Department of Chemistry and Biochemistry Research Opportunities
RESEARCH GROUPS BY DISCIPLINE:
Organic: Dr. Allen Schoffstall
Dr. Schoffstall's lab research is in the area of synthetic organic chemistry that features modern methodologies. One goal is to produce synthetic medicinal analogs with the potential for application to new routes to prepare candidate compounds as pharmaceuticals.
Recently we have synthesized a number of 1,2,3-triazole derivatives for the purpose of complexing with base metals (First row of the transition metals) to test as possible remediation agents (collaboration with Dr. Henry). A poster detailing the synthetic organic work is among the posters on display in the hallway outside the office suite. Two posters of students from our lab will be presented at Mountain Lion Day and three will appear at CSURF. In addition, we are hopeful of preparing some compounds for testing as possible hexokinase inhibitors later this year (collaboration with Dr. Braun-Sand).
Students who have an interest in making new organic compounds for various purposes are encouraged to consider joining our group. We currently have six (five undergraduate) active researchers in our group here and one MSc. at the Air Force Academy. We also have a very experienced former industrial organic research chemist working in our laboratory, Dr. Hagedorn is very helpful for our researchers on a day-to-day basis. We are always looking for additional, well-motivated students to join our group.
Analytical: Dr. Janel Owens, Dr. David Weiss
My research goals are focused on developing extraction protocols using so-called “green” chemistry principles to reduce the use of solvents and laboratory supplies in the investigation of fate and transport mechanisms of emerging environmental contaminants, which include pharmaceuticals, brominated flame retardants, silver nanoparticles, and hydraulic fracturing fingerprint chemicals. A second area of research interest includes the use of green extraction methods for the analysis of compounds found in plants that are of significant health interest, and whose concentrations may be affected by agricultural practices and exposure to pesticides. The third research aim is to use these green extraction protocols for the analysis of drugs of abuse (both illicit and pharmaceutical) in forensically-relevant samples. This third research aim has allowed for a strong collaboration with the El Paso County Coroner's Office Toxicology Laboratory.
I don't currently have any available spots in my research program but please have interested students talk to me.
I generally prefer that students have taken at least the first semester of organic chemistry before working with me but I will take advanced students who have completed General Chemistry II.
Research in the Weiss group is focused on developing new analytical approaches to monitor diseases and disease states. A current focus of our research has involved developing new methods for analysis of neurotransmitters in physiological solutions. This research will enable further investigation into the study the interrelationship between a group of neurotransmitters and depression, schizophrenia and high altitude mountain sickness. Research in our group is conducted primarily by undergraduates, and is often collaborative with other departments. They present their research at local and national conferences as well as author papers in peer-reviewed journals with Dr. Weiss.
Dr. Weiss is also heavily involved in chemical education and is investigating the advantages of clickers (an audience response system) in conjunction with cooperative learning in his General Chemistry and Analytical Chemistry courses.
Physical: Dr. Kevin Tvrdy
The Tvrdy lab focuses on the synthesis, characterization and implementation of nanomaterials. Recently his group has investigated the separation of semiconducting single walled carbon nanotubes based on chirality, an endeavor which will enable use in nanoscale electronics, solar cells, and biological imaging. Students working for Dr. Tvrdy can expect to gain a range of skills, from computational modeling to bench chemistry to manuscript preparation.
Dr. Tvrdy has room for one undergraduate and one master’s level student, starting in the fall of 2015.
Biochemical: Dr. Jarred Bultema, Dr. Wendy Haggren, Dr. Megan Carter, Dr. Sonja Braun-Sand
Dr. Bultema’s research lab is focused on understanding how a type of biological vesicles, known as exosomes, are produced, function, and how they can be adapted and modified for use as therapeutics. In particular, Dr. Bultema focuses on bio-engineering and developing methods to produce designer exosomes with specific contents and biological activity. The lab focuses on protein engineering, cell engineering, and production and purification techniques to make therapeutics suitable for human and animal use.
1. Protein engineering to develop methods to directly control the content of exosomes.
2. Cell engineering to determine how to control the maturation and activation state of immune cells and the exosomes they produce.
3. Characterization of exosome sub-populations from immune cells and biological fluids.
4. Investigation of the molecular mechanisms used for exosome secretion.
5. Study the molecular properties of tetraspanin proteins and their role in exosome biogenesis and uptake.
Unfortunately, I will not be accepting any new students for FA15, but may have open positions starting SP16. Requirements are completion of Gen. Chem I&II and Organic Chemistry. Research students must be a declared Biochemistry major.
Biofuels: The yeast, Saccharomyces cerevisiae, has been used extensively to ferment ethanol from glucose derived from starchy field crops, in particular corn. We propose to use a unique starch source, the Buffalo Gourd root, to serve as a feedstock for yeast fermentations. A different strain of yeast, S. diastaticus, which naturally contains the starch digestive enzyme, glucoamylase, will be genetically modified to contain variable copy numbers of the alpha-amylase starch digestive enzyme to increase starch breakdown efficiency.
Mutagenic analysis of protein function: in collaboration with Dr. Sonja Braun-Sand. Yeast hexokinase I (HxKI) from the single-celled bread yeast Saccharomyces cerevisiae shares a 33% amino acid sequence similarity to the human hexokinase isozyme IV (glucokinase). Low expression of glucokinase in liver characterizes Type 2 diabetes, and seems to be a result of several naturally occurring human mutations that affect regulation of glucokinase production or its ability to bind glucose. We use yeast as a cellular model in which to manipulate the expression level of hexokinase. Here we present several approaches we are taking to overexpress cloned yeast hexokinase I in a yeast cell which is also expressing its native version of the protein. The goal is to purify the cloned enzyme for kinetic analysis as well as to introduce mutations into the active site of hexokinase I and to purify the mutated proteins in order to correlate hexokinase structure to its function in diabetes.
Bacterial evasion of antibiotics and sliver nanoparticles: in collaboration with Dr. Janel E. Owens. Indole, produced from tryptophan by many bacteria, serves an inter-cellular signaling molecule. In the presence of antibiotic, indole secreted by resistant cells has been shown induce protective measures in non-resistant cells (specifically, up regulation of efflux pumps). This study investigates indole production by bacterial communities in the presence of starch-capped silver nanoparticle (AgNPs), which have been shown to kill bacterial cells. Cell-free supernatants were prepared for high performance liquid chromatography (HPLC). Indole was detected at 280 nm using a photodiode array detector. The HPLC assay, sensitive to micromolar amounts of indole, showed the robust resumption of indole production following exposure of Escherichia coli to AgNPs as compared to a slower response following exposure of E. coli to 10 µg/mL ampicillin, which is lower than the minimum inhibitory concentration. This methodology will provide information about how the cells of a bacterial population communicate among themselves in the presence of AgNPs.
Production of bacterial biofilms: in collaboration with Dr. Kevin Tvrdy.
Engineering E. coli to select specific chiralities of carbon nanotubes and build nanostructures through which electric current can be sent. Ultimately, the goal is to direct the migration of human cells as they grow.
Dr. Haggren may have research position available Fall 2015. Please contact her if interested.
Carter Research Group
The MutT Homolog 1 (MTH1) protein hydrolyzes oxidized nucleotide bases and prevents their incorporation into DNA, therefore performing a mechanism important for cell survival. MTH1 demonstrates specificity for its oxidized nucleotide ligands, 2-OH-dATP and 8-oxo-dGTP, compared to the non-oxidized their non-oxidized counterparts. Although the X-ray crystal structure of this protein in complex with 8-oxo-dGMP is published in the Protein Data Bank (PDB) the mechanism of substrate specificity has remained elusive. It has been hypothesized that MTH1 substrate recognition relies on ionization of key residues in the active site; therefore it is useful to determine the hydrogen placement in the MTH1 structure. Data resolution of this structure prevents placement of hydrogen atoms from crystallographic data alone. In the present work, we use the semi-empirical optimization and QM/MM computational methods PM7 to model the MTH1 protein, provide chemically accurate placement of hydrogen atoms, and investigate the mechanism for substrate recognition and specificity. It has recently been demonstrated that MTH1 is critical for the survival of cancer cells, where oxidative damage to dNTPs is prominent. For these reasons, MTH1 inhibition has shown great potential as a novel strategy to treat cancer – a concept coined ‘cancer phenotypic lethality’. The results of this work will guide further structural studies of MTH1 and provide additional knowledge for selective targeting of this protein.
Dr. Carter is not taking students in Fall 2015, but will potentially have space in the spring.
Dr. Braun-Sand’s research laboratory applies various computational chemistry methods to the study of ligand binding and enzyme mechanisms. Currently, her laboratory has collaborations with Dr. James Stewart (Stewart Computational Chemistry, developer of MOPAC software) and Dr. Megan Carter (University of Stockholm). Students are working on three main projects.
1) Using MOPAC, a semiempirical software package to investigate the mechanism of the digestive enzyme chymotrypsin. Chymotrypsin is believed to play a role in pancreatitis. Despite its role in this disease, the mechanism of action has never been investigated computationally.
2) Using MOPAC to investigate the mechanism of action of aspartyl protease. Aspartyl proteases are important anti-HIV drug targets, so understanding the mechanism of action is important and may help inform drug development.
3) Using MOPAC and Gaussian09 to investigate the selectivity of human MTH1. Human MTH1 sanitizes the dNTP pool in cells, and is upregulated in cancer. Understanding the selectivity of MTH1 will be important for finding potential drugs that inhibit MTH1 in cancerous cells.
Dr. Bruan-Sand will not be taking students for the 2015 – 2016 school year.
Inorganic: Dr. Renee Henry, Dr. Ronald Ruminski
Currently, we are working on a joint project with Dr. Schoffstall to create ligands for metal binding studies. The ligands are synthesized using copper catalyst “click” chemistry reaction to give a 1,4-disubstituted 1H-1,2,3-triazoles with varying carboxylic acid functional groups. These ligands are of interest as carboxylate groups are commonly found in plant siderophores to sequester iron atoms. Binding studies of Fe2+/3+ cations, after the ligands are de-protonation to give carboxylate anion, are in the early stages. A systematic binding study of the first row transition metals with varying metals will begin this summer with four female REU students.
I like to take students from second semester general chemistry but I only require that students can do more than one year of research in my group. At the end of each semester students are required to submit, in varying forms, the progress of their research project.
Yes, I am taking students. Students would start working in the laboratory towards the end of the summer work with REU students or at the start of the fall semester.
Current research work involves the synthesis and photophysical, electrochemical and NMR characterization of transition metal complexes that have overlapping properties in applications including photodynamic therapy, renewable energy resources and carbon sequestration.
The majority of actual research time is spent in the synthesis and purification area.
Accepting up to 2 undergraduates starting Fall 15. Minimum prerequisites include General Chemistry + at least 1 semester of Organic Chemistry and Organic Chemistry Lab.