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Chemistry Seminar Series


Weekly: EDUC 112 – 1:30 pm to 2:20 pm


Friday, November 30, 2018

Patrick Schwartz and Ben Lew, MS Students, Department of Chemistry & Biochemistry, Boise State University


Friday, November 16, 2018

Dr. Ramesh Jasti, Department of Chemistry & Biochemistry, University of Oregon
Title: “Nanohoops as New Architectures in Molecular and Materials Design”

Abstract

In their simplest form, nanohoops can be thought of as short slices of carbon nanotubes.  In this lecture, I will describe my research group’s impetus for developing synthetic methods to prepare a wide range of these types of structures. I will also detail the unique size-dependent properties of these molecules, which are direct manifestations of the unusual radially oriented π-systems.  Finally, I will share our most recent results to elaborate this new class of nanoscale building blocks into materials with unique function.


Friday, November 9, 2018

Dr. Nick Dickenson, Utah State University, Department of Chemistry & Biochemistry
Title: “In vitro to in vivo: Regulating Shigella virulence through controlling Spa47 ATPase activity”

Abstract

Many Gram-negative pathogens, including Shigella spp., use conserved type three secretion systems (T3SS) as key virulence factors. The Shigella T3SS relies on an associated needle-like type three secretion apparatus (T3SA) which penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. A great deal is now understood about the complex structure of the Shigella T3SA, however, the specific mechanisms of formation, secretion activation, and regulation remain unclear. Sequence homology of the Shigella protein Spa47 to known T3SS ATPases and its location within the sorting platform of the T3SA suggest that perhaps it is an ATPase responsible for providing the energy for T3SA formation and secretion. We have recently overcome the long standing hurdle of producing active recombinant Spa47 provide the first direct evidence that Spa47 is in fact a bona fide ATPase. Biophysical characterization of the recombinant Spa47 identifies multiple discrete oligomeric species with the highest order representing a unique Spa47 trimer exhibiting >8 fold higher ATP hydrolysis activity than the monomeric form. Additionally, access to active recombinant Spa47 permitted us to investigate the influence on Spa47 oligomerization and activity by several factors, including active site Walker motif residues, the protein N-terminus, key interactions with other T3SS proteins, and design of small molecule inhibitors that shut down Shigella protein secretion. Together, these results identify Spa47 as a Shigella T3SS ATPase and suggest that its activity is linked to oligomerization, perhaps as a regulatory mechanism controlled through interaction with chaperone proteins such as MxiN. The in vitro characterization of Spa47 structure and function described here provides a strong platform for additional studies dissecting its role in virulence and identifies an attractive target for much needed anti-infective agents against Shigella spp.


Friday, November 2, 2018

Dr. Karen Lewis, Texas State University, Department of Chemistry & Biochemistry
Title: “Structure and function of the RNA-binding protein LARP6 using a fish model system”

Abstract

All members of the La-Related Protein superfamily use an RNA Recognition Motif (RRM) in tandem with a conserved La Motif to bind RNA ligands. However, LARP6 has evolved unique structural and functional characteristics within the La Module that distinguish it from other LARP subfamilies. In particular, the La Motif—RRM interdomain linker and the RNA binding surface in the RRM appear to be specific to the LARP6 subfamily. To identify critical sequences and motifs that are involved in the structure and function of LARP6, we have employed a comparative phylogenetic approach using the LARP6 proteins from two teleost fish, Danio rerio and Xiphophorus maculatus. As these fish represent significant evolutionary divergence from each other and from humans, they also provide a natural suite of sequence variants within regions of interest in the RRM. Using an iterative, filter-based screening assay, we successfully purified biochemical quantities of the full-length fish LARP6 proteins. Electrophoretic mobility shift assays demonstrated that these non-mammalian vertebrate LARP6 proteins exerted robust RNA binding activity. The fish proteins have provided a system in which to evaluate several features of LARP6 structure. First, limited trypsinolysis and mass spectrometry identified a stable domain in the fish proteins, comprised of the uncharacterized N-terminal domain (NTD) and the La Module. These results indicated that there is direct contact between the NTD and La Module. We are currently employing a suite of biochemical and biophysical approaches to study this intramolecular interaction as a novel mechanism by which the RNA binding activity of LARP6 is regulated. Additionally, the fish La Modules have been amenable to several structural analyses, including solution NMR and small-angle X-ray scattering. In collaboration with the Warner Lab at Boise State, we are using these approaches to determine the relative orientation of the La Motif and RRM within the LARP6 La Module, which is hypothesized to be more extended than what is observed in the La Modules of the nuclear La-related proteins.


Friday, October 26, 2018

Leanna Marquart, M.S. Student, Department of Chemistry & Biochemistry, Boise State University
Title: “Regulating Dopamine Release from Nerve Cells: A Story of Troubleshooting”

Abstract

Dopaminergic nicotinic acetylcholine receptors (nAChRs) are transmembrane ligand-gated ion channels consisting of various subunit combinations. They are implicated in a variety of neurological disorders, including Parkinson’s disease (PD), nicotine addiction, and schizophrenia. Current drug therapies for PD lack prolonged efficacy and have many side effects. We hypothesize that molecular probes designed to selectively target the specific nAChRs deficient in PD patients will lead to alternative drug therapies with prolonged efficacy and fewer side effects. However, a gap exists in our understanding of the molecular mechanism of nAChR-ligand binding. To improve the process of informing our understanding of nAChR isoform-specific binding paradigms, we propose to develop a simple, accessible, rapid bioactivity assay using PC12 cells. The PC12 assay will provide a yes or no response to the question of whether a peptide or small molecule drug directly impacts DA release from nAChRs. Bioactivity of future lead compounds will be characterized in a time and cost efficient manner. Successful development of this assay will be a powerful advancement for understanding the pathophysiology of PD and other neurological functions involving the release of DA.

Melissa Roberts, M.S. Student, Department of Chemistry & Biochemistry, Boise State University
Title: “The Investigation of Thermally Altered Meteorites for Indicators of Fischer Tropsch-type Syntheses ”

Abstract

It is widely believed that organic compounds were delivered to the early (and prebiotic) Earth via extraterrestrial materials such as meteorites. We propose to investigate several thermally altered carbonaceous chondrites and ureilites for aliphatic and aromatic hydrocarbons. Recent experimental work suggested that Fischer Tropsch-type (FTT) synthesis may have been responsible for amino acids detected in thermally altered carbonaceous chondrites and ureilites. As a consequence, both aliphatic and aromatic hydrocarbons should be synthesized due to FTT synthesis and detectable (if amino acids can survive these conditions). This research will help answer fundamental questions regarding the diversity and abundance of organic compounds and their likely origin in extraterrestrial small bodies.


Friday, October 19, 2018

Kelsey Skluzacek, M.S. Defense, Department of Chemistry & Biochemistry, Boise State University
Title: “Structure-Based Drug Design of Novel Therapeutics Targeting Oncostatin M”
Advisor: Dr. Don Warner
Committee Members: Dr. Cheryl Jorcyk, Dr. Matthew King, Dr. Lisa Warner

Abstract

At 30% of all new diagnoses, the most prevalent malignancy for women is breast cancer, which in the United States will result in an estimated 266,000 new cases this year alone. Of the patients diagnosed with breast cancer, approximately 10-15% will develop distant metastases within three years of the initial detection of a primary tumor. For comparison, the five-year survival rate for localized breast cancer is 99%, whereas, the survival rate for metastatic breast cancer drops drastically to only 27%. The significant difference in survival rates is indicative of a need for a novel treatment strategy for metastatic breast cancer.

Oncostatin M (OSM), a member of the interleukin-6 family of cytokines, has been shown in the context of breast cancer to promote epithelial to mesenchymal transition (EMT), promote tumor cell detachment and invasiveness, increase circulating tumor cell (CTC) numbers, induce the expression of proangiogenic factors, and promote lung and bone metastases. For these reasons, the work presented describes the structure-based drug design, synthesis, and preliminary testing of small molecule inhibitors (SMIs) of OSM to be used as a therapeutic treatment method for metastatic breast carcinomas. Based on synthetic accessibility and computational screening, SMIs were synthesized and subsequently evaluated for inhibition of OSM-induced signaling using an enzyme-linked immunosorbent assay (ELISA). The SMIs were further assessed for binding affinity toward OSM using isothermal titration calorimetry (ITC). The results suggested that SMIs capable of inhibiting OSM-induced signaling also exhibited binding to OSM. Furthermore, SMIs not able to bind to OSM correlated with poor inhibition of OSM-induced signaling. Therefore, the preliminary results suggest: specific SMI-OSM binding occurs, SMIs are capable of inhibiting OSM-induced signaling, and that additionally optimized SMIs have the potential to be used as novel therapeutic treatment options for metastatic breast cancer.


Friday, October 12, 2018

Nick Craven, Idaho State Police Forensic Lab
Title: “Strategies for Landing a Career in Forensics”

Abstract

Due in part to the popularity of shows like CSI, NCIS, and Law & Order, the interest in the field of forensic science has increased over the last 20 years. Even though the forecast for forensic employment is promising, the Bureau of Labor Statistics reported that Forensic Technician jobs will increase by about 17% through 2026, many of the job openings see dozens if not hundreds of applicants. This presentation will discuss the strategies that the forensic job seeker can utilize to land a career in forensics.


Friday, October 5, 2018

Dr. Scott Phillips, Micron School of Materials Science and Engineering, Boise State University
Title: “Design and Preparation of Metastable Polymers for Amplified Responses in Soft Materials”

Abstract

Biological materials in Venus Flytraps and touch-me-nots display rapid, amplified responses that allow the plants to change rapidly on the macro scale when touched fleeting. Stimuli-responsive polymeric materials, in contrast, typically require continuous supplies of abundant signals before they change. To bridge this gap between synthetic and biological materials, we have developed two general autonomous signal amplification strategies for use in polymeric materials. Our approaches do not mimic the mechanisms or functions of biological materials, but they do impart macroscopic—and sometimes global—changes in polymeric materials when the materials are exposed to trace levels of specific signals. One of our approaches is based on a new class of self-immolative polymers that depolymerize from end to end continuously and completely in response to specific stimuli. This presentation will explore how we design and prepare new members of this class of polymers, and will illustrate examples of how these polymers may be used in the context of stimuli-responsive materials (e.g., debondable adhesives).


Friday, September 28, 2018

Dr. David Y. LeeDepartment of Chemistry and Materials Science & Engineering Program, Washington State University
Title: “Radical-Induced Topography and Physical Property Modifications of Materials Surfaces”

Abstract

Ultra-high-vacuum scanning tunneling microscopy and spectroscopy (STM and STS) are used to spatially resolve the topography and the electronic band modifications on graphene by atomic oxygen in the nanometer scale. We show that oxygen radicals, even at a low surface coverage of O/C = ~1/150, form random surface distributions and clusters of various sizes. These oxygen adsorbates are also observed to be p-type dopants, which leads to site-dependent partial and full band modifications up to a gap of few hundred meV. The degree of band gap opening and the number of O-atom induced charge-holes per area are inversely proportional to the distance to the nearest adsorbate. However, the number of holes contributed per oxygen atom was found to be a site-independent constant of 0.15±0.05. This presentation will begin with a brief but detailed introduction to high resolution surface imaging.


Friday, September 21, 2018

Dr. Deanne SammondNational Renewable Energy Lab
Title: “Using computational protein modeling to develop cost-competitive renewable biofuels”

Abstract

I use and develop structural informatics and rational protein design approaches to improve enzymes used to produce renewable fuels and chemicals. For example, cellulase enzymes deconstruct plant cell walls to release sugars used in fuel production. Cellulases, however, are inhibited by the plant cell wall polymer, lignin. I use computational tools to understand what causes cellulase inhibition and design improved enzymes to lower the cost of biofuels production. Also, state-of-the-art metabolic engineering approaches to produce fuels and chemicals from renewable resources often require introducing enzymes into non-native organisms. Many organisms ideal for the production of biofuels thrive in extreme environments, which can challenge our ability to import non-native enzymes. Protein engineering can rationally evolve enzymes for extreme environments by altering features such as stability, activity and substrate or cofactor specificity.


Friday, September 14, 2018

Dr. Picklestein, aka Associate Professor Henry Charlier, Department of Chemistry & Biochemistry, Boise State University
Title: “Chrazy, Chool Chemistry!”

Abstract

Chemicals get a bad rap in our world today. People seem to be searching for healthy “chemical free” foods, drinks, etc. Guess what? Nothing like that exists. Every substance in our world is made of chemicals. This includes our food and drink. Water, dihydrogen monoxide, is a chemical. We live in a chemical world. So, in order to counter the negative perceptions of chemicals, we are going to demonstrate just what chemicals can do and how amazing they are. So be prepared to be mystified and amazed by Chrazy, Chool Chemistry.


Friday, September 07, 2018

Dr. Ken Cornell, Department of Chemistry & Biochemistry, Boise State University
Title: “New Treatments for Acute and Chronic Infectious Diseases”

Abstract

Infectious diseases account for approximately one third of the annual human mortality on the planet. With the rise in antibiotic resistance and co-morbidities associated with epidemic obesity and diabetes, the death rate for infectious disease is expected to rival cancer and heart disease in the next 20 years. In this talk, I will summarize a lot of the projects that have been ongoing in my lab in the past decade to develop new therapeutics that function to interrupt critical nutrient salvage pathways in pathogens such as E. coli O157:H7, Borrelia burgdorferi, and Giardia. I will also present recent work we have been involved in to develop a “plasma scalpel” to treat MRSA and other microbes responsible for chronic wound infections.