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Project 1: Sexy Signals: The molecular basis of male ornamentation in sepsid flies

Dr. Julia Bowsher, Mentor and Project Lead

In many organisms, females choose mates based on ornamentation. These ornaments are often elaborate and costly, and have no function outside of courting females. The mechanisms by which they initially evolved are often unknown. We hypothesize that the developmental basis of sexually dimorphic traits influences their evolution.   We test this hypothesis using multiple fly species in the family Sepsidae. Male sepsid flies have abdominal appendage-like structures that they use to court females. We investigate the molecular genetics of these bizarre and novel structures, motivated by the following questions:

  1. How do these structures function during courtship? Can the shape of these abdominal appendages be explained by female choice?
  2. How do secondary sex traits like these appendages develop?  Do they use the same genes that are involved in primary sex determination?
  3. How do developmental processes shape evolutionary outcomes? By understanding genetics and selection pressure, can we explain the evolutionary history and diversity of these structures?

Students choosing to work in the lab can investigate any of the above questions, or are welcome to generate their own lines of inquiry.   After a summer in the lab, students will be able to do the following:

  • Generate their own hypotheses and design experiments to test them.
  • Explain the board biological questions that motivate their research, as well as the specific rationale for the experiments they conduct.
  • Generate, analyze and interpret data
  • Apply some or all of the following molecular techniques: PCR, gene expression analysis through antibody staining or in situ hybridization, and bioinformatics.

Project #2: Asymmetric Synthesis Using Green Sustainable Methods

Dr. Greg Cook, Project Lead

We are interested in developing selective organic reactions for organic synthesis utilizing organometallic and catalytic processes. An overriding theme of our research is the development of new reactions that lessen the negative environmental impact. We accomplish this through the advancement of new catalytic methods to increase efficiency in organic processes and expand on new processes that utilize non-toxic and non-harmful catalysts, reagents and solvents. Our methods are applied in the synthesis of new materials and compounds of biological interest. We are investigating novel isoform-selective inhibitors for histone deacetylses (HDAC) enzymes involved in epigenetic regulation. HDAC inhibitors have broader impacts in therapeutics for cancer and other diseases.

At the end of this research experience, students will be able to:

  • Make organic molecules using sustainable catalysis
  • Synthesize potential anti-cancer compounds
  • Purify organic molecules using chromatography
  • Analyze organic compound structure using NMR spectroscopy

Project #3: Intrinsically Conductive Polymers for Corrosion Protection of Metal Alloys

Dr. Victoria Gelling, Project Lead

Joseph Byrom, Graduate Student Mentor

Intrinsically conductive polymers (ICPs) are a class of polymeric materials that exhibit electrical properties inherent to traditional semi-conductor and metallic materials. Included with these novel properties is the ability to promote passivation of metallic substrates reducing their susceptibility to corrosion, thus improving the lifetime of the system. Students participating in Dr. Gelling's lab will study the chemical reactions of polypyrrole and polyaniline and how various reaction variables can affect the final polymer architecture and corrosion inhibition of the synthesized pigments when used in a paint formulation.

Goal of Project: The main focus for this project is to determine the effects of various reaction parameters pertaining to the synthesis of polypyrrole and polyaniline doped with ionic acrylates on the final electrical and corrosion resistant properties when implemented into a UV-curable paint system.

Throughout this research experience students obtain knowledge in:

 Polymer synthesis techniques

  • Coatings formulation
  • Mechanical properties evaluation
  • Various electrochemical and visual techniques pertaining to the assessment of corrosions

Specific techniques include:

  • Atomic Force Microscopy
  • Thermal Gravimetric Analysis
  • Fourier Transform Infrared Spectroscopy
  • Dynamic Mechanical Analysis
  • Electrochemical Impedance Spectroscopy
  • Linear Polarization
  • Scanning Vibrating Electrode Technique
  • Accelerated weathering methods

Project #4: Developmental physiology of insects

Dr. Kendra Greenlee, Project Lead

Development of physiological traits is a critical aspect of evolutionary and ecological physiology. Development plays an important role along the pathway from gene to phenotype, since in any situation where a new trait has evolved, alterations in ontogeny must also have occurred.

The Greenlee Lab seeks to understand the mechanisms and consequences of developmental changes in physiology.  Insects are excellent models for understanding physiological changes that occur with growth, because they are typically fast growing and have juvenile and adult morphologies that may be either different (insects that metamorphose) or similar (hemimetabolous insects).  Development of respiratory system is particularly interesting, because, as all organisms grow in size, total oxygen demand varies with age.  Variation in respiratory system capacity among life stages may have important ecological consequences, such as life-stage specific limitations on activity or acceptable habitats.  Equally interesting is development of the immune system, because as habitats change across life stages, potential pathogen exposures may also vary.  In my lab, we use the alfalfa leafcutting bee, Megachile rotundata, to understand how temperature changes during development affect bee development.  We also use tobacco hornworm caterpillars, Manduca sexta to understand how the respiratory and immune systems change throughout juvenile development. 

A student in the Greenlee Lab will be expected to participate in lab research activities, including weekly lab meetings and social activities.  During lab meetings, students read and discuss scientific literature or present experimental results.  By the end of the summer, students will be able to collect, analyze, and graphically represent data, prepare a scientific poster, present their findings to a general audience. 

Depending on the project, students in the Greenlee lab could learn the following specific techniques:

  • Insect care and maintenance
  • Measurements of growth and energy balance
  • Immune system assays
  • Respirometry
  • PCR or QPCR
  • Western blotting
  • Microscopy
  • microCT

Project #5: Guilt by association: Investigation into novel protein interactions with a biological complex essential for proper genome duplication and maintenance to prevent mutation

Dr. Stuart Haring, Mentor and Project Lead

Timothy Wilson, Graduate Mentor and Project Personnel

Erica Mueller, Graduate Mentor and Project Personnel

Kaitlin Dailey, Graduate Mentor and Project Personnel

Amber Severson, Graduate Mentor and Project Personnel

Replication Protein A (RPA) is a protein complex conserved in all eukaryotes from yeast to humans that is essential for DNA replication, repair/recombination, and cell cycle regulation.  Defects in any of these processes can and do lead to genomic mutation, which can dramatically affect cellular function.  The central research question of this project is, "How does RPA function mechanistically to perform the above processes?"  A common method for identifying molecular mechanism is to identify the protein partners with which a protein associates.  Therefore, the purpose of the research is to identify and characterize protein interactions through which RPA functions.  We have utilized a two-hybrid system approach to identify proteins that interact with RPA, and we have thus far identified 38 candidate protein interactors.

Further characterization of RPA associations will aid in the understanding of how RPA maintains the integrity of the genome, and this project focuses on characterizing these identified protein interactions by:

  • Defining specific protein regions important for interaction
  • Measuring if the interaction is conditional (e.g., dependent on DNA damage)
  • Measuring if the interaction is dependent on post-translational modifications of RPA
  • Determining how the disruption of protein interaction affects the physiology of the cell

At the end of this research experience, students will be able to:

  • Isolate, manipulate, and engineer DNA
  • Grow and maintain a model organism (i.e., yeast cell culture)
  • Knockout or replace genes in yeast cells
  • Understand and perform molecular and cellular biology assays
  • Generate, record, and interpret data
  • Understand primary literature
  • Present research to a general audience

Project #6: Light initiated chemical processes

Dr. Sivaguru Jayaraman, Project Lead

The proposed project for the prospective REU student in the sivagroup involves evaluation of several catalysts for photochemical transformations. This project is in collaboration with Prof. Mukund Sibi. Such an endeavor will provide some insights into the asymmetric light driven processes. In carrying out this research the prospective REU student will learn several synthetic and analytical skills that include, setting up of organic reactions that involve multistep synthesis, monitoring and determining the products through chromatographic, spectroscopic techniques and evaluate light driven catalytic transformation. In addition to this, the student will also learn about good lab practices and safety techniques in handling hazardous chemicals. This exposure will serve as a good learning ground for the preparation into graduate/professional career. 

Project #7: Surface Chemistry of Quantum Dots: Insights from Theory and Computations

Dr. Svetlana Kilina, Project Lead

In many respects, colloidal quantum dots (QDs) - a tiny semiconductor crystals of a few nanometers in size - possess a unique combination of electronic and optical properties, which open new ways to utilize them in next generation of solar energy conversion and solid-state lighting technologies. However, the main roadblock for practical applications of QDs is the sensitivity of their optical properties to their surface chemistry and chemical environment. While much is known about the size-dependence of the QD properties due to quantum confinement, considerably less is understood about the effects the surface morphology and passivation layer of organic ligands have on the photoexcited process in QDs. Experimentally this task is difficult since conventional spectroscopic techniques cannot directly probe surface properties, as electronic transitions associated with surface states are usually optically forbidden. As such, theoretical and computational modeling could provide a valuable insight into our limited understanding of the QD surfaces and interfaces and their role in photophysics of QDs. We will model different types of QDs, such as PbSe and CdSe, with various small organic ligands passivating their surfaces using density functional theory (DFT) and time dependent DFT (TDDFT). The acquired knowledge will allow for a better explanation and interpretation of experimental data, and facilitate rational design of new nanostructures with controllable and enhanced properties, fundamental to a myriad of technological applications ranging from sensing, imaging, and optoelectronics, to solar energy harvesting.

At the end of this research experience, students will be able to:

  • Use Unix operation system and run calculations at high performance clusters
  • Use common quantum chemistry software, such as Gaussian-09
  • Construct geometries and analyze calculated data using visualization software Gausview-5
  • Model properties of various molecules at their ground and excited state using density functional theory (DFT) and time dependent density functional theory (TDDFT)
  • Understand the main concepts and principles of computational chemistry, in general, and DFT-based molecular design, in particular.
  • Estimate the capabilities, limitations, and reliability of DFT-based methods
  • Perform computational studies in a tight collaboration with experimentalists

Project #8: Materials for Organic Electronics

Dr. Seth Rasmussen, Mentor and Project Lead

Kristin Konkol, Graduate Student Mentor

Conjugated organic materials include polymers or plastics that exhibit semiconducting properties. As such, these materials have found applications in growing field of organic electronics, including display technology (organic light emitting diodes or OLEDs) and alternative energy (organic solar cells), and provide the future possibility of flexible electronics. Students in the Rasmussen lab will have the opportunity to prepare thiophene-based small molecules and apply them to the generation of new materials (oligomers and polymers).

Through this experience, students will:

  • Develop synthetic skills in organic and organometallic chemistry
  • Gain experience in various physical, optical, and electronic characterization techniques of materials chemistry.

Specific techniques include:

  • Gel permeation chromatography (GPC) to determine molecular weight
  • Absorption and fluorescence spectroscopy for study of light absorption and emission, and
  • Cyclic voltammetry for study of redox properties.
  • If time allows, characterization will include both solution and solid-state techniques.

Project #9: Heme and the Biological Battle for Iron

Dr. Kenton Rodgers, Mentor and Project Lead

We use a variety of biophysical methods, including LASER-based spectroscopies, to probe the structural basis of function and mechanism in a variety of heme proteins and enzymes.

Bacterial heme transport.  We are investigating mechanistic aspects of the pathways through which bacterial pathogens acquire iron from their hosts.  The pathways we study involve protein-based systems that "steal" heme, the red iron-containing pigment of blood, from host organisms.  The bacteria internalize heme via membrane transport systems, metabolize it, and assimilate the iron.  Interestingly, if the ability to acquire heme is diminished, the organism's ability to infect the host is compromised.  Thus, a major impetus for this work is the prospect that mechanistic understanding of these iron assimilation steps will underpin the rational design of new therapeutic approaches to preventing and treating bacterial and even drug-resistant bacterial infections.

Objectives.  The objectives of this project are two fold.  After producing, isolating and purifying the proteins, we will use steady state absorbance, resonance Raman scattering and EPR spectroscopies to characterize the heme-bound states of a cognate pair of heme-donor and heme-acceptor proteins from a bacterial heme trafficking pathway.  Using their respective spectroscopic fingerprints, we will pursue insight into the heme transfer mechanism by tracking the heme in real time as it is passed from the donor to the acceptor protein.  This will be accomplished using rapid kinetic methods, including stopped flow spectrophotometry and laser flash photolysis.

The student's summer research experience.  A student working in our laboratories would participate fully in our group research activities, including experiments, presentation of their results in weekly group meetings, and discussion of recent scientific literature.  The student would gain experience in biochemical procedures and methodologies, such as:

  • heterologous protein expression
  • protein purification
  • bioanalytical techniques for verifying protein purity
  • biochemical assays for protein integrity and enzyme activity.

The student would also participate in spectroscopic experiments, including

  • resonance Raman scattering spectroscopy
  • EPR spectroscopy
  • UV-visible absorbance spectroscopy.

The rapid kinetic experiments in which the student could participate include

  • laser flash photolysis
  • stopped flow spectrophotometry.

Inquiries from interested students are welcome.  Feel free to contact Prof. Kenton Rodgers by phone (701-231-8746) or email ( at your convenience.

Project #10: Want to Save the World? Come and do Research in Renewable Resources

Dr. Mukund Sibi, Project Lead

Materials science will play a critical role in addressing issues of sustainability in the 21st century. Materials are the fundamental building blocks of human civilization. Sustainability in materials science encompasses such issues as materials based on renewable raw materials, materials having extraordinarily long lifetimes, materials used for energy conversion, and adoption of highly efficient research methodology. My research group is interested in developing novel and efficient methodologies for the preparation of monomers from renewable resources (biomass).  Thus they will provide a sustainable alternative to chemicals currently obtained from fossil fuels. One area of focus is the preparation of terephthalic acid from biomass. Terephthalic acid is currently obtained from fossil fuels and is used in the preparation of plastic water bottles. The biomass-derived monomers will also be utilized for the synthesis of designed polymers with novel properties.

Through this experience, students will:

  • Develop synthetic skills in organic chemistry
  • Gain experience in characterization of small organic molecules
  • Gain an appreciation for how renewable resources will impact life in the 21st century

 Specific techniques include:

  • Nuclear magnetic resonance (NMR) spectroscopy to determine molecular structure
  • Purification techniques such as automated column chromatography
  • High performance liquid chromatography (HPLC) for chemical analysis
  • Use of microwave technology for organic synthesis
  • Mass spectroscopy for molecular weight determination

Project #11: Mechanism-based drug design

Dr. DK Srivastava, Mentor and Project Lead  

The overexpression of several enzymes result in causing human diseases, and thus there is a growing interest in developing  small molecular weight compounds as inhibitors in treating those diseases. However, there are several analogous enzymes (known as isozymes) which are physiologically important and they should be protected while inhibiting their pathological counterparts.  Clearly, the drug designing endeavor must take into account this discriminatory feature in order to avoid potential side effects. In view of structural-functional and mechanistic features of enzymes, our group is involved in developing mechanism based isozyme selective inhibitors of pathogenic enzymes. Currently, we are working on various isoforms of histone deacetylase (HDAC) and sirtuins as drug targets. These enzymes are involved in epigenetic regulations of genes, and their overexpression is linked to different forms of cancers, cardiovascular and immunological diseases.  The overall objective will be accomplished via two approaches:

  1. Clone, express and purify selected isoforms of HDACs and sirtuins and their mutant variants and perform detailed kinetic, thermodynamic and spectroscopic studies.
  2. Evaluate the potentials of various (mechanism based designed) small molecular weight compounds to serve as the isozyme selective inhibitors as potential drug candidates.

Students in the Srivastava lab will:

  • Gain skills in basic molecular biology and protein chemistry techniques as applied to obtaining purified forms of HDACs and sirtuins.
  • Develop basic skills in assaying enzyme activity, and performing kinetic, thermodynamic, and spectroscopic analysis of proteins in the presence of ligands.
  • Screen and evaluate mechanism based inhibitors as potential drug candidates.

Project #12: Polymers for Renewables

Dr. Dean Webster, Project Lead

Polymers are used by everyone every day and often taken for granted. Most polymers are derived from petrochemicals and are, therefore, not renewable or sustainable. At some point in the future we won't be able to use petrochemicals to synthesize polymers and so it is time today to design polymers from renewable raw materials. Products derived from plants such as seed oils and chemicals derived from lignocellulose can serve as the building blocks for the materials of the future. These are further derivatized to incorporate reactive functional groups and then reacted to form a crosslinked or thermoset material. Thermosets have uses in a variety of important applications such as adhesives, coatings, and composites. One overall goal of the research is to design thermoset systems using bio-based raw materials that have performance properties that meet or exceed that of the currently used petrochemical polymer material.

In this project the student will learn:

  • How to synthesize and characterize functional resins beginning with bio-based starting materials;
  • How to prepare formulations and crosslinked polymer samples;
  • How to characterize the properties of the materials using state-of the art instrumental methods such as differential scanning calorimetry, dynamic mechanical analysis, tensile testing, etc.;
  • How to relate the structure and composition of the materials to the properties of the materials.

Project #13: Rational Design of New Organotransition Metal Catalysts for Eco-Friendly Chemical Synthesis

Dr. Pinjing Zhao, Mentor and Project Lead

Praveen Kilaru, Graduate Student Mentor

We are interested in the discovery, mechanistic details, and synthetic applications of new homogeneous catalytic reactions based on transition metal organometallic chemistry. Our studies are based on a combination of organic synthesis, organometallic synthesis, and physical organic techniques. Guided by in-depth reaction mechanism understanding, we aim at the rational design and improvement of catalytic processes with novel bond-formation and bond-cleavage sequences, high catalyst efficiency and selectivities, and eco-friendly reaction conditions with reduced energy input and waste production.

With the financial support from National Science Foundation and the North Dakota EPSCoR program, our group is currently investigating the following main projects: (1) Rhodium(I)- and ruthenium(II)-mediated stoichiometric and catalytic decarboxylation reactions; (2) Domino catalytic reactions by C-H bond activation and multiple C-C bond formations; (3) New catalytic methods for N-heterocycle synthesis with high atom efficiency; (4) Biomass-based monomer synthesis and modification for sustainable polymer materials.

At the end of this research experience, students will be able to:

  • Synthesize and characterize organometallic complexes using multinuclear NMR spectroscopy (1H, 13C, 31P and 19F) and single-crystal X-ray diffraction methods  
  • Use glovebox and Schlenk line techniques to study air- and moisture-sensitive compounds and carry out chemical synthesis under inert-atmosphere protection
  • Participate in the development of new homogeneous catalytic reactions for synthetic applications
  • Practice standard organic techniques for substrate synthesis and product purification
  • Apply modern physical organic chemistry concepts and experimental methods to study organometallic reaction mechanisms   

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