CORE Fellows


Gretchen Marie Peters, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Fellow
Department of Chemistry
Email: gretchen.peters@austin.utexas.edu

Calix[4]pyrrole gels: media for ion extraction and environmental remediation

Gretchen Marie Peters received her B.A. degree in Chemistry in 2010 from Luther College in Decorah, IA. Subsequently, she moved to the University of Maryland and worked with Professor Jeffery T. Davis, earning her PhD in 2015. While in the Davis group, her research focused on the development of functional guanosine receptors for small molecule transport and elucidating the structural composition and practical applications of guanosine-borate hydrogels. Currently, Gretchen is a postdoctoral researcher at the University of Texas at Austin working with Professor Jonathan L. Sessler. At UT Austin, Gretchen’s research focuses on designing calix[4]pyrrole receptors to function as anion hosts and ion extractants. In particular, Gretchen is interested in employing the molecular recognition properties of these calixpyrrole receptors to develop novel soft materials for ion separation and environmental remediation applications.  


Erin Taylor, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Fellow
Department of Molecular Biosciences
Email: elmimich@utexas.edu

Characterization of mitochondrial polymerase γ mutants and their role in mitochondrial disease

Erin Taylor earned a B.S. in biochemistry and molecular biology at Otterbein College in 2010 and a Ph.D. in biochemistry at the University of Michigan in 2015. Her graduate research focused on kinetic mechanisms of DNA repair glycosylases in the base excision repair pathway. As a postdoctoral fellow in the Kenneth Johnson lab, she is studying polymerase gamma (γ), which is responsible for replication and repair of the mitochondrial genome (mtDNA). Mutations in Pol γ lead to errors and degradation of mtDNA, causing a set of disorders termed mitochondrial disease. Using a humanized yeast model system and purified proteins, she will characterize the kinetic mechanisms of various Pol γ mutants and their relationships to human disease phenotypes. Erin is interested in teaching and mentoring undergraduates at small liberal arts institutions. 


Michael Cammarata, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Fellow
Division of Chemistry
Email: mbcammara@gmail.com

Development of High Performance Mass Spectrometry Applied to Structural Biology: Utilizing UVPD for Determination of Macromolecular Protein Complex Topology

Michael Cammarata graduated with a B.S. in Chemistry from Trinity University in San Antonio and earned his Ph.D. from University of Texas at Austin in Chemistry. His graduate studies included developing new techniques for structural biology with the use of mass spectrometry, specifically ultraviolet photodissociation (UVPD) for ion activation implemented as a top-down (intact protein) methodology. He applied this strategy in conjunction with covalent modification techniques to measure surface accessibility of proteins as well as crosslinking experiments to elucidate spatial information. Additionally, UVPD was used to characterize native-like proteins with and without bound cognate ligands or specific inhibitors. Changes in UVPD fragmentation between these bound and unbound states were indicative of regions of conformational changes of the protein. This methodology was successfully applied to study interactions of known inhibitors as well as novel inhibitors with dihydrofolate reductase (DHFR). The strategy has also been applied to the characterization of the structure of oncogene KRas to elucidate the dynamic conformational changes mediated by G12X mutations. Michael is continuing his work with Jennifer S. Brodbelt to study the topology of macromolecular protein complexes through protein crosslinking and native mass spectrometry.


Michael G. Chiorazzo, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Fellow
Division of Medicinal Chemistry
Email: mchio@utexas.edu

Understanding the role of maternal embryonic leucine zipper kinase (MELK) in cancer

Michael Chiorazzo earned a B.S. in Chemistry and Biology from Ramapo College of New Jersey and a Ph.D. in Pharmacology from the University of Pennsylvania. During his graduate studies, he worked on developing long wavelength activatable fluorophores, to serve as contrast agents in near infrared (NIR) fluorescence guided surgery of cancer. NIR fluorescence guided surgery has rapidly gained attention in the field of surgical oncology for its ability to increase rates of complete tumor resection and thus decrease rates of recurrence and metastasis. Michael developed a fluorophore specific towards cytosolic phospholipase A2, which has increased activity in triple negative breast cancer versus healthy tissue, and demonstrated its ability to image triple negative breast cancer in cellular and mouse models. As a postdoctoral fellow, Michael is investigating a protein kinase, maternal embryonic leucine zipper kinase (MELK) for its role in the progression and therapeutic response of triple negative breast cancer. Michael’s research under the guidance of Kevin N. Dalby and Karen M. Vasquez seeks to understand the biological mechanisms related to the role of MELK in DNA repair and transcriptional regulation. This research has the potential to elucidate the impact of anti-MELK therapy in addition to identifying novel therapeutic targets in triple negative breast cancer.


Peggy Williams, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Scholar
Department of Chemistry
Email: peggy.williams@utexas.edu

Development and applications of UVPD-MS strategies for characterization of lipopolysaccharides (LPS) from gram-negative bacteria

Peggy Williams earned a B.S. in Chemistry from Indiana State University in 2009 and a Ph.D. in Chemistry at Purdue University in 2014. Her graduate research focused on characterizing free radicals and studying their reactivity toward small biomolecules in both the gas phase and in solution. Her gas-phase ion chemistry research employing ion-molecule reactions in a mass spectrometer led her abroad to Australia where she developed robust HPLC methods that were coupled to advanced ion-molecule reaction based mass spectrometric methods for the differentiation of isomeric lipids. Her experience abroad in lipid analysis brought her back to the US and to UT Austin where her work as a CORE postdoctoral fellow is focusing on developing and applying ultraviolet photodissociation (UVPD) approaches for characterization of lipopolysaccharides (LPS) from gram-negative bacteria. This research has the potential to allow for a deeper understanding of how the structure of LPS influences immune stimulation and facilitate the development of bacterial vaccines and new antimicrobial drugs.


Timothy Cleland, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Scholar
Department of Chemistry
Email: tpcleland@utexas.edu

"UV Photodissociation for analysis of intact proteins"

Timothy Cleland earned a B.S. in geosciences at Colorado State University in 2007 and a Ph.D. in molecular paleontology at North Carolina State University in 2012. His graduate research focused on mass spectrometry characterization of proteins from fossil bone and soft tissues. His research has led him to broad studies of the bone proteome, especially related to osteoporosis and bone fragility. His work as a CORE postdoctoral fellow is focusing on applying ultraviolet photodissociation (UVPD) for characterization of intact proteins and their post-translational modifications in a high-throughput way. This research has the potential to allow for a deeper understanding of protein changes associated with disease.


Oana I. Lungu, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Scholar
Department of Chemical Engineering
Email: oilungu@gmail.com

Structural modeling and characterization of the paired VH-VL human immunoglobulin repertoire

Oana Lungu earned a B.S. in biochemistry from the University of Minnesota Twin Cities and a Ph.D. in Biochemistry from the University of North Carolina at Chapel Hill. During her graduate studies, she worked on computationally designing, expressing, and characterizing light-activated proteins, which allow for the manipulation of protein signaling networks. As a Postdoctoral fellow, Oana is applying her knowledge of computational protein structure modeling to a different problem: antibody structure prediction. Diversity in the sequences and structures of antibodies that constitute the human immune repertoire is critical for mounting an effective response against foreign antigens. The naïve B cell immunoglobulin repertoire, in particular, which has had no prior antigen exposure and has not been diversified through hypermutation, must have a large enough structural diversity to bind any possible novel antigen, while at the same time minimizing binding to any self-antigens. Oana’s research under the mentorship of George Georgiou and Andrew Ellington seeks to characterize and understand the structural antibody repertoire and its relationship to sequence in B cell populations, including naïve B cells. This research has the potential to further our understanding of how adaptive immune reactions develop in response to various antigens, such as those caused by cancers or immunizations.

 

Hugo V. Miranda, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Scholar
Department of Molecular Biosciences
Email: hvmiranda@austin.utexas.edu

“Characterization of horizontally acquired genetic elements that contribute to Vibrio cholerae fitness”

Hugo V. Miranda earned a B.S. and a Ph.D. in microbiology and cell science from the University of Florida. During his graduate studies, his research focused on the identification and characterization of protein modifiers in the haloarchaeon Haloferax volcanii. These protein modifiers are analogous to the eukaryotic protein ubiquitin. Two of the three protein modifiers identified were also shown to be potentially involved in sulfur transfer pathways for the biosynthesis of biomolecules. Currently, his postdoctoral research, under the direction and leadership of Dr. Bryan Davies at the University of Texas at Austin, focuses on identifying factors that affect the fitness and pathogenicity of Vibrio cholerae, the causative agent of the potentially deadly disease cholera. He is particularly interested in factors that may impact the evolution and shifts of pandemic V. cholerae strains. His current research seeks to identify protein effectors encoded within the horizontally acquired Vibrio 7TH pandemic island-1 (VSP-1) that may contribute to colonization of the host intestine and/or facilitate survival within the host. The VSP-1 is one of only two pathogenicity islands unique to the current pandemic El Tor V. cholerae strains, and in part, may be contributing to the success of El Tor biotypes as pandemic strains. Understanding how VSP-1 contributes to the fitness of V. cholerae may provide insight into potential new targets for prevention and/or therapeutic options.


Lindsay Morrison, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Fellow
Department of Chemistry
Email: lmorrison21@gmail.com

Lindsay Morrison earned a B.A. in Chemistry at Colorado College in 2009 and a Ph.D. in analytical chemistry at Ohio State University in 2014. Her graduate work focused on improving the understanding of collision based activation methods in mass spectrometry in order to develop mass spectrometry as a structural biology tool for probing protein structure. Native mass spectrometry approaches are rapidly developing as accepted structural biology tools as the characterization of the primary, sequence, structure of proteins and quaternary architecture proteins is possible by activating and dissociating intact proteins in the gas phase.  Using well-characterized helical peptides and proteins, she demonstrated that protein secondary structure exists in fragment ions following collision based activation of the precursor molecule, a result that has important implications for using tandem mass spectrometry methods to investigate protein secondary structure. Her work as a Core postdoctoral fellow is directed at developing applications of ultra-violet photo-dissociation (UVPD), a relatively new activation technique, for the characterization of protein and lipid structures. Because UV photons are highly energetic, activation by UVPD permits cleavage of high energy bonds, cleavage of which is not typically possible by collision-based activation techniques. In lipids and lipid containing molecules, this often results in the formation of unique fragment ions that provide highly informative structural information. Lindsay is using UVPD and an alternative technique, activated ion negative electron dissociation (AI-nETD), to characterize lipid A and ganglioside molecules. The short timescale of the activation event and rapid deposition of energy inherent to photoactivation permits retention of non-covalent interactions during dissociation. Lindsay is researching ways to exploit this feature in native proteins, including using the relative abundance and charge state of the fragments to identify salt bridge partners. 


Felix R. Perez, Ph.D.
University of Texas at Austin
Department of Chemistry
Email: perez.felix.r@gmail.com

Rapid Synthesis of Abietanes via a Geranylation-Polyene Cyclization Sequence

Felix Perez obtained his BS in Chemistry from California State University, Fresno. Afterwards he went to UCLA and obtained a PhD with Michael E. Jung. He is a postdoc in the Krische group at the University of Texas at Austin developing asymmetric methods for natural products synthesis. 


Alfred Tuley, Ph.D.
University of Texas at Austin
NIH CORE Postdoctoral Scholar
Department of Chemistry
Email: alfred.tuley@gmail.com

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Alfred received his B.S. in chemistry from Texas A&M University-Corpus Christi and his Ph.D. in chemistry from Texas A&M University-College Station. During his graduate work, under the guidance of Prof. Wenshe Liu, Alfred studied genetic code expansion using a number of non-canonical phenylalanine derivatives. These phenylalanine derivatives include a series of aliphatic compounds designed to survey the substrate scope of a mutant pyrrolysyl-tRNA synthetase, as well as the development of a genetically encoded aldehyde for rapid protein labeling under physiologically relevant conditions. In addition to genetic code expansion, Alfred has performed extensive work to elucidate the reaction mechanism for the copper-catalyzed azide-alkyne cycloaddition (CuAAC), an important reaction that is ubiquitous in chemical biology research. Alfred is now a postdoctoral researcher in the laboratory of Prof. Walter Fast, where he will investigate the covalent modification of enzymes using halopyridines and similar scaffolds.


Sarah Wong, Ph.D.
University of Texas at Austin
NIH Core Postdoctoral Fellow
Department of Chemistry

Email: sjwong@utexas.edu

“Structural and Mechanistic Characterization of the Eukaryotic Elongation Factor 2 Kinase (eEF-2K)”

 

Sarah Wong earned her B.S. in Biology and Chemistry from Texas Lutheran University and her Ph.D. in Biochemistry from the University of Texas Health Science Center at San Antonio. Her graduate studies focused on the structural characterization of the Polycomb Repressive Complex 1 using x-ray crystallography and nuclear magnetic resonance. As a postdoctoral fellow, she has been working on the structural and mechanistic characterization of the eukaryotic elongation factor 2 kinase (eEF-2K) under the guidance of Dr. Kevin Dalby.


Diana Zamora-Olivares, Ph.D.
University of Texas at Austin
NIH Core Postdoctoral Fellow
Department of Chemistry

Email: dianapauzo@gmail.com

“Differential sensing of mitogen-activated protein kinases MAPKs”

 

Diana Zamora-Olivares earned a B.S. in pharmaceutical chemistry from the National Autonomous University of Mexico (UNAM) and a Ph.D. in organic chemistry from the University of Texas at Austin. During her graduate studies, she worked on developing differential sensing methods to detect and differentiate mitogen-activated protein kinases, which regulate signaling pathways that are involved in different malignances. During the last decade, organic and supramolecular chemistry in combination with fluorescent-based sensing methods have led to the development of chemical biology tools to study protein phosphorylation. However, further challenges remain present to develop better chemical approaches that can allow us to understand the activation/inhibition of specific kinase pathways. The use of differential sensing techniques has allowed classifying structurally similar analytes. Using this approach, one obtains a distinct fingerprint of composite signals produced by the sensor elements allowing for discrimination of different relevant MAP kinases. As a Postdoctoral fellow, Diana is developing new chemical biological tools to fingerprint MAPKs in different models. Overexpression of MAPKs is related with tumorigenesis and acquired drug resistance. Diana’s research under the guidance of Eric V. Anslyn and Kevin N. Dalby seeks to profile and evaluate the differences between healthy, disease and resistant cellular processes. This research has the potential to increase our understanding of targeted kinase therapies.