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2015 REU Summer Research Projects

Descriptions

 

Kwabena Boahen
"Modeling Sensorimotor Circuits for Eye Movements"

We experience the visual world by constantly moving our eyes towards objects of interest. These eye movements remain mostly unnoticed, leaving us with the illusion of stable visual perception. For example, what we perceive as a clam gaze at a distant tree is actually a series of abrupt and disjoint eye movements, called saccades. When saccades are eliminated by artificially fixing the eye in place, the quick result is perceptual blindness. The pattern of saccades is not random: each one is directed to bring an interesting object to the fovea, where visual acuity is greatest. To accomplish this, the sensorimotor circuits underlying these eye movements must predict the locations of interesting objects based on visual information obtained from the locations peripheral to the current point of fixation. Although such predictions are critical to vision, the underlying neural circuits are unknown.

Our lab joined forces with Dr. Tirin Moore’s neurophysiology lab, in order to test the hypothesis, that sensorimotor circuits underlying eye movements predict both the retinal location of moving targets as well as future eye position after a saccade, and exploit these predictions for shifting the gaze to optimal retinotopic locations. In this project we combine theory, modeling, physiology and behavior to unravel the nature of predictions occurring in macaque sensorimotor circuits for eye movements. The summer project’s primary goal is to build a neural network model of the sensorimotor circuit for eye movements, in order to make testable experimental predictions about statistical relationships between the sensory and motor neural signals during eye movements. If time permits, these predictions will be tested using neural recordings from Dr. Moore’s lab, where neural activity is recorded in monkey visual and prefrontal cortices during visually guided saccades. Interested student may implement the model using the state-of-the-art neuromorphic simulation platform Neurogrid recently developed in our lab. Neurogrid emulates a million neurons in real-time with a high level of biophysical detail.

Responsibility/desired skills: computational and simulation experience (e.g., Python, Matlab), basic understanding of dynamical systems and differential equations, basic understanding of statistics and probability theory, interest in the field and eagerness to learn. Experience with neural networks or systems neuroscience is a plus. During the summer, the student will learn neural circuit modeling, neural data analysis techniques, multivariate statistical models and the basics of visuomotor neurophysiology.

Please direct any questions about this project to Tatiana Engel via email at tatiana.engel@stanford.edu.

Positions Available: 1

David Camarillo
"Human Brain System Identification through Finite Element Modeling"

According for the Center for Disease Control and Prevention, every year an estimated 1.7 million people are diagnosed with TBI in the US alone. Of these cases, 80% are categorized as mild, with symptoms ranging from headache, dizziness, disorientation, to depression and loss of memory. TBI research, for the most part, has focused on the acute consequences of single events involving moderate to severe head impacts. Similarly, mild traumatic brain injury (mTBI) was thought to result in only transient symptoms from single head exposure. However, several recent clinical studies have shown that even in the absence of diagnosed concussion, repeated “mild” head exposures could lead to long-term progressive changes in white matter structure and abnormalities in functional MRI activation patterns. A study into the physics of repetitive low-acceleration head motions is required in order to understand the dependence of brain tissue’s motion and deformation as a result of different skull motions in order to understand injury mechanisms and devise effective prevention. Here, we propose a computational study of skull-brain interaction using a validated Finite Element model. We have previously measured skull motion kinematics during low severity soccer headers. We will devise a test matrix for simulation input space based on the range of these measurements and previously published literature.

We are looking for an undergraduate student to assist in investigating brain’s response (transfer function) to various loading inputs to the skull. The student will specifically help with design the test matrix, running the simulations, and analyzing strain calculations. The student will also be involved in developing hypotheses based on the observations. The ideal student would start working on this project during Spring quarter for research /independent study units and continue through the Summer.

Responsibilities/desired skills: Study design and execution, computational experience (MATLAB, LS-DYNA), basic understanding of undergraduate dynamics and system identification, interest in the field, and eagerness to learn.

Lab website: http://camlab.stanford.edu

Positions Available: 1

David Camarillo
"Sensor Fusion and Statistical Signal Processing for Robotic Surgery"

Here in the CAMlab we are aiming to robotically automate some of the most difficult tasks involved in cardiac ablation for treating atrial fibrillation. Using a robotically actuated cardiac catheter, our goal is to reduce the difficulty of performing these procedures by substituting robot automation for fine tasks. One of the most crucial elements of robotic control is accurate sensing, which is extremely difficult in the body. The summer students’ project will involve implementing (some or all of) the following sensing modalities – magnetic tracking, force sensing, fluoroscopic tracking using computer vision, EKG monitoring, temperature sensors, and accelerometers. With the help of graduate student supervision, the sensing signals will be used to measure patient heartbeat and breathing, its effect on the catheter robot, and finally be used as an input for robotic control. The project goals will be flexible and we will work to match the students’ strengths and interests in various aspects of this study.

Lab website: http://camlab.stanford.edu

Responsibilities/desired skills: The students should be independent enough to investigate and implement sensors with some help from a graduate student mentor. The students should be well-versed in MATLAB and/or C++. Familiarity with signal processing would be desirable; any experience with sensors and/or machine learning would be beneficial but not necessary

Positions Available: 1

David Camarillo
"Understanding and Prevention of Brain Injuries in Bicycle Accident"

Bicycling is the leading cause of sports-related traumatic brain injury (TBI). According to the American Association of Neurological Surgeons, bicycling was the reason in about 86,000 of the 447,000 sports-related head injuries treated in emergency rooms in 2009. A critical component of reducing the risk of brain injuries in bicycle accidents lies in the understanding of brain response during a direct impact. Currently used bicycle helmets are designed so as to protect the skull, but not the brain. Therefore understanding the limitations/effects of the helmets bicycle riders use in an accident is crucial to prevent TBI. This requires predicting the skull kinematics during an accident, which can be done by constructing rigid-body models including the helmets to simulate the accident. CAMLAB is looking for an undergraduate student to help investigate the performance of bicycle helmets in bicycle accidents. The student will specifically work on simple rigid-body simulations of bicycle accidents (with helmets), obtaining skull kinematics, and running the necessary finite element (FE) models to evaluate injury to the soft tissue of the human brain. The student will also be given the free space to test his/her hypotheses regarding the study. Ideally, we are looking for a student who should start working on this project during the Spring quarter for research / independent study units and continue through the Summer.

Lab website: http://camlab.stanford.edu

Responsibilities/desired skills: Required skills: Basic knowledge on dynamical system, motivation and discipline in learning and researching on the subject. Desired skills: Computational skills (MATLAB, LS-DYNA), dynamical system modeling and identification.

Please contact Mehmet Kurtat mkurt@stanford.edu for any further information.

Positions Available: 1

Markus Covert
"Developing High Time-resolution Transcription Sensors to Monitor Host-virus Interactions at the Single-cell Level"

The advent of synthetic biology has led to a dramatic increase in our ability to engineer biological systems to perform new tasks or to display novel features. One exciting area of synthetic biology that has received significant attention is the development of biosensors - biological devices that are capable of performing previously impossible measurements. Recent examples include the development of sensors that can sense force being exerted on a protein to sensors that report the activity level of different kinases.

In this REU project, you will help design and characterize new biosensors that will monitor transcription inside single bacterial cells with high time resolution. A number of key phenomena in bacteria, including the host-virus interactions that determine the outcome of viral infections, occur too quickly to be accurately monitored with the current generation of transcriptional reporters. Hence, new sensors are required to make these measurements and gain insights into this poorly understood facet of biology. While the aim of the project is in and of itself important, you will gain valuable hands-on experience in multiple areas of biology ranging from biosensor design, PCR, cloning, imaging, and single-cell analysis.

Lab website: http://web.stanford.edu/group/covert/

Responsibilities/desired skills: Experience with standard molecular biology techniques (cloning, PCR, Gibson assembly), synthetic biology (knowledge of commonly used parts such as plasmid origins of replications, promoters, ribosome binding sites, and transcription terminators), and MATLAB is desired but not necessary. Responsibilities will be distributed through out all aspects of the project, ranging from biosensor design, implementation, and testing.

Positions Available: 1

Jennifer Cochran
"Development of Protein-based Therapeutics Targeting Tumor-associated Receptor"

Cell signaling pathways are dysregulated in many cancers, and one such pathway is the platelet-derived growth factor (PDGF) pathway. The platelet-derived growth factor receptor (PDGFR) is overexpressed in many solid tumors, where their overexpression and aberrant signaling are believed to play a role in promoting angiogenesis and metastasis. Current anti-angiogenesis therapies have primarily focused on targeting the vascular endothelial growth factor (VEGF) and its receptor (VEGFR). However, resistance to these therapies occurs when alternate cell signaling pathways, such as PDGFR, compensate for the decrease in VEGFR. The objective of this research is to engineer biologics that are antagonists of the PDGFR pathway for the development of a therapeutic compound.

Responsibilities/desired skills: The REU student will express and purify engineered proteins, and perform assays to characterize the efficacy of these proteins, such as binding affinity, phosphorylation, and proliferation. The student will learn molecular biology techniques, biochemical assays, flow cytometry, and cell culture. Previous lab experience in any of these skills would be helpful.

Positions Available: 1

Scott Delp
"Assessing Muscle Biomarkers of ALS in Mice"

Amyotrophic Lateral Sclerosis (ALS) is a devastating disease where motor units progressively die off and there is no treatment. Our lab has a novel microendoscopy system that can be used to visualize motor unit responses in muscle to electrical stimulation. We hypothesize these motor units responses will change with progression of ALS, and we will image muscle at different time points in a mouse model in order to find how parameters change. The goal of this project is to establish biomarkers for progression and methods for how to monitor the disease in mice and in humans with our microendoscope. This method will hopefully lead to better diagnosis and monitoring to aid patients as well as therapy developers.

Responsibilities/desired skills: Must not have adverse reaction to animal studies/needles/seeing blood. / Responsibilities will include helping with microendoscopy experiments and data and image analysis. Independent experiments of muscle properties through other techniques in ALS mice is possible.

Positions Available: 1

Scott Delp
"Building a Customizable Biomechanical Simulation and Analysis Framework for OpenSim"

OpenSim is the most widely used musculoskeletal modeling and simulation platform in the world for biomechanics and rehabilitation research. OpensSim is opensource software that implements physics and physiology-based models of human and animal dynamics to simulate movement. It provides tools to solve model dynamics that include multibody, contact and muscle dynamics and capabilities to visualize and analyze simulated movements in great detail. The OpenSim team is looking for motivated computer science and software engineering students to help build the next generation of capabilities. This includes an API for controling data flow to and from external sensors (Kinect, IMUs, phones) and devices (haptics, exoskeletons) to measure and augment human performance. Furthermore, we need to facilitate the creation of custom workflows via scripting in Python and Matlab. The goal is to enable power users to construct high throughput workflows that can be used within an optimization framework to perform a design study, or to batch process calculations for hundreds of subjects or patients in a population study. The OpenSim software consists of C++ libraries at its foundation and we use SWIG to wrap C++ classes in Java and Python. The OpenSim GUI is written in Java and we are moving to implementing the visualization in WebGL.

Responsibilities/desired skills: We are seeking one or two enthusiastic computer scientists/engineers to implement the team vision. We are specifically looking for the following skills (in order of priority):

1. C++ proficiency for API development with interests in bio-computation and simulation 
2. SWIG knowledge for API wrapping in Java and Python and enabling tighter bindings 
3. Java/Python or MATLAB experience for scientific computing to create examples that exploit the new API features 
4. (Bonus) WebGL experience /

Positions Available: 1-2

Drew Endy
"Synthetic Biomineralization"

The production of high-performing hard materials occurs widely in biology, such as in the growth of bones, teeth, and seashells. An understanding of these biominerals, their evolution and synthesis, can provide a road-map for harnessing synthetic biology to biomanufacture technologically relevant inorganic materials. Inspired by this goal, this project will utilize metagenomic screening to re-engineer E. coli bacteria to create cell variants that are able to controllably biofabricate defined materials of interest. To accomplish this, large libraries of randomized gene cassettes isolated from bacterial consortia from diverse environmental niches will be transformed into E. coli. The transformed cells will be screened via fluorimetric readouts using a new micro-capillary array-based high-throughput screening platform that has recently been developed at Stanford. Materials targeted for synthetic biomineralization will include quantum dots, mineral carbonates, and silicates and other mineral oxides.

Responsibilities/desired skills: Specific responsibilities could involve gene library design and synthesis, cell culture with fluorimetric analysis and screening, DNA sequencing with bioinformatics analysis, materials characterization (e.g., electron microscopy), or some combination of the above. Specific sub-project roles and goals will be defined to suit your background and interest.

Lab website: http://openwetware.org/wiki/Endy_Lab

Positions Available: 2

Kerwyn Huang
"Mechanics of Bacterial Morphogenesis"

Bacteria morphogenesis (i.e., the attainment and maintenance of cell shape) is a central research subject in microbiology. In particular, there are many open questions regarding the mechanisms by which bacteria assemble and sculpt their cell walls, the organelle that determines their shape. In this REU project, the student will investigate fundamental questions related to cell wall synthesis. He or she may focus on a variety of specific topics, for example: 1) the mechanisms by which intracellular proteins coordinate in space and time to assemble the cell wall; 2) the physical/biochemical mechanisms by which the cell wall is reshaped during division; 3) the difference between cell wall synthesis strategies across different species. The experimental methods used to explore these topics will involve applying mechanical and/or chemical perturbations to bacteria cells as they grow and comparing the resulting phenotypes to "normal" phenotypes. The student may also develop simple mathematical models to explain his or her results.

Please contact KC Huang at kchuang@stanford.edu for any further information.

Lab website: http:whatislife.stanford.edu

Responsibilities/desired skills: The student should be majoring in a field related to biology, physics, and/or biochemistry. More importantly, the student should be willing to work in a highly interdisciplinary environment that may call upon concepts and experimental techniques from molecular biology, biophysics, biochemistry and mathematics. Although the student will be working closely with a postdoctoral mentor, he or she should also be self-motivated and independent.

Positions Available: 3

Craig Levin
"Molecular Imaging Techology"

We have several projects that explore advanced concepts in instrumentation (hardware) and algorithms (software) to create new imaging systems capable of enhanced visualization and quantification of molecular pathways of disease in living subjects.

Responsibilities/desired skills: Interest or skills in sensors, electronics, computation, physics, math

Please direct all questions to Dr. Levin via email at cslevin@stanford.edu.

Positions Available: 2

Michael Lin 
"Controlling Protein Folding using Photo-switchable Green Fluorescent Protein Dronpa and Light"

In this project, we aim to control the folding of a protein by light-induced association and dissociation of dimeric mutants of the green fluorescent protein Dronpa. We have engineered photodissociable dimeric Dronpa mutants that undergo association and dissociation in response to light. We are attempting to link the multimeric status of Dronpa to the folding state of another protein, and we have chosen red fluorescent protein as our first target so that we can have a visual readout of protein folding. The undergraduate student will assist in the design, building, and testing of fusions of Dronpa and red fluorescent proteins to identify designs showing the desired light-control over red fluorescence. Testing will be performed in vitro initially and in cultured cells with the most promising candidates. If successful, this project will lead to a new method for controlling protein activity with light. The student will learn protein design, expression, and characterization, and the iterative design-build-test cycle as applied to molecular engineering.

Responsibilities/Desired skills: The student should have excellent grades in biology, chemistry, and physics coursework. Prior experience with molecular cloning (PCR, enzyme reactions, gel electropheresis, plasmid purification) is required. Cell culture experience is preferred. The student will be expected to read the primary literature and troubleshoot procedures on their own. Most important is a desire to work hard and to learn.

Lab website: http://web.stanford.edu/~mzlin/

Positions Available: 1

Michael Lin 
"Molecular Engineering of Luminescent Reporters of Cardiac Stem Cell Differentiation"

We are developing protein-based reporters to iage the functional differentiation of cardiac stem cells into functional cardiomyocytes. These reporters produce light specifically in response to calcium influx within actively contracting cardiomyocytes. Prototype reporters exist but improvements in terms of brightness and responsiveness to contraction are desired. We will design, build, and test a series of reporter variants, covering the range of possible protein topologies and performing finer optimizations as well. Testing will be performed in vitro initially and in cultured cells with the most promising candidates. If successful, this project will lead to a new method for visualizing stem cell differentiation and cardiomyocyte function. The student will learn protein design, expression, and characterization, and the iterative design-build-test cycle as applied to molecular engineering.

Responsibilities/Desired skills: The student should have excellent grades in biology, chemistry, and physics coursework. Prior experience with molecular cloning (PCR, enzyme reactions, gel electropheresis, plasmid purification) is required. Cell culture experience is preferred. The student will be expected to read the primary literature and troubleshoot procedures on their own. Most important is a desire to work hard and to learn.

Lab website: http://web.stanford.edu/~mzlin/

Positions Available: 1

Manu Prakash
"Dancing Droplets - Applications"

We have uncovered and mechanistically explained an exciting new phenomena where droplets move under their own power, communicate with each other over a distance, and can be made to perform many novel functions. See video: https://www.youtube.com/watch?v=K8Wx2PHIYGI. The motion of these droplets is quite mesmerizing and beautiful. The unique physical mechanism gives these droplets their remarkable abilities. Since this phenonema is so new, there are a multitude of different completely unexplored applications and questions. Given our deep understanding and the ease of working with this system, rapid progress is easily attainable. The ideal student will explore, document and publish results on some of these applications.

Lab Website: http://web.stanford.edu/~manup/home.html

If you are interested in this project, please contact Nate Cira at ncira@stanford.edu.

Responsibilities/Desired skills: The ideal candidate will be independent, curious, creative, good with their hands, comfortable working on a fast paced project, possess good reading and writing skills, and be willing to work before/after the summer program.

Positions Available: 1

Manu Prakash
"Foldscope - Origami Based Optics for Large Scale Manufacturing"

Microoptics fabrication - optical characterization (prototyping optical test equipment) - disease biophysics for optical detection.

Lab Website: http://web.stanford.edu/~manup/home.html

Responsibilities/Desired skills: Optics, passion, and an interest in infectious disease and global health.

Positions Available: 4

Stephen Quake
"Electrically Actuated Microfluidic Valves"

Microfluidic technologies have enabled complex biological processing, such as single cell analysis, digital single molecule counting, and automation. Central to these innovations was the pneumatic valve which allowed routing of fluids on microfluidic chips. When these devices were first created, people envisioned widespread, low cost, portable, lab-on-a-chip devices that could be used as diagnostics, sensors, and reactors. However the dream of microfluidics outside of research labs is largely unrealized. A central obstacle is creating low cost devices that do not sacrifice the diverse abilities of laboratory setups. Existing pneumatic valve designs require bulky expensive setups to operate. We are addressing these challenges by creating a second generation valve type which is actuated by electricity. Students working on this project will: design, fabricate, and test new devices. Ultimately we hope to showcase the technology with a fully functional prototype which performs a relevant bioassay.

If you are interested in this project, please contact Nate Cira at ncira@stanford.edu.

Lab Website: http://thebigone.stanford.edu/

Required: Enthusiasm, creativity, independence, and ability to learn. Helpful: microfabrication experience, knowledge of clinical diagnostics, interest in working before and after the summer program is highly valued.

Positions Available: 2

Ingmar Riedel-Kruse

"Cloud Experimentation for Online Education, Citizen Science, and Biotic Games"

The Riedel-Kruse Lab (Bio-Engineering) is fascinated by multicellular pattern formation and interactive biology. This project seeks to develop interactive online interfaces and equipment that enable remote users (typically non-scientists) to interact with biological data and even run their own experiments. It is our vision to develop such online interfaces (often structured in game form given the motivational and educational power of games) to enable average citizen to help solving bio-medically relevant research questions ("human computation" / "crowd-sourcing" / "citizen science") and as a medium for large-scale informal and formal science online education (MOOCs). We also have a strong collaboration with Prof. Paulo Blikstein from the School of Education.

Responsibilities: There is a larger development effort going on in the lab, and we will jointly identify a sub-project that suits your background and interest. For example, your project could focus more on creativity and artistic game development, or programming web interfaces and data bases, or work on data analysis aspects, or actually building devices. Desired skills: The skills listed below are what you will likely encounter during the project - either by yourself or your team colleagues. In your application you should identify at least one of these skills that you would like to focus on and deepen further (and we provide the opportunity to build additional skills based on your interest). Programming (one or more of: Python, HTML5, databases, Matlab, Android, iOS) (Visual) Art (Educational) Game design Image and data analysis Mechatronics (arduino, solidworks, raspberry PI, 3D printing, LEGO mindstorm etc.) Basic microbiology Strong motivation and curiosity (required by all ;-))

Lab Website: http://www.stanford.edu/group/riedel-kruse/

Positions Available: 3

Ingmar Riedel-Kruse
"Engineering contact-dependent cell-cell signalling in bacteria"

To achieve ever expanding goals, synthetic biology is moving beyond the engineering of individual microbes, and towards the engineering of microbial consortia. To make this possible, we need to develop tools for cell-cell communication that coordinate behaviors on a population-level. Examples of such tools include repurposed quorum sensing pathways and phagemid transmission systems, which allow bacteria to communication with nearby neighbors. Communication in such systems is regulated by transport (eg. diffusion, convection) of soluble particles through the extracellular liquid environment. Currently there exists no cell-cell communication platform that is regulated by direct contact between neighboring cells. Plasmid conjugation is common phenomenon between neighboring cells in naturally existing biofilms, and plays a key role in signaling related to biofilm formation and development. The goal of this project is to re-engineer existing conjugative plasmid transfer systems into a controllable platform for contact-dependent cell-cell communication. Such a platform would allow for finer spatial control of signaling, particularly in structured microbial consortia such as biofilms.

Skills: molecular biology / cloning and microbial culture would be beneficial but not required. Strong motivation and curiosity is always required. Project can be tailored to student's strengths, but will likely involve mix of biological wet-lab bench work and possibly microfluidic chip design and mathematical modeling.

Lab Website: http://www.stanford.edu/group/riedel-kruse/

Positions Available: 1

Christina Smolke
"Characterizing Ribozyme Switches with Novel Sensing Capabilities"

Synthetic biology promises new ways of engineering biology for a variety of applications such as the biosynthesis of chemicals such as biofuels and drugs, hijacking cells and tissues for diagnostics and therapeutics, and fashioning environmental biosensors out of microbes. To achieve these, it relies on manipulating individual biological components and integrating them into systems of interacting parts. A molecular component of every living cell that is well suited for the dynamic control of gene expression is RNA, which is not only an information carrier but also often a catalyst of a range of regulatory processes enabled by its complex 3-D structures. Such regulatory RNA can be turned into devices that include riboswitches (“ribonucleic acid”+“switches”), ribozymes (“ribonucleic acid”+“enzymes”) and RNA interference effectors. Our lab has developed ribozyme switches that regulate gene expression in cells, and effectively applied to switching on/off T cell proliferation for enhancing adaptive immunotherapy, developing a high-throughput screen for evolving an enzyme caffeine demethylase, and controlling alternative splicing in response to cellular cues, among others. To further expand the capability of our ribozyme switch device, it is crucial that it can specifically sense, essentially, a limitless number of small molecule input signals. We are currently developing an automated and parallelizable selection method coupled with next-generation sequencing (NGS) as a high-throughput screen to accelerate the generation of RNA biosensors and switches de novo. This project will first involve testing potential switches that respond to targets such as metabolites in the benzyl isoprenoid alkaloid biosynthetic pathway in vivo in yeast, followed by optimizing genetic context and ribozyme loop sequence to improve properties such as dynamic range.

Desired skills: Basic molecular biology, general chemistry and (desirable but not required) basic familiarity with Matlab or Python or other programming language Responsibilities - Characterize novel ribozyme switches in vivo in yeast that respond to a therapeutic or metabolite target - Optimize ribozyme switch activity.

Lab Website: http://smolkelab.stanford.edu/

Positions Available: 2

Fan Yang
"Develop Controlled Drug Delivery system to direct Tissue Regeneration"

Both normal tissue development and wound healing processes are guided by sequential release of various soluble factors to promote stem cell recruitment, vascularization and tissue formation. Controlled delivery of multiple biological signals (e.g. proteins or genes) to cells in a temporally-controlled manner can provide a powerful tool to promote desired cellular processes and tissue regeneration. The goal of this project is to develop biomaterials-based drug delivery platforms to achieve sequential release of multiple biological factors,. The effects of varying biomaterials structures on drug loading and release kinetics will be examined, and the biological activity of the released drug will be tested using in vitro cellular based assays.

Desired skills: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.

Lab website: http://www.fanyanggroup.com/

Positions Available: 1

Fan Yang
"Engineering a Brain in a Dish: 3D in vitro Models for Studying Pediatric Brain Tumor using Biomimetic Hydrogels"

Brain tumors are the most common solid tumor in children, and represent the leading cause of death from childhood cancer. To address the urgent need for improving the outcomes for treating pediatric brain tumors, it is critical to develop in vitro models specifically optimized for pediatric brain tumors, with advanced understanding of the effects of microenvironmental cues on pediatric brain tumor growth and invasion. The brain tumor microenvironment is a complex niche consisting of biochemical and mechanical cues, and the interplay between multi-factorial niche signals play an important role in regulating brain tumor growth and invasion. Through working at the interface of biology, material science, bioengineering and medicine, this project aims to provide novel 3D in vitro models that bridge the gap between the 2D culture and animal models for studying pediatric brain tumor growth and invasion in a more defined manner. The student will work in a highly interdisciplinary group that integrates cancer biology, biomaterials, engineering and medicine.

Desired skills: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.

Lab website: http://www.fanyanggroup.com/

Positions Available: 1

Fan Yang
"Engineering Stem Cell Microenvironment Using 3D Biomimetic Materials"

Stem cells reside in a complex 3D niche in vivo including biochemical and mechanical signals. Before stem cells can be broadly useful for repairing lost tissues, methods must be developed to control stem cell fate towards desirable lineages. Biomaterials provide a powerful tool for recapitulating stem cell niche, and can be engineered to promote desirable cellular fates and tissue formation. Prospective undergraduate researcher will work in a highly interdisciplinary group that integrates biology, materials science, engineering and medicine. Such biomaterials platforms can be used for elucidating the mechanisms of stem cell-niche interactions, as well as for translational studies for repairing tissues such as cartilage, bone and blood vessels.

Desired skills: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.

Lab website: http://www.fanyanggroup.com/

Positions Available: 2

Fan Yang
"Harnessing Stem Cells to Catalyze Tissue Repair"

Stem cells are widely known for their potential to repair lost tissues via differentiating towards specific tissue lineages. Recent studies have shown that stem cells may also contribute to tissue repair via paracrine signaling, and interacting with other cell types residing in close proximity. The goal of this project is to harness the interplay of stem cells and other cell types to achieve catalyzed tissue regeneration. Our lab has recently developed novel 3D co-culture models that allow control of cell distribution in 3D, and employ 3D biomimetic materials to recapitulate the role of natural extracelluar matrix as binding reservoir for paracrine signals. These novel tools enable us to conduct mechanistic studies of cell-cell interactions in a spatially controlled manner, and outcomes of such studies will lead to novel tissue engineering therapies for repairing lost tissues such as cartilage.

Desired skills:Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.

Lab website: http://www.fanyanggroup.com/

Positions Available: 1

Peter Yang
"Development of Prevascularized Endothelial Cell Aggregates for Therapeutic Angiogenesis"

Cell-based therapeutic angiogenesis has shown a great potential for treatment of the damaged tissues, but there still remain challenges in protecting cells from poor vascularization and maintaining stable vascular network for anastomosis and microcirculation. Here, we will develop prevascularized human umbilical vein endothelial cell (HUVEC) based vasculature capable of enhancing functional vessel formation, preventing vessel regression over time, and recovering blood perfusion quickly. In this project, first, we will develop hydrogel systems with tunable physiochemical and mechanical properties. Second, we will evaluate the interaction between HUVEC, the specific tissue cells, and tunable hydrogels. Finally, we will evaluate the effect of pre-fabricated HUVEC aggregates on neo-vascularization in a murine ischemia model.

Responsibilities/Desired skills: Completion of basic molecular biology /chemistry courses. Prior lab experience is preferred but not required

Positions Available: 1

Peter Yang
"Engineering Antler-like Cells for Rapid Bone Regeneration"

This project is to study genes involved in the regeneration of deer antlers through gene overexpression. Deer antlers are bone tissues that regenerate annually at an astounding rate of 2 cm per day. We have recently isolated deer antler progenitor cells and performed RNA-seq analysis, identifying a set of candidate genes, which we wish to study. The details of experiments is subject to change depending on the project status and student interest. It may include cloning and testing the function of candidate genes involved in deer antler regeneration. Candidates will be taught how to prepare and isolate cDNA for cloning, design pcr primers for deer gene cloning and restriction enzyme digestion, perform transfection on mammalian cells, cytochemical and immunostaining as necessary.

Responsibilities/Desired skills: Interested candidates are expected to be familiar in molecular biology, meticulous in planning and execution of experiments, and hardworking. Scientific curiosity and independence are highly encouraged in our lab. We are also more than happy and willing to teach untrained undergraduates as long as they share the same passion as we do and are willing to dedicate their time for research. Recommended Courses/Readings: Molecular biology Desired Qualifications of REU Intern: Familiarity with molecular biology techniques especially in pcr-based gene cloning and plasmid transfection

Positions Available: 1

Peter Yang
"Hollow Fiber Membranes for Tissue Engineered Vascular Beds"

Large bone defect repair still remains a significant clinical challenge. Synthetic bone scaffolds show promise to regenerate damaged bone tissue without the need for harvesting autografts or allografts. However, scaffolds used to treat large bone defects are limited by poor revascularization in the region of regenerating tissue. The inclusion of a prefabricated engineered vasculature within critical size bone grafts could overcome this obstacle and supply the regenerating tissue with the necessary blood flow to increase the rate of successful healing and minimize the risk of graft necrosis. In order to engineer a preformed vasculature, our lab has developed small diameter vascular grafts (SDVG) from elastic hollow fiber membranes (HFM). These tubular constructs can be tuned to mimic many of the essential properties of native blood vessels. The HFM are biocompatible and biodegradable, with elastic mechanical properties and sufficient strength to be directly sutured to host blood vessels.

Hemocompatibillity testing indicated no significant increase in hemoglobin content, blood cell damage, or platelet adhesion after contact with blood under static or flow conditions. Additionally, the HFM surfaces have demonstrated appropriate cytocompatibility, with the ability to support human mesenchymal stem cells (hMSC) and human umbilical vein endothelial cells (HUVEC). Using a custom-made bioreactor, we have achieved successful proliferation HUVEC monolayers on both the inner and outer membrane surfaces. For effective integration of the engineered SDVG in vivo, it is essential that the HFM develop an extensive microvascular network.

The purpose of this study is to examine the ability of endothelial cells on the HFM surface to initiate and form microvascular sprouts into a suitable hydrogel/scaffold environment in vitro. The development of such a tissue engineered vascular bed could lead to great improvements in the regenerative medical treatment of critical size bone defects.

Requirements: Completion of a basic molecular biology /chemistry course. Prior lab experience is preferred but not required.

Positions Available: 2

Peter Yang
"The Effects of Varenicline on Gene Expression in Osteoblasts"

Smoking is harmful to musculoskeletal health and reduces bone healing in patients undergoing Orthopedic Surgery. Varenicline (Chantix) is an anti-smoking medication that achieves significantly higher rates of smoking cessation. However, the effects of varenicline on bone healing are not known. By gaining a better understanding of this, physicians can determine if this powerful medication compromises the outcomes they are trying to achieve. The results of this study will help establish clinical practice recommendations for clinicians who treat tobacco users undergoing Orthopedic Surgery. This project will investigate how varenicline affects gene expression in bone forming cells. In vitro cell culture experiments will be conducted on osteoblastic cell lines and the levels of collagen I, ALPL, and osteocalcin will be measured. By working on this project, the student will learn: tissue culture, RNA processing, RT-PCR, experiment design, and data analysis.

Responsibilities/Desired skills: Completion of a basic molecular biology course. Prior lab experience is preferred but not required

Positions Available: 1