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No. 1 From the Start

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Ph.D. student Jessica Ungerleider looks at one of her experiments in the lab of bioengineering professor Karen Christman at the Sanford Consortium.

UC San Diego Bioengineering ranked first by National Research Council since founding 50 years ago
San Diego, Calif., May 26, 2016 -- Bioengineers at the University of California San Diego have helped us understand why atherosclerosis develops and how it is impacted by blood flow. They have pioneered the development of very thin, small and flexible sensors that stick to the skin and monitor vital signs, such as the brain activity of a newborn. They also developed injectable hydrogels that can help muscle tissues heal after a heart attack.

Researchers celebrated their achievements over the past five decades and looked to the future during a three-day 50th anniversary celebration May 19 to 21.

“This department was created in the same spirit as our campus, as an innovative, collaborative and experimental place,” said Chancellor Pradeep K. Khosla during an anniversary gala at the Birch Aquarium. “We are proud that UC San Diego's Bioengineering Department has been a leader in the field since its founding, advancing our mission of education, research and service.”

 The bioengineering program at UC San Diego, which became a department in 1994, has maintained high national rankings throughout the years. Its graduate program has been consistently ranked number one in the nation by the National Research Council. It serves as a model for many of the more than 130 existing programs in bioengineering and biomedical engineering worldwide, said Chair Geert Schmid-Schonbein. Its anniversary was recognized with a proclamation both from the County of San Diego and the City, marking May 21 as Bioengineering Day.

“As we celebrate our 50th anniversary, we need to ask ourselves what we want to do better and what we can do differently,” Schmid-Schonbein said.

That is setting the bar high. The department is the coordinating entity for all bioengineering efforts within the University of California. Two faculty have received the National Medal of Science—program founder YC Bert Fung, a legend in the field, and department founding chair Shu Chien. 

A short history

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Professor Shu Chien helps students use sensors to measure muscle tension under different loads during a new hands-on pilot course for undergraduates in bioengineering.

Fung, then a professor at Caltech, with Marcos Intaglietta, also of Caltech, and Benjamin Zweifach, from New York University brought bioengineering to UC San Diego in 1966. Fung is now retired. He was a pioneer in analyzing the mechanical properties of tissues, including the lungs, blood vessels, heart, brain—and more. Intaglietta is still on faculty and pioneered the search for blood substitutes that may eventually replace human blood in transfusions. Zweifach passed away in 1997 after an illustrious career.

Since then, the program has graduated more than 6,000 students. “We’re constantly feeding new talent to industry, locally and nationally,” Chien said. “We teach a new generation of engineering students to work with living tissues, work in teams and apply innovative thinking, to serve them well in industry and academia.”

As it grew, the program strengthened its ties to industry. In its early years, most PhDs went on to join academia. Today, half go to work in industry. That percentage is even higher for undergraduates.

Three years ago, the department helped pioneer a design track that allows freshmen to take hands-on classes. All departments at the Jacobs School of Engineering have since adopted the approach. “Designing, building and testing are at the core of engineering,” Chien said.

Alumni entrepreneurs and leaders

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Cognionics, founded by bioengineering alumnus Mike Yu Chi, has developed a wearable EEG headset that's comparable to state of the art laboratory equipment.

Some of the department’s graduates have become entrepreneurs and are leading their own companies. Christophe Schilling is the CEO of Genomatica, a company that produces chemicals in a greener, more sustainable way. The company’s proprietary technology was licensed to chemical giant BASF and bioplastics leader Novamont. Iman Famili, one of Genomatica’s employees and an alumna, went on to co-found two more start-ups.

Other alumni have become leaders in their field. Ann Lee-Karlon is a vice president at biotech giant Genetech. Makoto Suematsu was appointed in 2015 by the Prime Minister of Japan as the founding director of the Japanese equivalent of the NIH. Dr. Brian Clary, who earned his bachelor’s in bioengineering here, is now surgeon in chief for the UC San Diego School of Medicine. Tom Skalak leads the science and technology programs at the Paul G. Allen Family Foundation, after serving as vice president at the University of Virginia.  

A leader in research

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Undergraduate researcher Gladys Ornelas fabricates sensors in the Nano 3 clean room  at Atkinson Hall for Professor Todd Coleman.

The department’s faculty are leaders in their research fields as well. They focus on analysis and design, said Schmid-Schonbein. That is, they analyze medical and biological problems and design a solution—just like a traditional structural engineer analyzes why a bridge collapsed—and then designs a solution---a stronger, better bridge.

A team of young rising stars that works at the cutting edge of bioengineering has been hired in recent years. Stephanie Fraley studies the physical and molecular mechanisms that drive complex cell behaviors in cancer and sepsis. Prashant Mali is an expert in the CRISPR/Cas9 gene editing technique that holds great promise for a wide range of therapies. Christian Metallo studies metabolism and its impact on disease such as obesity. Peter Yingxiao Wang is working with physicians at the School of Medicine to develop molecular biosensors and machineries to help treat multiple myeloma, a blood cancer.

Frontiers of bioengineering

In coming years, researchers envision a future where bioengineers bring together the very small and the very large into one comprehensive model of the human body. They will bring together molecules, cells, tissues and organs, he said. “We need to treat the whole person as an integrated system,” Chien said.

Bioengineers also probe the origins of aging and diseases that still challenge researchers, said Schmid Schonbein. “We look at the technologies used to support prevention, diagnosis and treatment,” Chien said. “We’re bringing everything together to improve people’s health and wellbeing.”

Research accomplishments

The department’s 24 faculty, junior and senior, boast a number of achievements in a wide range of fields, gravitating around genomics, regenerative medicine, diagnostic tools and treatment and prevention. Research landmarks include:

The Omics field

  • Bernhard Palsson, named one of the world’s most influential scientific minds by Thomson Reuters in 2016, studies cellular life by developing experimental and computational models for red blood cells, E. coli and several human pathogens. Last year, Palsson and his team defined the core set of genes and functions that bacterial cells need to sustain life.
  • Kun Zhang developed new techniques to reduce the cost and improve the accuracy of gene sequencing. Probing the genetic make-up of individual cells would help researchers identify and understand a wide range of organisms that cannot be easily grown in the lab from the bacteria that live within our digestive tracts and on our skin, to the microscopic organisms that live in ocean water.
     
  • Trey Ideker seeks to comprehensively map connections between the many genes and proteins in a cell and how these connections trigger or prevent disease. His current work focuses on DNA mutations that cause cancer.
     
  • Shankar Subramaniam is a pioneer in the field of large scale mathematical analysis to determine the metabolic functions of cells based on their genome. Last year, he and his team were able to explain why the flu vaccine is less effective in elderly people.
     
  • Sheng Zhong is the principal investigator on a $30 million, five-year grant from the National Institutes of Health to better understand how DNA is arranged within the cell’s nucleus in four dimensions (three-dimensional space, plus time).
     
  • Xiaohua Huang was a pioneer in the effort to understand the function of the smallest blood vessels, or capillaries, and their role in hypertension, diabetes and shock. He is regarded as a key player in the arenas of genomics, bioinformatics and nanotechnology-based molecular devices.
     

Diagnostic tools
 

  • Todd Coleman’s research brings together electronics for medical use, machine learning and public health. His team develops multi-functional, flexible bio-electronics and new analytic methods to help patients and medical decision makers.
     
  • Elliot McVeigh, the former chair of the Department of Biomedical Engineering at Johns Hopkins University who joined UC San Diego in 2015, aims to create a completely new imaging paradigm for cardiac care by developing imaging techniques that give patients and their doctors all the information they need to avoid heart attacks.
     
  • Andrew D. McCulloch pioneered the development of personalized computer models of the heart that serve to predict the outcome of treatments, which allows physicians to avoid ineffective therapies.  
     
  • Gert Cauwenbergs developed sensor systems that do not need to be in contact with the body to measure the electrical activity of the heart, brain, muscle and other tissues. Recently, he and colleagues built the first portable, 64-channel wearable brain activity monitoring system that’s comparable to state-of-the-art equipment found in research laboratories.
     
  • Michael Heller developed techniques to detect and measure fragmented DNA in blood to diagnose cancer extremely early on, a method known as “liquid biopsy.” Recently, he and his team developed a new technology that uses an oscillating electric field to easily and quickly isolate drug-delivery nanoparticles from blood. The technology could serve as a general tool to separate and recover nanoparticles from other complex fluids for medical, environmental, and industrial applications.
     

Therapy, treatment and prevention

  • Karen Christman has developed a new injectable hydrogel that can repair damage from heart attacks, help the heart grow new tissue and blood vessels, and get the heart functioning closer to a healthy heart. The gels are in clinical trials.
     
  • David Gough developed a long-term implantable blood glucose sensor that can provide information for better metabolic control in diabetics. The device is currently in clinical trials.
     
  • Robert Sah arrived at a basic understanding of diseased orthopedic joints that provides a basis for tissue engineering repair strategies. Sah's goal is to pave the way for successful tissue-engineered total joint replacement for people who suffer cartilage damage due to injury or aging.
     
  • John Watson helped in the development of the cardiac assist device that serves to save the life of desperately ill heart patients. His current mission is to find ways to reduce how long it takes medical technology to move from concept into the clinic.
     
  • Gabriel Silva pioneered research to restore retinal function restoration in eye disease. He studies the neurobiology of neural signaling at the cellular and cellular network scales to learn more about the mechanisms that underlie neural computation and information processing in the brain.  
     
  • Jeff Hasty designs and constructs gene circuits for use in living cells that can then be applied to cancer therapy. They use tools from physics and engineering to study the circuits, including microfluidic devices that they design themselves to constrain a bacterial population.
     
  • Schimd-Schonbein discovered a mechanism by which many cell functions fail in metabolic diseases due to breakdown of receptors on the cell’s membrane. He also discovered a mechanism by which the body can destroy itself via its own digestive enzymes (“autodigestion”) and a method to minimize this process in very ill individuals.
     
  • Pedro Cabrales studies how oxygen and other gases become available in the body, their biological function and how their levels are regulated. Recently, he was part of a team of bioengineers and physicians who showed that waiting 30 seconds between bites prevented excessive weight gain in children.
     

Regenerative medicine

  • Chien developed a basic understanding of why atherosclerosis occurs in arteries and how it is influenced by blood flow. He is also collaborating on multiple projects in regenerative medicine to develop a process to identify the best environments in which to grow stem cells.
     
  • Adam Engler developed a basic understanding about what stem cells require to differentiate into specific cell types for therapy. Recently, this team provided new insights on how hearts “stay young” and keep functioning over a lifetime despite the fact that most organisms generate few new heart cells.
     
  • Shyni Varghese is a pioneer in the field of bio-inspired materials, stem cells and regenerative medicine. Her work focuses on the interface of biomaterials and stem cells. Her research involves the development and application of biomaterials and engineering tools to understand the impact of interactions in the cell-microenvironment on stem cell differentiation and disease progression.

 

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Ioana Patringenaru
Jacobs School of Engineering
Phone: 858-822-0899
ipatrin@ucsd.edu

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