Angiosarcomas are aggressive cancers with a poor prognosis for patients. We utilize genetically engineered cell lines and in vivo models to study the molecular drivers of angiosarcoma. In recent work, we found that DICER1 and microRNAs may function as critical tumor suppressors. We have gone on to generate additional tumor models investigating other genes known to be altered in patients. In this project we will study a novel oncogene to determine its role in angiosarcoma and potential as a therapeutic target.

Biological Characterization and Imaging, Cellular Biology, Genetics

• No Major Restriction

Biological Sciences

Jason Hanna

Novel natural products from Streptomyces are challenging to discover, often because they are not produced under standard laboratory conditions. We are exploring methods of activating production of novel natural products using antibiotics.

Biological Characterization and Imaging, Cellular Biology

• No Major Restriction

Chemistry

Elizabeth Parkinson

Cell migration plays an important role in physiology and pathophysiology. Migrating cells are able to sense surrounding mechanical environments. For example, a number of experiments have demonstrated that nano- and micro-patterns can guide migration of cells. This migratory behavior is called the contact guidance and is of great importance in various physiological processes, such as cancer metastasis. In this research project, we aim to use a rigorous computational model and collaborate with experimentalists in order to investigate intrinsic mechanisms of the contact guidance. A participating student will run computer simulations and analyze data from the simulations to perform the research. If necessary, everything for this project can be done remotely.

Biological Simulation and Technology, Cellular Biology

• Mechanical Engineering
• Biomedical Engineering
• Biological Engineering - multiple concentrations
• Computer Engineering

Intermediate/Proficient C coding skills Sufficient experiences in MATLAB coding Basic knowledge of cell biology (optional)

Weldon School of Biomedical Engineering

Taeyoon Kim

The student will join a multi-disciplinary team investigating epigenetic processes, chromatin structure and gene regulation. This project will involve learning and applying biochemical, genetic and molecular biology strategies to build and characterize customized budding yeast (Saccharomyces cerevisiae) strains or mammalian cell lines for the investigation of evolutionarily conserved protein-protein interactions and post-translational modifications using state-of-the-art detection and quantification strategies. Biological targets may include histone modifying enzymes, histone modifications, histone variants and chromatin assembly and DNA replication factors.

Biological Characterization and Imaging, Cellular Biology, Genetics

• No Major Restriction

General Chemistry required, introduction to molecular biology, biochemistry, genetics preferred.

Biochemistry

Ann Kirchmaier

Breast cancer is the number one diagnosed cancer among women and affects over a quarter of a million people annually. The five-year survival rate is exceptional if the disease remains local, however, once breast cancer has metastasized, patient survival rates drop precipitously. There is a critical need to better understand the events required for breast cancer metastasis and how these events culminate in systemic tumor growth. During breast cancer metastasis, the composition and structure of the extracellular matrix (ECM) in the metastatic niche are dramatically altered before the arrival of colonizing cells. As such, the ECM is emerging as a potential therapeutic target for disrupting the metastatic process. Our goal is to determine how changes in the ECM are permissive to metastasis and to manipulate these events in order to inhibit metastatic disease. Our recent studies have demonstrated that Fibronectin (FN) is upregulated in the lungs before the arrival of metastatic cancer cells, and clinical evidence has shown that increased FN is predictive of decreased patient survival. Despite these findings, there remain fundamental gaps in determining how matrix remodeling events that occur during metastasis can dictate the cancer cell fate. In particular, the architecture of the FN matrix can induce phenotypic changes of invading cancer cells that can make the cells less sensitive to drug treatment. Additionally, changes in the local tissue architecture can direct a cell to enter a growth cycle or a dormant phenotype, which can diminish the clinical efficacy of ECM-targeted therapeutics.
Our group has recently observed that tumor-derived metastatic cancer cells express elevated levels of FN, but unlike fibroblasts and other stromal cells, the tumor cells do not deposit FN as a fibrillar matrix. Instead, tumor cells secrete FN in a soluble form which must be converted into insoluble fibrils through a cell-mediated event, exposing cryptic binding domains and transitioning the protein into a bioactive state. Our studies suggest that the assembly of fibrillar FN is dependent on a functional relationship between tumor cells and fibroblasts. Interestingly, we have demonstrated that the FN matrix produced and assembled by resident lung fibroblasts during pre-metastatic niche formation results in a highly aligned and organized FN matrix. However, the matrix formed by fibroblasts utilizing FN produced by tumor cells is less organized and more dispersed, which can significantly alter how forces are transmitted to local cells. To study the impact of FN architecture on the metastatic process independent of the confounding influence of other cell populations, our group has developed an advanced 3D cell culture platform that allows us to create a bioactive fibrillar FN network without the need for cell-mediated assembly. Utilizing this platform, we can tune the alignment of the resultant 3D fibrillar FN network to interrogate the role of the matrix on cell fate decisions. Based on our strong preliminary results, we hypothesize that dynamic changes in the FN network architecture will alter both biochemical and mechanical signaling within the niche, influencing the cell phenotype and dormancy and ultimately altering the cell sensitivity to drugs.

Through this project, we seek to evaluate the effect of FN architecture on dormancy. We will use genetic depletion strategies along with a rigorous panel of markers to determine the effect of matrix architecture on the entrance to or exit from dormancy.

Biological Characterization and Imaging, Cellular Biology, Medical Science and Technology

• No Major Restriction

BME

Luis Solorio

Neurons convert biochemical information (through binding of a neurotransmitter) to electrical signal (via action potential) and back to biochemical signal (through the release of neurotransmitters). These distinct and separable processes can be reconstituted in a synthetic neuron by using natural and engineered proteins, and a synthetic neuron platform can be used to understand the rules governing the emergence of the present morphology of a neuron and the architecture of the neuronal system. This project thus aims to construct a synthetic neuron with a modular design and a programmable synthetic neuronal network capable of recapitulating basic functions of a natural neuronal system (e.g., action potential, synaptic communication, and basic computation) and with a long-term vision of incorporating more advanced computation and potentiation.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology

• Chemical Engineering
• Biological Engineering - multiple concentrations
• Biomedical Engineering
• Neurobiology and Physiology

Chemical Engineering

Chongli Yuan

This project aims to develop drop-on-demand (aka inkjet) printing technology of soft biomaterials including cell-laden hydrogel and RNA containing materials. Specifically, the undergraduate student will formulate and characterize the mechanical and rheological properties of polymeric inks to print and cure for advanced tissue constructs or drug delivery systems.

Cellular Biology, Material Processing and Characterization, Medical Science and Technology, Nanotechnology

• Mechanical Engineering
• Chemical Engineering
• Biomedical Engineering

Course work of solid or fluid mechanics are required. Experience in LabVIEW, CAD software and Matlab are preferred. Cell biology background is plus but not required.

Mechanical Engineering

Bumsoo Han

Spinal cord injury is a significant human health problem affecting about 300,000 people in the US. Better treatment options are needed to overcome the limited regeneration potential of the human spinal cord. Zebrafish larvae are an emerging model system for drug screening for several reasons including large number of embryos per breeding, genetics, and availability of behavioral assays for drug testing. Our lab is conducting a large scale drug screen with an FDA-approved library to identify novel compounds that enhance functional recovery following injury as assessed by a swimming assay. The student will be involved with fish breeding, spinal cord injury, drug treatment, and behavioral assay. We hope that this work will identify new compounds with translational potential.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology, Medical Science and Technology

• Biology
• Cell Molecular and Developmental Biology
• Biochemistry
• Neurobiology and Physiology
• Genetics
• Microbiology

Cell Biology, Neurobiology, fine motor skills, working with zebrafish

Biological Sciences

Daniel Suter

From leopards to fish, many animals sport patterns (like stripes or spots) on their bodies. My group takes a mathematical approach to understand how patterns form in the skin of zebrafish, which are small striped with important biomedical applications. Zebrafish development takes months, but simulating pattern formation takes minutes. In this project, I will mentor a student in building image-processing software to make simulated zebrafish patterns look more like real fish.

Big Data/Machine Learning, Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology

• Mathematics
• Computer Science
• Biomedical Engineering
• Biological Engineering - multiple concentrations
• Engineering (First Year)
• Agricultural Engineering

Good team members who are excited about interdisciplinary research, have taken a course in linear algebra, and have strong programming skills.

Mathematics

Alexandria Volkening

This project will be a nexus of the design, imaging, and manufacturing science and engineering of tissue matrix by cellular engineering. The project will engage students in high-resolution imaging, building a 2D and 3D digital design construct of the cellular matrix, and application of AR/VR for the human-matrix interface. Students will learn convergence of imaging, design, tissue engineering, and visualization. This project will be conducted in the College of Engineering and the College of Agriculture.

Biological Characterization and Imaging, Cellular Biology, Other

• Agricultural & Biological Engineering

Junior and Senior students are preferred. Student's personality expectations- Self-motivated, able to "figure out" solutions, persistent, and trustworthy to complete assigned projects.

School of Mechanical Engineering

Ajay Malshe

The increasing worldwide demand for vaccines along with the intensifying economic pressure on health care systems underlines the need for further improvement of vaccine manufacturing. In addition, regulatory authorities are encouraging investment in continuous manufacturing process to ensure robust production, avoid shortages, and ultimately lower the cost of medications for patients. The limitations of in-line process analytical tools are a serious drawback of the efforts taken in place. In line analysis of viral particles are very limited, due to the large time required for the current techniques for detection, qualitative and quantitative analysis. Therefore, there is a need for new process analytical technology. This project has both experimental and computation components and two students will be recruited for perform different tasks. The student focusing on experiments will fabricate devices and test them. The student focusing on computations will focus on developing machine learning codes.

Big Data/Machine Learning, Biological Characterization and Imaging, Biological Simulation and Technology, Biotechnology Data Insights, Cellular Biology, Computer Architecture, Deep Learning

• No Major Restriction

For the experimental portion of the project: fabrication, cell culture, microfluidics, microscopy For the computational portion of the project: Coding, Python

Mechanical Engineering

Arezoo Ardekani

Cancer is a major threat for humans worldwide, with over 18 million new cases and 9.6 million cancer-related deaths in 2019. Although most common cancer treatments include surgery, chemotherapy, and radiotherapy, unsatisfactory cure rates require new therapeutic approaches. Recently, adoptive cellular immunotherapies with chimeric antigen receptor (CAR) engineered T and natural killer (NK) cells have shown impressive clinical responses in patients with various blood and solid cancers. However, current clinical practices are limited by the need of large numbers of healthy immune cells, resistance to gene editing, lack of in vivo persistence, and a burdensome manufacturing strategy that requires donor cell extraction, modulation, expansion, and re-introduction per each patient. The ability to generate universally histocompatible and
genetically-enhanced immune cells from continuously renewable human pluripotent stem cell (hPSC) lines offers the potential to develop a true off-the-shelf cellular immunotherapy. While functional CAR-T and NK cells have been successfully derived from hPSCs, a significant gap remains in the scalability, time-consuming (5 or more weeks), purity and robustness of the differentiation methods due to the cumbersome use of serum, and/or feeder cells, which will incur potential risk for contamination and may cause batch-dependency in the treatment. This project thus aims to develop a novel, chemically-defined platform for robust production of CAR-T and CAR-NK cells from hPSCs.

Biological Characterization and Imaging, Biological Simulation and Technology, Cellular Biology, Genetics, Medical Science and Technology

• No Major Restriction
• Chemical Engineering
• Biological Engineering - multiple concentrations
• Biochemistry
• any related major

Previous experience with cell culture and molecular biology is a bonus, but NOT required.

Davidson School of Chemical Engineering

Xiaoping Bao

We are interested in identifying how certain viruses are causing specific cancers. To this end, we hope to extract host and pathogen specific gene expression patterns from single cell omics technologies from public data.

Big Data/Machine Learning, Cellular Biology

• No Major Restriction

familiarity with genomics technologies are welcome

Computer Science

Majid Kazemian

We have identified a range of noncoding RNAs that are affected in cells of human adaptive immune system. We have identified potential biological pathways that are affected by these noncoding RNAs in silico. We now intend to modulate these noncoding RNAs in human and mice cells and measure their contribution to immune system function. Students will learn how to perform qPCR assays and knockdowns of these RNA species in human cells.

Cellular Biology

• No Major Restriction

basic molecular biology skills such as PCR, qPCR, WB are welcome

Biochemistry and computer science

Majid Kazemian