2020 BioMaP REU Research Projects

1. Immunomodulatory Nanovaccines Against Infectious Diseases – Experimental

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.

2. Drug and Gene Delivery – Experimental

Mentor: Surya Mallapragada

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.

3.  Hyperspectral Imaging of DNA and Protein-Linked Metal Nanoparticles – Experimental

Mentor: Andrew Hillier

The Hillier group focuses on synthesis and characterization of nanoscale materials with an emphasis on novel and highly tunable optical phenomena associated with these systems. Our recent efforts have exploited nanostructures that exhibit surface plasmon resonance for high fidelity sensing. Sensors based on surface plasmon resonance (SPR) have become increasingly popular as a label-free method for measuring the binding of analytes to functionalized surfaces and in the detection of immobilized biomolecules. SPR sensing has been exploited in the development of immunosensors, advancing proteomics, accelerating drug discovery, monitoring DNA hybridization, and detecting protein-DNA interactions. One of the key attributes of SPR sensing is that it gives a direct signal related to local binding, and eliminates the complex labeling/conjugation steps required of competing techniques that utilize fluorescently labeled molecules in detection assays. Noble metal nanoparticles can be used as precise markers for SPR-based sensing in that they give a strong optical response, and can also be tracked individually. The overall goal of this research is to assist in developing a hyperspectral imaging tool that can be used to detect the spectral signature of individual and collections of metal nanoparticles as they bind to and assemble into complex hybrid structures with biological macromolecules, such as DNA.

Example REU Project: The REU student will assist in the development and testing of a hyperspectral imaging system for the analysis of metal nanoparticles in isolation and in the presence of DNA and a selection of binding proteins. An optical microscopy system will be modified to allow multi-color imaging and high resolution spectroscopy in order to track the optical response of gold and silver nanoparticles bound to surfaces or suspended in solutions. This project integrates nanotechnology, optics, microscopy, and analytical chemistry.

4. Controlling Structure and Mechanical Properties to Understand and Guide Cell Migration – Experimental

Mentor: Ian Schneider

During tumor metastasis, cancer cells migrate out of the tumor into the surrounding tissue. They do this by sensing aligned fibers of insoluble extracellular matrix (ECM) proteins such as collagen and gradients in ECM stiffness. Both direct migration leading to invasion, metastasis and poor prognosis. The goal is to control collagen fiber alignment through self-assembly or mechanical rotation (Figure 1A&B) and stiffness through soft-stiff interfacial interactions in hydrogels tuned using unique topographies and surface chemistry (Figure 1C-E) in tumor-mimicking environments. These tools will be used in conjunction with fluorescent biosensors and live-cell light microscopy techniques that allow for the visualization of cell migration. Understanding how cells respond to precisely defined structural and mechanical properties will uncover fundamental mechanisms of cancer invasion and metastasis as well as guide the design of platforms to separate patient-derived cells based on directed cell migration guide.

Example REU Project:

Cancer cells will be seeded in 3D collagen-hyaluronan networks with varying degrees of fiber alignment. Hyaluronan is a polysaccharide various molecular weights that occupies pores and alters the mechanical properties of the collagen network. Collagen orientation and cell migration will be assessed in these 3D tumor-mimicking environments. The REU student will learn how to align 3D collagen networks and culture cells in those networks. The migratory behavior of cells and the extracellular processes of collagen rearrangement will be analyzed as a function of hyaluronan concentration and molecular weight. This project will expose the REU student to collagen alignment techniques, mechanical and structural property measurements, cell biology and quantitative light microscopy.

5.  Model Validation for Photosynthetically Active Radiation Transport in Algal Photobioreactors – Computational

Mentor: R. Dennis Vigil

Concerns about dwindling petroleum reserves, geopolitical instability, and the linkage of global climate change to fossil fuels has led to increased effort in developing biorenewable replacements. The cultivation of microalgae for producing biorenewable chemicals and fuels is particularly attractive because these aquatic systems offer several important advantages over terrestrial biomass, such as noncompetition with food agriculture, lower water demand, and significantly higher fuel yield potential due to solar radiation photoconversion efficiencies five times higher than land-based crops. Nevertheless, large-scale deployment of algaculture for partial replacement of petroleum products requires many technological advances including drastic improvements in the efficiency and scalability of processes and equipment for culturing algae and separating products. This project will address the need for improved process engineering and scaleup by developing and validating better models for computational simulation of the complex interplay between hydrodynamics and radiation, which are crucial factors determining the performance and scalability of algal photobioreactors. The importance of accurately simulating the coupling between radiation energy transport and fluid mixing springs from the fact that algae growth rates can be significantly influenced by the characteristic frequency that cells are exposed to lighter or darker regions within the reactor. This project aims at determining how hydrodynamics affect radiation penetration in model algae bioreactors.

Example REU Project: In view of the above considerations, it is evident that the rational design and scale-up of photobioreactors requires at a minimum the development of modeling tools that incorporate the following elements: (1) a two-phase computational fluid dynamics (CFD) code that can accurately predict the distribution of gas and liquid phases in the reactor, as well as intraphase mass transport of nutrients in the aqueous growth media and interphase transport of important reactants between gas bubbles and liquid growth media, such as oxygen and carbon dioxide; (2) a detailed light transport model; (3) a Lagrangian particle tracking simulation to predict the light history of microorganisms; and (4) a kinetic growth model for the microalgae. The REU student will develop and validate the first three of these essential elements of a comprehensive photobioreactor model.

6. Contribution of Membrane Proteins to Microbial Robustness – Experimental

Mentor: Laura Jarboe

The Jarboe group has identified a variety of naturally-occurring sequence variations that impact the membrane characteristics the model organism Escherichia coli. One of these variations occurs within outer membrane protein A (OmpA), a protein that has previously been implicated in microbial attachment and in pathogenesis. Another of these variations involves the global regulator CsrA. This variation has been shown to substantially improve the resistance of the E. coli membrane to biomass-derived inhibitors and thus may useful in improving the production of biorenewable fuels and chemicals.

Example REU Project: The REU student will characterize bacterial strains expressing the different protein variants, with the goal of understanding the relationship between the protein sequence variations and the microbial characteristics. Characterization will include survival in a variety of conditions, membrane integrity and production of model biorenewable compounds. Some strain engineering may also be performed and/or preliminary bioinformatic analysis, such as modeling the impact of sequence changes on protein structure.

7. Thermal Deconstruction of Biomass – Experimental

Mentor: Robert Brown

We are exploring the thermal deconstruction of lignocellulosic biomass into sugars, phenolic oil, and acetate. This contrasts with biological deconstruction, which uses enzymes and microorganisms to separate carbohydrate and lignin from plant fibers.  The thermal pathway offers a faster and less expensive pathway to deconstruction, the first step in converting biomass into biofuels and biobased products. The goal is to produce high yields of monomeric building blocks from both the carbohydrate and lignin.  We have demonstrated that fast pyrolysis, which is the rapid heating of biomass in the absence of oxygen, can produce anhydro monosaccharides (dehydrated sugars) from both cellulose and hemicellulose.  Success depends upon blocking the catalytic activity of naturally occurring alkali and alkaline earth metals in biomass, which otherwise promotes pyranose and furanose ring fragmentation, converting polysaccharides into light oxygenates instead of the preferred anhydro monosaccharides. With support from the National Science Foundation, we have recently begun fundamental studies to understand the mechanism by which plant polysaccharides are thermally depolymerized. The goal of this research is to measure the chemical kinetics of thermal deconstruction of biomass through time-resolved measurements of condensed phase reactions. Most previous studies of thermal deconstruction kinetics have measured weight loss of samples undergoing relatively slow heating, which yields little information about elementary reactions occurring in the solid biomass. This research will demonstrate the utility of Controlled Pyrolysis Duration (CPD) – Quench reactors developed at Iowa State University for studying condensed phase elementary chemical reactions.

Example REU Project: The REU student in collaboration with graduate students and research staff will conduct experiments with two versions of CPD – Quench reactors. The first, capable of investigating reactions that occur on the order of a few seconds, will be used to study unzipping of small oligosaccharides to form the anhydro-monosaccharide levoglucosan.  The second, capable of investigating much faster reactions, will be used to study cracking of cellulose to oligosaccharides early in the depolymerization process. These apparatus will also be employed to study thermal depolymerization of hemicellulose and lignin. The student will learn to analyze pyrolysis products using various analytical instruments including GC/MS, GPC and HPLC.

8. The Artificial Pancreas Project – Experimental and Computational

Mentor: Derrick Rollins

Type 1 diabetics often experience extreme variations in glucose concentrations which can have long- and short-term adverse effects such as seizures, coma and organ degeneration. Studies have established that there is a need to maintain the glucose levels within a normal range to avoid complications caused by diabetes. However, initial attempts to regulate blood glucose levels using insulin infusion, multiple injections or their combinations have had limited success as they lack the ability to decide the appropriate rate and/or amount of insulin infusion based on the current metabolic state of the body. An “artificial pancreas” consisting of a continuous glucose monitor, an insulin infusion pump, and a control algorithm has the potential to improve glucose regulation by intelligently deciding the proper amount of insulin delivery at the proper time.

In this research, we are developing patient-specific dynamic, block-oriented, multivariable models that can predict how various disturbances (inputs) such as food consumption, activity and stress affect glucose concentrations. The modeling methodology chosen has the ability to determine causality even from correlated inputs, which invariably results in free-living real subject studies. Since glucose levels are highly dependent on the metabolic and physiologic states of the body, the models includes several non-invasive variables that are related to activity, stress, food consumption, etc. as inputs to the model so that the affect of their interactions can be explicitly taken into account.

Example of REU Project: The student will help with assist in our inpatient and outpatient clinical trials in data collection, processing, modeling and analysis. This work is supported by the Juvenile Diabetes Research Foundation (JDRF) and the National Institute of Health (NIH). Our partners on engineers, doctors and nurses at the Illinois Institute of Technology (IIT), the University of Ill at Chicago, and the University of Chicago Medical Center. Students on this project will have an opportunity to analyze and develop models using real subject data and could assist with our data collection with the patients in a hospital setting. Student may also have an opportunity to assist with the development of a new non-invasive continuous-time glucose monitor that uses data from an armband as shown with several sensors to measure activity and stress.

9. Polymer Properties that Selectively Target Tumor-Associated Macrophages – Experimental

Mentor: Kaitlin Bratlie

We are interested in understanding what material parameters can be exploited to discriminately deliver drugs to tumor-associated macrophages (TAMs). TAMs promote tumor growth through the release of angiogenic – blood vessel forming – molecules. These growth factors provide nutrients to the tumor and enable metastasis. TAMs are alternatively activated macrophages (M2) that can be reprogrammed to classically activated macrophages (M1), which kill neoplastic cells through the release of cytotoxic molecules, such as tumor necrosis factor. Our goal is to determine what materials properties will allow for selectively targeting of these alternatively activated macrophages (Figure 2). We will examine how the cytokine expression of classically and alternatively activated macrophages changes in response to different functional groups. We will also monitor internalization of the liposomes in polarized macrophages.

Example REU Project: The REU student will learn how to polarize macrophages into classically (M1) and alternatively (M2) activated cells. The macrophages will be cultured with functionalized liposomes. The viability of the macrophages in the presence of liposomes loaded with chemotherapeutics will be measured through a colorimetric assay. The cytokines expressed will also be studied through colorimetric enzyme linked immunosorbant assays (ELISA) to quantitatively detect the presence of antigen. The ultimate goal for this project is to examine all of the data generated through these assays and determine how the particle parameters influence the two different macrophage polarizations. This study will lay the groundwork for future studies in targeted drug delivery. The REU student will learn sterile cell culture technique, scientific communication skills, how to process data, and how to perform biochemical assays.

10. Understanding the Relation Between Aptamer Structure and Function for Sensors and Synthetic Biology – Computational

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.

11. Developing New Oral Vaccines through the Minigut Mucosal System– Experimental

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.

12. Probiotic Engineering – Experimental

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).

13. Resonant Biosensors for Enzyme Activity, Protein Binding, and Ion Detection – Experimental

Mentor: Nigel F. Reuel

nigel-reuel-project-graphicThe Reuel lab works to bridge the logic system of biology (molecules and enzyme gates) to the logic system of modern electronics (electrons and semiconductor gates) through novel materials and synthetic-biologic interfaces. We are especially interested in transducing biologic events within closed systems, as these are the most commercially relevant and impactful to the “real world” (living models, soil systems, bioreactors, etc.). We are rapidly producing a new class of resonant sensors (ACS Sensors N. Reuel et al. 2016) that are able to transduce changes in the local dielectric environment wirelessly, via short wave radio frequencies (1-100MHz). By engineering the surface coating and geometry of the sensors we can tailor the resonators to measure enzyme activity, protein binding, ion sensitivity, tissue health, and biofilm growth. Our lab work is a balance of raw material synthesis, prototype development (hardware and software), and application testing. This summer project will focus on real world problems with our growing list of collaborators (animal models with ISU Vet Med, diabetic foot ulcers at Baylor, field studies with ISU Agronomy, biofilms with ISU Microbiology, etc.).

Example REU Project: Student will help design and build resonant sensors for biologic analytes (ions, proteins, cells, and tissue types). They will work with a Ph.D. student and a larger team of undergraduate researchers. This project will involve material synthesis (custom and vendor supplied), hardware automation (basic Python programming and stepper motor control will be taught), handling and use of commercially available proteins, some custom protein synthesis (E. coli expression, ­in vivo or cell free), and back-end software development to analyze experimental results (Python and Matlab).

14. Lignin-Based Engineering Thermoplastics – Experimental

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.

Contact Information

BioMaP REU
Chemical and Biological Engineering
Iowa State University
618 Bissell Road
Ames, IA 50011-1098
515 294-6533
biomap@iastate.edu