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Projects and Mentors

The Clemson REU Program: Nature’s machinery through the prism of physics, biology, chemistry and engineering has mentors in Physics, Chemistry, Materials Science, Bioengineering, Genetics and Biochemistry, and Biology. All the mentors have extensive experience in supervising undergraduate research students. Participants will work in pairs with in a dynamic research team led by two principle investigators to:

      • design and conduct experiments;
      • use modern research equipment;
      • learn applied and theoretical methods;
      • analyze data and draw conclusions;
      • present results in multiple formats;
      • enjoy an engaging, academically stimulating, and highly collaborative interdisciplinary
      • research environment.
  • Active matter driven by molecular motor proteins

    Mentors: Dr. Joshua Alper, Physics and Astronomy, and Dr. Olga Kuksenok, Materials Science and Engineering

    Introduction: Engineered active polymer gels have the potential to revolutionize the next generation of smart biomedical devices and tissue-engineering scaffolds. The cytoskeleton is essentially a naturally occurring active gel found in nearly every eukaryotic cell. It is capable of forming structures, changing shape, and driving oscillations both spontaneously and in response to external cues. Recently, there has been increased interest in building active materials from cytoskeletal filaments and motors and using viscoelastic material theory and computational models to describe their properties. However, these studies only hint of what is possible with biomimetic active gels engineered from components of the cytoskeleton.

    Research Plan: Two participants will collaborate to study motor protein-driven active gels. One participant, primarily engaged in experimental research in the Alper Lab, will reconstitute active polymeric gels using microtubules, crosslinking microtubule associated proteins (Ase1 and inactive motors), and motor proteins (axonemal dyneins). The participant will measure the passive and active properties of the gels using high-resolution microscopy and force spectroscopy (optical tweezers). The other participant, primarily doing theoretical and computational work in the Kuksenok Lab, will model the passive and active properties of these gels. This participant will adapt existing models developed and validated for similar systems to predict and explain the behaviors of these active biological gels. Together, the participants will design, build, model, and engineer nature’s machinery to generate active gels with novel properties. The participants will make significant contributions to this exciting field of active nano-biological materials by expanding the molecular constituents used in the design of these gels.

    Equipment/techniques participants will learn and use: fluorescence microscope; optical tweezers; general biochemical and biophysical equipment including centrifuges, gel electrophoresis, and spectrophotometers; high performance computer cluster.

  • Dielectrophoretic forces in the diagnosis of parasitic disease

    Mentors: Dr. Rodrigo Martinez-Duarte, Mechanical Engineering, and Dr. James Morris, Genetics and Biochemistry

    Introduction: Diagnosis of infection by the kinetoplastid parasites, including Trypanosoma brucei, Leishmania spp., and Trypanosoma cruzi, remains challenging, in part, due to the technical challenges associated with performing microscopy-based tests in remote settings. Dielectrophoresis (DEP) forces, which result from exposing the parasites to an electric field gradient, can selectively concentrate parasites in specific locations within a microfluidic chip and greatly facilitate their detection. However, the response of kinetoplastids to the DEP force likely depends on the properties of the parasite, which can change due to growth, environmental conditions, and exposure to sub-curative doses of different anti-parasitic agents.

    Research Plan: Two participants will collaborate to study how growth, environmental factors, and exposure to drugs affect the DEP behavior of T. brucei. One participant primarily engaged in mechanical and biological engineering research in the Martinez-Duarte Lab will develop an experimental platform to study the response of parasites to various electric fields. This participant will use hydrodynamic and electrical forces to manipulate parasites of interest inside microfluidic systems selectively. The other participant, primarily doing molecular parasitology research in the Morris Lab, will use molecular genetics approaches to generate parasites that express distinct fluorescent markers. This participant will clone fluorescent protein genes into trypanosome expression vectors, transfect them into parasites, and score the expression of these proteins by flow cytometry and microscopy. Together, the participants will determine whether DEP can distinguish between subtle differences in trypanosomes. Ultimately this research will lead to better diagnostic techniques for parasitic disease with the potential to impact the lives of millions of people worldwide.

    Equipment/techniques participants will learn and use: Molecular cloning, in vitro parasite culture, transfection approaches, flow cytometry, microfluidics, dielectrophoresis. 

  • The effects of radiation on cells and tissues

    Mentors: Dr. Endre Takacs, Physics and Astronomy, and Dr. Delphine Dean, Bioengineering

    Introduction: High dose radiation treatment is commonly used to kill diseased cells within a target tissue, but healthy cells near to the target also get exposed to low doses of radiation. Recently, there has been some evidence that suggests various tissues react to low doses of radiation, potentially altering their underlying physical, chemical, and biological pathways during irradiation. However, precisely how tissues respond to low dose radiation and whether we can create materials to make cells more or less radio-sensitive remains unknown.

    Research Plan: Two participants will collaborate to study the interaction between low levels of monochromatic soft x-ray radiation and biological tissues. One student, primarily working on tissue engineering in the Dean Lab, will grow breast cells and characterize their properties in response to radiation and radiosensitizing materials using various biological assays. The other student, primarily performing medical physics research in the Takacs Lab, will characterize the low dose x-rays and model their effects on tissue. Together, the participants will precisely quantify the radiation that cell cultures receive and use well-defined protocols to understand how low levels of radiation affect individual biological machinery in cells and cell cultures.

    Equipment/techniques participants will learn and use: mini-x-ray tubes, solid-state x-ray detectors, single-photon counters, spectral analysis software, statistical analysis software, cell culturing, optical microscopy and image analysis, cell proliferation and cell cycle analysis, cell function and differentiation assays

  • The Role of Defects in Nanomaterial-Biomolecular Interactions

    Mentors: Dr. Ramakrishna Podila, Physics and Astronomy, and Dr. Terri Bruce, Bioengineering

    Introduction: Nanomaterials have many exciting potential biological and biomedical applications, including in diagnostic and therapeutic devices. Nanomaterials are more chemically reactive than their bulk counterparts because they possess a high density of naturally occurring structural defects (e.g., atomic vacancies). The altered chemical reactivity of nanomaterials leads to pronounced interactions with biomolecules and increases their ability to efficiently cross physiological barriers (e.g., blood-brain barrier). In this scenario, it is critical to understand the interactions between biomolecules and defects within nanomaterials to both predict the fate of nanomaterials and develop safe nanomaterials by design. 

    Research Plan: Two participants will collaborate to study how defects in graphene effect protein interactions from the individual protein level to the complex biological milieu. One participant, primarily doing nanotechnological research in the Podila Lab, will use defected graphene sheets to study the interactions between defects and individual proteins (e.g., fibrinogen) using a comprehensive array of techniques, including high-resolution transmission electron microscopy, Raman spectroscopy, and atomic force microscopy. This participant will also determine the impact of defects on the formation and composition of protein corona through detailed proteomics studies on pristine and defected graphene incubated in fetal bovine serum. The other participant, primarily doing cell biological and biochemical research in the Bruce Lab, will evaluate the physiological responses to defected graphene with and without protein corona using cell viability and oxidative stress assays, flow cytometry, and hyperspectral microscopy. Together, the participants will explore how defects in nanomaterials influence their interactions with biomolecules. Ultimately this research be used to guide the development of novel biomedical devices.

    Equipment/techniques participants will learn and use: Electron microscopy, Raman and X-ray photoelectron spectroscopy, atomic force microscopy, proteomics, mammalian cell culture, flow cytometry, ELISA, and LDH cytotoxicity assay

  • Small GTPases that organize septins essential for the pathogenesis of Cryptococcus neoformans

    Mentors: Dr. Feng Ding, Physics and Astronomy and and Dr. Lukasz Kozubowski, Genetics and Biochemistry

    Introduction: Cryptococcus neoformans is a major opportunistic fungal pathogen worldwide and a leading cause of death in AIDS patients. Like all microbial pathogens, C. neoformans must cope with stress in the adverse environment of the host, and thus inhibiting its stress response pathways is a promising therapeutic strategy. Recently, proper organization and dynamics of septin filaments, which act in cell division and morphogenesis, have been identified as essential to the C. neoformans stress response, and Cdc42, a small GTPase, has been identified to play a significant role in septin organization. However, the mechanisms by which Cdc42 organizes septin assembly and dynamics and its connections to the stress response in C. neoformans remain unknown. 

    Research Plan: Two participants will collaborate to study the role that Cdc42 and other small GTPases play in organizing C. neoformans septins. One participant, primarily engaged in cell biological and biochemical research in the Kozubowski Lab, will use an allele of the Cdc42 protein that we engineered to be light-sensitive to study its role in C. neoformans cells. The participant will investigate how Cdc42 and other small GTPases regulate septin complex assembly and dynamics using fluorescent and confocal microscopy. The other participant, primarily doing computational biophysics and protein engineering in the Ding Lab, will design and model additional light switchable proteins to be subsequently tested in C. neoformans. This participant will use discrete molecular dynamics and other computational techniques to predict and model the dynamics of these proteins in silico. Together, the participants will define the mechanisms responsible for C. neoformans cell division and survival in the host and could potentially reveal new targets for therapeutic interventions.

    Equipment/techniques participants will learn and use: molecular modeling; computational protein engineering; molecular dynamics simulations; fluorescent microscopy; confocal microscopy.

  • Intrinsically disordered proteins in membraneless organelles 

    Mentors: Dr. Sapna Sarupria, Chemical Engineering, and Dr. Hugo Sanabria, Physics and Astronomy

    Introduction: Membraneless organelles, including nucleoli, Cajal bodies, P-bodies, postsynaptic densities, and stress granules, are formed by the condensation of intrinsically disordered proteins (IDPs) due to a process known as liquid-liquid phase separation. These ubiquitous, highly specialized compartments are critical for multiple physiologically relevant cellular functions, including the storage and processing of molecular information. The discovery of IDPs and membraneless organelles has challenged the traditional protein structure-function paradigm. In particular, weak and transient interactions between the IDPs in membraneless organelles have been hypothesized to drive function.

    Research Plan: Two students will collaborate to study the process of liquid-liquid phase separation using engineered peptide sequences that are thought to generate the weak and transient interactions between intrinsically disordered regions of molecules found in membraneless organelles. One student, primarily involved in experimental research in the Sanabria Lab, will perform fluorescence spectroscopic measurements and imaging at the ensemble and single-molecule levels to quantify the dynamics of these peptides inside the liquid-liquid phase-separated droplets. The other student, primarily involved in computational research in the Sarupria Lab, will perform atomistic and coarse-grained molecular dynamics (MD) simulations of these same peptides that capture observable quantities. Together, the students will quantify the dynamic behavior of biomolecules in these condensates by combining sensitive state of the art ensemble and single-molecule fluorescence spectroscopy techniques with various molecular dynamics simulation approaches. The participants will significantly advance this field by identifying how the dynamic behavior of biomolecules in these condensates can lead to their function. 

    Equipment/techniques participants will learn and use: Fluorescence spectroscopic tools, first principles of polymer phase separation, high-performance computing, molecular dynamics simulations, basic bash and python scripting, scientific visualization.

  • Redox Chemistry Models for Alcohol-induced Cardiac Dysfunction

    Mentors: Dr. Will Richardson, Bioengineering, and Dr. Andy Tennyson, Chemistry

    Introduction: Chronic alcohol abuse is a substantial health problem that can cause cardiac dysfunction through altered tissue structural remodeling. This tissue remodeling results from pathological cell signaling governed, in part, by the redox chemical reactions involved in alcohol metabolism, amongst other biochemical and biophysical signals. Therefore, understanding how redox reactions modulate cell signaling behavior could help us develop new therapeutic approaches for alcohol abuse-related cardiac dysfunction. Unfortunately, these redox reactions interact within a large and complex network of signaling pathways, making it difficult to predict their effect.

    Research Plan: Two participants will collaborate to study how redox chemistry relates to alcohol-induced cell signaling pathway dysfunction in cardiac cells. One student, primarily performing biochemical and cell biological research in the Tennyson Lab, will synthesize and characterize novel organometallic complexes that interfere with the reactive oxygen species (ROS) that contribute to redox stress. Once synthesized, the participant will treat cardiac cells in culture with these complexes and test their effect on various cell functions. The other participant, primarily performing systems biological modeling in the Richardson Lab, will use a computational model of cardiac cell signaling networks to identify the particular signaling molecules and pathways that are most strongly affected by ROS. This participant will also perform virtual drug screens to identify other novel therapeutic targets for future study. Together, the participants will help discover how oxidative stresses contribute to alcohol-induced tissue damage and new potential therapeutic compounds to prevent this damage in the first place.

    Equipment/techniques participants will learn and use: general biochemical and biophysical equipment including centrifuges, gel electrophoresis, and spectrophotometers; mammalian cell culture equipment; optical and fluorescent microscopy; network systems modeling; high-performance computer cluster.