Computer engineer Densmore and team aim to advance synthetic biology
By Michael G Seele
The rapidly growing field of synthetic biology has made long strides in recent years as researchers have modified the genetic makeup of living organisms to get them to behave in different ways — flagging the presence of toxins in the environment, for example. Researchers have done this by breaking down biology into basic building blocks. However, using these building blocks has been increasingly difficult without a clear design methodology and supporting quantitative metrics researchers could use to make decisions.
Associate Professor Douglas Densmore (ECE, BME) would like to take the guess work out of biological design and speed the development of synthetic biology in the process. Working under a new $10 million National Science Foundation “Expeditions in Computing” grant, Densmore will lead the Living Computing Project, a comprehensive effort to quantify synthetic biology, using a computing engineering approach to create a toolbox of carefully measured and catalogued biological parts that can be used to engineer organisms with predictable results. These parts will allow the entire field to understand better what computing principles can be applied repeatedly and reliably to synthetic biology.
Densmore and assistant professors Ahmad Khalil (BME) and Wilson Wong (BME), and Research Assistant Professor Swapnil Bhatia (ECE) will take the lead on the project, partnering with colleagues at MIT and Lincoln Laboratory over the course of the five-year grant. The award marks the first time explicitly exploring computing principles in multiple living organisms and openly archiving the results has been funded.
“This puts a stake in the ground to make synthetic biology more rigorous,” Densmore said. “We want to build a foundation that’s well understood, built to use software tools, and that can serve as an open-source starting place for many advanced applications.”
Synthetic biologists take snippets of DNA and combine them in novel ways to produce defined behavioral characteristics in organisms. For instance, Densmore envisions a day when one might engineer a cell to change state when it detects cancer. The cell could be introduced into a patient, retrieved after a time and read like the memory of a computer, enabling detection of disease much earlier and less invasively than is now possible. Engineering that cell could be far easier and faster if researchers had a detailed inventory of parts and corresponding software tools they could use to create it.
Densmore is a core member of — and the only computer engineer in — BU’s new Biological Design Center. He has long been applying the kinds of tools used in computer engineering to synthetic biology. His software aims to identify and characterize biological parts — segments of DNA — and assemble them into complex biological systems. The NSF Expeditions in Computing grant will allow for expansion of that effort, but there are significant challenges in applying computer engineering principles to natural systems.
“What is power consumption in biology?” Densmore cites as an example. “What are the metrics in biology that make sense, can be repeated, and are reliable? You can’t make decisions in engineering without metrics and quantifiable information.”
“Programming a flower to change color, a cell to repair damaged tissue, or a mosquito to defeat malaria, is likely to require a different computational model than programming an app for your laptop,” said Bhatia. “Discovering this new type of computational thinking in partnership with synthetic biologists is what I am most excited about.”
Densmore hopes this project will take synthetic biology from an artisanal endeavor to a true engineering discipline with a solid, quantified foundation.
“Computation is important for moving any field forward and that’s what we’re trying to do with synthetic biology,” Densmore said. “We’re trying to build a library based on computing principles for the whole community, an open-source repository of biological pieces that use those principles reliably, repeatedly, and with broad applicability.”
“The Expeditions in Computing program enables the computing research community to pursue complex problems by supporting large project teams over a longer period of time,” said Jim Kurose, NSF’s head for Computer and Information Science and Engineering. “This allows these researchers to pursue bold, ambitious research that moves the needle for not only computer science disciplines, but often many other disciplines as well.”
126 Researchers Convene on Campus
By Michael G Seele
One hundred and twenty six materials researchers from as near as Boston and as far away as California and Iran convened in the Photonics Center on September 25 for the BU Materials Day symposium, “Nanomaterials in Medicine: Improving Healthcare Through Small Innovations.”
The day-long event featured an array of speakers who addressed the promise and use of nanomaterials in drug delivery, biomedical imaging, and fighting cancer and infectious diseases.
Dean Kenneth Lutchen welcomed the symposium participants and noted the wide-ranging, interdisciplinary strength of the College of Engineering’s Materials Science & Engineering Division. Materials research, he said, will play an important role in advancing society, particularly in healthcare.
“The current challenges facing health care call for biomaterials solutions,” he said. “It is an inherently complex, multi-scale problem you are trying to address.”
Two College of Engineering faculty affiliated with MSE — Professor Mark Grinstaff (Chemistry, BME) and Assistant Professor Allison Dennis (BME) — made presentations at the symposium.
Grinstaff’s presentation focused on his lab’s work in using drug-infused nanoparticles to treat mesothelioma, a highly fatal cancer associated with asbestos exposure. Mesothelioma progresses locally, Grinstaff noted, and current chemotherapy treatments — which infuse toxic drugs throughout the body for a relatively brief period — have not been effective.
Grinstaff’s approach has been to develop nanoparticles on the order of 100 nanometers that are infused with the chemotherapy drug paclitaxel. The particles are small enough to be admitted into a cancer cell, where the more acidic environment causes the nanoparticles to expand to 1,000 nanometers and begin releasing the drug. The cells are not able to quickly expel the nanoparticles, which can release paxlitaxel into the cell — and only the cell — for up to two weeks.
The research has produced excellent results in vivo, Grinstaff noted, and he hopes that this approach may also benefit patients suffering from breast, lung and ovarian cancers.
Dennis’ presentation focused on her work with quantum dots, which she described as semi-conductor nanocrystals with optical properties. Quantum dots have many applications in solid-state lighting and consumer electronics, as well as biomedical imaging.
She described how her lab has been working to manipulate the dots to change the color of light they emit. Dots emitting multiple colors can be used to more effectively conduct tissue-depth imaging, she said. Some of the dots are exceptionally bright, making their detection easier.
More recently, she said, she has been working with the chemistry of quantum dots in order to find an alternative to the toxic element cadmium so the dots can be used more readily in biomedical applications.
Other speakers and their topics at the symposium included:
- Vladimir Torchilin, distinguished professor of pharmaceutical sciences at Northeastern University, “Stimuli-sensitive Combination Nanopreparations of siRNA and Chemotherapeutic Drugs to Treat Multidrug Resistant Cancer.”
- Alnylam Pharmaceuticals Senior Vice President of Drug Discovery Muthiah Manoharan, “Making Drugs Out of siRNAs.”
- University of California, Los Angeles professor of chemistry and biochemistry Heather Maynard, “Bio-inspired and Degradable Nanomaterials for Delivery of Proteins.”
- University of Washington bioengineering Professor Patrick Stayton, “Intracellular Delivery of Biologic Drugs Diagnostics.”
- Niren Murthy, professor of bioengineering at the University of California Berkeley, “New Strategies for Imaging Infectious Diseases and Oxidative Stress.”
- Anna Moore, professor of radiology at Massachusetts General Hospital and Harvard Medical School, “Image-guided RNA-based Cancer Therapies.”
- University of Pennsylvania Associate Professor of bioengineering Andrew Tsourkas, “Engineering Targeted Nanoparticles for Molecular Imaging and Therapeutic Applications.”
Assoc. Prof. Tyrone Porter (ME, MSE) organized the symposium and moderated the discussions that followed each presentation.
“Nanomaterials in medicine is such a timely subject as we have seen unprecedented activity in the design and production of biologically and medically relevant materials on the nanoscale,” Porter said. “The symposium featured leaders in the field who are pushing the boundaries to generate novel constructs and platforms that ultimately will revolutionize how we image, diagnose, detect, and treat disease.”
US News and World Report released its college and undergraduate rankings today. Compared to last year’s rank of #14, Boston University Biomedical Engineering has moved up to #12. Among programs also accredited by ABET, BU BME is ranked #9, matching this year’s grad-program rankings.
“These rankings reflect the quality of our students and programs, and the esteem with which we are held by our peers.”
-John A. White, Ph.D.
Professor and Chair
BU Biomedical Engineering
BME Professor Muhammad Zaman featured in new NPR article, “One Man’s Quest To Combat Counterfeit Drugs — With A Suitcase”.
Research Could Bolster Nanoscale 3D Printing, Catalysis and Sensor Design
By Mark Dwortzan
A study led by Assistant Professor Scott Bunch(ME, MSE) has demonstrated the ability to measure and control the transport of gas through a single molecule-sized pore in graphene, a strong, flexible material made of one-atom-thick sheets of carbon atoms. By using gold nanoparticles to block and unblock such pores in a graphene membrane, Bunch and his research team have provided the first evidence of controlling the transport of gas through a molecule-sized opening in any existing membrane material.
“These nanopore molecular valves provide the unique ability to control a single-file flow of molecules, and may lead to important applications in nanoscale 3D printing, catalysis and sensor design,” said Bunch.
Nanoscale 3D printing could be used to manufacture high-precision devices ranging from micro-needles to nano-robots. New applications in catalysis, the acceleration of chemical reactions, could yield new chemical compounds for scientific and commercial applications. The research may also improve the performance of graphene-based separation membranes, which can be used to purify gas, capture carbon from power plant carbon dioxide emissions, and perform other applications.
Bunch and collaborators at Boston University, MIT, University of Colorado and National University of Singapore used two methods to create the nanopores in the graphene membranes. They either applied a voltage pulse with an atomic force microscope, or exposed the graphene to ultraviolet light. They also used an atomic force microscope to monitor the flow of hydrogen, nitrogen and other gases.
The research, which was funded by the National Science Foundation, is described in the online edition ofNature Nanotechnology.
Master’s students can now specialize in these fast-growing fields
By Janet A. Smith (ENG) and Amy Laskowski (BU Today)
In an effort to train its graduate students in rapidly expanding fields, this fall the College of Engineering will begin offering three new master’s degree specializations in the fields of data analytics, cybersecurity, and robotics.
“The corporate sector has voiced frustration with the shortage of trained engineers in key sectors of the innovation economy,” says Kenneth Lutchen, dean of ENG. “By combining a master’s degree in a foundational engineering discipline with a specialization in a fast-growing, interdisciplinary field, students will be well positioned to meet this need and impact society. This unique combination should greatly enhance the power of their degrees in the marketplace.”
The specialization programs are open to all master’s degree candidates in ENG. Students who opt to add a specialization will select at least four of their eight required courses from a list specific to that field. Specializations will be noted with the degree title on students’ final transcripts.
Classes for the fall 2015 semester begin September 2, and master’s degree students who are interested in focusing on one of the three fields should contact the Graduate Programs Office for more information.
Two years ago, the Harvard Business Review noted that jobs in the field of data analytics are expected to continue to increase. Glassdoor.com reports that the average data scientist salary is currently $118,700. ENG’s new data analytics specialization will emphasize decisions, algorithms, and analytics grounded in engineering application areas. Students choosing to specialize in data analytics can expect to find jobs in finance, health care, urban systems, commerce, pharmaceuticals, and other engineering fields.
Recent, brazen cyber attacks on companies such as Target and Sony Pictures as well as the data breach thought to originate in China that compromised the records of 21.5 million Americans who had applied for government security clearances over the past 15 years highlight the growing importance of cybersecurity.
ENG’s cybersecurity specialization will teach students security-oriented theory and train them in practical cybersecurity applications including software engineering, embedded systems, and networking. It will also provide a context for cybersecurity threats and mitigation strategies ranging from protecting corporate and government systems, to home and building automation accessories and medical devices.
Global spending on robotics is predicted to increase to $67 billion by 2025 from just $15 billion in 2010. Today, robotics are used in everything from prosthetics and telemedicine to autonomous vehicles, feedback control systems, and brain-machine interface. The new ENG specialization will prepare master’s students for careers in research and development and deployment and operation of advanced individual or multi-coordinated robotic systems.
Tom Little, an ENG professor of electrical and computer engineering and systems engineering and associate dean of educational initiatives, says these new specializations are meant to be complementary to the numerous existing master’s degree programs. Come fall, someone getting a master’s degree in mechanical engineering, for instance, could specialize in cybersecurity, and learn how to prevent a car’s computer system from being hacked.
“These are all very exciting areas that are emerging,” Little says. “ENG is active in doing research, but also active in developing the next generation of scientists and engineers who can contribute to companies who want to build applications that have an impact.”
BU to Host Symposium: BU MATERIALS DAY 2015 – Nanomaterials in Medicine: Improving Healthcare Through SMALL Innovations
Boston University, the Division of Materials Science & Engineering and the Center for Nanoscience and Nanobiotechnology will be hosting BU MATERIALS DAY 2015: Nanomaterials in Medicine: Improving Healthcare Through SMALL Innovations on September 25, 2015 in the Photonics Center.
All are welcome to attend! Registration is required.
Registration deadline is September 14, 2015.
There will be a poster session, but space for posters is limited, so please register early.
The impact of nanomaterials on the practice of medicine far exceeds its dimensions. Nanomaterials have unique physicochemical, electromagnetic, and pharmacological properties that enable innovative strategies for diagnosing and treating disease. Targeted imaging probes engineered with nanomaterials allows clinicians and scientists to detect anatomical and pathological abnormalities indicative of disease with biomedical imaging systems. Nanomaterials have also been co-opted for chemical modification or packaging of therapeutic agents, augmenting their bio-distribution, increasing their specificity, and enhancing their efficacy while minimizing off-target adverse effect. In this symposium, leading scientists will present on medical breakthroughs that have been made possible through novel formulations and constructs of nanomaterials.
Program and Abstracts
Vladimir Torchilin, Ph.D.
Distinguished Professor, Pharmaceutical Sciences
Director, Center for Pharmaceutical Biotechnology and Nanomedicine
Stimuli-sensitive combination nanopreparations of siRNA and chemotherapeutic drugs to treat multidrug resistant cancer
Heather Maynard, Ph.D.
University of California, Los Angeles
Professor, Chemistry and Biochemistry
Director of the Chemistry Biology Interface Training Program
Associate Director of Technology and Development for the California NanoSystems Institute
Bio-inspired and degradable nanomaterials for delivery of proteins
Mark Grinstaff, Ph.D.
Professor, Chemistry, Biomedical Engineering, and Materials Science & Engineering
Director, Center for Nanoscience and Nanotechnology
Title of talk: TBA
Patrick Stayton, Ph.D.
University of Washington
Washington Research Foundation Professor, Bioengineering
Director, Institute for Molecular Engineering and Sciences
Director, Center for Intracellular Delivery of Biologics
Intracellular Delivery of Biologic Drugs
Anna Moore, Ph.D.
Massachusetts General Hospital/Harvard Medical School
Director, Molecular Imaging Laboratory at the
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging,
Image-guided RNA-based cancer therapies
Niren Murthy, Ph.D.
University of California, Berkeley
New strategies for imaging infectious diseases and oxidative stress
Andrew Tsourkas, Ph.D.
University of Pennsylvania
Associate Professor, Bioengineering
Associate Director, Program in Targeted Therapeutics, Institute of Translational Medicine and Therapeutics
Engineering targeted nanoparticles for molecular imaging and therapeutic applications
Allison Dennis, Ph.D.
Assistant Professor, Biomedical Engineering and Materials Science & Engineering
Engineering Thick-shelled Quantum Dot Heterostructures for Biosensing and Bioimaging
Associate Professor ME, MSE
By Mark Dwortzan
Professor Elise Morgan (ME, BME, MSE) was selected as a recipient of INSIGHT Into Diversitymagazine’s 100 Inspiring Women in STEM Award. INSIGHT Into Diversity is the oldest and largest diversity magazine and website in higher education.
This award recognizes 100 women whose work and achievements as researchers, teachers and mentors encourages women currently engaged in science, technology, engineering and math fields, and inspires a new generation of young women to consider STEM careers. Boston University recipients Morgan and Cynthia Brossman, director of the Learning Resource Network, will be profiled in the magazine’s September issue along with 98 other Women in Stem honorees.
“I’m extremely honored to receive this recognition, particularly alongside people like Cynthia who exemplify tireless commitment to lighting a spark in the next generation of women in STEM,” said Morgan. “I always hope that I am making an impact through the research that my group does and by connecting with young people. It’s absolutely critical to help everyone around us understand the importance of STEM for society.”
Since joining the College of Engineering faculty in 2003, Morgan has worked to advance understanding of the role of the mechanical function of tissues and organs in skeletal health, repair and development, with the ultimate goal of pinpointing causes and treatments for osteoporosis, osteoarthritis and poor bone healing.
As director of the Orthopaedic and Developmental Biomechanics Laboratory, Morgan studies the interplay among the mechanical behavior, structure and biological function of tissues. Drawing on methods from engineering mechanics, materials science, and cell and molecular biology, and combining experimentation and computational modeling, Morgan’s lab investigates how mechanical factors contribute to the development, adaptation, failure and regeneration of bone and cartilage. Current projects include the use of mechanical stimulation to promote bone regeneration, the biomechanics of spine fractures and bone healing, non-invasive diagnostics of bone healing, and inflammatory bone loss. This work has been funded by the National Institutes of Health, the National Science Foundation, private foundations and industry sponsors.
Morgan, who was inducted this year as an American Institute for Medical and Biological Engineering (AIMBE) Fellow, has received a Ruth L. Kirschstein National Research Service Award for Senior Fellows from the National Institutes of Health, a Young Investigator Research Award from the International Osteoporosis Foundation and Servier Research Group, the 2013 Kappa Delta Young Investigator Award from the American Association of Orthopaedic Surgeons, and an Early Career Research Excellence Award and Distinguished Faculty Fellow Award from the College of Engineering. She has published more than 50 peer-reviewed articles in major engineering journals and has delivered more than 40 seminars and invited talks. She is also the co-founder of a successful outreach program, Summer Pathways, which engages high school girls in a week-long sequence of activities in science, engineering and math.