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Photothermally Induced Optical Property Changes Of Poly (N-Isopropylacrylamide) Microgel-Based Etalons, Molla R. Islam, Jessica Irvine, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Poly(N-isopropylacrylamide) microgel-based optical devices were designed such that they can be stimulated to change their optical properties in response to light produced by a light-emitting diode (LED). The devices were fabricated by sandwiching the synthesized microgels between two Cr/Au layers all supported on a glass coverslip with gold nanoparticles (AuNPs) deposited. Here, we found that these devices can be stimulated to change their optical properties when exposed to green LED light, which excites the AuNPs and increases the local temperature, causing the thermoresponsive microgels to decrease in diameter, resulting in a change in the devices’ optical properties. We also found …

Steroid Receptor Isoform Expression In Drosophila Nociceptor Neurons Is Required For Normal Dendritic Arbor And Sensitivity, Aidan L. Mcparland, Taylor L. Follansbee, Gwendolyn D. Vesenka, Alexandra E. Panaitiu, Geoffrey K. Ganter

Biology Student Publications

Steroid hormones organize many aspects of development, including that of the nervous system. Steroids also play neuromodulatory and other activational roles, including regulation of sensitivity to painful stimuli in mammals. In Drosophila, ecdysteroids are the only steroid hormones, and therefore the fly represents a simplified model system in which to explore mechanisms of steroid neuromodulation of nociception. In this report, we present evidence that ecdysteroids, acting through two isoforms of their nuclear ecdysone receptor (EcR), modulate sensitivity to noxious thermal and mechanical stimuli in the fly larva. We show that EcRA and EcRB1 are expressed by third instar larvae in …

The Rna World: 4,000,000,050 Years Old, Niles Lehman

Chemistry Faculty Publications and Presentations

The notion that molecular systems such as RNA can display a wide range of evolutionary processes in the absence of fully formed cellular life continues to gain support. Understanding how RNA can behave in an abiotic context is a key piece of our picture of how life developed and expanded on the Earth, and by proxy, elsewhere. We can study how RNA behaves in this regard through a combination of in vivo work (with small regulatory RNAs and larger catalytic RNAs alike), experimental work in the laboratory, and through powerful analytical and simulation studies. These efforts will not only grant …

Two-Ply Channels For Faster Wicking In Paper-Based Microfluidic Devices, Conor K. Camplisson, Kevin M. Schilling, William L. Pedrotti, Howard A. Stone, Andres W. Martinez

Chemistry and Biochemistry

This article describes the development of porous two-ply channels for paper-based microfluidic devices that wick fluids significantly faster than conventional, porous, single-ply channels. The two-ply channels were made by stacking two single-ply channels on top of each other and were fabricated entirely out of paper, wax and toner using two commercially available printers, a convection oven and a thermal laminator. The wicking in paper-based channels was studied and modeled using a modified Lucas–Washburn equation to account for the effect of evaporation, and a paper-based titration device incorporating two-ply channels was demonstrated.

Using Nitrate, Chloride, Sodium, And Sulfate To Calculate Groundwater Age, Kimm Crawford, Terry Lee

Sinkhole Conference 2015

Regression analysis is used to identify monotonic trends to assign water age using ion data from two large well water databases from southeast Minnesota (SE MN). Nitrate (NO3-N), chloride (Cl), sodium (Na), and sulfate (SO4) ions in the commonly used aquifers in SE MN can be used as groundwater tracers since they are either entirely or partly anthropogenic in their sources, their loading occurs on a regional scale, and they are almost entirely conserved. Ion concentrations over time are used to establish six trend patterns. Two patterns are unchanging (background and stable above background), and four are changing (linear up, …

Bis(Spirolactam) 1,3-Double-Armed Calix[4]Arene Compounds And Their Application As Extractants For The Determination Of Heavy Metal Ions, Fintan Kelleher, Mary Deasy, James Ward, Li Li, Fiona Regan

Articles

A number of double-armed calix[4]arene compounds, with proline-derived spirolactam ligating groups on the lower rim, have been synthesised and investigated as extractants of toxic heavy metal ions from aqueous solution. Pedersen’s extraction technique was employed to determine the capability of these new 1,3-distal derived calix[4]arene spiroalactams to extract selected heavy metal ions (e.g. Pb²⁺, Cd²⁺, Zn²⁺, Cu²⁺, Ni²⁺, Co²⁺) from an aqueous phase into an organic phase. The percentage extraction was calculated using UV-vis spectroscopy. All of the compounds synthesised demonstrated good selectivity for the heavy metals selected …

Chemometric And Bioinformatic Analyses Of Cellular Biochemistry, Bradley Worley

Department of Chemistry: Dissertations, Theses, and Student Research

The amount of information collected and analyzed in biochemical and bioanalytical research has exploded over the last few decades, due in large part to the increasing availability of analytical instrumentation that yields information-rich spectra. Datasets from Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), infrared (IR) or Raman spectroscopy may easily carry tens to hundreds of thousands of potentially correlated variables observed from only a few samples, making the application of classical statistical methods inappropriate, if not impossible. Drawing useful biochemical conclusions from these unique sources of data requires the use of specialized multivariate data handling techniques.

Unfortunately, proper implementation of …

Cobalt-Centred Boron Molecular Drums With The Highest Coordination Number In The Cob16− Cluster, Ivan A. Popov, Tian Jian, Gary V. Lopez, Alexander I. Boldyrev, Lai-Sheng Wang

Chemistry and Biochemistry Faculty Publications

The electron deficiency and strong bonding capacity of boron have led to a vast variety of molecular structures in chemistry and materials science. Here we report the observation of highly symmetric cobalt-centered boron drum-like structures of CoB16⁻, characterized by photoelectron spectroscopy and ab initio calculations. The photoelectron spectra display a relatively simple spectral pattern, suggesting a high symmetry structure. Two nearly degenerate isomers with D8d(I) and C4v (II) symmetries are found computationally to compete for the global minimum. These drum-like structures consist of two B8 rings sandwiching a cobalt atom, which has the highest …

Cladribine Analogues Via O6-(Benzotriazolyl) Derivatives Of Guanine Nucleosides, Sakilam Satishkumar, Prasanna K. Vuram, Siva Subrahmanyam Relangi, Venkateshwarlu Gurram, Hong Zhou, Robert J. Kreitman, Michelle M. Martínez Montemayor, Lijia Yang, Muralidharan Kaliyaperumal, Somesh Sharma, Narender Pottabathini, Mahesh K. Lakshman

Publications and Research

Cladribine, 2-chloro-2′-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O6-(benzotriazol-1-yl)-2′-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic …

Two Distinct Modes Of Metal Ion Binding In The Nuclease Active Site Of A Viral Dna-Packaging Terminase: Insight Into The Two-Metal-Ion Catalytic Mechanism, Haiyan Zhao, Zihan Lin, Anna Y. Lynn, Brittany Varnado, John A. Beutler, Ryan P. Murelli, Stuart F.J. Le Grice, Liang Tang

Publications and Research

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A° . Such proximity of the two metal ions may play an essential role in catalysis by …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Faculty members from Chemistry and Biology Department Recived a Sustainability Fee Grant
• Teaching Scholarship

• CEMITURE 2015- Research Experience for Undergraduates

Temporal Variation In Optical Properties Of Chromophoric Dissolved Organic Matter (Cdom) In Southern California Coastal Waters With Nearshore Kelp And Seagrass, Catherine D. Clark, Warren J. De Bruyn, Paige Aiona

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Optical properties of chromophoric dissolved organic matter (CDOM) were measured in surf zone waters in diurnal field studies at a Southern California beach with nearshore kelp and seagrass beds and intertidal plant wrack. Absorption coefficients (aCDOM(300 nm)) ranged from 0.35 m21 to 3.7 m21 with short-term variability<1 h, increases at ebb and flood tides and higher values (6 m21) during an offshore storm event. Spectral slopes (S) ranged from 0.0028 nm21 to 0.017 nm21, with higher values after the storm; S was generally inversely correlated with aCDOM(300 nm). 3-D excitation–emission matrix spectra (EEMs) for samples with lower S values had humic-type peaks associated with terrestrial material (A, C), marine microbial material (M) and protein peaks, characteristic of freshly produced organic material. Samples with high S values had no or reduced protein peaks, consistent with aged material. Fluorescent indexes (f450/f500 >2.5, BIX>1.1) were consistent with microbial aquatic sources. Leachates of senescent kelp and seagrass had protein and humic-type EEM peaks. After solar simulator irradiation (4 h), protein peaks rapidly photochemically degraded, humic-type peak C increased in intensity and peak M disappeared. Optical characteristics of kelp leachates were most similar to field samples, …

The Nicotine Metabolite, Cotinine, Alters The Assembly And Trafficking Of A Subset Of Nicotinic Acetylcholine Receptors, Ashley M. Fox, Faruk H. Moonschi, Christopher I. Richards

Chemistry Faculty Publications

Exposure to nicotine alters the trafficking and assembly of nicotinic receptors (nAChRs), leading to their up-regulation on the plasma membrane. Although the mechanism is not fully understood, nicotine-induced up-regulation is believed to contribute to nicotine addiction. The effect of cotinine, the primary metabolite of nicotine, on nAChR trafficking and assembly has not been extensively investigated. We utilize a pH-sensitive variant of GFP, super ecliptic pHluorin, to differentiate between intracellular nAChRs and those expressed on the plasma membrane to quantify changes resulting from cotinine and nicotine exposure. Similar to nicotine, exposure to cotinine increases the number of α4β2 receptors on the …

Small Molecule Inhibitor Design For Anaplastic Lymphoma Kinase Inhibition, Theodore D. Hansel, David J. Grabovsky

Interface Compendium of Student Work

The Anaplastic Lymphoma Kinase (ALK) gene has been linked to tumorigenesis in a number of human cancers, including anaplastic large cell lymphoma (ALCL) and neuroblastoma. While ALK mutations in ALCL and many other cancers occur as a result of gene fusions with wild type kinase domains, those in neuroblastoma stem from single nucleotide polymorphisms (SNPs) in the kinase domain. These lead to autophosphorylation and constitutive signaling by ALK for cell growth and division, ultimately causing cancer. Crizotinib, an ATP-competitive ALK inhibitor, has proven to be an effective inhibitor of both ALKWT and ALKMutant kinase domains, and is in the middle …

Chemistry Department Newsletter 2015, Ken Overway

Chemistry Department Newsletters

This document contains a summary of news and events from the chemistry department from the 2014-2015 academic year.

Ligand Discovery For The Alanine-Serine-Cysteine Transporter (Asct2, Slc1a5) From Homology Modeling And Virtual Screening, Colas Claire, Christof Grewer, Nicholas J. Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger

Chemistry Faculty Scholarship

The Alanine-Serine-Cysteine transporter ASCT2 (SLC1A5) is a membrane protein that transports neutral amino acids into cells in exchange for outward movement of intracellular amino acids. ASCT2 is highly expressed in peripheral tissues such as the lung and intestines where it contributes to the homeostasis of intracellular concentrations of neutral amino acids. ASCT2 also plays an important role in the development of a variety of cancers such as melanoma by transporting amino acid nutrients such as glutamine into the proliferating tumors. Therefore, ASCT2 is a key drug target with potentially great pharmacological importance. Here, we identify seven ASCT2 ligands by computational …

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Avera Health and Science’s 5th Year Celebration
Page 3 Harvest Table Food Drive — Round Two
Page 4 New Graduates Students
Page 5 Department to Host CHEM Ed 2017
Page 6 ACS Student Affiliate Chapter Activities
Page 7 Faculty and Staff News
Page 8 Publications & Grants

Distributed Approach For Peptide Identification, Naga V K Abhinav Vedanbhatla

Masters Theses & Specialist Projects

A crucial step in protein identification is peptide identification. The Peptide Spectrum Match (PSM) information set is enormous. Hence, it is a time-consuming procedure to work on a single machine. PSMs are situated by a cross connection, a factual score, or a probability that the match between the trial and speculative is right and original. This procedure takes quite a while to execute. So, there is demand for enhancement of the performance to handle extensive peptide information sets. Development of appropriate distributed frameworks are expected to lessen the processing time.

The designed framework uses a peptide handling algorithm named C-Ranker, …

Expression And Purification Of Unlabelled And Isotopically Labelled Human Fibroblast Growth Factor-1 And Its Receptor Relevance In Cancer Research, Oluwadamilola Filani

Masters Theses & Specialist Projects

Studies show that fibroblast growth factors (FGFs) control variety of cellular activities such as mitosis, cell differentiation, survival and angiogenesis. The FGF family consists of 23 different heparin-binding proteins. One of the most intensively studied members is human FGF-1 (hFGF-1) because of its critical role in the formation of blood vessels and cell proliferation in some types of cancer. The biological activities of FGFs are primarily mediated via interactions with fibroblast growth factor receptors (FGFR) and are a potent target in cancer. In this study, we report an efficient affinity column purification of hFGF-1 and the D2 domain of FGFR-2 …

A Sem Study Of Copper Corrosion In Bowling Green Supply Lines, Reema M. Alghamdi

Masters Theses & Specialist Projects

Recently, the rate of corrosion of copper water pipes in Bowling Green, Kentucky has unexpectedly accelerated. The specific reasons for this are unknown. Our aim is to elucidate the factors enhancing the corrosion and help understand the primary mechanisms of action. This will help in combating and reducing future corrosion incidents leading to pipe failure, thus reducing losses experienced when these pipes are replaced. This study seeks to explore the characteristics and factors involved. The scanning electron microscopy was used to obtain elemental composition, and images of both inside and outside of the corroded pipes. Strikingly, corrosion primarily occurred on …

The Periodical Fall 2015, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 2, issue 2 of the Periodical includes articles about the Chemistry Department's partnership with Georgia-Cumberland Academy, a pictorial listing of December 2015 graduates, new service-learning tutoring classes, and an alumni spotlight.

Multi-Dimensional Glycan Microarrays With Glyco-Macroligands, Satya Nandana Narla, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

Glycan microarray has become a powerful high-throughput tool for examining binding interactions of carbohydrates with the carbohydrate binding biomolecules like proteins, enzymes, antibodies etc. It has shown great potential for biomedical research and applications, such as antibody detection and profiling, vaccine development, biomarker discovery, and drug screening. Most glycan microarrays were made with monovalent glycans immobilized directly onto the array surface via either covalent or non-covalent bond, which afford a multivalent glycans in two dimensional (2D) displaying. A variety of glyco-macroligands have been developed to mimic multivalent carbohydrate-protein interactions for studying carbohydrate-protein interactions and biomedical research and applications. Recently, a …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Mass Spectrometry Based Proteomics And Lipidomics Studies, Huan Kang

Theses and Dissertations

Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C₄₀H₆₀NO, provided PRMD prediction with 90.0% sensitivity at …

Mixed Valent Metal Pincer Complexes And Reactivity Of Metal Complexes Of Extended Pincer Ligands, Jeewantha Sampath Hewage

Dissertations (1934 -)

Historically, the study of mixed valence complexes has been critical for advancing our understanding of electron transfer processes in biological and abiological systems. The recent use of mixed valence complexes in electrochromic materials, and the promise of their use in future technological or molecular electronic applications, has spurred further interest in this class of compound. Previous studies by our research group have shown that gallium(III) or tricarbonylrhenium(I) complexes of pincer-type ligands with diarylamido anchors and either pyrazol-1-yl (pz) or diarylphosphino (PAr2) flanking donors are electroactive species with quasi reversible ligand-centered oxidations. Moreover, the one-electron oxidized derivative with pz flankers, [Ga(L)(L+)]2+ …

S-Nitrosothiols: Electronic Structure And Substituent Effects, Matthew Flister

Dissertations (1934 -)

S-nitrosothiols (RSNOs) are biologically important molecules involved in the storage and transport of nitric oxide (NO) and account for much of its signaling activity in living organisms. RSNOs have significant impact on NO signaling through, S-nitrosation, a major post-translational modification of proteins. These unstable thiol derivatives readily undergo homolytic dissociation of the S–N bond to release NO. RSNOs have potential therapeutic applications as NO donors, although the development of novel RSNOs has been slow due to the complex electronic structure of the –SNO group. A specific focus on the impact of the –R group on RSNO properties via substituent effect …

Ligand Frameworks For Transition-Metal Complexes That Model Metalloenzyme Active, Denan Wang

Dissertations (1934 -)

Advances in the field of biomimetic inorganic chemistry require the design of sophisticated ligand frameworks that reflect the amazing complexity of metalloenzyme active sites. For instance, most active sites feature extensive hydrogen-bonding interactions between ligands bound to the metal center (the “first” coordination sphere) and nearby units in the outer (or “second”) sphere. Since these interactions modify the structural and electronic properties of the active sites, a number of inorganic chemists have sought to design ligands that permit outer-sphere functional groups to interact with first-sphere donors. This dissertation describes our contribution to these broader efforts to model the second coordination …

Role Of Annexin A6 In Cancer (Review), Houbao Qi, Shuqing Liu, Chunmei Guo, Jiasheng Wang, Frederick T. Greenaway, Ming Zhong Sun

Chemistry

Annexin A6 (AnxA6) is a member of a conserved superfamily of Ca2+-dependent membrane-binding annexin proteins. It participates in membrane and cytoskeleton organization, cholesterol homeostasis, membrane trafficking, cell adhesion and signal transduction. The expression levels of AnxA6 are closely associated with melanoma, cervical cancer, epithelial carcinoma, breast cancer, gastric cancer, prostate cancer, acute lymphoblastic leukemia, chronic myeloid leukemia, large-cell lymphoma and myeloma. AnxA6 exhibits dual functions in cancer, acting either as a tumor suppressor or promoter, depending on the type of cancer and the degree of malignancy. In several types of cancer, AnxA6 acts via Ras, Ras/MAPK and/or FAK/PI3K signaling pathways …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

Density Functional Theory For The Investigation Of Transition Metal Complexes: Structure, Binding, And Spectroscopy Of Metal-Siderophores And The Catalase-Peroxidase Enzyme, Bonnie I. Kruft

Dissertations, Theses, and Capstone Projects

Since the development of quantum mechanics in the 1920's and with the introduction of the Schrödinger equation in 1926, various methods to solve the Schrödinger equation have evolved. With advances in these computational methods, we are now able to solve the Schrödinger equation for systems that did not seem possible less than a century ago. Density functional theory (DFT) is a valuable tool for the exploration of the molecular properties of biological systems, and is based upon the theory that the exact energy could be determined from the knowledge of the electron density. The purpose of this dissertation is to …