Research Projects

Mentor: Balaji Narasimhan

We have designed novel biodegradable amphiphilic polyanhydrides that have the ability to enhance the immune response and stabilize protein antigens. These capabilities have important implications for the design of single dose vaccines for diseases ranging from cancer and HIV to anthrax and plague to tetanus and diphtheria. We have fabricated nanoparticles based on sebacic acid (SA), 1,6-bis(p-carboxyphenoxy)hexane (CPH), and 1,8-bis(p-carboxyphenoxy)3,6-dioxaoctane (CPTEG) and demonstrated the stability and immunogenicity of antigens released from these nanoparticles. Our overall goal is to understand the cellular and molecular mechanisms by which these polymeric nano-adjuvants enhance and activate host immune responses. This work will be in collaboration with Professors Wannemuehler and Bellaire from the Veterinary Microbiology and Preventive Medicine department at ISU.

Example REU Project: Two REU students will learn to fabricate antigen-loaded nanoparticles (200-800 nm) using CPH:SA and CPTEG:CPH copolymers. The antigens of interest include ovalbumin, F1-V (plague antigen), influenza hemagglutinins, and rPA (recombinant protective antigen against anthrax). The students will learn to characterize these nanoparticles using electron microscopy and a Zetasizer (for size distribution). One REU student will study how the blank nanoparticles (i.e., no antigen) are uptaken by antigen presenting cells of the immune system using confocal laser scanning microscopy. The second REU student will immunize mice with these antigen-loaded nanoparticles with the appropriate controls. The immune response in these animals will be characterized using both antigen-specific antibody responses and T and/or B cell proliferative responses. Together, all these studies will provide molecular and cellular information about how polymer chemistry enhances and activates host immune responses. This project will expose the students to nanotechnology, materials science, biochemistry, animal studies, and applied immunology.

The Mallapragada group has designed and synthesized novel smart bioinspired multi-block copolymers that exhibit pH and temperature sensitivity. These polymers are ionic and undergo thermoreversible gelation at body temperatures. Above a critical gelation temperature and polymer concentration, the micelles formed by the multi-block copolymers described above self-assemble to form macroscale thermoreversible physical gels. Since the critical gelation temperatures are close to physiological temperatures, these polymers can be used as injectable delivery devices and have significant advantages over other crosslinked stimuli-sensitive hydrogels that have been investigated. These physical gels eventually dissolve in the body. These polymers are ideal candidates for self-regulating systems for drug delivery. These cationic polymers exhibit complexation with DNA and serve as excellent injectable controlled gene delivery vectors, with selective transfection in fast growing cells such as cancer cells as opposed to normal cells.

Example REU Project: The REU student will investigate transfection of reporter gene in co-cultures of cancer and normal cells using the novel pentablock copolymer. Furthermore, this transgene system is also serum resistant and able to be injectable for sustained release, which makes it promising as an ideal sustained transgene vector. The student will investigate transfection using both dissolved vector as well as high enough concentrations where the vector forms polyplex gels which will dissolve slowly to release polyplexes. Through this experience, the student will learn 1) cell culture and sterile technique 2) transfection techniques 3) working in an interdisciplinary environment integrating engineering and biological approaches.

Mentor:  Rizia Bardhan

Stimuli-responsive nanocarriers have transformed the landscape of multiple diseases by enabling spatiotemporally-controlled drug delivery. The localization of such nanocarriers in cells is controlled by their physicochemical properties, and the type and phenotype of cells that they encounter. In this project we will modulate the mechanical (i.e. stiffness or rigidity) properties and molecular properties (i.e. surface ligands) of hybrid liposomal nanocarriers, and by simultaneously leveraging both of these properties we will achieve better cell- and phenotype-specific uptake and drug delivery across the blood brain barrier (BBB), that remains a critical challenge in most central nervous system (CNS) disorders. These project aims will be realized in an in vitro model of BBB constituting three distinct cell lines – brain microvascular endothelial cells, astrocytes, and microglia. We will examine the endocytosis pathway and intracellular trafficking of hybrid liposomal nanocarriers in these cell types and finally also study photothermally actuated drug delivery of rosiglitazone, a drug specific to CNS disorder.

Example REU Project: The REU student will synthesize the hybrid nanocarriers, characterize their various properties, and interrogate their uptake in various cells of the BBB. The student will learn cell culture techniques, nanomaterial synthesis, characterization techniques, and drug transport in in vitro3D models (neurospheroids) of the BBB. Through these skill sets the student will achieve mechanistic understanding of drug delivery controlled by nanocarrier mechanomolecular properties.

Mentor: Ian Schneider

Many diseases or conditions are caused by a misregulation of cell-level forces. Examples include fibrosis in the lung, liver and joints, cancer and other less common conditions like decompression sickness. Delivering drug to these sites specifically will require drug constructs that can release cargo in response to aberrant cell-level forces. Drug constructs that control the release over time as well as those that release drug in response to temperature or pH changes are commonplace. The goal of this project is to generate a new class of drug release constructs that can release payload in response to a variety of environmental inputs including mechanical force.

Example REU Project: We will use an approach called DNA origami to engineer hollow structures that can be loaded with drug and opened in response to environmental signals. The student will use nucleotide chemistry, particle characterization, fluorescence and microscopy techniques to assemble, characterize, load and release drug from these structures. Understanding how these structures operate will allow for the design of drug release constructs that can be deployed in a variety of disease and conditions.

Mentor: R. Dennis Vigil

We are developing a state-of-the-art methodology for fermenter design and scale-up that will be translatable to different microbial strains and processes, thereby helping accelerate technology commercialization in the biomanufacturing industry. Simulation and scale-up of bioreactors is difficult because microorganisms, which function as small chemical factories, are heavily influenced by both the microenvironment that they are in, and also the microenvironment’s trajectory, or history.  As the bioreactor size increases the heterogeneity of microenvironments increases, which makes prediction of the overall performance of the bioreactor more difficult. This is the problem we are trying to address by first understanding how microorganisms perform in a uniform homogeneous environment.

Example REU project: This project involves constructing a new continuous-flow fermenter to produce fatty acids while simultaneously extracting the product in the same device. The work will primarily be experimental, but will also involve data analysis.

Mentor: Laura Jarboe

Microbial cell factories, such as yeast, convert the carbon in substrate molecules to the desired product. This project aims develop yeast strains that can use low-value lipid-rich materials to produce valuable biomolecules. Metabolic activity requires that cells be provided with nitrogen so that they can form the enzymes that perform biochemical reactions. This project will explore methods to improve yeast utilization of complex mixtures of lipids while using sustainable sources of nitrogen.

Example REU project: The REU student will characterize utilization of various non-conventional lipid substrates and nitrogen sources by yeast and relate this data to the relevant physical and chemical properties of the molecules. The student will have the opportunity to work with several yeast species and learn multiple characterization techniques for soft materials. Finally, the REU student will characterize changes in yeast physiology or composition associated with utilization of these carbon and energy sources.

Mentor: Ratul Chowdhury

Alpha helical proteins are proteins which have a helix shape and come in different lengths. They either exist singly, or in bundles (of three or four) with other identical helices. They are held upright by a layer of fat which is known as the cell membrane. These proteins help our cells to interact with the outside as part of this helices are exposed to the outside, a part of it is embedded in the membrane, and a part of it is exposed towards the cell interior. Depending on whether they exist solo or in a bundle, they posit a single pore down the middle of the helix itself, or a square-ish pore guarded by multiple helices. While nature has made for us several thousand helical proteins for various life sustaining tasks, we will learn from those proteins using deep learning and AI, and build, from scratch, completely new helical proteins with transport properties we care about.

Example REU project: The student will execute multiple iterations of the deep-learning AlphaFold algorithm, Rosetta energy minimization, and molecular dynamics.  The work will make use of the Python programming language – so students with prior experience with Python are encouraged. Proteins candidates emerging from simulations of the student will be tested by our experimental collaborators.

Mentor: Molly Kozminsky

Cancer is the second leading cause of death in the United States, and yet every individual’s disease is different. This is in part due to the selective pressures of metastasis, the multi-step process by which cancer spreads that is responsible for 90% of cancer deaths. The different events in metastasis—from the intravasation of the tumor cell into the blood stream to shear stress and immune response experienced while circulating to extravasating and forming colonies in distant sites—present obstacles that can lead to different outcomes. There is heterogeneity both in traits inherent in the tumor cells and in their experiences along the metastatic cascade. This high degree of difference in inherent tumor cell properties, barriers presented by the metastatic cascade, and interactions with the other cells in primary and secondary location present challenges to modeling the inputs and interactions at the root of a patient’s disease trajectory that would lead to a better understanding of diverse outcomes. Current state-of-the art tools and methods cannot dissect key contributing factors— spatial organization and interactions with multiple microenvironments and cellular populations—that lead to disease progression. To overcome these shortcomings, we will use a DNA-directed patterning technique to build models of these microenvironments. DNA-directed patterning allows high-resolution, high-spatial complexity immobilization of cells, ligands, antibodies over a wide range of length scales, from nanometers to millimeters. This platform combines the numerous highly advantageous features necessary to probe the tumor heterogeneity that is at the root of cancer progression and variable response to treatment.

Example REU Project: The REU student will investigate the contribution of specific immune cell populations to cancer cell behavior in the tumor microenvironment. The REU student will gain experience in cell culture, immunofluorescence staining, and immunofluorescence microscopy. The student will additionally have the opportunity to work in the Keck Microfabrication facility to learn the fundamentals of photolithography used in the DNA-directed patterning technique. Combining these skill sets, the student will perform cell patterning and learn image processing techniques required for data analysis.

Mentor: Zengyi Shao

The long-term goal of the Shao group is to (1) study the functional genomics of high-performing microbial species that have unique biochemical and biomedical potentials and (2) leverage these relatively simple and fast-growing testbeds to decipher critical steps in cellular commands, and eventually elucidate fundamental mechanisms in higher eukaryotes. Shao group has established expertise in exploring the unique properties of non-model species as microbial factories to produce compounds with biopolymer, biolubricant, nutraceutical, and pharmaceutical applications. To promote the efficiency to exploit these non-model species, we gear our research towards elucidating systematic rules and developing platform technologies to create generic strain-engineering solutions.

Example REU Project: Genomes serve as scaffolds for transmitting information through both genetic and epigenetic means. Eukaryotes face an information packaging challenge because DNA molecules of each chromosome need to be folded within a tiny space in the nuclei. Accumulating evidence demonstrates that the spatial arrangement of the genomes in eukaryotes is far from random. We are interested in studying the influence offered by different genome contexts on heterologous pathway performance, which is directly correlated to the productivity when the host is engineered as a microbial factory to produce high-value chemicals (e.g., biofuels, biopolymer precursors and other compounds used as nutraceuticals and pharmaceuticals). The REU student will be exposed to frontier research topics such as high throughput DNA assembly and CRISPR-based genome editing technology, and also learn the techniques to generate recombinant DNAs, perform flow cytometry, and gene knock-in/knock-out.

Mentor: Jing Wang

In metastasis, tumor cells travel from the primary site to distant organs through the blood or lymph system.  We are interested in a three-dimensional (3D) spatial analysis to decipher how far tumor cells can penetrate the lung tissues (the most common metastasis site for multiple cancers) from the blood vessels. This study cannot be performed directly with lung tissues because the abundance of tumor cells in the lungs at the early or middle stage of cancer is extremely low, which is < 100 tumor cells per mouse lung. To address this issue, we have designed a subcutaneous model with a 3D scaffold implant, which can develop vasculature and recruit lung-tropic tumor cells from the blood in a mouse model bearing a metastatic tumor. This lung-mimicking subcutaneous model can enrich circulating tumor cells. A scaffold that has a size ten times smaller than a mouse lung can collect > 3000 tumor cells at the early stage of cancer. We will analyze the distance of each tumor cell from the adjacent blood vessel in this lung-mimicking subcutaneous model to advance our understanding of lung metastasis.

Example REU project: The REU student will learn two major technologies in this project. The first is immunofluorescence staining, including fixing and permeabilizing scaffolds explanted from the mouse and staining the tumor cells and blood vessels with fluorescently labeled antibodies. The second one is whole-tissue imaging. The student will learn how to use light sheet ultramicroscopy (UM) to acquire 2D images and splice them to present the 3D distributions of tumor cells and blood vessels in the scaffolds. Finally, the student will work with a group from the Computer Science Department at Iowa State University to quantify the distance of tumor cells to the blood vessels and analyze their 3D spatial relationships.

Mentors: Monica Lamm and Marit Nilsen-Hamilton

Aptamers are short nucleic acids that fold uniquely to specifically recognize other molecules (Figure 3). They have some superior properties to antibodies for applications in sensor platforms in that they are stable to dehydration, high temperatures and long storage. They also have the capability of being used in synthetic biology to control gene expression, which is something for which we cannot use antibodies. A very exciting aspect of aptamers is their great flexibility in structure and in methods by which they can be controlled. We need to understand this molecular flexibility to properly design sensor components for engineering applications and gene regulators for synthetic biology. For this we are using molecular dynamics simulations paired with biochemical analysis of the aptamer functions in the laboratory. Our goal is to develop a computational approach to consistently and accurately predict an aptamer’s mobility and target (ligand) recognition that can be validated in the laboratory by our collaborator, Professor Marit Nilsen-Hamilton (Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology).

Example REU Project: The REU student will use modeling and simulation software to investigate aptamer structure and dynamics. The student’s investigation will involve generating variants of an aptamer that has an established structure to test hypotheses about the role of certain nucleotide bases in ligand recognition and structural rearrangement upon binding the ligand. The model variants will be studied using docking methods, followed by molecular dynamics simulation to characterize the structural changes in the aptamer between its unoccupied and ligand-occupied states.

Mentor: Qun Wang

Gastrointestinal (GI) mucosal delivery of vaccines has practical advantages over vaccination by intravenous injection or subcutaneous injection, including both cost efficiency and increased safety. Our long-term goal is to explore ex vivo gut models to study new oral vaccine delivery systems for the treatment of infectious diseases. In pursuit of this goal, our overall objective in this project is to determine how nanoparticles-based vaccine delivery systems transport within an ex vivo intestinal mucosal system built by primary intestinal stem cells (ISCs) derived intestinal organoids (Miniguts). The rationale for the proposed research is that in-depth knowledge of the mechanisms involved in the progressive induction and differentiation of ISCs into M-cells in vivo and guided transport of oral vaccine delivery in vivo will be gleaned. The harvested knowledge will further equip us to understand epigenetic changes of ISCs during reprograming progression and offer new insights to develop orally available vaccination strategies to treat inflammatory and infectious diseases. We plan to (1) to determine how M cells can be incorporated into miniguts to create an ex vivo and in vivo model of the mucosal immunological system; (2) to determine the enhancement of the transport of gold nanocages through minigut mucosal system by surface modification with MRV σ1 protein; (3) to determine how the surface modification with MRV σ1 protein onto nanoparticles to enhance the transportation of encapsulated model vaccines and oral immunization

Gastrointestinal (GI) mucosal delivery of vaccines has practical advantages over vaccination by intravenous injection or subcutaneous injection, including both cost efficiency and increased safety. Our long-term goal is to explore ex vivo gut models to study new oral vaccine delivery systems for the treatment of infectious diseases. In pursuit of this goal, our overall objective in this project is to determine how nanoparticles-based vaccine delivery systems transport within an ex vivo intestinal mucosal system built by primary intestinal stem cells (ISCs) derived intestinal organoids (Miniguts). The rationale for the proposed research is that in-depth knowledge of the mechanisms involved in the progressive induction and differentiation of ISCs into M-cells in vivo and guided transport of oral vaccine delivery in vivo will be gleaned. The harvested knowledge will further equip us to understand epigenetic changes of ISCs during reprograming progression and offer new insights to develop orally available vaccination strategies to treat inflammatory and infectious diseases. We plan to (1) to determine how M cells can be incorporated into miniguts to create an ex vivo and in vivo model of the mucosal immunological system; (2) to determine the enhancement of the transport of gold nanocages through minigut mucosal system by surface modification with MRV σ1 protein; (3) to determine how the surface modification with MRV σ1 protein onto nanoparticles to enhance the transportation of encapsulated model vaccines and oral immunization

Example REU Project: The REU student will participate to establish protocols to produce surface modified nanoparticles with the MRV σ1 to investigate nanocarriers transport mechanism through a minigut epithelial wall and incorporate M cells into the Mini-gut model to create an ex vivo mucosal immunological transport system. First, we will optimize RankL concentration for induction of M cells ex vivo and determine how to encapsulate RankL into nanoparticles for delivery to ISCs and reprogram ISCs to M cells ex vivo and in vivo. Second, we will separate and purify MRV σ1 protein and produce M-cell-targeting nanocage with the MRV σ1 protein. Third, we will determine whether surface modification with MRV σ1 protein will enhance antigen loaded PLGA NPs through M cells and induce immune response in vivo.

Mentor: Thomas Mansell

The probiotic E. coli strain Nissle 1917 is a gut isolate from a WWI soldier resilient to Shigellosis (dysentery). Now sold in Canada and Europe as Mutaflor for protection against traveler’s diarrhea, it is a good gut colonizer that is non-pathogenic: a perfect model probiotic. The Mansell lab is interested in understanding the mechanisms of Nissle’s probiotic effects as well as its demonstrated resilience to many biofuel and short chain fatty acid challenges. We have been performing various genome engineering experiments with Nissle which have led to the production of useful probiotic small molecules (Figure 4). Additionally, we are beginning to test Nissle’s probiotic effects in mouse and other gut microbiome models.

Example REU project: The REU student will use genome and genetic engineering techniques to explore Nissle’s probiotic nature, adding and deleting metabolic pathways to determine which traits are most useful in Nissle. The project may also involve production of therapeutic molecules (e.g., immunomodulating cytokines, small molecules, antimicrobial peptides, or therapeutic proteins).

Mentor: Nigel F. Reuel

The promise of stem cells for regenerative medicine cannot be fully realized unless the manufacturing cost and quality of differentiated cell therapies is improved. A recent report from the US national academies indicates that reproducibility in manufacturing is a critical, un-met attribute that increases cost and limits development timeline and patient access. Much work has been done on identifying chemical, physical, and electrical cues that can direct differentiation of stem cells into mature, functional cell types. These static recipes give some ability to control direction in manufacturing; however, phenotypic variability and process perturbations result in heterogeneous differentiation and batch-to-batch variation. The current manufacturing process is analogous to driving a car blind-folded: stem cells are pointed in the desired direction, set on their way at a constant rate, and no adjustments are made despite the random bumps or crosswinds encountered in the environment. The end-product must be sorted and purified at great cost and unacceptable yield or pooled and used at lower potency. A critical gap in our understanding is the dynamic interplay of these control actions and how they can be modulated throughout the differentiation process to limit variability.

Example REU project: This project tests the hypothesis that a real-time control system framework built on reinforcement learning (RL) will improve intra- and inter-batch stem cell differentiation homogeneity vs. static recipes. This would, in effect, take the blind fold off and give autonomous control to respond to process and phenotypic variations. The REU student will will contribute to research aims that are designed to test this hypothesis and determine the level of differentiation improvement from dynamic control as well as the effect of RL training iteration number on control quality. These are R1: build the control framework, R2: enable training of the control framework, and R3: benchmark dynamic control against static recipes on model cells.

Mentor: Eric Cochran

Professor Cochran’s research group focuses on the development of new plastics from bio-based monomers that can compete with their petroleum based analogues on the basis of cost and performance. A particular area of focus is the application of controlled radical polymerization to manage branching in multifunctional monomers to yield biobased thermoplastics from a variety of sources previously only considered as thermosets, such as soybean oil.

Example REU Project: The REU student will chemically modify lignin fragments such that they undergo radical polymerization reactions. The properties of the resultant thermoplastic lignin will be tuned such that a melt-spinnable resin can be produced, suitable as a precursor to carbon fibers. Through this project, the student will learn (1) techniques for the synthesis and basic characterization of acrylic polymers, (2) polymer processing techniques such as extrusion and (3) mechanical characterization techniques such as dynamic shear rheology and tensile testing.