Mentor: Adam Bauer, Assistant Professor of Radiology, Assistant Professor of Biomedical Engineering
Lab description: Two major themes running through our lab’s research are mapping functional brain organization in the mouse and examining how changes in local neural activity are related to corresponding changes in blood flow. We are very interested in mapping functional network connectivity in the mouse brain, and how those connections evolve in healthy mice and models of disease, in particular stroke. To help us answer our questions, we use the latest advances mouse genetics and optogenetic targeting strategies.
1) Mapping brain activity and behavior in mice following focal ischemia.
2) Using deep learning to characterize functional vs. compensatory recovery after stroke.
For either project, the student would be involved in experimental design, data collection (e.g. functional neuroimaging) and image analysis. Depending on interests, students would also be able to take on a larger role in hardware development and data processing/analysis.
Mentor: Matthew Bersi, Assistant Professor, Department of Mechanical Engineering & Materials Science
Lab description: Research in the Bersi lab is generally focused on mechanisms of soft tissue remodeling in cardiovascular disease. Specific research interests include the interplay between immune cell activation and the mechanobiology of vascular cells in the context of remodeling in response to intraluminal vascular injury, hypertension, and aneurysm. We are particularly interested in the role of T cell polarization along the Th17/Treg axis on promoting phenotyping alterations of vascular smooth muscle cells as well as the impact of cell-cell adhesion proteins (e.g., cadherin-11) on cardiovascular tissue remodeling. Techniques in the Bersi lab include small animal surgical models of cardiovascular disease, soft tissue mechanical testing and material characterization, optics-based approaches such as histology and whole-mount tissue imaging, in vitro assays for assessment of cellular phenotype, analysis of gene transcription, immune cell isolation and polarization, and mathematical modeling. Using a combination of engineering approaches and molecular biological tools, we are investigating disease progression and therapeutic approaches in cardiovascular medicine.
Project: Ongoing projects in the Bersi lab with opportunities for student involvement are related to the development of a system for in-situ arterial pressurization in the mouse. Biomechanical analysis is a common ex vivo technique used to determine mechanical properties of aortic tissues such as distensibility, stiffness, and stored elastic energy. Traditional approaches require that tested segments be removed from the body, cleaned of excess perivascular tissues, and mounted in devices capable of measuring quantities such as arterial pressure, force, and diameter. However, increasing evidence suggests that such perivascular structures provide non-negligible external mechanical support and may be an important reservoir for effector cells that have direct impacts on vascular mechanobiology. To circumvent these limitations of traditional biomechanical analysis, the current project seeks to develop an in-situ mechanical testing system comprised of controlled intravascular pressurization and image-based measurement of vascular deformation. Outcomes of this project will be focused on 1) biomechanical characterization of perivascular tissues in different regions of the aorta, 2) in-situ pressurization of small vascular segments that are not testable using standard methods, and 3) tissue deformation near aortic branch sites. Students working on this project will gain experience with biomechanical analysis of vascular tissues, optical coherence tomography imaging, image processing (including segmentation and quantification), small animal tissue dissection, and various molecular biology techniques including histology and/or gene expression analysis.
Mentor: Yao Chen, Assistant Professor of Neuroscience, Cell Biology and Physiology, and Biomedical Engineering
Lab description: Neuromodulators such as dopamine, acetylcholine, and neuropeptides have profound effects on neural circuits and behavior. Altered neuromodulation is associated with most psychiatric disorders, major neurodegenerative disorders, and neuromodulatory systems are targets of almost all drugs of abuse. While specific behaviors have been linked to specific neuromodulators, and while many neuromodulator receptors and their downstream signaling pathways are known, how neuromodulators regulate behavior remains enigmatic.
The knowledge gap exists because our understanding of molecular signaling networks remains largely a static diagram of connections between molecules. Our laboratory attempts to fill the gap between molecular neuroscience and animal behavior by elucidating the spatial and temporal dynamics of biological signals, because their dynamics carry critical information that explain subsequent modifications of cells, circuits, and behavior.
Specifically, we aim to understand how the dynamics of neuromodulators and intracellular signals contribute to the function of neuromodulators, to learning, and to the function of sleep. We combine biosensor development, two photon fluorescence lifetime imaging microscopy, electrophysiology, as well as molecular, cellular, and biochemical approaches in mice to visualize molecular dynamics in action, perturb them with precise spatiotemporal control, and analyze the functional consequences. Our research promises to uncover principles of neuromodulator action, illuminate how molecular mechanisms produce behaviorally relevant features, and ultimately help treat psychiatric disorders.
Project: Despite the importance of sleep, it is unclear how sleep promotes many important functions (e.g. cardiovascular health, emotions, learning, immune functions). We will use fluorescence lifetime photometry combined with EEG/EMG analysis to identify biological signals that change between sleep and wakefulness. They will immediate generate hypotheses on the cellular functions of sleep. The student interested in this project needs to be comfortable handling live mice, detail oriented, and not afraid of new technology/software. The student will receive extensive mentoring and support.
Mentor: Abhinav Diwan, MD, Professor, Department of Medicine, Cardiovascular Division
Lab description: The Diwan lab is investigating the regulation of lysosome function in physiology and disease. Their program has discovered evidence for acquired lysosome dysfunction in cardiac myocytes and macrophages in the setting of myocardial infarction and cardiomyopathies and in protein aggregate induced cardiomyopathy and heart failure. His lab employs molecular, genetic, and surgical modeling techniques in animal models to investigate lysosome biology in cardiac stress and homeostasis using basic research approaches.
Projects: Specific research projects in the Diwan lab that will offer interdisciplinary training opportunities for undergraduate students are as follows. Project 1: The first project focuses on elucidating the role of specific genes (n=6) uncovered in a genetic screen of starvation survival in lysosome biogenesis transcription factor-deficient worms in regulating the starvation response in worms and mammalian cells. Students will test the role of individuals genes in mutant worm lines and cells targeted for loss of function of these genetic pathways to evaluate their role in starvation stress. Project 2: will focus on uncovering the redundancy of three members of the lysosome biogenesis transcription factor family, namely TFEB, TFE3, and Mitf, in genetically targeted murine embryonic fibroblasts. These data will be correlated with murine models with cardiac myocyte-specific deficiency of these transcription factors to understand their role in cardiac homeostasis. Project 3: is to evaluate the role of genetic mutations and stress-induced post-translational modifications in CRYAB, a cardiac enriched chaperone protein, in causing aberrant phase separation and protein aggregation, leading to proteotoxic cardiomyopathy. The undergraduates will work with targeted phase separation assays, as well as generic tool compounds to disrupt phase separation to assess the mechanisms whereby CRYAB becomes aggregate-prone. Project 4: A fourth project is focused on zinc-induced lysosomal remodeling in worms and mammalian cells. This is based on preliminary observations that toxic metals are sequestered within lysosomes to attenuate cellular toxicity. Students will evaluate worm models of gain and loss of function of the lysosome biogenesis program and quantify metals in the lysosomal compartment using state-of-the-art organelle isolation strategies and mass spectroscopy-based chemical assays.
Mentor: Adam Eggebrecht, Assistant Professor of Radiology
Lab description: Our Brain Light Lab of the Biophotonics Research Center, is a diverse and interdisciplinary team whose research focuses on developing novel tools that extend mapping of brain function beyond current limitations. We harness the power of diffuse optics to create portable and wearable systems for minimally constrained imaging of brain function. This technology facilitates mapping brain function in participants who are especially challenging to study with fMRI such as toddlers and children with autism and patients undergoing surgery or intensive care. Our efforts are focused on three broad areas: hardware development, software and algorithm development, and applications from basic science to clinical care. Hardware development projects concentrate on optimizing signal-to-noise, image quality, subject comfort, and portability. Software and algorithm projects include Finite Element Modeling of light propagation, image reconstruction speed and accuracy, spatial registration of multiple data types, and development of a self-contained toolbox, NeuroDOT (https://www.nitrc.org/projects/neurodot/), for acquisition and analysis of diffuse optical tomography data and extensions for uncovering statistically meaningful relationships between metrics of brain function and behavior. Current funded applications of focus include childhood development of brain function and behavior as it relates to autism spectrum disorder and congenital heart disease.
Project: While mortality rates have improved for children born with congenital heart disease, morbidity rates for patients who undergo corrective surgery and/or extracorporeal membrane oxygenation (ECMO) can have life-long effects. Current neuromonitoring technologies that can be deployed at the bedside have low sensitivity and predictive value for detecting changes in physiology that may underlie deleterious outcomes. The summer project provides opportunities for data collection during surgery and/or ECMO maintenance with our custom bedside neuroimaging device. Additionally, the project would involve opportunities for data analyses including the development of new strategies to relate variability in physiological status and brain networks with outcomes. The student would interact with team members from a variety of disciplines, work with state-of-the-art technology, and obtain computational experience.
Mentor: Song Hu, Associate Professor, Department of Biomedical Engineering
Lab description: Our laboratory combines optics and ultrasound for in vivo high-resolution imaging of structural, functional, metabolic, and molecular contrasts at multiple spatial and temporal scales. Our research efforts encompass three main aspects: pushing the technical envelope to cover temporal scales that range from fast cellular dynamics to chronic disease progression, revealing novel optical / acoustic contrast mechanisms to enhance imaging sensitivity and specificity, and bridging the gaps between mechanistic studies in animals and clinical practice in humans.
Project: Development of a high-speed miniature photoacoustic microscopy system for intravital imaging of the beating mouse heart. In this project, the intern is expected to work with a postdoc in the Hu lab on the system development, image acquisition, and data analysis, with a primary focus on the analytical aspect.
Mentor: Nathaniel Huebsch, Associate Professor, Department of Biomedical Engineering
Lab description: We use induced pluripotent stem cells, micro-fabrication and image processing technologies to study how mechanical stress combines with genetics to trigger the pathophysiology and molecular signatures of genetically inherited cardiomyopathy.
Project: The student will work with Huebsch lab team members to form arrays of cardiac micro-tissues derived from human induced pluripotent stem cells, perform high speed video microscopy of the tissues and use Matlab coding routines to convert these videos into information on tissue-level contractility, voltage and calcium handling. He/she will also assist in structural and biochemical analysis of the tissues and gain proficiency in these techniques.
Mentor: Kory Lavine, Assistant Professor of Internal Medicine
Lab description: Our laboratory is interested in understanding how the immune system can be manipulated to reduce inflammation, improve tissue healing, and leveraged to develop regenerative approaches.
Project: This project will explore the functions of human pluripotent stem cells-derived macrophages within the mouse heart. Key areas of interest will include how transplanted macrophages influence the organization, morphology, and transcriptional signatures of native endothelial cells, fibroblasts, and cardiomyocytes.
Mentor: Jeanne M. Nerbonne, PhD, Alumni Endowed Professor of Molecular Biology and Pharmacology, Departments of Medicine, Cardiovascular Division, and Developmental Biology
Lab description: A major goal of the research program in the Nerbonne lab is to define the physiological mechanisms that control the expression, properties, and functioning of myocardial Na+ (Nav) and K+ (Kv) channels, which are key determinants of myocardial membrane excitability, affecting the waveforms of action potentials in individual myocytes and the propagation of electrical activity through the heart. In addition, we are exploring the pathophysiological mechanisms contributing to the dysregulation of Nav and Kv channels in inherited and acquired cardiovascular diseases. A major focus of ongoing research in the lab is identifying the components of native myocardial Nav channels and defining the mechanisms involved in the regulation and modulation of these channels by accessory proteins. The following research project is presently accepting interested undergraduates to work under the direct oversight of a graduate student or postdoctoral fellow and with the guidance and mentorship of Dr. Nerbonne.
Project: Mechanisms linking voltage-gated sodium (Nav) channel accessory subunits to the regulation and dysregulation of membrane excitability in the mammalian heart: Considerable evidence suggests that native cardiac Nav channels function in macromolecular complexes of the Nav1.5 α subunit and multiple accessory proteins. The Nav1.5 α subunit, which forms the Na+ selective channel pore, has four homologous domains (DI-DIV), each with six transmembrane segments (S1-S6), connected by cytoplasmic linkers. The S1-S4 segments form the channel voltage-sensing domains, and the S5-S6 segments form the ion-selective pore. On depolarization, the voltage-sensing domains move and coupled to the pore through intracellular S4-S5 linkers, cause channel opening. Hydrophobic amino acids in the DIII-DIV linker, the IFM motif, are essential for inactivation. Native Nav channel function, however, is determined not only by the α subunit but also by the associations with intracellular and transmembrane accessory subunits. In collaboration with the laboratory of Jon Silva, Associate Professor of Biomedical Engineering, ongoing studies are detailing the molecular mechanisms underlying the regulation of myocardial Nav1.5-encoded channels by intracellular fibroblast growth factor 12 (iFGF12), the predominant iFGF expressed in the human heart. We are also testing the hypothesis that the iFGF12A variant, which we have found is upregulated in failing human hearts, has functional effects on the biophysical and pharmacological properties of myocardial Nav1.5-encoded channels distinct from the effects of iFGF12B. An additional goal is to test the hypothesis that another intracellular Nav channel auxiliary subunit, calmodulin (CaM), which binds to the C-terminus of Nav1.5 very near to the site of iFGF12 binding, modulates the effects of iFGF12B and/or iFGF12A on Nav1.5 channel gating. We are combining cellular electrophysiological and molecular genetic approaches to accomplish these goals. We are also developing a mathematical model of the Nav currents in native (mouse and human) myocytes and will use these in dynamic clamp experiments to manipulate the properties or the amplitudes of the Nav currents computationally in situ and in real-time during current-clamp recordings. In addition, biochemical and mass spectrometry-based proteomic approaches are being employed to identify the molecular components of native (mouse and human) myocardial Nav channel macromolecular protein complexes.
Mentor: Colin Nichols, Carl Cori Professor, Department of Cell Biology and Physiology
Director, Center for the Investigation of Membrane Excitability Diseases
Lab description: The Nichols Lab develops, introduces and uses a wide range of molecular biological and biophysical approaches, as well as in vivo gene manipulation to address questions in proteins, cells and animals, and now in humans. These efforts are leading them to a detailed understanding of both molecular mechanisms of channel activity, and roles of ion channels in multiple disease processes including diabetes, heart failure, pulmonary disease and epilepsy.
Project: The student will use cell lines expressing Cantu Syndrome mutant KATP channels and assess the efficacy of candidate inhibitory drugs for therapy, using fluorecence based high throughput assays.
Mentor: Michelle Oyen, Associate Professor, Department of Biomedical Engineering
Lab description: Our lab is developing engineering tools to understand and intervene into preterm birth, with a focus on the placenta and the maternal-fetal interface. The maternal and fetal vasculatures do not directly mix but the transport distances for oxygen and nutrients between them are small. One major cause of preterm birth is pre-eclampsia, when the placenta causes potentially fatally high blood pressure to develop in the mother. We use both experimental tools and computational modeling to try and understand the placenta’s role in this and related conditions.
Project: Both maternal and fetal outcomes in pregnancy are reliant on the first trimester development of the placenta, the maternal-fetal interface. Fetal trophoblast cells invade the maternal uterine lining and direct the remodeling of uterine spiral arteries. The signaling cues that direct this invasion are not fully known, nor are there diagnostic criteria to indicate that this process has been suboptimal. Poor outcomes in pregnancy, including pre-eclampsia and fetal growth restriction, occur when the placental vascular bed is insufficient for transport. Clinical signals of poor maternal and fetal outcomes may not appear until the third trimester, long after the early placental development has ceased. To study this process, we are developing assays using biomimetic hydrogels as an artificial extracellular matrix to model the physical and chemical environment during trophoblast invasion. The work is being conducted in collaboration with scientists in developmental biology, who derive trophoblast-like cells from induced pluripotent stem cells. The long-term goal of the project is to develop biomarker assays for signaling either poor or adequate trophoblast invasion, to allow for early diagnosis of future potential placental malfunction.
Mentor: Stacey Rentschler, M.D., Ph.D., Associate Professor, Department of Medicine, Cardiovascular Division
Research in the Rentschler lab is centered around three broad themes: defining the developmental and molecular mechanisms underlying congenital and acquired arrhythmias, defining the transcriptional and epigenetic mechanisms that regulate the programming and reprogramming of cellular electrophysiological phenotypes, and harnessing the power of developmental signaling cascades to treat conduction disorders. Specifically, we focus on the transcriptional and epigenetic pathways activated in response to Notch and Wnt signaling during development and in response to cardiac injury, which mediate changes in ion channel gene expression and cellular electrophysiology. Our group previously demonstrated that reactivation of developmental signaling pathways including Notch and Wnt could electrically remodel cardiomyocytes or “reprogram” them to adopt a new electrical phenotype in animal models. In heart failure, reactivation of the Notch signaling pathway may contribute to transcriptional changes influencing ion channel gene expression that may predispose to the development of lethal arrhythmias. In contrast, reactivation of distinct signaling networks within the adult myocardium may provide new avenues for regenerative medicine approaches for the treatment of arrhythmias, such as in the development of a biological pacemaker.
Projects: Current projects in the Rentschler lab include the development of a methodology for culturing organotypic cardiac slices from atria and ventricles from explanted human donor hearts rejected from transplantation. Functional readouts include optical mapping with voltage-sensitive dyes to visualize and quantify electrophysiological properties, as well as microelectrode recordings to assess changes in cellular physiology. In addition, we are performing genome-wide gene expression and epigenetic studies on mouse and human cardiac tissue to decipher the complex regulatory mechanisms that govern the expression of important regulators of electrophysiology within regions of the heart in both health and disease states. This methodology will allow us to test the response of human cardiac tissue to selected therapeutics, with the goal of expediting the prolonged process involved in getting new therapeutics validated for use in humans. More recently, Dr. Rentschler has built a team-science approach and led a multidisciplinary group of pathologists, cancer biologists, radiation oncologists, and cardiac electrophysiologists at Washington University to understanding mechanisms of cardiac irradiation to treat ventricular tachycardia first observed in the ENCORE-VT clinical trial.
Mentor: Jonathan Silva, Associate Professor, Department of Biomedical Engineering
Lab description: We want to develop precision approaches to arrhythmia therapy by identifying biophysical features of ion channels that predict patient drug response.
Project: We have developed an automated protocol to assess anti-arrhythmic drug response in patients with different genetics. Students involved with this summer project would help with the collection of this data and working on predictive methods to connect it to patient response.
Mentor: Jessica Wagenseil, Vice Dean for Faculty Advancement & Professor, Department of Mechanical Engineering & Materials Science
Lab description: The Wagenseil Vascular Mechanics Laboratory focuses on the mechanical behavior of large, elastic arteries during development and disease. We are interested in how the arterial wall remodels to maintain appropriate mechanical properties for heart function.
Project: Elastic fibers are critical for elastic recoil in the large arteries during the cardiac cycle. Elastic fiber assembly can be compromised and elastic fiber degradation can be expedited in genetic and acquired vascular disease, compromising arterial function. The student will perform studies to determine whether or not specific reagents can increase elastic fiber assembly and/or prevent elastic fiber degradation. Methods include biochemistry, cell culture, microscopy, and in vitro mechanical testing of mouse aorta.
Mentor: Christian Zemlin, Associate Professor of Surgery, Division of Cardiothoracic Surgery, Director of the Cardiothoracic Surgery Research Lab
The Zemlin laboratory studies cardiac arrhythmia mechanisms, particularly the mechanism of atrial fibrillation. We use both optical mapping with voltage-sensitive fluorescent probes and extracellular electrodes to monitor cardiac electrical activity. We are also interested in the surgical treatment of cardiac arrhythmias, and we are developing a new ablation modality for cardiac tissue based on electroporation with nanosecond pulsed electric fields.
Projects: One of our current projects that would be interesting for undergraduate students to participate in is sonogenetics. In this project, we study rat hearts that have been transfected with mechanosensitive ion channels, in particular, how sensitive these hearts are to stimulation with ultrasound. We have an existing optical mapping set up to monitor the electrical activity of rat hearts, which needs to be extended in several ways: 1) We need to extend our setup to allow for the placement and manipulation of different ultrasound probes; 2) We need to perform optical mapping experiments in which we use the ultrasound probes to stimulate the genetically modified hearts; 3) the movies that are recorded during or stimulation attempts need to be processed and evaluated to determine the efficacy of ultrasound stimulation. All these tasks offer great opportunities for undergraduate student participation.
Mentor: Tiezhi Zhang, Associate Professor of Radiation Oncology
Lab description: We are developing novel x-ray imaging technologies for image guided radiotherapy and diagnostic imaging. Cardiac ablation is a hot topic in radiotherapy. We are developing micro-CT with cardiac gating for small animal studies.
Project: Micro-CT is of importance for preclinical research. We are developing a novel inverse-geometry micro-CT that can improve the radiation dose efficiency and super-high resolution. However, cardiac motion causes artifacts in the images. We will need a device to monitor the cardiac cycles of the mice for cardiac gated micro-CT imaging. The summer fellow will work togher with the PI and graduate students to develop an ECG device for mice and interface with micro-CT system.
Mentor: Jie Zheng, Associate Professor of Radiology
Our lab is focusing on development and translational of cardiovascular imaging techniques for basic science research and clinical study. The major imaging modalities are magnetic resonance imaging (MRI) and positron emission tomography (PET). Current projects involve applications of myocardial oxygenation in cardiac patients and peripheral tissue perfusion / metabolism measurements in patients with diabetes and peripheral arterial disease (PAD).
Project 1: This study will evaluate a newly developed cardiac MRI method in human subjects (normal volunteers and cardiac patients). Some of MRI data will be compared with PET images for cross correlation. The goal is to develop and translate a robust non-invasive method for fast assessment of myocardial oxygen extraction fraction (OEF) that represent the balance of oxygen supply and demand. This will enhance clinical understanding to the severity of various cardiac diseases including coronary artery disease, heart failure, etc.
Project 2: We developed comprehensive MRI tools for evaluating peripheral perfusion and metabolism. The goal of this project is to apply and evaluate the disorders in peripheral muscle associated with vascular and metabolic diseases in skeletal muscle of patients with diabetes, heart failure, PAD, etc. This project involves exercise physiology, imaging acquisition, and data analysis.
Mentor: Chao Zhou, Associate Professor, Department of Biomedical Engineering
Lab description: We are interested in developing novel optical imaging technologies for biomedical applications, especially in developing optical coherence tomography (OCT) and microscopy (OCM) technologies to perform “optical biopsy” and generate 3D in situ images of tissue morphology, function and pathological status in real-time without the need to remove and process specimens.
We are also interested in applying these technologies to a variety of biological and clinical applications, including cancer research, neuroscience, developmental biology and tissue engineering.
Project: In order to effectively place a gene of interest into a tissue of interest, a driver gene must be used. In optogenetics, this gene of interest encodes for an opsin that, such as channelrhodopsin or halorhodopsin, and in our lab, we design crosses so that these opsins are specific to the heart region, utilizing the GAL4-UAS system. Previous work in our group has shown that the Hand driver is effective at producing flies with heart specific opsins that are able to respond to heart pacing experiments. As we explore ways to further optimize our cardiac optogenetic pacing experiments, we would like to explore more drivers, comparing their effectiveness at delivering the gene of interest to the heart for optogenetic pacing experiments, both through looking at tissue specificity, using tools such as multiphoton imaging and fluorescent markers, and by comparing the results of pacing experiments at different laser power levels.