkeley

October 18, 2007 Thomas N. Wight, Ph.D.

Professor, Pathology Benaroya Research Institute

University of Washington

October 24, 2007—J. David Hellums Lecture Steven Quake, Ph.D.

Professor, Bioengineering Stanford University

October 25, 2007 Andre Levchenko, Ph.D.

Assistant Professor, Biomedical Engineering Johns Hopkins University

November 15, 2007 Daniel A. Hammer, Ph.D.

Professor and Chair, Bioengineering and Chemical Engineering University of Pennsylvania

November 27, 2007 Alice Y. Ting, Ph.D.

Associate Professor, Chemistry Massachusetts Institute of Technology (MIT)

November 29, 2007 Luke P. Lee, Ph.D. Professor, Bioengineering

University of California, Berkeley

December 6, 2007 William L. Murphy, Ph.D.

Assistant Professor, Biomedical Engineering University of Wisconsin - Madison