Chemistry Commons^™

Antibiotic Sensitivity Testing Of Foodborne Bacteria Using Surface-Enhanced Raman Spectroscopy, Joshua Gukowsky

Doctoral Dissertations

The spread of antibiotic resistant bacteria around the world has become a major public health issue, and it is essential that effective detection methods exist for identifying these organisms and preventing them from spreading throughout our food systems and into the environment. The goal of this research is to develop a novel analytical procedure that is capable of easily identifying antibiotic resistance in bacterial samples, and also provides more information about the biochemical characteristics of the bacteria and their responses to antibiotic exposure. Surface-enhanced Raman Spectroscopy (SERS), an analytical technique that uses light scattering to produce a spectrum based on …

Computational Approaches For The Multimodal Imaging Of Nanomaterials And Their Biochemical Effects, Laura J. Castellanos

Doctoral Dissertations

Nanomaterial delivery systems constitute a group of drug delivery vehicles that have been used extensively in biodelivery. The proper characterization of the therapeutic function of these nanomaterials requires analytical methods to track the presence of the cargo and its biochemical effects. In some cases, the detection of the cargo and biochemical changes are not attainable in the same experiment, and more than one technique might be needed for the proper analysis of the drug delivery system. In this case, separate analysis of adjacent tissue sections is performed by techniques that offer complementary information such as MALDI-MS and LA-ICP-MS. However, the …

Advanced Materials Design Using Application-Based Processing Techniques, Daniel S. Camarda

Doctoral Dissertations

This dissertation pertains to generating advanced materials using application-based processing techniques. First, billets consisting of PTFE sintering powders are evaluated using Thermomechancal Analysis. It was found that both shape change and volume change are associated with enthalpic and entropic recoil, respectively. These phenomena, due to melting and stored energy during the powder compaction process, were found to be molecular weight dependent. Additionally, kinetics of the recovery and sintering process were found to be slower in blended specimens than pure samples. Next, the creation of graft copolymers by selectively grafting a second polymer to the amorphous fraction of a semi-crystalline polymer …

Amyloidogenesis Of Β-2-Microglobulin Studied By Mass Spectrometry And Covalent Labeling, Blaise G. Arden

Doctoral Dissertations

Amyloid-forming proteins are implicated in a number of debilitating diseases. While many amyloid-forming proteins are well studied, the early stages of amyloidosis are still not well understood on a molecular level. Covalent labeling, combined with mass spectrometry (CL-MS), is uniquely well suited to provide molecular-level insight into the factors governing the early stages of amyloidosis. This dissertation leverages CL-MS techniques to examine the early stages of β-2-microglobulin (β2m) amyloidosis. β2m is the protein that forms amyloids in the condition known as dialysis-related amyloidosis. An automated CL-MS technique that uses dimethyl(2-hydroxy-5-nitrobenzyl) sulfonium bromide as a labeling reagent was developed and used …

Systematic Evaluation Of A Novel Self-Healing Poly(Acrylamide-Co-Vinyl Acetate)/Alginate Polymer Gel For Fluid Flow Control In High Temperature And High Salinity Reservoirs, Jingyang Pu, Baojun Bai, Thomas P. Schuman

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Preferential fluid flow often occurs when water and CO₂ is injected into mature oilfields, sig-nificantly reducing their injection efficiency. Particle gels have been evaluated and applied to control the short circulation problems. This study systematically investigated a novel poly(acrylamide-co-vinyl acetate)/alginate-based interpenetrated gel system (Alg-IPNG) which is designed to control the preferential fluid flow problems in high-temperature reservoirs. Chromium acetate was incorporated into the gel system to provide the delayed crosslinking feature of the particle gels. The alginate polymer system can also take advantage of the Ca²⁺ ions in the formation water, which exist in most reservoirs, to reinforce …

Cyclic Peptide-Gadolinium Nanocomplexes As Sirna Delivery Tools, Amir Nasrolahi Shirazi, Muhammad Imran Sajid, Dindyal Mandal, David Stickley, Stephanie Nagasawa, Joshua Long, Sandeep Lohan, Keykavous Parang, Rakesh Kumar Tiwari

Pharmacy Faculty Articles and Research

We have recently reported that a cyclic peptide containing five tryptophan, five arginine, and one cysteine amino acids [(WR)₅C], was able to produce peptide-capped gadolinium nanoparticles, [(WR)₅C]-GdNPs, in the range of 240 to 260 nm upon mixing with an aqueous solution of GdCl₃. Herein, we report [(WR)₅C]-GdNPs as an efficient siRNA delivery system. The peptide-based gadolinium nanoparticles (50 µM) did not exhibit significant cytotoxicity (~93% cell viability at 50 µM) in human leukemia T lymphoblast cells (CCRF-CEM) and triple-negative breast cancer cells (MDA-MB-231) after 48 h. Fluorescence-activated cell sorting (FACS) analysis indicated …

The Ion Pair Thermal Model Of Maldi Ms, Shiyue Fang

Michigan Tech Publications

The ion pair thermal model for MALDI MS is described. Key elements of the model include thermal desorption and ionization, strong tendency to neutralization via ion pair formation and proton transfer in the gas phase, thermal equilibrium, overall charge neutral plume, and thermal energy assisted free ion generation via ion pair separation by ion extraction potential. The quantities of ions in the solid sample and in the gaseous plume are estimated. Ion yields of different classes of molecules including peptides, nucleic acids, permanent salts and neutral molecules are estimated at the macroscale and single ion pair levels. The estimated ion …

Designed, Highly Expressing, Thermostable Dengue Virus 2 Envelope Protein Dimers Elicit Quaternary Epitope Antibodies, Stephen T. Kudlacek, Stefan Metz, Devina Thiono, Alexander M. Payne, Thanh T.N. Phan, Shaomin Tian, Lawrence J. Forsberg, Jack Mcguire, Ian Selm, Shu Zhang, Ashutosh Tripathy, Joseph S. Harrison, Nathan I. Niceley, Sandrine Soman, Michael K. Mccracken, Gregory D. Gromowski, Richard G. Jarman, Lakshmanane Premkumar, Aravinda M. De Silva, Brian Kuhlman

College of the Pacific Faculty Articles

Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.

Scaffold-Based [Fe]-Hydrogenase Model: H2 Activation Initiates Fe(0)-Hydride Extrusion And Non-Biomimetic Hydride Transfer, S. A. Kerns, J. Seo, V. M. Lynch, Jason M. Shearer, S. T. Goralski, E. R. Sullivan, M. J. Rose

Chemistry Faculty Research

We report the synthesis and reactivity of a model of [Fe]-hydrogenase derived from an anthracene-based scaffold that includes the endogenous, organometallic acyl(methylene) donor. In comparison to other non-scaffolded acyl-containing complexes, the complex described herein retains molecularly well-defined chemistry upon addition of multiple equivalents of exogenous base. Clean deprotonation of the acyl(methylene) C-H bond with a phenolate base results in the formation of a dimeric motif that contains a new Fe-C(methine) bond resulting from coordination of the deprotonated methylene unit to an adjacent iron center. This effective second carbanion in the ligand framework was demonstrated to drive heterolytic H₂ activation …

The Bioinformatics Virtual Coordination Network: An Open-Source And Interactive Learning Environment, Benjamin J. Tully, Joy Buongiorno, Ashley B. Cohen, Jacob A. Cram, Arkadiy I. Garber, Sarah K. Hu, Arianna I. Krinos, Philip T. Leftwich, Alexis J. Marshall, Ella T. Sieradzki, Daan R. Speth, Elizabeth A. Suter, Christopher B. Trivedi, Luis E. Valentin-Alvarado, Jake L. Weissman, Bvcn Instructor Consortium

Faculty Works: Biology, Chemistry, and Environmental Studies

Lockdowns and “stay-at-home” orders, starting in March 2020, shuttered bench and field dependent research across the world as a consequence of the global COVID-19 pandemic. The pandemic continues to have an impact on research progress and career development, especially for graduate students and early career researchers, as strict social distance limitations stifle ongoing research and impede in-person educational programs. The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative ways to carry out their research. The BVCN was founded in April …

Chitosan Graphene Composite Fabrication And Characterization For Treatment Of Harmful Algal Blooms And Toxins, Sarah Zetterholm

Master's Theses

Chitosan graphene composites were fabricated and characterized as a management strategy for harmful algal blooms (HABs) caused by various species of cyanobacteria. These chitosan graphene materials were compared to previously studied chitosan graphene-oxide composites in both material properties and HAB treatment. In previous studies, adsorption of the cyanobacteria onto the surface of the composite materials has been observed. Investigations of the pure materials for these composites are also included in this study to determine whether removal is a result of charge interactions with the composite, or as an inherent property of the graphene or graphene oxide. Initial results suggest that …

Comparison Of Design Approaches For Low-Cost Sampling Mechanisms In Open-Source Chemical Instrumentation, Greggory Murray, Samuel Bednarski, Michael Hall, Samuel W. Foster, Sijun Jin, Joshua J. Davis, Wei Xue, Eric Constans, James P. Grinias

Faculty Scholarship for the College of Science & Mathematics

Robotic positioning systems are used in a variety of chemical instruments, primarily for liquid handling purposes, such as autosamplers from vials or well plates. Here, two approaches to the design of open-source autosampler positioning systems for use with 96-well plates are described and compared. The first system, a 3-axis design similar to many low-cost 3D printers that are available on the market, is constructed using an aluminum frame and stepper motors. The other system relies upon a series of 3D printed parts to achieve movement with a series of linker arms based on Selective Compliance Assembly Robot Arm (SCARA) design …

New Approach For Assigning Mean Oxidation Number Of Carbons To Organonitrogen And Organosulfur Compounds, Pong Kau Yuen, Cheng Man Diana Lau

Faculty Publications

Organonitrogen and organosulfur compounds are abundant in the natural environment. To understand the biological redox pathways properly, it is important for learners to be able to count the oxidation number of organic carbons. However, the process of counting is not always easy. In addition, organonitrogen and organosulfur molecules are seldom studied. To compensate these problems, this paper explores the bonddividing method, which can effectively determine the mean oxidation number of carbons of organonitrogen and organosulfur molecules. This method uses the cleavage of carbon-sulfur and carbon-nitrogen bonds to obtain the organic and inorganic fragments. The mean oxidation numbers of carbon atoms, …

Editorial: Discovery And Development Of Drugs For Neglected Diseases: Chagas Disease, Human African Trypanosomiasis, And Leishmaniasis, Gildardo Rivera, Navin B. Patel, Debasish Bandyopadhyay

Chemistry Faculty Publications and Presentations

Twenty tropical diseases have been listed by the World Health Organization (WHO) as Neglected Tropical Diseases (NTDs). These tropical diseases are called “neglected” for three primary reasons: 1) These diseases are widespread worldwide among the economically weaker (neglected?) section of the society; 2) Although the total number of mortality, morbidity, disability, and health disparity caused annually by the NTDs is more than that attributed by the so-called elite diseases like cancer, diabetes, human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), cardio- or neurological diseases but NTD patients do not receive comparable attention or treatment opportunities either from the governments or healthcare professionals …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Effects Of Redwood Bark And Leaf Leachate On Different Lichen Populations Found Within The Redwood Forest Of Arcata, Ca, Courtney Michelle Harris, Phoebe Hughes

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

No abstract provided.

A Study Of The Mammalian High Mobility Group Protein At-Hook 2 (Hmga2) And Its Interactions With Dna, Linjia Su

FIU Electronic Theses and Dissertations

The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three positively charged “AT-hooks” and a negatively charged C-terminal motif. It is a multifunctional nuclear protein linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Previous results showed that HMGA2 is a potential therapeutic target of anticancer and anti‐obesity drugs through inhibiting its DNA‐binding activities. Here a miniaturized, automated AlphaScreen ultra‐high‐throughput screening assay is developed to identify inhibitors targeting HMGA2‐DNA interactions. After screening the LOPAC1280 library, several compounds are identified that strongly inhibit HMGA2‐DNA interactions including suramin, a negatively charged antiparasitic drug. …

3d-Printable And Open-Source Modular Smartphone Visible Spectrophotometer, Brandon Winters, Nick Banfield, Cassandra Dixon, Anna Swensen, Dakota Holman, Braxton Fillbrown

Chemistry Faculty Publications

The past four decades have brought significant and increasingly rapid changes to the world of instrument design, fabrication, and availability due to the emergence of 3D printing, open-source code and equipment, and low-cost electronics. These, along with other technological advances represent a nexus in time ripe for the wide-spread production and availability of low-cost sophisticated scientific equipment. To that end, the design of a 3D printable and open-source, modular spectrometer is described. This specific instrument is distinctly different from others that have been reported in recent years in that it was designed outside of the “black box” paradigm of …

Physical Chemistry, Ruth E. Stark

Open Educational Resources

This is a provisional syllabus for Physical Chemistry I (Thermodynamics), to be taught using an OER Textmap in Fall, 2021.

College Of Natural Sciences Newsletter, October 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 10

Page 1 Dean's Message
Page 2 Awards and Recognition; Introducing Natural Sciences Student Ambassadors
Page 3 Media Coverage of CNS
Page 4 Spooky Science Outreach
Page 5 The BIG Event Outreach
Page 6 Geography Club Road Trip
Page 7 Aamlid Family Anatomy Lab
Page 8 Hobo Day Recap
Page 10 Open PRAIRIE Data; Grants Awarded in CNS