IRP Focus: Biomedical Engineering & Biodesign: Research Projects
Design of "Cellular FedEx Systems"
T. Kyle Vanderlick, Department of Chemical & Environmental Engineering; James McGrath, Yale School of Medicine; Gabor Huszar, Yale School of Medicine
Nature relies on compartmentalization at the cellular level and her packaging material of choice is molecularly-thin membranes formed primarily of phospholipids and proteins. It’s surprisingly easy to create man-made phospholipid membrane sacs—often called vesicles or liposomes—and to load these membrane “containers” with various types of cargo, such as drugs or pesticides. Polymeric analogs—called polymersomes—can also be readily fabricated, and both types of systems can be created at the nano- and micron-size scale. There are many potential applications for membrane-based “shipping containers” especially if novel transportation mechanisms can be developed.
The Vanderlick research team is partnering with other research groups across Yale to develop such systems, using naturally motive cells as transportation vehicles. One of the most promising and exciting research directions is the use of spermatozoa as the motive cell fleet, delivering cargo such as RNA or proteins directly to an oocyte at the moment of fertilization. This work is being carried out in collaboration with Yale School of Medicine researchers.
Of course, the largest and most diverse fleet of motile cells belongs to the bacterial world, and Vanderlick’s team and collaborators in SEAS are also investigating methods to couple liposome and polymersomes to the complex outer membranes of selected prokaryotic cells. Potential applications here abound, from bioremediation in soils to oil clean-ups in the ocean.
Developing Optical Materials Informed by Bird Feather Structures
Eric Dufresne, Dept. of Mech. Eng. & Mats. Sci., Dept. of ChE & EnvE, Dept. of Physics, Dept. of Cell Biology; Simon Mochrie, Dept. of Physics, Dept. of Applied Physics; Hui Cao, Dept. of Physics, Dept. of Applied Physics; Richard Prum, Dept. of E&EB, Peabody Museum of Natural History
Some of the most stunning colors in nature are not created by pigments, but are instead the result of light scattered by nanoscale structures. The vivid blues observed in the feathers of Bluebirds and Blue Jays are just one such example.
In a step toward uncovering how these structures form, a team of Yale engineers, physicists, and evolutionary biologists discovered that the color-producing structures in feathers appear to self-assemble in much the same manner as materials undergoing phase separation: Bubbles of water form in a protein-rich soup inside the living cell and are replaced with air as the feather grows, creating a structure similar to that of beer foam.
This research has important implications for the role color plays in birds’ plumage, as the color produced depends entirely on the precise size and shape of these nanostructures. But mechanical engineering professor Eric Dufresne is also interested in the potential technological applications of the finding. He is leading a team that is mimicking the approach to make a new generation of optical materials in the lab.
Applying Fluctuation Spectroscopy to Clinical Use
Michael Levene, Department of Biomedical Engineering
A technique known as fluctuation spectroscopy has been around since 1970. Widely used in the biophysics community, it is useful for measuring absolute concentrations of particles in fluids.
The Levene Lab is pursuing the use of fluorescence fluctuation spectroscopy in the clinic to quickly and effectively measure the concentration of proteins in blood. Specifically, their approach could be useful for diagnosing von Willebrand Disease, a common inherited clotting disorder, and other blood coagulation disorders
Because von Willebrand Disease is caused by a defect in the protein known as von Willebrand factor that is necessary for blood clotting, fluorescence fluctuation spectroscopy can be used to label the proteins and measure the concentration and size of those proteins in the blood.
While existing tests for von Willebrand Disease involve running a gel that can take 16 hours, involves radioactivity, and often returns poor results, the Levene Lab’s fluorescence fluctuation spectroscopy technique can provide accurate and reproducible results quickly.
It could have applications in diagnosing, classifying, and monitoring disease, as well as in elucidating specifics about the pathogenetic mechanism of thrombotic thrombocytopenia purpura, and as a new tool for assessment of coagulation or bleeding risk in a variety of common systemic conditions.
Frontiers in Optics
Exploiting the Novel Properties of Bulk Metallic Glass
Themis Kyriakides, Dept. of Biomedical Eng., Yale School of Medicine; Jan Schroers, Dept. of Mech. Eng. & Mats. Sci.
In the field of biomedical implants, device developers rely on materials whose surface properties can be controlled and modified, that can function in nanoscale devices, and that are biocompatible. Having struck on novel methods for exploiting the unique properties of metal alloys known as bulk metallic glasses, mechanical engineers and materials scientists in the Schroers Lab are collaborating with biomedical engineering colleagues in the Kyriakides Lab to expand that materials’ application to medical uses.
They have shown bulk metallic glasses to be superior to other materials used in biomedical implants. BMGs exhibit an excellent combination of properties and processing capabilities desired for versatile implant applications, from stents to bone replacement. Unlike most metals, BMGs have an amorphous structure that yields many advantages: high strength (three times that of steel), elasticity, corrosion resistance, and durability. Most notable, they can be molded like plastics with nanoscale precision and complex geometries.
The Yale Engineering collaborators now are putting the outstanding properties of bulk metallic glasses to the test. So far, they have shown that BMGs can, indeed, be implanted in the human body. And in vitro and in vivo study results indicate that the BMGs are compatible with cell growth and tissue function.
In the news:
New Material for Biomedical Applications Offers Superior Properties
Yale Engineers Revolutionize Nano-device Fabrication Using Amorphous Metals
Designing Functional Proteins that Move Electrons
Corey J. Wilson, Dept. of ChE & EnvE
Caltech theoretical chemist Rudolph A. Marcus won the Nobel Prize in 1992 for his contributions to the theory of electron transfer reactions in chemical systems. But he did not present an instruction manual for replicating them.
Chemical and environmental engineers in the Wilson Lab are integrating experimental and computational modeling approaches to design synthetic electron transfer systems. They began by deconstructing Marcus Theory and translating it into a design algorithm for building proteins that are capable of accepting and donating electrons. To accomplish this, the Wilson Lab modeled protein energetics—analogous to stability analysis of buildings whereby civil engineers use accurate computer models to evaluate designs before they are built—using Yale’s Bulldog high-performance-computing clusters. With blueprints in hand, the experimental nano-scale construction work commenced. To date, the team has succeeded in designing functional proteins that propagate electrons and continues toward the goal of perfecting biological mimics.
The potential applications of the work are numerous and exciting. Synthetic electron transfer systems could eventually be used to generate energy in the human body, for instance by mimicking cellular respiration, or in products such as exterior house paints that could imitate photosynthesis to capture and translate light to power the home.
Extending the Impact of Multiphoton Microscopy
Michael Levene, Dept. of Biomedical Eng.
From the first microscopes to Zernike's phase contrast and modern laser scanning fluorescence microscopes, each advance in microscopy technology has opened up new windows onto the mechanisms of life. A team of engineers led by Professor Michael Levene is working to extend the impact and reach, in particular, of multiphoton microscopy and optical spectroscopy through elegant technological innovations, many of which are ready for rapid adoption by biologists who are otherwise naive in optical physics.
One breakthrough from the Levene biomedical engineering lab has been the development of 3D models of whole, intact mouse organs. Combining multiphoton microscopy with “optical clearing,” which uses a solution that renders tissue transparent, the engineers are able to scan mouse organs and create high-resolution, 3D, images of the brain, small intestine, large intestine, kidney, lung, and testicles. They then create 3D models of the complete organs.
Until now, this was only possible by slicing the organs into thin sections or destroying them in the process. When combined with optical clearing, multiphoton microscopy—so called because it uses two photons to excite naturally fluorescent cells within the tissue—can image a larger field-of-view at much greater depths. Once the tissue is cleared, the researchers shine different wavelengths of light on it to excite the inherently fluorescent tissue. The fluorescence is displayed as different colors that highlight the different structures and tissue types.
Now that the concept has been tested on mouse organs, Levene’s team is moving to human samples, focusing on prostate, liver, and breast tissue. Long term, the engineers hope to translate the technology to be used for 3D virtual biopsies to detect or rule out cancer.
Developing New Materials at Warp Speed
Jan Schroers, Dept. of Mech. Eng. & Mats. Sci.
In recent decades, high-throughput screening of chemical compounds revolutionized the pharmaceutical industry. Now, Yale engineers are set to revolutionize the understanding and development of materials with a technique they’ve dubbed “high-throughput characterization.”
Mechanical engineering & materials science professor Jan Schroers and his colleagues are known for their work on a class of materials called bulk metallic glasses. In the past, Schroers' five-person team spent a year and $500,000 to develop a single new bulk metallic glass. The process entailed weighing and combining various amounts of metals such as gold, silver, palladium, copper, and silicon, putting the combination into a vacuum, and characterizing the result. Working fast, the team produced one new alloy per day, and produced one combination a day for a year to come up with the one that could be blow-molded as a bulk metallic glass.
Now, with their massively parallel approach that sprays four different metals in various ratios onto a substrate, they can process 750 new combinations in a day. They are systematically creating large composition libraries of materials and characterizing them to find properties of interest. The vast stores of information will enable the engineers to produce stronger experimental data points to compare their theories against, and scale up materials development to a pace not seen before.
Engineering Faster MR Imaging
Todd Constable, Dept. of Biomedical Eng., Yale School of Medicine
Magnetic resonance imaging has been used in medical imaging for 30 years. Engineers working to improve the technology today address two main issues: imaging speed and quality. Faster imaging would reduce costs by enabling higher use of MRI machines, and improvements in image resolution would enhance a physician’s ability to make a proper diagnosis.
Todd Constable, professor of biomedical engineering, diagnostic radiology and neurosurgery, leads a team of engineers who are working to both accelerate and improve the quality of MR imaging by spatially encoding the data an MR imager records.
Most recent improvements in the speed of MRI have been made by introducing arrays of small coils that receive signals from the body. Data from the coils are spatially encoded by magnetic field gradients—that’s what produces the loud clanging sound a patient hears inside the magnet. Instead of adding more coils, the Constable team’s approach has been to change the gradient encoding strategy. They’ve switched from using linear to nonlinear magnetic field gradients to encode spatial information in a manner that's maximally complementary to what is provided by receiver coil arrays.
Indeed, the approach increases the efficiency of data acquisition and allows excellent images to be obtained using less data and, therefore, less time. At current rates, an MRI imaging sequence may take up to 10 minutes to acquire. For complete scans, patients often must lie still in the machine for a full hour. The Constable Lab’s new method could produce images from 2 to 16 times faster. Alternatively, instead of speeding up the acquisition time, the technology could be used to produce higher resolution images than what are currently available.
Constable and colleagues have filed two patents on the approach and are working on a licensing agreement with Siemens Medical to incorporate it into a clinical platform. They estimate that within five years their technology could be built into all clinical magnetic resonance scanners, doubling throughput and reducing medical costs, or producing higher resolution images at current times.
Publications: Stockmann JP, Ciris PA, Galiana G, Tam L, Constable RT, O-Space imaging: Highly efficient parallel imaging using second-order nonlinear fields as encoding gradients with no phase encoding, Magn. Reson. Med., 64(2): 447-456, 2010.
Predicting the Course of Cardiovascular Disease with Computer Models
Jay Humphrey, Dept. of Biomedical Eng.
In the emerging field of predictive medicine, cardiovascular disease is a prime target. Being able to chart its progression could enable physicians to prognosticate and prescribe a course of treatment, as well as save countless time, pain, and expense for cardiac patients. Meeting that challenge requires collaboration among engineers, computational scientists, and geneticists.
With a focus on whole arteries and aneurysms, the Humphrey team tackles the problem as a mechanobiological one, aiming to understand the mechanical stimulus and subsequent biological response at the cellular level that manifests at the tissue and organ level. Access to such a tool could create a new niche for biomedical engineers. Because the computational models that the Humphrey engineers are developing would likely be too sophisticated for a general practitioner to employ, they could create a demand for engineers in the clinical environment who would be able to interface with the data and offer interpretations to the physician.
Humphrey JD, Taylor CA (2008) Intracranial and abdominal aortic aneurysms: Similarities, differences, and need for a new class of computational models. Ann Rev Biomed Engr 10: 221-246.
Taylor CA, Humphrey JD (2009) Open problems in vascular mechanics: Hemodynamics and arterial wall mechanics. Comp Meth Appl Mech Engr 198: 3514-3523.
Bazilevs Y, del Alamo JC, Humphrey JD (2010) From imaging to prediction: Emerging non-invasive methods in pediatric cardiology. Prog Ped Card 30: 81-89.
Speedier Gene-Sequencing through Molecule Trapping
Mark Reed, Dept. of Electrical Eng.
Faster and cheaper gene sequencing is the Holy Grail of personalized medicine, which is why developers of “next-generation” sequencing technologies have been striving for nearly a decade to reduce the cost of reading a human genome to under $1,000. One vexing obstacle to this goal has been the difficulty of isolating single DNA molecules in their natural water-based environment.
Electrical Engineering Professor Mark Reed is leading a Yale team that is collaborating with a team in the Physics Division at Oak Ridge National Laboratory led by Predrag Krstic to take an innovative approach to the problem. The partnership is employing an ion trapping method that uses oscillating electric fields to confine charged particles to a nanometers-sized space.
Until now, this method, known as a “Paul trap,” has only been used to isolate particles in a vacuum. But Reed, Krstic, and colleagues are using ion-trapping to confine micrometer-sized charged polystyrene beads in aqueous solution to an accuracy of 10s of nanometers. They’ve demonstrated proof-of-principle on test beads recently. Next, they intend to reduce the device size further, to isolate nanometer-sized particles, and eventually to confine DNA. The team hopes to have a working DNA molecule trap within a few years. Analyzing nucleic acids that way could enable quicker, less costly disease diagnostics and treatment, or lead to speedier drug discovery and development.
PNAS, June 7, 2011 vol. 108 no. 23 9326-9330 "Paul trapping of charged particles in aqueous solution”
In the News:
Particle Trap Paves Way for Personalized Medicine
Interpreting and Quantifying Images with Computers
Hemant Tagare, Yale School of Medicine, Dept. of Biomedical Eng., Dept. of Electrical Eng.; Frederick Sigworth, Yale School of Medicine, Dept. of Biomedical Eng.; Hongwei Wang, Dept. of MB&B
Teaching a computer to understand and interpret an image is a difficult problem that engineers have long been trying to solve with sophisticated mathematics and computational power. The problem becomes especially challenging when the image is noisy, out of focus, or contains confusing extraneous information.
Hemant Tagare’s lab is developing algorithms that process biological or medical images to filter out the noise, detect weak signals, and quantify their geometric content. One example is the lab's new effort in creating three-dimensional protein structure from two-dimensional electron microscopy images of the protein. Electron microscopy protein images can be as unclear as the view through a window in a heavy rainstorm, but Tagare’s team takes noisy images of the protein from a variety of angles and processes them to recreate the protein's 3D structure.
In collaboration with Yale professors Frederick Sigworth and Hongwei Wang, the Tagare team is trying to create 3D models that capture the flexible structure of the Dicer protein. Dicer is known for its ability to chop up viral RNA that enters a cell. Modeling its structure could help explain how it does this, and perhaps enable scientists to manipulate or mimic that mechanism in other proteins. What sets Tagare’s efforts apart from engineers elsewhere who are trying to model Dicer is the interdisciplinary approach that relies on close collaboration among biophysicists, biochemists, and image processing experts.
A Control Theoretic Analysis of Biological Neural Systems
K.S. Narendra, Dept. of Electrical Eng.; Stephen Robinson
The brain is frequently described as the most complex machine in the known universe, yet our scientific understanding of how it works is still in its infancy. New tools and techniques have fueled the growth of a body of observations in biological systems that present a great opportunity for further analysis, and a richer understanding of these processes in action.
Professor K. S. Narendra and Dr. Stephen Robinson are pursuing a systems theoretic investigation across several areas of neuroscience. Specifically they aim to apply systems theory to inspect and investigate the underlying structures of interaction that exist within these biological systems. Areas of focus include motor control of primitive organisms to the higher order cognitive processes of attention, decision making and synchronization of multiple competing sub-systems.
The goal is to illuminate neural processes from a fresh interdisciplinary perspective, one from which new ideas can be developed to help spur further investigation.
Application of Systems Engineering To Human Motor Control
Kumpati Narendra, Dept. of Electrical Eng.
Controlling the human body is a formidable task. It takes the newborn baby countless experiments with its limbs to acquire motor control skills needed to ambulate. Most people take for granted the ability to control movement, unless of course they are afflicted with a movement disorder.
Since 2006, Kumpati Narendra has been collaborating with Peter Reeves (formerly a graduate student at Yale, now at Michigan State University) to apply systems engineering and control theory to the study of human motor control. For the past six years, they have been investigating the effects of control impairments on common conditions such as back pain; more recently they have initiated a study of Parkinson’s Disease (PD).
Research on Back Pain: Interest in controlling human movement has had a long and distinguished history. For instance, Giovanni Alfonso Borelli applied mechanistic theory in the 17th century to predict how much effort was required by muscles in the spine to support the body and external loads. Others developed more sophisticated models of the spine to predict loading on the spine and related it to risk of injury. However, it wasn’t until fairly recently that researchers started to investigate how a motor control error, an unintentional mistake in muscle recruitment, could lead to injury under relatively nominal loads.
To elaborate on this work, Reeves and Narendra examined, in a series of papers, how the central nervous system maintains stability of the spine, and suggested how different types of control impairments may be responsible for back pain.
N. P. Reeves, K. S. Narendra, and J. Cholewicki, “Spine Stability: The six blind men and the elephant.” Clinical Biomechanics, vol. 22, pp. 266-274, 2007.
N. Reeves, J. Cholewicki, and K. S. Narendra, “Effects of reflex delays on postural control during unstable seated balance.” Journal of Biomechanics, vol. 42, pp. 164-170, 2009.
N. P. Reeves, K. S. Narendra, and J. Cholewicki, “Spine Stability: lessons from balancing a stick.” Clinical Biomechanics, vol. 26, pp. 325-330, May 2011.
Research on Parkinson’s Disease
Jean Martin Charcot, father of neurology, coined the term Parkinson’s Disease, after a London doctor, James Parkinson, who wrote a paper entitled “An Essay on the Shaking Palsy” in 1817. However, it was only after Sherrington’s work on the nervous system was well established that PD was related to malfunctions within motor circuits.
At present PD is considered as a set of neurodegenerative conditions affecting humans. While no single cause is known to be responsible, it is attributed to the composite result of defects or changes in a number of benign biological processes. Narendra and Reeves believe (following the significant work done at the Hamilton Institute in Maynooth, Ireland), that a systems approach can be a most effective one for the study of PD. They are investigating systematically the effects of small changes in different cellular and metabolic subsystems on motor control. They also believe that the same models can be used to propose corrective actions that may be best suited for an individual.
An alternative form of treatment for PD is through external electrical stimulation. In the 1990s, experiments were described which showed spectacular results using such an approach. Stimulation of the subthalamic nucleus was shown to dramatically reduce Parkinson’s Disease symptoms and restore normal motor function. Since that time, this form of stimulation has evolved into a second form of treating PD. Recently, Narendra and Reeves have also initiated research on the effect of external stimulation on electro-chemical signals in biological systems.
Targeting Chromatin to Combat Viruses
Kathryn Miller-Jensen, Dept. of Biomedical Eng.
Typically, when a person is infected by a virus, the host cell expresses the viral DNA, leading to proliferation in the body. Some HIV-infected cells, however, fail to express viral DNA. These cells are immune to conventional antiviral therapy, but they can reactivate later. Consequently, HIV patients must continuously take antiviral therapy. It remains unclear why infections in some cells become latent, while infections in other cells, even in the same patient, lead to active viral replication.
One reason could be randomness. Every cell population exhibits differences–or “noise”–between individual cells, even when the cells are genetically identical and the environment is carefully controlled. Biomedical engineers in the lab of professor Kathryn Miller-Jensen are trying to understand what governs these differences, in order to design more effective therapies. In one innovative approach, the Miller-Jensen team and colleagues at the University of California, Berkeley, are using the HIV virus as an experimental model for studying chromatin—the genetic structures that regulate gene expression. That’s because chromatin modification patterns differ within a population of HIV-infected cells, and Miller-Jensen and her colleagues believe the resulting differences in gene expression may influence whether a virus becomes active or latent.
The engineers suggest their findings may inform efforts to combat diseases by targeting and modifying chromatin, the mechanisms responsible for these phenotypic differences. If all viral infections could be driven towards replication, then all viruses would be susceptible to antiviral drugs. As an alternative strategy, if infection could be forced into a permanent latent state, then the viral genomes could persist without phenotypic consequences. There could be numerous specific therapeutic options for targeting chromatin modification, and the implications of gene expression regulation in treating cancer are also great.
Trends in Biotechnology, June 21, 2011, Varying virulence: epigenetic control of expression noise and disease processes
In the News:
Miller-Jensen and Colleagues Propose Targeting Chromatin to Combat Viruses
Unraveling Microalgae Genetics to Perfect Biofuels
Jordan Peccia, Dept. of ChE & EnvE
Though the idea of producing biofuels from algae is not new, scientists as yet know little about the genes that algae use to make lipids—fats that can be used as biofuel—or how they can be turned off and on under different environmental conditions. As attention to alternative energy sources increases, however, renewed attention is being paid to the genetic makeup of microalgae.
A team of environmental engineers led by Professor Jordan Peccia is using a high-throughput DNA sequencing technology known as 454 pyrosequencing to unravel the genomes of lipid-rich microalgae. There are several goals of their work. If they can determine how the algae ramp up lipid production, and identify those algae that are most capable of producing lipids, the information could be useful in enhancing biofuel production. In addition, the Peccia team is using the technology to create a genetic library of the hundreds of thousands of species of algae in order to identify those that are ripe for genetic modification for biofuel production and those that are pure, lipid-enriched strains.
Because lipid creation is an energy-intensive process, the algae that are the best producers are also the weakest when it comes to surviving in an environment among competitors. So the Peccia team is also researching how to keep one particularly strong lipid producer, S. dimorphus, growing in a reactor contaminated by other algal species. By making genetic libraries of the algae and bacteria that thrive in a reactor as S. dimorphus dies off, they can trace population declines to particular causes and perhaps devise a solution. They are also exploring ways of promoting S. dimorphus growth, such as increasing CO2 content, which many competing algae species cannot tolerate. With information like that, microalgae may soon reach its true potential as a sustainable biofuel.
In the news:
Microbial Diversity: From Genetic Sequencing to Biofuels
Developing In Vivo Microscopy for Fundamental Neuroscience
Michael Levene, Dept. of Biomedical Eng.
Major areas of experimental neuroscience, from micro-circuitry to gene function to basic anatomy, are best studied optically. Yet conventional microscopy approaches can only reach about 5 percent of the intact mouse brain. One goal of the Levene Lab is to image the remaining 95 percent using optical microscopy.
Levene and colleagues have engineered a technique using micro-optics,which overcomes the major hurdle to viewing the recesses of the live brain: the inability to get adequate optical access in vivo due to the strong scattering of light. Their method works by examining the brain longitudinally through a microscope that shines light through a tiny prism embedded in the brain of a live mouse. The prism allows a view deep into the brain, where firing neurons can be viewed. The approach is like using a periscope to peer into the brain, and the Levene team has been able, using calcium-sensitive dyes, to witness neurons responding when the mouse’s whiskers are tweaked.
The technique has implications for basic science as well as therapeutic interventions. Deep in vivo imaging could lead to a greater fundamental understanding of how the brain works and also has implications for understanding diseases such as epilepsy. Potential clinical applications include image-guided surgery. Levene and team continue to work with colleagues in Yale’s Neurosurgery Department to develop these ideas.
Addressing Key Challenges in Biomaterials
Paul Van Tassel, Dept. of ChE & EnvE
Biomaterials are ubiquitous in modern medicine, from prosthetic limbs to device coatings, and hold promise for future applications like scaffolding for tissue regeneration. Biomaterial design presents a key challenge, however: applications often require materials to be both mechanically rigid (to promote strong cell adhesion) and bioactive (i.e. able to communicate specific cues to contacting cells). To date, achieving one of these features usually required sacrificing the other.
Van Tassel and his group have developed an idea that appears to address this challenge: a thin polymer film biomaterial offering both high rigidity and bioactivity. The approach involves forming the film in the presence of sacrificial nanoparticle templates. The film is first rigidified through a chemical cross-linking procedure; then, the template species are selectively dissolved, leaving behind a pore structure. These pores can then be filled with proteins able to communicate with cells, rendering the film bioactive.
The new approach – part of an ongoing effort toward polymeric thin film biomaterials – achieves mechanical rigidity in conjunction with bioactivity, and, notably, allows for embedding high quantities of biological species without regard to size (previous methods were limited to lower quantities of smaller drug or protein species).
Publications: Advanced Functional Materials