Controlled environment agriculture methods like hydroponics allow for the growth of crops indoors, providing a stable and controlled conditions for year-round food production, even in urban areas. Despite the high level of control, the growth of microbes can be difficult to control and threatens crop viability. Biofilms develop on system surfaces, and can harbor pathogens harmful to plant or human health.

In this project, biofilm development will be investigated in piped systems using flow cytommetry, imaging, and molecular biology methods. Students will grow plants with hydroponics systems and investigate the factors that control biofilm growth. Since biofilms can develop similarly in any piped system, students will also operate a variety of piped systems with controlled conditions. Students will learn a variety of environmental characterization methods and design and develop controlled experiments.

Biological Characterization and Imaging, Cellular Biology, Ecology and Sustainability, Engineering the Built Environment

• No Major Restriction

While no background is required, a student with biology and/or biology lab experience and background is preferred.

Environmental and Ecological Engineering

Caitlin Proctor

Cell division is essential for life, underlying the development of mammals from embryo to full-grown adult, regenerative processes, such as wound healing, and diseases such as cancer. The intracellular aspects of mammalian cell division have been revealed through two-dimensional culture studies, where cells simply grow and then release from the substrate to divide in an unrestricted manner. However, physiologically, many cells divide in mechanically confining microenvironments, including dense extracellular matrices (ECMs) with distinct viscoelastic, viscoplastic, and nonlinear elastic characteristics, often surrounded by other cells, as in tumors. In this project, we will illuminate how cells modulate extracellular forces to facilitate and sustain cell division in confining microenvironments, using a computational model.

Biological Simulation and Technology, Cellular Biology

• Biomedical Engineering
• Mechanical Engineering

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

Weldon School of Biomedical Engineering

Taeyoon Kim

Students will perform microscopic studies to understand meristem cell division and growth in Ceratotperis gametophytes in response to phytohormones, environmental signals, and mechanical perturbations. This study will help reveal the cellular basis of stem cell proliferation and meristem development in plants.

Biological Characterization and Imaging, Cellular Biology

• Plant Science
• Biology
• Cell Molecular and Developmental Biology
• Biochemistry

Botany and Plant Pathology

Yun Zhou

Although engineers add disinfectant residual to drinking water to prevent microbial growth, as water travels many miles through distribution pipes this disinfectant is lost. Microbial growth is often unavoidable - including the growth of opportunistic pathogens that can cause disease in immunocompromised populations. The three opportunistic pathogens (OPs) recognized by the scientific community to be of major concern are Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa. These bacteria often grow in biofilm, a microbiological layer formed along the inner surface of pipes.
This project will investigate the microbial diversity of drinking water bacteria through a variety of molecular biology methods. Opportunistic pathogens will be quantified through qPCR methods within samples from rural drinking water and controlled experiments on Purdue's campus. Additionally, students will help with more advanced molecular methods including sequencing and bioinformatics. Results from this project will provide insight into the dynamics of pathogens within drinking water.

Biological Characterization and Imaging, Cellular Biology, Engineering the Built Environment, Environmental Characterization

• No Major Restriction

While no background is required, a student with biology and/or biology lab experience and background is preferred.

Environmental and Ecological Engineering

Caitlin Proctor

EMBRIO Institute has an opening in the Zhang lab in the Comparative Pathobiology department for a SURF student to work on establishing calcium reporter zebrafish genetic lines. The student will learn more about the zebrafish model, and prepare for a future career in research. This project is part of the larger effort to determine how tissue-wide organization of connected epithelial sheets emerge.

Cellular Biology, Genetics

• No Major Restriction

student must be determined.

Comparative Pathobiology

GuangJun Zhang

Project 1: This summer research project will use high resolution imaging test the hypothesis that decoding of Ca2+-flux frequency by CaM and CaMKII plays a major role in dynamic actin polymerization and dendritic spine morphology. Student will learn basic laboratory skills, primary cell culture, immunohistochemistry, confocal imaging and image analysis.

Project 2: This summer research project will use computational modeling of Ca2+/Calmodulin and CaMKII interactions in dendritic spines to test the hypothesis that decoding of Ca2+-flux frequency by CaM and CaMKII plays a major role in dynamic actin polymerization and dendritic spine morphology. Computational tools that will be used include ordinary and partial differential equations and machine learning techniques to rapid explore model parameter space.

Research Question Overview:
Neuronal synapses are tightly regulated intercellular junctions that rapidly convey information from an upstream pre-synaptic neuron to a downstream post-synaptic neuron. Dynamic strengthening or weakening of synaptic connective strength, known as synaptic plasticity, is a critical feature of neuronal function. The direction of synaptic plasticity (increased connective strength (LTP) versus decreased connective strength (LTD)) depends on the timing of action potentials (AP), which is translated into frequency signals of Ca2+ ion flux through NMDA
receptors (NMDAR) located on dendritic spines (100-500nm mushroom-like protrusions that form the post-synapse).

The timing and direction of synaptic plasticity is also exquisitely regulated by dynamic organization and spatial localization of synaptic adhesion molecules, signaling receptors, ion channels, and the intracellular cytoskeleton within spines. However, it not clear to how these electrical, biochemical, and mechanical cues are integrated to produce robust, repeatable, and highly dynamic synaptic plasticity that lasts over the lifetime of a neuron (decades). Our recent work has shown that competition for CaM-binding can influence the Ca2+ frequency-dependence of protein activation and downstream signaling. In particular, the highly expressed Ca2+/calmodulin-dependent kinase II (CaMKII) plays a key role in synaptic plasticity via two
important aspects of its function: (1) CaMKII is highly involved in Ca2+-dependent signal transduction via phosphorylation of a number of downstream proteins including ion channels, guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and transcription factors, and (2) CaMKII acts as a multivalent scaffold that binds multiple proteins simultaneously and localizes them to post-synaptic spines, including both filamentous and monomeric actin and may regulate actin polymerization in the spine.

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

• No Major Restriction

Weldon School of Biomedical Engineering

Tamara Kinzer-Ursem

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, Cellular Biology, Genetics, Medical Science and Technology

• No Major Restriction

GPA > 3.5, BME, ABE and CHE preferred

Davidson School of Chemical Engineering

Chongli Yuan

The goal of this Summer undergraduate research program is to develop cell-based immunotherapies for glioblastoma (GBM) with engineered natural killer (NK) cells by targeting mechanisms of immunosuppression in the tumor microenvironment. Specifically, the project is focused on engineering the immune functions of NK cells to generate CAR-NK and CRISPR KO variants of NK cells to multispecifically, via synthetic genetic circuits, interact with the tumor microenvironment and rescue NK cell activity from dysfunction. In this context, the project will characterize and optimize a multi-specific CAR-NK cell product for the treatment of glioblastoma, designed to co-target multiple elements of NK cell dysfunction in the tumor microenvironment. This project builds on the lab’s recent publication describing the very first triple-engineered NK cell platform for GBM addressing antigen escape and immunometabolic reprogramming via CD73, and will incorporate elements that reprogram the cells’ metabolic function via, among other oncometabolite and glutamine targeting. These engineered NK cells will be developed from induced pluripotent stem cells as well as peripheral blood.

The student’s role in the project will be to isolate and differentiate immune cells, characterize and learn how to effectively engineer these cells to express various multispecific constructs, learn how to manipulate NK cell activity in the context of metabolic modulation via adenosine and glutamine, and perform functional assays including cytotoxicity, degranulation and immunophenotyping.

The student will also be involved in learning some computational analysis to analyze RNAseq and CRISPR screen data. The student will learn skills incell-based immunotherapy and immunoengineering, cancer biology, cell therapy product development and formulation, synthetic biology and genetic engineering.

In terms of lab participation, the student will be involved in weekly lab meetings with the rest of the lab where they will present their findings, and in regular individual meetings with the PI. The student will be trained and mentored by a graduate student.

Cellular Biology, Medical Science and Technology

• No Major Restriction

Industrial and Physical Pharmacy

Sandro Matosevic

Neurite outgrowth is a physiological process where neurons generate farther projections, which is essential for wiring nervous systems during development and regeneration after trauma or disease. The neurite outgrowth is known to be driven mainly by interactions between cytoskeletal components, such as microtubules, cross-linkers, and dynein motors. Previous studies suggested that dynein motors interact with and walk on a pair of neighboring microtubules which are transiently linked by cross-linkers. However, it still remains elusive how these molecular interactions result in neurite elongation at larger scale. To investigate the mechanisms of neurite elongation, we developed an agent-based model that consists of essential cytoskeletal elements with consideration of their mechanical properties and physical interactions. In this project, using the agent-based model, a student will explore extensive parametric spaces to find intrinsic mechanisms of the neurite outgrowth.

Biological Simulation and Technology, Cellular Biology

• Bioengineering
• Mechanical engineering
• Biochemistry

MATLAB, C language

Weldon School of Biomedical Engineering

Taeyoon Kim

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. The students recruited will help to engineer stem cells with gene editing tools, differentiate stem cells into immune cells, and perform molecular and cellular assays to characterize the cells.

Cellular Biology, Medical Science and Technology

• No Major Restriction
• Chemical Engineering
• Biological Engineering - multiple concentrations
• Cell Molecular and Developmental Biology
• Biomedical Engineering

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

Davidson School of Chemical Engineering

Xiaoping Bao