Embedded Files
Rotation Schedule
Rotation 1: August 19 - September 27 (Agreement due Aug 12)
Rotation 2: September 30 - November 9 (Agreement due Sept 23)
Rotation 3: November 11 - December 21 (Agreement due Nov 4)
You can download the agreement form here. Please send it to bioe-grad@umd.edu before the due date.
Fischell Department of Bioengineering labs are listed first, followed by affiliated labs, both on- and off-campus, in alphabetical order by the PI's last name.
Fischell Department of Bioengineering Faculty Labs
PI Name: Dr. William Bentley
PI E-mail: bentley@umd.edu
Lab Name: Bentley Lab
Lab Address (room, building, campus): 5th floor, A. James Clark Hall, College Park
Lab Overview:
We explore cell-cell communication among microbes. We recently proposed "electrogenetics" as a way to electronically programming genetic circuits. We are exploring the creation of devices that enable electrogenetics.
Project Description
We will electroassemble genetically engineered cells onto electrodes and then activate them by providing a reducing potential to generate H2O2. This signaling is used to activate circuits using the OxyR regulon.
Project skills/experience to be gained
Electroassembly, bacterial cell culture, quorum sensing signal assays.
Project expectations/requirements
We would like to have a powerpoint presentation at the end of the rotation.
PI Name: Dr. Alisa Clyne
PI E-mail: aclyne@umd.edu
Lab Name: Vascular Kinetics Laboratory
Lab Website: https://vascularkinetics.com/
Lab Address (room, building, campus): 4113, A. James Clark Hall, College Park
Lab Overview:
Our laboratory uses engineering methods to understand vascular diseases ranging from atherosclerosis to cancer to Alzheimer's disease. We study how cells respond to mechanical forces (e.g., blood flow) and metabolic changes (e.g., high glucose) by integrating in vitro, ex vivo, in vivo, and in silico methods. We believe bioengineering benefits from diverse voices and an inclusive environment. Each individual adds to our lab in unique ways, and we work together to build equity in bioengineering.
Project #1 Description
We know that high fat and high sugar foods are bad for our bodies, but we don’t know how nutrient excess impacts our blood cells and blood vessels in all their complexity. Our laboratory is using computational metabolomics, 3D in vitro models (artery-on-a-chip), animal models (high fat diet fed rats), and human samples (blood from people with diabetes) to quantitatively study how the nutrients in your blood impact the interactions between blood cells (red blood cells, leukocytes) and blood vessels.
Project #1 skills/experience to be gained
Skills and experiences include: human endothelial cell culture, human red blood cell and monocyte isolation, extracellular vesicle isolation, metabolomics, proteomics, computational models.
Project #2 Description
We are engineering a contractile artery-on-a-chip to study how environmental factors and blood cells impact vascular health. We plan to create models to study peripheral arteries and brain arteries for diseases as diverse as atherosclerosis and Alzheimer’s disease. We will also use the artery-on-a-chip to explore vascular differences in men and women and in people with diabetes.
Project #2 skills/experience to be gained
Skills and experiences include: 3D endothelial and smooth muscle cell culture, biomaterials synthesis, microfluidics, 3D printing, confocal microscopy, mouse models, pressure myography, human studies, flow-mediated vasodilation
Project expectations/requirements
The student is expected to be an active participant in all lab activities, including weekly lab meetings, individual meetings, and journal clubs. Each week, the student will submit a progress report and at the end of the rotation, the student will present his/her results to the rest of the lab.
PI Name: Dr. Gregg Duncan
PI E-mail: gaduncan@umd.edu
Lab Name: Respiratory NanoBioengineering Lab
Lab Website: http://duncan.umd.edu
Lab Address (room, building, campus): 4113, A. James Clark Hall, College Park
Lab Overview:
Our research group aims to understand how the lung microenvironment influences the onset and progression of pulmonary diseases such as asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD). We integrate nanobiotechnology and bioengineering approaches to study the fundamental processes critical to lung health such as mucus clearance and viral infections to inform the design of novel therapeutic platforms.
Project Description
Mucociliary clearance (MCC) provides our first line of defense against potentially harmful inhaled materials. Disruption of this apparatus has immense consequences in those afflicted with chronic, potentially life-threatening lung diseases. Our knowledge of this important biological process is incomplete and requires the development of new models to define what makes effective mucus in health and what leads to dysfunction in disease. Building on prior work [Song et al, Science Advances (2022)], we seek to develop CRISPR/Cas9 engineered tissue culture models to allow for direct control of mucus composition and hypersecretion that better mimic the pathophysiology of asthma. Developing the models will provide new tools in understanding important aspects of the lung airway microenvironment.
Project skills/experience to be gained
3D cell culture techniques, CRISPR/Cas9 gene editing, particle tracking microrheology, confocal microscopy
Project expectations/requirements
Students will meet weekly with Dr. Duncan to discuss research progress and plan experiments. At the end of the rotation, students will give a final presentation to discuss their results.
PI Name: Dr. John Fisher
PI E-mail: jpfisher@umd.edu
Lab Name: Tissue Engineering & Biomaterials Lab
Lab Website: https://tebl.umd.edu
Lab Address (room, building, campus): 3121, A. James Clark Hall, College Park
Lab Overview:
The Tissue Engineering and Biomaterials Laboratory (TEBL) investigates biomaterials, stem cells, bioprinting, and bioreactors for the regeneration of lost tissues, particularly bone, cartilage, and dermal tissues, as well as the fabrication of tissue models. The laboratory has published over 225 articles, book chapters, editorials, and proceedings (17,400+ citations / 74 h-index). Dr. Fisher has advised over 25 doctoral students - these students have received numerous awards, including a Fulbright Fellowship, NIH Pre/Postdoctoral Fellowship, NSF Graduate Fellowship, and TERMIS Outstanding Graduate Student Researcher. TEBL has funded projects from NIH, MSCRF, the Royal Society of New Zealand, and the Osteo Science Foundation.
Project Description
Rotation students will gain a broad set of skills emphasized in TEBL. Working with existing TEBL graduate students, rotation students will experience efforts in polymer synthesis and biomaterials fabrication, cell culture, stem cell biology, bioink preparation, computer-aided design of engineered tissues, 3D printing, and bioprinting. In addition, TEBL has a growing effort in AI/ML directed tissue engineering with an emphasis on precision printing. These efforts will be executed in the context of orthopedic tissues, dermal tissues, and tissue models. At the end of the rotation, students interested in working in TEBL will discuss with Dr. Fisher the specific projects available for their doctoral thesis work.
Project skills/experience to be gained
biomaterials, cell culture, molecular biology, 3D printing, bioprinting, bioreactors
Project expectations/requirements
Rotation students are expected to experience (1) TEBL emphasized skills, (2) TEBL’s approach to solving critical research problems, and (3) TEBL’s day-to-day work environment.
PI Name: Dr. Xiaoming He
PI E-mail: shawnhe@umd.edu
Lab Name: Multiscale Biomaterials Engineering (MBE) Laboratory
Lab Website: https://shawnhelab.umd.edu/
Lab Address (room, building, campus): 3124, A. James Clark Hall, College Park
Project #1 Description
Cancer tissue engineering
Project #1 skills/experience to be gained
microfluidics, hydrogel microencapsulation, cancer stem cell culture and characterization
Project #2 Description
Cancer immunotherapy
Project #2 skills/experience to be gained
Nanotechnology, drug delivery, cancer stem cell culture and characterization
Project expectations/requirements
Weekly progress report with data from experiments and data analysis
PI Name: Dr. Steve Jay
PI E-mail: smjay@umd.edu
Lab Name: Jay lab
Lab Website: https://jaylab.weebly.com/
Lab Address (room, building, campus): 3113, A. James Clark Hall, College Park
Lab Overview:
Our research aims to uncover new biological insights towards the design, production, and delivery of biotherapeutics. We are particularly interested in cell-derived products from both humans and bacteria, especially extracellular vesicles (EVs, including exosomes) and bacterial extracellular vesicles. Overarching goals of the lab include developing therapeutics towards clinical translation and endowing trainees with the skills and knowledge necessary to become leaders in the biotechnology and pharmaceutical industries.
Project Description
We will work together to define and address big questions/challenges related to bacterial extracellular vesicle (BEV) therapeutic development. Topics of current interest include investigating the role of BEVs in host-pathogen interactions, exploring the potential of BEVs as neurotherapeutics, and developing novel technology to control BEV cargo and biodistribution.
Project skills/experience to be gained
Molecular biology techniques, cloning, DNA/RNA purification, BEV separation (chromatography) and characterization (immunoblots, particle analysis, microscopy).
Project expectations/requirements
1. Learn hands-on skills in the lab; contribute to ongoing project working with current lab personnel.
2. Work with me to develop a potential thesis project plan (1-2 page write-up)
NEWLY ADDED PI Name: Dr. Sara Molinari
PI E-mail: saramol@umd.edu
Lab Name: Living Material Design Lab
Lab Website: https://molinari.umd.edu
Lab Address (room, building, campus): 3107, A. James Clark Hall, College Park
Lab Overview:
Engineered Living Materials (ELMs) are composites of living cells embedded into a biopolymer matrix. They are inspired by natural living materials but use synthetic biology to introduce non-natural properties. We aim to engineer multifunctional ELMs for transformative applications in different fields.
Project Description
The students rotating in the Molinari Lab will work on genetically engineering bacterial cells to functionalize their extracellular surface. Based on the specifics of the functionalization, modified cells will be screened for their ability to aggregate and/or adhere to a specific surface.
Project skills/experience to be gained
Cloning pipeline: synthetic DNA plasmids design and assembly. Includes, primer design for PCR, Gel extraction, Golden Gate Assembly, and interpretation of sequencing results. Depending on the progress of the students, the rotation could also involve optical and confocal microscopy.
Project expectations/requirements
Students are expected to complete the cloning of at leat one plasmid under the guidance of current graduate students in the lab.
PI Name: Dr. Erika Moore
PI E-mail: emt@umd.edu
Lab Name: Moore Lab
Lab Website: https://www.themoorelab.com/
Lab Address (room, building, campus): 3113, A. James Clark Hall, College Park
Lab Overview:
The Moore Lab mission is to engineer biomaterial models that leverage the regenerative potential of the immune system across health inequities. We have 4 major projects which include: 1) investigating how the extracellular matrix directs macrophage function, 2) investigating the role of age in macrophage-microvessel development, 3) developing a model of lupus-induced vasculitis, and 4) investigating how ancestry dictates macrophage function. We execute on our projects by developing compassionate innovators equipped to transform biomedical research.
Project #1 Description
Macrophage immune cells determine tissue homeostasis, wound healing, and tissue regeneration through signals from their microenvironment. While we understand how some cues direct macrophage function, as a field we do not understand how the extracellular matrix (ECM) directs macrophage function. The goal of this project is to understand how the ECM, specifically, ECM ligands, direct macrophage function through design of biomaterial tools. The ability to direct macrophage function and therefore, determine whether an acute wound will become a non-healing chronic wound, or fully heal and regain proper tissue homeostasis is determined in part by integrin ligand receptor interactions. There is a critical knowledge gap as we do not understand how ECM integrin ligands direct macrophage function. The central hypothesis is that ECM-derived ligands from collagen, laminin, and fibronectin direct macrophage activation towards an inflammatory state (via 61 and 41) or towards a tissue healing state (via 21 and 11). Our preliminary work targeting 21integrin signaling via collagen-1 derived peptide, DGEA, inhibits inflammatory macrophage activation. The proposed work will combine a peptide-polymer strategy to achieve three research objectives: 1) Quantify integrin ligands influence on macrophage function via 3D peptide screening, 2) Design combinatorial ECM ligand biomaterials to quantify ECM niche impact on macrophage function; and 3) Quantify the influence of age on human-donor macrophage function via combinatorial ECM ligand biomaterials.
NOTE: This is a NSF CAREER Funded project!
Project #1 skills/experience to be gained
Skills/experiences associated with this project include: (1) learning about integrin receptor-ligand interactions, (2) synthesis of polymer composites, (3) analysis of macrophage phenotype for immunocytochemistry, genetic expression, and protein expression, and (4) primary macrophage isolation/culture from multiple donors.
Project #1 expectations/requirements
Skills/experiences associated with this project include: (1) learning about integrin receptor-ligand interactions, (2) synthesis of polymer composites, (3) analysis of macrophage phenotype for immunocytochemistry, genetic expression, and protein expression, and (4) primary macrophage isolation/culture from multiple donors.
Project #2 Description
Aging is a multifaceted process influenced by a combination of genetic, environmental, and lifestyle factors. In our project, we aim to understand how aging impacts macrophage cell function and communication, particularly in the context of tissue regeneration and wound healing. While it is well-documented that aging affects clinical wound healing, the underlying cellular and molecular mechanisms remain poorly understood. Our hypothesis is that aging leads to distinct changes in macrophage cellular responses during wound healing. The overall goal of our research program is to utilize biomaterial models to explore how aging influences the wound healing process.
Our proposed research will address two main questions: (1) How does aging influence macrophage cellular physiology? (2) How does aging affect cellular phenotype?
Project skills/experience to be gained
Skills and experiences associated with this project include:
Understanding how aging impacts macrophage cell functions.
Synthesizing and characterizing polymer composites for biomaterial scaffolds.
Analyzing cell phenotypes using immunocytochemistry, genetic expression, and protein expression techniques.
Isolating and culturing primary cells from donors of different ages.
Project expectations/requirements
Conduct a literature review on the contributions of aging to cellular function and present a synthesis/summary of the findings.
Design a study to create ECM environments that mimic different stages of wound healing in aged and young tissues.
Successfully encapsulate macrophages into a hydrogel system.
Create and analyze the two ECM wound environments, correctly interpret the results, and present your findings.
The final deliverable will be a PowerPoint presentation detailing the study design, methods, results, and proposed next steps.
PI Name: Dr. Jenna Mueller
PI E-mail: mueller7@umd.edu
Lab Name: Global Biomedical Devices Laboratory
Lab Website: https://mueller.umd.edu/
Lab Address (room, building, campus): 4107, A. James Clark Hall, College Park
Lab Overview:
Over 70% of cancer-related deaths occur in low and middle-income countries (LMICs), primarily due to a lack of access to cancer diagnosis and treatment services. The Mueller lab develops affordable, accessible diagnostic and therapeutic technologies to improve the management of cancers in LMICs. We use engineering design methods, rapid prototyping and fabrication, various types of bioimaging, chemical ablation, bench testing, and tissue and animal models to develop biomedical technologies for improving cancer management.
Project #1 Description
Laparoscopic surgery is the standard of care in high-income countries for many procedures, including cancer excisional surgeries, in the chest and abdomen. It avoids large incisions by using a tiny camera and fine instruments manipulated through keyhole incisions, but it is generally unavailable in low- and middle-income countries (LMICs) due to the high cost of installment (>$200,000), lack of qualified maintenance personnel, unreliable electricity, and shortage of consumable items. Patients in LMICs would benefit from laparoscopic surgery, as advantages include decreased pain, improved recovery time, fewer wound infections, and shorter hospital stays. We are developing a low-cost, durable, and reusable laparoscope called the KeyScope laparoscope for use in LMICs. Rather than having an expensive light source and camera coupled to a fragile fiber optics, the KeyScope laparoscope prototype contains a color complementary metal-oxide-semiconductor (CMOS) detector and ring of LEDs that has been moved to the front of the device. This enables a significant decrease in cost and complexity (cost of goods ~$1000) while also maintaining the image quality of a standard-of-care laparoscope. We are currently: 1) optimizing the design of the KeyScope laparoscope and 2) developing a portable testing chamber to evaluate the performance of each unit.
Project #1 skills/experience to be gained
Skills/experiences associated with this project include: (1) learning about surgery in LMICs and laparoscopic equipment, (2) rapid prototyping and fabrication, (3) optics and optomechanics, and (4) engineering design to improve on an aspect of either the KeyScope or portable testing chamber.
Project #1 expectations/requirements
Expectations/requirements associated with this project include: (1) reading literature on surgery in LMICs and laparoscopic equipment and presenting a synthesis/summary of the literature, (2) building a prototype of the KeyScope laparoscope and testing/analyzing its performance, (3) brainstorming/demonstrating how to improve an aspect of the KeyScope or portable testing chamber, and (4) the final deliverable will be a powerpoint presentation of the prototype, testing methods, and results.
Project #2 Description
In low and middle-income countries (LMICs), up to 80% of women diagnosed with pre-cancerous lesions in the cervix do not return for follow-up care, primarily due to treatment being inaccessible. High mortality rates are a consequence. We have developed an accessible treatment, which involves injecting ethanol into a lesion to cause necrosis, to treat women at the time of diagnosis. Addition of a water-insoluble but ethanol-soluble polymer, ethyl cellulose, to the ethanol results in a phase change within tissue, which acts to localize ethanol within the target zone. The ethanol-rich gel provides prolonged contact between ethanol and tissue, leading to effective localized treatment within lesions. We are currently investigating interacting effects of multiple injection parameters vs. the resulting distribution volume in tissue. These experiments are guiding design of an injection device to ablate the zone needed to treat cervical pre-cancers.
Project #2 skills/experience to be gained
Skills/experiences associated with this project include: (1) learning about cervical cancer in LMICs and different types of ablative therapies, (2) learning about different types of bio-imaging (CT, ultrasound, fluorescence microscopy) and how they can be used to image distribution volume of ethanol in tissue, (3) learning how to work with cervical tissue, and (4) conducting studies in cervical tissue to investigate how injection parameters impact distribution volume.
Project #2 expectations/requirements
Expectations/requirements associated with this project include: (1) read literature on cervical cancer in LMICs and ablative therapies and present a synthesis/summary of the literature, (2) design a study to fully investigated one delivery parameter and its impact on distribution volume in cervical tissue, (3) successfully use a bioimaging device to evaluate distribution volume, (4) conduct the proposed study in cervical tissue, correctly analyze the resulting images, and present your data. The final deliverable will be a powerpoint presentation of the study design, methods, and results.
PI Name: Dr. Giuliano Scarcelli
PI E-mail: scarc@umd.edu
Lab Name: translational photomedicine
Lab Website: http://www.umdoptics.com
Lab Address (room, building, campus): 1st Floor, A. James Clark Hall, College Park
Lab Overview:
Our lab studies the interaction of light and matter to devise novel technology for biological research and clinical medicine. We cover all stages of the translational spectrum as we develop advanced optical technology; we build instruments; and, we use our instruments for biological research and in clinical trials. We have developed modalities to map properties (e.g. mass, stiffness) that are impossible to measure with traditional techniques but with important applications.
Project #1 Description
In the past few years, we have been developing an all-optical approach, named Brillouin microscopy, which uses the longitudinal elastic modulus as a label-free imaging contrast at high resolution, non-perturbatively, and without contact. We have also previously established Brillouin microscopy sensitivity for mechanical analysis of relevant biology applications. However, current Brillouin microscopy instruments rely on point-scanning and are limited in speed making it difficult to perform rapid and/or volumetric analysis of many phenomena in the metastatic cascade. To overcome these challenges, we are developing a multiplexed Brillouin microscopy (MBM) configuration with dramatically increased instrument speed/accuracy and validate our microscopy platform for biology studies.
Project #1 skills/experience to be gained
optical alignment
spectroscopy
biomechanics
Project #1 expectations/requirements
Commitment to learn optics and instrument development
Project #2 Description
Keratoconus and surgical correction of myopia are separate but interrelated issues of major significance for which a clear unmet need is the measurement of local corneal biomechanical properties. Indeed, the lack of effective biomechanical measurements forces clinicians to rely on morphologic surrogates, e.g. curvature and thickness, which are insufficient. We have developed a highly sensitive clinical instrument based on Motion-Tracking (MT) Brillouin microscopy and demonstrated the superior performance of biomechanical vs morphologic imaging in identifying early-stage and subclinical keratoconus; and, characterized biomechanical alterations after refractive surgery. Here, we will work with a next generation instrument to realize the clinical potential of MT-Brillouin microscopy to predict keratoconus progression risk. This project for the student side can go in many directions from measurement and cornea biomechanics application, to hardware/software for rapid acquisition and image processing, to Finite Element Modeling to use mechanical maps in clinical outcome predictions.
Project #2 skills/experience to be gained
biomechanics
hardware/software
image processing
FEM
Project #2 expectations/requirements
Commitment to learn and deepen one of the aspects of this research program.
PI Name: Dr. Ian White
PI E-mail: ianwhite@umd.edu
Lab Name: Amplified molecular sensors lab
Lab Website: https://terpconnect.umd.edu/~ianwhite/
Lab Address (room, building, campus): 3107, A. James Clark Hall, College Park
Lab Overview:
Molecular diagnostics, especially infectious disease, and frequently point-of-care diagnostics.
Project Description
Point-of-care diagnostics of viral disease.
Project skills/experience to be gained
qRT-PCR, RT-LAMP, assay preparation.
Project expectations/requirements
Independently perform point-of-care assays, present weekly research updates.
PI Name: Dr. Alex Xu
PI E-mail: alexmxu@umd.edu
Lab Name: Xu Spatial Biology Lab
Lab Website: https://blog.umd.edu/xuspatialbio/
Lab Address (room, building, campus): 3120, A. James Clark Hall, College Park
Lab Overview:
I'm joining the department this fall, and I'm interested in how cells and proteins organize in tissue to drive cancer behavior and immunotherapy. We'll use highly multiplexed spatial protein and RNA analysis and bioinformatic strategies to study cancer (lymphoma, ovarian cancer, colorectal cancer), with the goal of predicting patient outcomes, predicting therapy targets, and eventually developing novel immunotherapy.
Project #1 Description
Spatial architecture of lymphoma: We collected tissue from hundreds of patients with different types of lymphoma and analyzed them with spatial methods. We want to discover how immune cells and tumor interact spatially and if there are spatial features that predict outcomes
Project #1 skills/experience to be gained
Bioinformatics, spatial omics, cancer biology, biomarkers, clinical collaborations
Project #1 expectations/requirements
Mostly dry lab to start, familiarity with R/Python, interest in math/bioinformatics.
This project is nearing completion, would love for the student to get started here to join the publication.
If time allows, we will begin wet lab work, processing slides for multiplexed imaging/histology.
Project #2 Description
Machine learning predictors of cell therapies: We developed a strategy to use machine learning to predict how spatial features of tissues are controlled. We want to apply the method to new types of cancers and develop it further to predict how cell-specific or extracellular signals contribute
Project #2 skills/experience to be gained
Bioinformatics, spatial omics, cancer biology, machine learning
Project #2 expectations/requirements
Mostly dry lab to start, familiarity with R/Python, interest in math/bioinformatics
This project is more focused on bioinformatic methods, not a particular disease
If time allows, we will begin wet lab work, processing slides for multiplexed imaging/histology
Please note that Dr. Xu is a new faculty member joining the department in August 2024.
PI Name: Dr. Nan Xu
PI E-mail: nanxu@umd.edu
Lab Name: INSPIRE (Imaging and Neurocomputations for Precision Informatics Research) Lab
Lab Website: https://www.inspirelab.site/
Lab Address (room, building, campus): A. James Clark Hall, College Park
Lab Overview:
Our research lies in the interphase of data science and brain science. We aim to uncover brain function and cognitive mechanisms by modeling and analyzing the spatiotemporal brain dynamics. Employing multimodal functional neuroimaging data (e.g., fMRI-BOLD, LFP, optical imaging, MEG, etc.) from animals, humans, and patients, we decode complex processes shaping brain function and disease. This approach yields innovative insights for both fundamental and translational brain science.
Project #1 Description
This project investigates brain activity dynamics across species using functional neuroimaging data to analyze the consistency and differences in spatiotemporal patterns between rodents and humans. It employs analytical methods such as correlation-based detection and complex principal component analysis to identify these patterns. Initial findings indicate similarities in spatiotemporal patterns across both species, highlighting three distinct patterns observed in rodents and humans. Comparative analysis will validate these findings and assess the efficacy of various analytical approaches. During the rotational session, the tasks are as follows:
Task 1: Implement various preprocessing methods and utilize different analytical toolkits to detect spatiotemporal brain activity patterns in rodents and humans.
Task 2: Evaluate these patterns across cortical and subcortical gradients to compare species and analyze differences between analytical procedures.
Project #1 skills/experience to be gained
Neuroimaging data preprocessing skills.
Advanced neuroimaging data analysis using correlation-based detection and complex principal component analysis (PCA).
Comparative analysis of spatiotemporal brain activity patterns between rodents and humans.
Proficiency in using Matlab and Python toolkits for pattern detection in neuroimaging data.
Interdisciplinary research experience integrating neuroscience and data science methodologies.
Project #1 expectations/requirements
Proficiency in Matlab and Python
Basic knowledge in data science and statistics.
Familiarity with or a willingness to learn about neuroscience principles applicable to both rodents and humans.
Project #2 Description
Obesity is a rising concern in US children, affecting nearly 40% of the population. There's growing evidence of its neurological implications. Through fMRI, we can explore these neural interactions and patterns related to obesity. In collaboration with collaborative with Dr. Ellen Schur’s team at the UW Medicine Diabetes Institute, this project focuses on crafting new fMRI biomarkers to depict brain dynamics in obese children. With the identification of hypothalamus inflammation as a key factor in obesity influencing significant network connectivity, we'll explore new fMRI biomarkers based on large-scale spatiotemporal patterns, spotlighting wakefulness cycles potentially controlled by the hypothalamus. During the rotational session, the tasks are as follows:
Task 1: process the fMRI data to extract different parcellated timeseries.
Task 2: Using Matlab to identify dynamic patterns associated with wakefulness cycles.
Task 3: Examining the relationship between these patterns and obesity effects. Conclude with a detailed report.
Project #2 skills/experience to be gained
fMRI Data Processing and analyses
fMRI biomarker development based on large-scale spatiotemporal patterns to depict brain dynamics in the context of obesity and hypothalamic influences.
Neuroscience and Obesity Research: Exposure to interdisciplinary research involving neuroscience and its implications in understanding obesity, particularly in children.
Project #2 expectations/requirements
Proficiency in Matlab and Python
Basic knowledge in data science and statistics.
Familiarity with or being willing to learn about basic neuroscience principles related to obesity.
Please note that Dr. Xu is a new faculty member joining the department in January 2025. She will be supervising lab rotations virtually. Please contact her for more details.
Affiliate Faculty Labs (On Campus)
NEW PI Name: Dr. E. Smela
PI E-mail: smela@umd.edu
Lab Address (room, building, campus): 2112, Martin Hall, College Park
Project Description: Developing a Cell-Based Sensor for Odorant Identification
Despite having artificial vision (cameras), hearing (microphones), and touch (pressure sensors), we still have no general-purpose artificial olfaction (an e-nose), and therefore still employ the noses of humans, dogs, and rats for odor identification. Applications for an e-nose would be in a wide range of fields, from medical diagnostics (animals can smell cancer and covid) to human safety (moldy food, toxic chemical spills, search and rescue) and agriculture (detecting insect infestations of orchards, provenance of olive oil). An interdisciplinary team (including Dr. Abshire from ECE, Dr. Shrivastava in CS, Dr. Araneda in Biology, and Dr. Tomblin in STS) is developing an e-nose based on engineered, desiccatable insect cells (see https://today.umd.edu/umd-researchers-are-creating-a-bio-nose-that-smells-for-real ). The graduate student will participate in studying the cell responses and/or in creating technologies for a portable device based on the cells.
PI Name: Dr. Reza Ghodssi
PI E-mail: ghodssi@umd.edu
Lab Name: MEMS Sensors and Actuators Lab (MSAL)
Lab Website: https://umdmsal.com
Lab Address (room, building, campus): 2201, JM Patterson Building, College Park
Lab Overview:
Our lab focuses on application-driven technology development using micro-nano-bio engineering approaches and “systems integration” to provide holistic solutions for real-world use. The focus of our work is aimed at in situ biomedical and clinical applications, specifically toward gastrointestinal diagnostics and platforms for investigating gut-brain interactions. Our devices incorporate system-oriented design elements relying on MEMS materials and fabrication technology, novel biosensing and biofabrication processes, microelectronics integration, and 3D printed hierarchical structure and packaging techniques.
Project #1 Description
Gastrointestinal (GI) diseases, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), pancreatitis, and GI cancer are critical health conditions that require burdensome procedures for diagnosis. Additionally, drug delivery systems to treat these diseases and others have significant limitations due to their non-localized administration. The current methods for the diagnosis of GI disease often suffer drawbacks of low specificity/sensitivity or are successful at too late a stage to begin effective treatment. Traditional endoscopic screenings usually involve sedation that requires advanced facilities and can have trouble accessing specific regions of the GI tract (small intestine). To address these shortcomings, we are working toward developing an integrated ingestible capsule device for real-time, in situ location of GI pathology and subsequent localized drug delivery. Currently, we are developing a prototype ingestible capsule to allow for the in vivo measurement of aqueous biomarkers associated with inflammation within the GI tract, while simultaneously measuring the epithelial barrier integrity with an embedded impedance sensor to monitor inflammation-induced changes in the GI lumen. Additionally, we are working toward therapeutic intervention and biopsy methods in the GI tract including drug delivery and tissue sampling via microneedle integrated actuators. The rotation project will involve aiding in the design, fabrication, or validation of key components of the ingestible capsule or drug delivery system. Potential project tasks include: (1) fabrication of microneedle drug delivery system components using microscale 3D-printing and molding techniques; (2) design and fabrication of capsule prototypes demonstrating the capability to withstanding the simulated GI environment while retaining sensor function and integrity; (3) design or in vitro characterization of capsule sensors; (4) design fabrication and evaluation of actuators for tissue sampling.
Project #1 skills/experience to be gained
Introduction to ingestible capsule systems
Learn about the field of microsystems technology and traditional fabrication techniques
Optimize fabrication strategies for various thin film biosensors, actuators, microneedles, and ingestible device packaging
Communicate with a principal graduate student and participate in group meetings, as well as meetings with our collaborating medical practitioners
How to achieve an effective literature review
Project #1 expectations/requirements
Applying with the intent to commit at least 20 hours/week, including 2 hours for group meetings on Fridays (10 AM-12 PM).
Keep a laboratory notebook and share results with their team for feedback and guidance
Protocol design for novel experiments and an end of rotation report
Project #2 Description
Many physiological functions and conditions are modulated via signaling molecules known as neurotransmitters. While best known for their role in neuronal signal propagation, neurotransmitters such as serotonin (5-HT) and dopamine (DA) play a critical role in other organ systems as well. Real-time monitoring of neurotransmitter dynamics is critical in understanding their role in the modulation of behavior, pathology, and organ function. To this end, our lab aims to develop biosensors and platforms to interrogate communication via these signaling molecules by quantifying their dynamics both in vitro and in vivo. Currently, we are developing carbon fiber and microneedle electrochemical sensors that aim to detect 5-HT in complex environments. The rotation project will involve aiding in the design, fabrication, and validation of key components of the electrochemical sensors. Potential project tasks include: (1) design and fabrication of carbon fiber microelectrode sensors, (2) functionalized and characterization of sensors, and (3) fabrication of microneedle components using microscale 3D-printing and molding techniques.
Project skills/experience to be gained
Introduction to electrochemical detection of molecules
Basic fabrication methods: 3D printing, electrode fabrication and modification, packaging assembly
Sensor characterization and validation
Communication of results in meetings and with mentor graduate student
General learning about challenges associated with electronic biosensor integration
Project expectations/requirements
Applying with the intent to commit at least 20 hours/week, including 2 hours for group meetings on Fridays (10 AM-12 PM)
Keep a lab notebook and communicate with the team for guidance and to share results
Individually reading literature for your own education on the topic
End of rotation report to document methods and achievements
PI Name: Dr. Srinivasa Raghavan
PI E-mail: sraghava@umd.edu
Lab Name: Complex Fluids and Nanomaterials Group
Lab Website: https://complexfluids.umd.edu
Lab Address (room, building, campus): 1138, Chemical & Nuclear Engineering Building, College Park
Lab Overview:
We invent new materials to improve our health and thus ‘change the world’! Examples:
Surgery using electroadhesion of gels
Bleeding control using biopolymers
Engineered living materials using capsules
Pancreatic cancer imaging using liposomes
We are the ONE lab at UMD that has translated a product that you can buy at pharmacies (Rapid-Seal Wound Gel, to stop bleeding).
We love to have students interested in launching companies! Article on our lab: https://www.snexplores.org/article/electricity-glue-hard-metals-soft-materials
Project #1 Description
Gluing Hydrogels to Tissues: A Simple Way to Do Surgery
We have discovered that hydrogels can be glued to human tissues by applying an electric field for a few seconds. This is a super-simple way to repair cuts and tears!
Read our paper in Nature Communications: Reversible electroadhesion of hydrogels to animal tissues for suture-less repair of cuts or tears (https://complexfluids.umd.edu/papers/170_2021g.pdf)
This is an exciting discovery with the potential to transform surgery! It could make surgery simpler and quicker. It won ‘Invention of the Year’ at UMD in 2022.
We are looking for a student who can advance this discovery on both the technology side as well as the scientific side.
Project #1 skills/experience to be gained
Students will create gels, study their properties under electric fields, and will work with surgeons (at Children’s National Hospital) on using these gels for surgeries.
Students will get to be a part of a project that could be the most exciting work we have ever done in our lab. You will be part of a team that includes BioE professors such as Dr. Ian White and surgeons at Children’s such as Dr. Tony Sandler.
Project #1 expectations/requirements
We are looking for students who want their PhD to have an impact on the world. The most important requirement that the student should have is a deep curiosity about the world.
A background in the areas related to this research is NOT required.
But if a student has experience in any of the following, please let Dr. Raghavan know:
Chemistry, polymers, hydrogels
Electrical effects on tissues
Tissue anatomy
Surgery (working with surgeons, performing surgeries)
Note: Read a blog post about our discovery: https://bioengineeringcommunity.nature.com/posts/a-new-discovery-that-could-revolutionize-surgery-gels-can-be-adhered-to-animal-tissues-by-applying-an-electric-field. Read this news article about our 'Invention of the Year' winner: https://research.umd.edu/articles/inventions-year-umd-researchers-create-develop-adhesive-alternative-surgical-sutures.
Project #2 Description
Stopping Bleeding via Sandcastles: Biopolymer Granules form a Sandcastle-Like Gel Around a Wound by Capillary Adhesion
We have found that when biopolymer granules are contacted with blood, they form a gel by capillary adhesion.
This is akin to common granular structures found in nature, such as sancastles on a beach.
The resulting granular gel is sufficiently robust that it forms a seal around the wound, thereby stopping the bleeding!
This is an exciting discovery that could be commercialized into a product to stop bleeding in surgical settings.
We are looking for a student who will work closely with Medcura, a company formed from our lab by a UMD BioE PhD student.
Project #2 skills/experience to be gained
Students will learn about polymer chemistry, colloidal interactions, wetting, and the science behind hemostasis (stopping bleeding)
Come and be part of a team that is looking to make an impact in bleeding control.
Project #2 expectations/requirements
We are looking for students who want their PhD to have an impact on the world. The most important requirement that the student should have is a sense of curiosity.
A background in the areas related to this research is NOT required.
But if the student has experience in any of the following, please let Dr. Raghavan know:
Chemistry, polymers
Wound healing
Hemostasis
Note: Read a news article about Medcura and our product to stop bleeding: https://fischellinstitute.umd.edu/news/story/umdborn-bleeding-management-tech-available-nationwide.
NEWLY ADDED PI Name: Dr. Ryan Sochol
PI E-mail: rsochol@umd.edu
Lab Name: Bioinspired Advanced Manufacturing (BAM) Laboratory
Lab Website: https://bam.umd.edu/
Lab Address (room, building, campus): Room 2152, Glenn L. Martin Hall, College Park
Lab Overview:
Prof. Ryan D. Sochol’s Bioinspired Advanced Manufacturing (BAM) Laboratory pioneers micro/nanoscale additive manufacturing or “3D printing” strategies that advance the life sciences and biomedical applications to, ultimately, benefit human health and well-being. These efforts rely primarily on “Two-Photon Direct Laser Writing”—a 3D micro/nanoprinting technique with feature resolutions on the order of 100 nanometers.
Project Description
3D-Nanoprinted Soft Robotic Microcatheters for Minimally Invasive Surgery
Project skills/experience to be gained
Gain experience related to “Direct Laser Writing (DLW)”, which is a two-photon (or multi-photon) polymerization 3D micro/nanoprinting approach that entails rapidly scanning a tightly focused pulsed laser to crosslink (i.e., solidify) a photoreactive material at designed locations and, ultimately, produce 3D objects with feature resolutions down to the 100 nanometer range.
Project expectations/requirements
Strong personal/professional qualities (e.g., excellent written/verbal communication skills, driven, thoughtful, independent-minded, meticulous, self-starter, strategic long-term thinking).
Affiliate Faculty Labs (Off Campus)
PI Name: Dr. Seth Ament
PI E-mail: sament@som.umaryland.edu
Lab Name: Ament Lab / Inst for Genome Sciences
Lab Website: http://amentlab.org
Lab Address (room, building, campus): HSF3-3182, 670 W Baltimore St., Baltimore, MD
Lab Overview:
The Ament lab conducts basic and translational studies of brain disorders, using genome sequencing, single-cell and spatial genomics of human and rodent brains, human pluripotent stem cells, and clinical samples.
Project Description
Most rotation projects for BIOE students will involve the development and application of machine learning tools to analyze large genomic and clinical datasets. Representative problems include:
Development and applicaiton of algorithms to model the gene regulatory networks underlying human brain development
Development and application of algorithms to predict patient outcomes from combinations of clinical and genomic data
Development and application of algorithms to model the diversity of neuronal synapses and predict their functions, using super-resolution confocal imaging and electrophysiological data]
Students will also have the opportunity to develop new high-throughput datasets using genomic techniques, stem cells, microscopy, etc.
Project skills/experience to be gained
Applications of machine learning / AI in genetics, genomics, neuroscience, and clinical settings.
Project expectations/requirements
Students should have a solid foundation in statistics and data science.
To learn more about the project, watch the video here.
PI Name: Dr. Rong Chen
PI E-mail: rchen@som.umaryland.edu
Lab Name: Biomedical data mining lab
Lab Address (room, building, campus): 100 N Greene, Baltimore
Lab Overview:
Dr. Chen’s research focuses on leveraging machine learning, theory, and computational methods to understand the relationship between brain and behavior across scales, leading to next-generation AI and a deeper understanding of mechanisms of cognition, emotion, and decision making. His lab analyzed multimodal neuroimaging and genetic data to understand the neuropathology of Alzheimer's disease, Parkinson's disease, Autism, and sickle cell disease.
Project Description
Neural decoding focuses on harnessing machine learning techniques to predict behavioral or clinical variables based on neural signals. Neural decoding can generate predictive models for diagnosis, prognosis, and personalized medicine. It is a critical component of precise neuromodulation and brain-computer interfaces. In machine learning, neural decoding is formulated as a supervised learning problem. However, recorded neural datasets from multiple subjects demonstrate significant heterogeneity. A naïve approach that pools these datasets together often leads to a model with poor generalizability. This project centers on developing a machine learning method to address this problem. The study focuses on single-neuron spike activities in the human medial frontal cortex, hippocampus, and amygdala.
Project skills/experience to be gained
Neural decoding and Machine learning
Project expectations/requirements
The candidate is also expected to develop algorithms for neural decoding.
Note: Students can work remotely.
PI Name: Dr. Vivek Garg
PI E-mail: vgarg@som.umaryland.edu
Lab Name: Garg Lab
Lab Website: http://www.vgarglab.com
Lab Address (room, building, campus): 655 West Baltimore St. BRB 5-039, Baltimore
Lab Overview:
Biophysics of mitochondrial membranes. Our lab works on the molecular physiology of mitochondrial ion channels and transporters, structure-function relationships and their role in mammalian physiology.
Project Description
Molecular physiology of mitochondrial calcium uniporter and the role of mitochondrial calcium signaling in mammalian physiology.
Project skills/experience to be gained
Mammalian cell culture, SDS-PAGE. Western blot and/or microplate-reader based assays.
Project expectations/requirements
Basic understanding of the cell/cell biology. Depending on prior experience, their are opportunities to learn more.
PI Name: Dr. Xiaofeng Jia
PI E-mail: xjia@som.umaryland.edu
Lab Name: Translational Neuroengineering & Neuroscience Lab
Lab Website: https://www.medschool.umaryland.edu/xjia/
Lab Address (room, building, campus): UMB campus, MSTF 8-16 C, 8-21, 8-22, 8-23, 8-34A, Baltimore
Lab Overview:
The PI is the director of Neurosurgical Stem Cell Research at UMB. He is a professor with tenure in the Department of Neurosurgery at the University of Maryland School of Medicine, Department of Orthopaedics, Anatomy Neurobiology, and an adjunct professor of the Department of Biomedical Engineering and Anesthesiology at Johns Hopkins University School of Medicine. He has been a Faculty since 2007 and was the Associate Research Professor at Johns Hopkins University.
Project #1 Description
Brain Recovery after Cardiac Arrest
This project will develop and optimize a novel glycan-based intervention via metabolic glycoengineering to promote neural stem cell interaction in vitro and to improve neurological outcomes after cardiac arrest. It will track the fate of transplanted neural stem cells and explore related mechanisms with enhanced cell survival. We also focus on developing novel translational tools for uncovering mechanisms of brain injury after cardiac arrest, monitoring and tracking neurological injuries, and guiding treatments like therapeutic hypothermia. Our lab will also investigate the effect of stem cell-derived extracellular vehicle therapy in cardiac arrest induced brain injury animal models.
Project #1 skills/experience to be gained
In vitro study, quantitative analysis, animal behavior studies after brain injury
Project #2 Description
Peripheral Nerve Injury and regeneration
This project will enhance adipose stem cell adhesion and differentiation in vitro via stem cell surface modification, and improve nerve regeneration after critical-sized nerve repair with sugar-analog-treated adipose stem cells. Our lab will also investigate the effect of stem cell-derived exosome therapy in peripheral nerve crush injury and nerve defect repair animal models.
Project #2 skills/experience to be gained
In vitro study, quantitative analysis, animal behavior studies after peripheral nerve injury
Project expectations/requirements
cell study, behavioral assessment, histology with quantitative analysis
PI Name: Dr. Yajie Liang
PI E-mail: yajie.liang@som.umaryland.edu
Lab Name: In vivo Cellular Dynamics
Lab Website: https://sites.google.com/yajieliangneurolab.com/liangresearchlab/home
Lab Address (room, building, campus): HSF3, 1150, Baltimore
Lab Overview:
We are using advance 2-photon imaging to study cellular dynamics and function in the brain of living animals, trying to gain insights on disease mechanisms and finding new therapies.
Project Description
Cellular dynamics in stroke or brain cancers
Project skills/experience to be gained
stem cell/brain cancer cell culture, vector design, cell transduction, cell tracking and 2P imaging
Project expectations/requirements
Basic skills in molecular cloning and cell culture, experience in handling mice or brain surgeries.
PI Name: Dr. Jung Soo Suk
PI E-mail: jsuk@som.umaryland.edu
Lab Name: Nanomedicine and therapeutic development
Lab Address (room, building, campus): HSF III 9110, UMB Medical Campus, Baltimore
Project #1 Description
Development and preclinical evaluation of human protein nanocage capable of reverting the immunosuppressive tumor microenvironment to enhance therapeutic efficacy of cancer immunotherapy.
Project #1 skills/experience to be gained
Protein production, purification, and characterization
Particle characterization (e.g., DLS, TEM, etc.)
Molecular biology techniques (e.g., ELISA, western blot, RT-PCR, IHC, etc.)
Cell culture
Animal experiments - preclinical pharmacokinetics, efficacy, and safety assessments
Project #2 Description
Development and preclinical evaluation of novel immune stimulating antibody conjugate that promotes innate and adaptive immune responses against hematologic and solid malignancies
Project #2 skills/experience to be gained
Antibody-drug conjugate production, purificaiton, and characterization
Molecular biology techniques (e.g., ELISA, western blot, RT-PCR, IHC, etc.)
Cell culture and primary cell isolation and differentiation
Animal experiments - preclinical biodistribution, efficacy, and safety assessments
Project expectations/requirements
Self-motivation and commitment, strong work ethic, inter-personal skill (e.g., ability to work as a team)
Fundamental understanding of molecular biology
Prior experience with wet lab experiments is desired
PI Name: Dr. Yifan Yuan
PI E-mail: yyuan@som.umaryland.edu
Lab Name: Yuan Lab
Lab Website: https://sites.google.com/view/yuanlab/home
Lab Address (room, building, campus): S109, Health Science Research Facility II, University of Maryland School of Medicine, Baltimore
Lab Overview:
Our lab is focused on integrating molecular biology, bioengineering, and computational biology to delineate biological mechanisms in the vascular microenvironment and to develop a native-mimicking modeling system during homeostatic and diseased states.
Project Description
Diseases of the lung vasculature are difficult to study due to the lack of functional ex vivo models. Conventional culture systems are typically limited in their ability to represent human pathophysiology for the study of disease and drug mechanisms. The overall objective of this project is to develop an experimental platform that mimics the pulmonary microvasculature during normal homeostasis and during disease states. The lung microvascular niche characteristics, such as paracrine factors, hemodynamics, and extracellular matrix composition are all of pivotal importance for regulating endothelial maturation and maintaining vascular homeostasis. Leveraging single-cell RNA-seq (scRNAseq), we developed computational tools to identify the paracrine signals in human distal lungs. We also made a prototype vascular platform using acellular whole lung scaffolds that recapitulate the native ECM microenvironment in the lung vascular tree. In this study, we will leverage these tools to identify novel, important locally acting soluble factors in a functional lung microvascular niche to improve pulmonary microvascular maturation in acellular lung scaffolds. During the last year, we determined a group of important and novel soluble factors that could improve endothelial maturation in 2D culture. During the rotation, the students will be testing the impact of these soluble factors in in vitro flow device and 3D endothelial repopulated lung platform. The students will have the opportunity to familiarize themselves with the biological, computational, and engineering tools in the lab, such as the bioengineered whole organ culture system and multi-omics.
Project skills/experience to be gained
The student will have the chance to gain skills in dynamic cell culture, whole organ culture using decellularization/recellularization strategy, single-cell RNA-seq analysis
Project expectations/requirements
The candidates are expected to have great interest in bioengineering, molecular biology, and translational research. Candidates with additional experience in the following skills and areas will be preferred but not required: human primary cell culture, computational biology, qRT-PCR, western blot, flow cytometry, and familiar with 3D cell culture systems such as organoids and/or organ on chips.
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