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Developing A New Sensing Technology For Double-Stranded Dna Detection Utilizing Engineered Zinc Finger Proteins And Nanomaterials, Dat Thinh Ha

Masters Theses & Specialist Projects

A specific double-stranded DNA sensing system is of great interest for diagnostic and other biomedical applications. Zinc finger domains, which recognize double-stranded DNA, can be engineered to form custom DNA-binding proteins for recognition of specific DNA sequences. As a proof of concept, a sequence-enabled reassembly of TEM-1 β- lactamase system (SEER-LAC) was previously demonstrated to develop zinc finger protein (ZFP) arrays for the detection of a double-stranded bacterial DNA sequence. Here, we implemented the SEER-LAC system to demonstrate the direct detection of pathogenspecific DNA sequences present in E. coli O157:H7 on the lab-on-a chip. ZFPs customdesigned to detect shiga toxin …

Responses Of Daphnia Magna To Chronic Exposure Of Cadmium And Nickel Mixtures, Edgar Pérez, Tham C. Hoang

School of Environmental Sustainability: Faculty Publications and Other Works

The present study assessed the chronic toxicity of cadmium (Cd) and nickel (Ni) mixtures to Daphnia magna. Using a titration design, Ni concentrations of 20, 40, 80, 100, 120, 140, and 160 μg/L were tested alone and simultaneously titrated in increments against a constant concentration of 1.5 μg/L Cd. The results demonstrated that Cd at 1.5 μg/L was highly toxic to D. magna, and Ni alone concentrations ≥80 μg/L were toxic to D. magna survival, reproduction, and growth. No Ni alone concentration was found to induce a toxic effect on undeveloped embryos and the time to first brood. …

Chemistry Matters Fall 2018, Otterbein University Chemistry Department

Chemistry Matters Department Newsletter

In this issue:

Fall 2017 Sabbatical in Cambridge, UK/New Study Abroad Course in Chemistry/Students and Faculty Present at the 255th ACS National Meeting in New Orleans, March 2018/Exploring Biodiesel Chemistry in Multiple Lab Courses

Synthesis And Evaluation Of Protein-Phenylboronic Acid Conjugates As Lectin Mimetics, Joshua Whited, Czharena Kay Rama, Xue-Long Sun

Chemistry Faculty Publications

Glycan-binding molecules, such as lectins, are very important tools for characterizing, imaging, or targeting glycans and are often involved in either physiological or pathological processes. However, their availability is far less compared to the diversity of native glycans. Therefore, development of lectin mimetics with desired specificity and affinity is in high demand. Boronic acid reacts with 1,2- and 1,3-diols of saccharides in aqueous media through reversible boronate ester formation and are regarded as synthetic lectin mimetics. In this study, bovine serum albumin (BSA)-phenylboronic acid (PBA) conjugates were synthesized in a density-controlled manner by targeting both aspartic and glutamic acids to …

Regulation Of Kv11.1 Potassium Channel C-Terminal Isoform Expression By The Rna-Binding Proteins Hur And Hud, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The potassium voltage-gated channel subfamily H member 2 (KCNH2) gene encodes the Kv11.1 potassium channel, which conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation and forms a functional, full-length Kv11.1a isoform if exon 15 is polyadenylated or a nonfunctional, C-terminally truncated Kv11.1a-USO isoform if intron 9 is polyadenylated. The molecular mechanisms that regulate Kv11.1 isoform expression are poorly understood. In this study, using HEK293 cells and reporter gene expression, pulldown assays, and RNase protection assays, we identified the RNA-binding proteins Hu antigen R (HuR) and Hu antigen D (HuD) as regulators of Kv11.1 …

Polymer Coated Gold-Ferric Oxide Superparamagnetic Nanoparticles For Theranostic Applications, Muhammad Raisul Abedin, Siddesh Umapathi, Harika Mahendrakar, Tunyaboon Laemthong, Holly Coleman, Denise Muchangi, Santimukul Santra, Manashi Nath, Sutapa Barua

Chemistry Faculty Research & Creative Works

Background: Engineered inorganic nanoparticles (NPs) are essential components in the development of nanotechnologies. For applications in nanomedicine, particles need to be functionalized to ensure a good dispersibility in biological fluids. In many cases however, functionalization is not sufficient: the particles become either coated by a corona of serum proteins or precipitate out of the solvent. We show that by changing the coating of magnetic iron oxide NPs using poly-l-lysine (PLL) polymer the colloidal stability of the dispersion is improved in aqueous solutions including water, phosphate buffered saline (PBS), PBS with 10% fetal bovine serum (FBS) and cell culture medium, and …

Thermochemistry: Heat Of Neutralization And Hess’S Law [Chemistry], Kevin Mark, Phil Mercier, Janet Gonzalez, Burl Yearwood

Open Educational Resources

The General Chemistry 1 (SCC 201) course has been designated for the core competency of Inquiry and Problem Solving along with the Written Communication Ability. These abilities are best observed in the laboratory section of the course where SCC 201 students are asked to submit weekly written lab reports that range in chemistry topics from chemical structures to the chemical analysis of polluted environments. SCC 201 will be implementing a new experiment in the laboratory portion of the course entitled, “Thermochemistry: Heat of Neutralization and Hess’s Law.” The design of the experiment incorporates many elements of LaGCC’s Core Competencies and …

Air Pollution [Liberal Arts: Math And Science/Natural Science], Ian Alberts

Open Educational Resources

This assignment was designed for students in the pathways introductory chemistry class and the first year seminar and aligns with the Inquiry and Problem Solving core competency. In this context, there is a focus on “framing the issues” (identifies and/or addresses questions and problems), “evidence gathering” (assembles, reviews and synthesizes evidence from several diverse sources), “evidence” (analyze the data to address the questions posed) and “conclusions” (critical thinking, reflect on the outcomes, draw conclusions and generate new knowledge). There is also a Global Learning component based on comparing data collected locally with corresponding data from other locations or countries. The …

Folding Of Gα Subunits: Implications For Disease States, Matthew Najor, Brian D. Leverson, Jesse L. Goossens, Saad Kothawala, Kenneth W. Olsen, Duarte Mota De Freitas

Chemistry: Faculty Publications and Other Works

G-proteins play a central role in signal transduction by fluctuating between “on” and “off” phases that are determined by a conformational change. cAMP is a secondary messenger whose formation is inhibited or stimulated by activated Giα1 or Gsα subunit. We used tryptophan fluorescence, UV/vis spectrophotometry, and circular dichroism to probe distinct structural features within active and inactive conformations from wild-type and tryptophan mutants of Giα1 and Gsα. For all proteins studied, we found that the active conformations were more stable than the inactive conformations, and upon refolding from higher temperatures, activated wild-type subunits recovered significantly more native structure. We also …

Vitamin D: Controversy Cancer And Beyond, Cristian J. Rosales, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Vitamins are an essential part to wellbeing. This was not something always known however, as the Germ theory was the accepted thesis of the 18th century. It was found that certain accessory factors helped mitigate and even cure these diseases such as beriberi, scurvy, and rickets. Accessory factors, later coined vitamins by Casimir Funk, are an essential constituent of the human diet. Vitamin D is technically not a vitamin but functions as a steroid hormone whose most well-known purpose is calcification of the human skeleton. This helps prevent osteomalacia in adults and rickets, a serious problem in children due to …

Advanced Cotton Fibers Exhibit Efficient Photocatalytic Self-Cleaning And Antimicrobial Activity, Jared Jaksik, Phong Tran, Veronica Galvez, Isaac Martinez, Darian Ortiz, Andy Ly, Monica Mcentee, Erin M. Durke, Sayeeda Tj Aishee, Margaret Cua, Ahmed Touhami, H. Justin Moore, M. Jasim Uddin

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Functional cotton fibers have a wide range of applications in domestic, commercial, and military settings, and so enhancing the properties of these materials can yield substantial benefits. Herein, we report the creation of functional fibers that are self-cleaning, anti-microbial, and protective against UV radiation. A uniform, and high surface area films of TiO2 were deposited on cotton fibers and gold/silver nanoparticles were directly incorporated on the nanostructured TiO2 surface. The synthetic method is simple and the produced TiO2 film is homogenous and the nanoparticles were shown to be effectively distributed on the surface using a simple photocatalytic reduction method. …

Development Of A Fluorescence Imaging Photometer-Based Method For Characterization Of Phytoplankton Communities, Cameron Maxwell Rekully

Theses and Dissertations

The development of methods for real-time characterization of phytoplankton community structure has important implications for environmental monitoring and the prediction of harmful algal blooms. Our research group has developed an instrument, the Fluorescence Imaging Photometer (FIP), which is capable of rapid classification of phytoplankton via imaging single-cell chlorophyll a fluorescence under different excitation conditions. Discrimination of cells from different taxonomic groups is achieved using optical bandpass filters that have been chosen to selectively excite pigments which occur in characteristic ratios that vary from one group to the next. The relative fluorescence intensity emitted by cells under these different excitation conditions …

Development Of Bioactive Peptidomimetics, Fengyu She

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic foldamers that expected more resistant to proteolytic degradation and enormous chemodiversity when compared with peptides. To date, the functional peptidomimetics such as β-peptides, peptoids, oligoureas, etc have been developed in many science fields. In order to explore the unnatural foldameric architectures, it’s necessary to discover the novel frameworks and molecular scaffolds. γ-AApeptides were reported to be a new class of peptidomimetics that showed its potential applications in drug discovery and chemical biology. However, a wide function and property of γ-AApeptides need to be further explored. To expand the potential application of γ-AApeptides in biochemistry, I have been …

Solution And Solid-State Emission Toggling Of A Photochromic Hydrazone, Baihao Shao, Massimo Baroncini, Laura Bussotti, Mariangela Di Donato, Alberto Credi, Ivan Aprahamian

Dartmouth Scholarship

The proliferation of light-activated switches in recent years has enabled their use in a broad range of applications encompassing an array of research fields and disciplines. All current systems, however, have limitations (e.g., from complicated synthesis to incompatibility in biologically relevant media and lack of switching in the solid-state) that can stifle their real-life application. Here we report on a system that packs most, if not all, the desired, targeted and sought-after traits from photochromic compounds (bistability, switching in various media ranging from serum to solid-state, while exhibiting ON/OFF fluorescence emission switching, and two-photon assisted near-infrared light toggling) in an …

Efforts Towards The Discovery Of Novel Methods For The Synthesis Of Pharmacologically Relevant Molecular Scaffolds, Graham Joseph Haun

Theses and Dissertations

With the introductions of pharmaceuticals into modern day society many people have been using them to improve their lives. Due to this high increase in demand along with the ever-growing concern of environmental impact pharmaceutical companies have been pressed to synthesis new and existing drugs at a higher rate. This increased rate can cause low yield drugs or have a heavy environmental impact. As the use of pharmaceuticals becomes more widespread the need for greener and simpler organic synthesis methods to make these pharmaceuticals becomes more needed.

Herein is reported the methodological development of different pharmacologically relevant scaffolds. This work …

The Role Of Proton Transport In Gating Current In A Voltage Gated Ion Channel, As Shown By Quantum Calculations, Alisher M. Kariev, Michael E. Green

Publications and Research

Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGIC) to carry Na⁺ and K⁺ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently the structure of a number of VGIC was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains …

Triel-Bonded Complexes Between Trr3 (Tr = B, Al, Ga; R = H, F, Cl, Br, Ch3) And Pyrazine, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes between TrR3 (Tr = B, Al, Ga; R= H, F, Cl, Br, CH3)molecules and pyrazine have been characterized at the MP2 and CCSD(T) levels of theory. The adducts can be grouped according to the type of molecular arrangement. The first situation places the Tr atom in the plane of the pyrazine ring and contains a triel bond to the N lone pair. For the boron complexes the orbital interaction energy is almost equal to the electrostatic component, while the former is only half the latter for Tr= Al and Ga. The two monomers are stacked above one another in …

Isolation Of Rna From A Mixture And Its Detection By Utilizing A Microgel-Based Optical Device, Molla R. Islam, Shakiba Azimi, Faranak Teimoory, Glen Loppnow, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this investigation, we show that RNA can be separated from a solution containing DNA and RNA and the isolated RNA can be detected using poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons). The isolation of RNA was accomplished by using hairpin-functionalized magnetic beads (MMPDNA) and differential melting, based on the fact that the DNA–RNA hybrid duplex is stronger (i.e., high melting temperature) than the DNA–DNA duplex (i.e., low melting temperature). By performing concurrent etalon sensing and fluorescent studies, we found that the MMPDNA combined with differential melting was capable of selectively separating RNA from DNA. This selective separation and …

Unraveling The Stereodynamics Of Cold Controlled Hd−H2 Collisions, James F. E. Croft, Naduvalath Balakrishnan, Meng Huang, Hua Guo

Chemistry and Biochemistry Faculty Research

Measuring inelastic rates with partial-wave resolution requires temperatures close to a Kelvin or below, even for the lightest molecule. In a recent experiment, Perreault, Mukherjee, and Zare [Nat. Chem. 10, 561 (2018).] studied collisional relaxation of excited HD molecules in the v=1, j=2 state by para- and ortho-H2 at a temperature of about 1 K, extracting the angular distribution of scattered HD in the v=1, j=0 state. By state preparation of the HD molecules, control of the angular distribution of scattered HD was demonstrated. Here, we report a first-principles simulation of that experiment which enables us to attribute the main …

Ability Of Ir And Nmr Spectral Data To Distinguish Between A Tetrel Bond And A Hydrogen Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The placement of a nucleophile X along the R-CH3 axis of a methyl group can be described as either a trifurcated H-bond or as a tetrel bond between C and X. Quantum calculation of the vibrational and NMR spectral features of a number of systems are used to provide a framework by which to distinguish between the presence of a tetrel or H-bond. Both cationic and neutral methyl-containing Lewis acids (SMe3+, NMe4+, SMe2) are paired with both neutral and anionic Lewis bases (NH3, OH2, OCHNH2, OCH3-, OH-, HCOO-). As the base is moved away from the R-CH3 axis of the …

Short-Term Low Salinity Mitigates Effects Of Oil And Dispersant On Juvenile Eastern Oysters: A Laboratory Experiment With Implications For Oil Spill Response Activities, Meagan N. Schrandt, Sean Powers, F.Scott Rikard, Wilawan Thongda, Eric Peatman

University Faculty and Staff Publications

Following the Deepwater Horizon oil spill, eastern oyster (Crassostrea virginica) reefs in the northern Gulf of Mexico were exposed to oil and various associated clean-up activities that may have compromised oyster reef health. Included in the exposure was oil, dispersant, and in some locales, atypical salinity regimes. Oil and dispersants can be detrimental to oysters and the effects of salinity depend on the level. In addition to these extrinsic factors, genetic diversity of oyster populations may help the oysters respond to stressors, as demonstrated in other systems. We used a 3×3×2 factorial design to experimentally examine the effects …

Deep Soils Modify Environmental Consequences Of Increased Nitrogen Fertilizer Use In Intensifying Amazon Agriculture, Kathijo Jankowski, Christopher Neill, Eric A. Davidson, Marcia Macedo, Ciniro Costa Jr., Gillian L. Galford, Leonardo Maracahipes Santos, Paul Lefebvre, Darlisson Nunes, Carlos E. P. Cerri, Richard Mchorney, Christine S. O'Connell, Michael T. Coe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Agricultural intensification offers potential to grow more food while reducing the conversion of native ecosystems to croplands. However, intensification also risks environmental degradation through emissions of the greenhouse gas nitrous oxide (N₂O) and nitrate leaching to ground and surface waters. Intensively-managed croplands and nitrogen (N) fertilizer use are expanding rapidly in tropical regions. We quantified fertilizer responses of maize yield, N₂O emissions, and N leaching in an Amazon soybean-maize double-cropping system on deep, highly-weathered soils in Mato Grosso, Brazil. Application of N fertilizer above 80 kg N ha⁻¹ yr⁻¹ increased maize yield and N …

Gold-Catalyzed Conversion Of Lignin To Low Molecular Weight Aromatics, Yang Song, Justin K. Mobley, Ali Hussain Motagamwala, Mark Isaacs, James E. Dumesic, John Ralph, Adam F. Lee, Karen Wilson, Mark Crocker

Chemistry Faculty Publications

A heterogeneous catalyst system, employing Au nanoparticles (NPs) and Li–Al (1 : 2) layered double hydroxide (LDH) as support, showed excellent activity in aerobic oxidation of the benzylic alcohol group in β-O-4 linked lignin model dimers to the corresponding carbonyl products using molecular oxygen under atmospheric pressure. The synergistic effect between Au NPs and the basic Li–Al LDH support induces further reaction of the oxidized model compounds, facilitating facile cleavage of the β-O-4 linkage. Extension to oxidation of γ-valerolactone (GVL) extracted lignin and kraft lignin using Au/Li–Al LDH under similar conditions produced a range of aromatic monomers in high yield. …

Preparation And Characterization Of Chemically-Modified Biomaterials And Their Application As Adsorbents Of Penicillin G, Jesie Silva, Lizebel Morante, Tesfamichael Demeke, Jacqueline Baah-Twum, Abel E. Navarro

Publications and Research

The prevalence of antibiotics in water creates microbial resistance and has a negative impact on the ecosystem. Biomaterials such as spent tea leaves are rich in functional groups and are suitable for chemical modification for diverse applications. This research proposes the use of spent tea leaves of chamomile (CM), green tea (GT), and peppermint (PM) as structural scaffolds for the incorporation of carboxyl, sulfonyl, and thiol groups to improve the adsorption of Penicillin G (Pe). Adsorbents characterization reported a higher number of acidic functional groups, mainly in thiolated products. Scanning electron microscopy (SEM) analysis showed changes on the surfaces of …

Synthesis And Evaluation Of 4-Cycloheptylphenols As Selective Estrogen Receptor-Β Agonists (Serbas), K. L. Iresha Sampathi Perera, Alicia M. Hanson, Sergey V. Lindeman, Andrea Imhoff, Xingyun Lu, Daniel S. Sem, William A. Donaldson

Chemistry Faculty Research and Publications

A short and efficient route to 4-(4-hydroxyphenyl)cycloheptanemethanol was developed, which resulted in the preparation of a mixture of 4 stereoisomers. The stereoisomers were separated by preparative HPLC, and two of the stereoisomers identified by X-ray crystallography. The stereoisomers, as well as a small family of 4-cycloheptylphenol derivatives, were evaluated as estrogen receptor-beta agonists. The lead compound, 4-(4-hydroxyphenyl)cycloheptanemethanol was selective for activating ER relative to seven other nuclear hormone receptors, with 300-fold selectivity for the β over α isoform and with EC₅₀ of 30–50 nM in cell-based and direct binding assays.

Archean Phosphorus Liberation Induced By Iron Redox Geochemistry, Barry Herschy, Sae Jung Chang, Ruth Blake, Aivo Lepland, Heather Abbott-Lyon, Jacqueline Sampson, Zachary Atlas, Terence P. Kee, Matthew A. Pasek

Faculty Articles

The element phosphorus (P) is central to ecosystem growth and is proposed to be a limiting nutrient for life. The Archean ocean may have been strongly phosphorus-limited due to the selective binding of phosphate to iron oxyhydroxide. Here we report a new route to solubilizing phosphorus in the ancient oceans: reduction of phosphate to phosphite by iron(II) at low (<200 >°C) diagenetic temperatures. Reduction of phosphate to phosphite was likely widespread in the Archean, as the reaction occurs rapidly and is demonstrated from thermochemical modeling, experimental analogs, and detection of phosphite in early Archean rocks. We further demonstrate that the …

Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach

Chemistry Faculty Research

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …

Native V. Californicum Alkaloid Combinations Induce Differential Inhibition Of Sonic Hedgehog Signaling, Matthew W. Turner, Roberto Cruz, Jordan Elwell, John French, Jared Mattos, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Veratrum californicum is a rich source of steroidal alkaloids such as cyclopamine, a known inhibitor of the Hedgehog (Hh) signaling pathway. Here we provide a detailed analysis of the alkaloid composition of V. californicum by plant part through quantitative analysis of cyclopamine, veratramine, muldamine and isorubijervine in the leaf, stem and root/rhizome of the plant. To determine whether additional alkaloids in the extracts contribute to Hh signaling inhibition, the concentrations of these four alkaloids present in extracts were replicated using commercially available standards, followed by comparison of extracts to alkaloid standard mixtures for inhibition of Hh signaling using Shh-Light II …

High Resolution Imaging Of Single Nanoparticles And Two-Dimensional Nano-Material By Scanning Electrochemical Microscopy, Tong Sun

Dissertations, Theses, and Capstone Projects

Electrochemistry at nanostructured interfaces is of significant current interest. Metal nanoparticles (NPs) and two-dimensional semiconductor nanomaterial are particularly important because of their applications in catalysis, energy conversion and storage, sensors, and medicine. Electrocatalytic processes at such nanostructured interfaces are essential for the generation of hydrogen and other types of fuels and photochemical energy conversion. Nanoscale electrochemical experiments require the fabrication and characterization of nanometer-size electrochemical probes. The main advantages of the nanoprobes include very fast mass-transfer rate, high signal-to-noise ratio and extremely fine spatial resolution of electrochemical imaging. During my Ph.D. research, nanoscale disk-type platinum electrochemical probes were developed for …

Nmr Characterizations Of Candidate Battery Electrolytes, Stephen A. Munoz

Dissertations, Theses, and Capstone Projects

Enormous strides have been made in next-generation power sources to build a more sustainable society. Energy storage has become a limiting factor in our progress, and there are huge environmental and financial incentives to find the next step forward in battery technology. This work discusses NMR methods for characterizing materials for use in battery application, with a special focus on relaxometry and diffusometry. Examples are provided of various recent investigations involving novel candidate electrolyte materials with different collaborators. Works discussed in this thesis include: the characterization of a new disruptive solid polymer electrolyte technology, investigations of the dynamics of super …