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Research Projects and Laboratories

Before filling out your application, read each of the laboratory descriptions below. Several of the labs offer more than one project. If you are selected to work in a particular lab, you can discuss the projects with your mentor.
 

Thrust 1: Implantable / Wearable Photonic Devices

Faculty mentors: Walfre Franco, Gary Tearney, Andy Yun. This research area is focused on developing novel photonic devices using principles, materials, and structures that are implantable, biodegradable, wearable, and that often mimic nature at scales from nano to macro levels. Such devices are primarily used for sensing, diagnostics, and therapeutic applications, solving the limitations of conventional optical devices and conventional approaches. Furthermore, novel lasers that are biocompatible and small enough to be inside a cell — cell laser — promise to open new avenues in the applications of light in biomedical research.

Fiber capsule endoscope in Tearney Lab.Project 1: Smart tethered capsule endoscopes. The current standard endoscopy has many limitations as it is invasive, costly and suffers tissue sampling error. To overcome these limitations, the Tearney lab has developed tethered capsule endomicroscopy [2-5], which involves swallowing a tethered capsule that acquires three-dimensional microscopic images of the entire esophageal wall as it traverses the luminal organ via peristalsis or is pulled up towards the mouth using the tether (photo). REU students will design, fabricate, and validate prototype capsules with integrated position sensing capabilities and develop imaging processing algorithms for real time diagnosis of esophageal disorders.

Project 2: Implantable wireless microscope. The Tearney Lab is currently developing an implantable microscope that could one day provide real-time images from inside the body via a wireless transmitter [6]. The implantable microscope is self-contained, battery-powered, and wirelessly transmitting images, allowing physicians to see if cancer is developing, if a heart attack is imminent or if a transplanted organ is on the verge of being rejected. Students will have hand-on experience in the design, fabrication, and/or assembly of components into a working prototype, and in testing the device with biological tissues ex vivo.

Implantable hydrogel fibers in Yun LabProject 3: Implantable hydrogel optical waveguides. The Yun lab makes pioneering efforts in the field of biomaterial-based photonic devices, such as light-guiding hydrogels [7] and biocompatible waveguides [8-10], to create implanted optical devices for health monitoring and therapies. Students working on this topic will design, fabricate, and characterize novel polymer-based or hydrogel-based waveguides, and they will acquire knowledge on waveguide optics, biomaterials, nanofabrication, and their applications.

Project 4: Development of mobile phone-based imaging devices. In the Franco Lab in collaboration with the Hasan Lab, students will help to develop computer vision algorithms and optical methods for quantifying and analyzing variations in the optical environment of cutaneous tissues using a mobile phone camera platform primarily for evaluating the spatial and temporal features of cutaneous lesions [11]. Additionally, the students will learn how to leverage optical hardware to probe tissues and improve image Implantable hydrogel fibers in Yun Lab quality and resolution while minimizing motion and lighting artifacts. The hardware and software developed will create simple-to-use low-cost technologies for diagnosis and evaluation of treatment response of common dermatologic lesions.

Project 5: Wearable optical sensors. Light emitting diodes and optical sensors can be integrated into flexible substrates for wearable patches for longitudinal measurement of tissue optical properties for tracking spectroscopic changes in tissue [12-15]. In the Franco lab in collaboration with Yun lab, students will learn about electronic circuit design, spectroscopy and wearable devices, and help to develop non- invasive probes for tracking changes in tissue, sub-millimeter dynamics of cutaneous lesions or oxygenation states. These sensors may ultimately be deployed in wound care settings and, in collaboration with biologists [16], free-diving seals.

Students learn intracellular lasers in Yun lab [Cover of Nature Photonics 2015]Project 6: Biological cell lasers. The Yun lab is pioneering the field of bio- lasers. The group has demonstrated fluorescent-protein lasers, cell-dye lasers, all- biomaterial laser, and intracellular micro-lasers [17-24]. These works, which are supported by NSF grants, have received considerable public exposure through numerous news media and awards. These new lasers have potential for imaging, biological sensing, and cell tracking [25]. Students will learn how to generate and detect laser light from micro-cavities, how cells uptake micro lasers, how the intracellular environment affects the output characteristics of the lasers, and the novel applications of cell lasers.

Thrust 2: Optical Imaging

Faculty mentors: Brett Bouma, Charles Lin, Gary Tearney. In this research area, the projects are focused on developing optical imaging modalities, such as optical coherence tomography (OCT) and intravital fluorescence microscopy and cytometry, that address challenges in basic biomedical science and diagnosis. Light is uniquely well suited for non-invasively interrogating the microscopic structure, molecular composition, and biomechanical properties of biological tissues. Students will experience novel intrumentation and image processing using multidisciplinary approaches.

Project 1: Intravascular polarimetry. Intravascular OCT provides high resolution, cross sectional images of the subsurface microstructure of the coronary arteries in human patients. Polarization sensitive measurements further offer refined insight into microstructural arrangement and composition of individual tissue types. Projects in the Bouma lab focus on investigating specific polarization signatures with experimental measurements of isolated plaque components and by devising new processing strategies. These projects are positioned between electrical and mechanical engineering, as well as computer science and will help students to gain a solid understanding of the physical principles underpinning state-of-the-art OCT technology.

Project 2: OCT imaging of intact brains of Alzheimer’s disease mouse model. OCT combined with tissue clearing agents enables high throughput imaging deep into intact tissues. This method facilitates large-scale investigation into complex biological systems. Students will develop tools to process and segment the multi-terabyte volumetric datasets with a special focus on the detection of Amyloid beta plaques.

Project 3: Development and validation of OCT quantitative angiography. The Bouma lab is in the process of developing quantitative angiography using OCT, integrating valuable functional imaging into OCT structural imaging with clinical applications in cardiology and ophthalmology [26-33]. The students will learn the basis of the study of the random fluctuations of light present in coherent imaging, and how they can be used to infer sample dynamical information. Students will help in the development of OCT quantitative angiography, they will learn to design and perform validation experiments in the lab using phantom setups and will obtain experience in processing OCT datasets beyond direct image reconstruction [34-39].

Students will learn state-of-the-art in vivo fluorescence microscopy in Lin lab [Nature 2014]Project 4: In vivo analysis of circulating blood cells. The ability to perform noninvasive blood analysis will be useful in situations where repeated blood sampling is problematic in newborns and patients with leukemia and HIV, for example. The Lin lab has developed fluorescence-based in vivo flow cytometry [40-42] for real- time detection and quantification of circulating cells without needing to draw blood samples [43,44]. The project aims to extend this technique to label-free detection in two complementary approaches: cellular autofluorescence and light scattering. Participating students conduct instrumentation and signal analysis directed at circulating cell count.

Project 5: Imaging central nervous system inflammation through the eye. The retina is an optically accessible part of the central nervous system [45]. Under normal conditions the retinal parenchyma is sepatered from the circulatory compartment by the blood-retina barrier. Similar to the barrier in the brain, the blood-retina barrier can be breached in the condition of inflammation. The project in the Lin lab utilizes home-built state- of-the-art scanning laser ophthalmoscopy and mouse models of multiple sclerosis and brain injury to study central nervous system inflammation. Students will participate in the development of a scanning laser ophthalmoscope with adaptive optics for imaging inflammation in humans.

Project 6: Optical characterization of the bone marrow microenvironment. All blood cells are made from blood stem cells (hematopoietic stem cells) in the bone marrow. Blood cancer also originate in the bone marrow. The Lin lab is developing optical techniques to track normal and malignant cells and to study their interaction with the bone marrow microenvironment [46-50]. Students will learn to perform 3D image analysis and quantitative measurements in vivo, including the rate of bone formation, cell migration, proliferation, blood flow, vascular permeability, and local oxygen concentration using various fluorescent tracers and sensors.

Project 7: Imaging central nervous system inflammation through the eye. The retina is an optically accessible part of the central nervous system [45]. Under normal conditions the retinal parenchyma is sepatered from the circulatory compartment by the blood-retina barrier. Similar to the barrier in the brain, the blood-retina barrier can be breached in the condition of inflammation. The project in the Lin lab utilizes home-built state-of-the-art scanning laser ophthalmoscopy and mouse models of meningitis and multiple sclerosis to study central nervous system inflammation. Students will participate in the development of a scanning laser ophthalmoscope with adaptive optics for imaging inflammation in humans.

Thrust 3: Optical Biomechanics—from Brillouin imaging to crosslinking

Faculty mentors: Seemantini Nadkarni, Andy Yun. In this research area, we develop and apply novel photochemical and biophotonic methods to modulate, control and measure the biomechanical properties of tissue-engineering materials, tissues, and cells. The biomechanical properties of extra- and intra-cellular matrices and cell scaffolds play important roles in cell migration and mechanotransduction, and they have been linked to a variety of diseases, including atherosclerosis and cancer metastasis. Several engineering projects are available for REU students that may have long-term impact on the diagnosis and treatment of the related diseases, particularly regarding fundamental knowledge and technical innovation.

Students will learn Brillouin microscopy to study cell biomechanics [Nat. Methods 2015].Project 1: Brillouin optical microscopy for cell biomechanics. The Yun lab has previously developed high-resolution Brillouin light scattering microscopy for studying cell biomechanics [51]. By measuring the optical frequency shift of the scattered light, Brillouin measurements probe the local spontaneous pressure waves in the intracellular environments, from which one can determine high frequency longitudinal modulus that is related to the modulus of individual cytoskeletal components, network crosslinking, compressibility of the local microenvironment, and solid-liquid volume fraction. In this project, REU students can participate in new instrumentation [51-56] and use a state-of-the-art setup to measure the stiffness of the extracellular and intracellular matrices and study their interplay in stem cell differentiation, in synergy with an ongoing NSF-funded research.

Project 2: Photo-crosslinking of tissues. Photochemical crosslinking is a powerful technique to control the stiffness of tissues for treatments of wounds and diseases [57-67]. The project in Yun lab aims to develop a novel two-photon crosslinking technique to enhance the local mechanical modulus of tissue with specific optimal spatial patterns with three-dimensional resolution [66]. The students will conduct two-photon crosslinking on tissues, perform biochemical assays for assessing the light-induced changes in the tissues, and conduct various mechanical measurement methods including tensile test, Brillouin microscopy, and fluorescence microscopy to determine matrix structure and cell viability following crosslinking. Students can also be involved in the development of waveguide-assisted deep-tissue crosslinking methods [67].

Project 3: Viscosity-based optical blood coagulation sensor. The goal this project is to develop a low-cost, multi-functional blood coagulation sensor that can measure a patient’s coagulation status within 5 minutes using a drop of blood [68,69]. This device addresses the critical unmet need to identify and manage patients with an elevated risk of life-threatening bleeding or thrombosis, the major cause of in- hospital preventable death. In addition, this innovation will enable rapid coagulation testing in the doctor’s office or at home for over 15 million patients worldwide who routinely receive oral anticoagulants to prevent venous and arterial thrombosis, the world’s number one killer. Students will build a simple optical setup, conduct measurements, and analyze the data.

Project 4: Laser speckle microrheology to evaluate the mechanical hallmarks of tumor malignancy. There is growing recognition that the stiffness of the extracellular matrix (ECM) is a powerful regulator of cell response, and the differentiation, proliferation and malignant transformation of tumor cells can be modulated by tuning ECM mechanical properties. These insights indicate that cancer is mediated by a dialogue between ECM mechanical cues and oncogenic signaling, and therefore knowledge of ECM mechanics is important for advancing current understanding of tumorigenesis and for developing new therapeutic paradigms. In this project students will learn about the principle of speckle and microrhesology and the instrumentation and operation of speckle microrheology [70-74], and their applications in conjunction with confocal microscopy to investigate the structural and mechanical hallmarks of tumor malignancy.

Thrust 4: Nano-technologies for light-activated therapy and diagnostics

Faculty mentors: Tayyaba Hasan, Conor Evans, Gary Tearney. Most cancer-related deaths are associated with the multitude of disseminated metastatic lesions that occur throughout the body. These lesions are often far too small and widespread to detect and resect and may become resistant to therapeutic intervention. Our long-term goal is to develop effective cancer therapy by using light-activated multifunctional drugs. Students will use state-of-the-art optical imaging to gain insights into the bio-physical barriers in drug delivery into tumors and learn synthesis of nanoscale drug carriers.

A photo-activated nanoconstruct for cancer therapy [Nat. Nanotech 2015].Project 1: Photoactivatable nanoscale drug delivery. Nanoscale drug delivery vehicles facilitate multimodal therapies of cancer by promoting tumor-selective drug release. The Hasan lab recently developed a photoactivatable multi-inhibitor nano-liposome that imparts light-induced cytotoxicity in synchrony with photo-initiated and sustained release of inhibitors that suppress tumor regrowth and treatment escape signaling pathways [74-76]. Students will test this technique on state-of-the- art tumor cell cultures to develop and optimize spatiotemporal control of drug release whilst reducing systemic drug exposure and associated toxicities.

Project 2: Engineering molecular probes for multifocal imaging. Recent advances in 3-D cell cultures, organoids, and organ-on-chips promise to accelerate biomedical drug discovery without relying on experimental animals. The Hasan lab aims to develop, test, and apply various 3-dimensional tumor cell model for the development of photodynamic therapy [78-80]. Students will conduct engineering molecular probes for multifocal imaging of complex biological samples and application of a unique video-rate hyperspectral microscopic imaging system.

Project 3: Quantification of near single molecule level ligand binding to white blood cells. Binding of as few as 10 antigens to white blood cells can alter the cell’s behavior and promote tumor immune evasion. State of the art detection methods, however, cannot routinely detect this low level of protein binding. The Evans lab is developing a novel plasmonic nanoparticle-based imaging platform to detects single-molecule levels of antigen binding in patient blood samples to improve cancer detection and immunotherapies [81,82]. Students will work to functionalize plasmonic nanoparticles, understand their optical characteristics, visualize their binding to leukocytes, and work to quantify white blood cell-antigen binding in clinical samples.

Project 4: Nano-enabled imaging devices. Nanotechnologies can be integrated with optical imaging devices to increase their medical utility. The Tearney Lab is developing such optical imaging and biopsy devices that incorporate nanoparticles and nanotubes to provide enhanced imaging capabilities and multimodality sensing features. Students who participate in these projects will build nano-enabled imaging devices and validate them in phantoms and animals to demonstrate performance for particular multimodality assays.