Digital Commons Network^™

Length And Charge Of Water-Soluble Peptoids Impact Binding To Phospholipid Membranes, Madeleine R. Landry, Jacenda L. Rangel, Vivian P. Dao, Morgan A. Mackenzie, Fabiola L. Gutierrez, Kalli M. Dowell, Anna L. Calkins, Amelia A. Fuller, Grace Y. Stokes

Chemistry and Biochemistry

In this study, we provide a quantitative description of the adsorption of water-soluble N-substituted glycine oligomers (peptoids) to supported lipid bilayers that mimic mammalian plasma membranes. We prepared a small array of systematically varied peptoid sequences ranging in length from 3 to 15 residues. Using the nonlinear optical method second harmonic generation (SHG), we directly monitored adsorption of aqueous solutions of 3- and 15-residue peptoids to phospholipid membranes of varying physical phase, cholesterol content, and head group charge in physiologically relevant pH buffer conditions without the use of extrinsic labels. Equilibrium binding constants and relative surface coverages of adsorbed peptoids …

Consumption Of Black Raspberries Altered The Composition Of The Fecal Microbiome In Mice Fed A Western Type Diet (Or04-01-19), Abby D. Benninghoff, Sumira Phatak, Korry Hintze

Chemistry and Biochemistry Faculty Publications

Dietary strategies to reduce colonic inflammation and promote gut homeostasis may markedly reduce the risk of colitis-associated colorectal cancer. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption a Western type diet in mice. In this study, our goal was to assess the impact of consumption of the TWD with and without black raspberry supplementation on the composition of the fecal microbiome over the course of disease development.

Dietary Intervention With Black Raspberries To Reduce Colitis Symptoms In Mice Fed Either Standard Ain93g Diet Or The Total Western Diet (P05-021-19), Daphne Michelle Rodriguez Jimenez, Michaela Brubaker, Elizabeth Park, Canyon Neal, Korry Hintze, Abby D. Benninghoff

Chemistry and Biochemistry Faculty Publications

Approximately 1.4 million people suffer from inflammatory bowel disease, which is a major risk factor for developing colitis associated colorectal cancer (CAC). Dietary interventions with the goal to reduce colon inflammation and encourage gut microbiome homeostasis may be a strategy to reduce the risk of CAC. The antioxidants and anti-inflammatory compounds present in black raspberries (BRB) have demonstrated protective effects in the colon epithelium and may alter the composition of the gut microbiome. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption of a Western type diet in mice. The …

Integration Of Random Forest Classifiers And Deep Convolutional Neural Networks For Classification And Biomolecular Modeling Of Cancer Driver Mutations, Steve Agajanian, Odeyemi Oluyemi, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to …

Approaches For Sample Characterization And Lithography With Nanoparticles Using Modes Of Scanning Probe Microscopy, Jayne C. Garno, Temitope O. Jegede, Kathryn B. Mckee, Melissia Porter, Autumn E. Webb, Jin Gyun Lee, Neepa Mk Kuruppu Arachchige, Justin R. Ragains, Noémie Elgrishi

Faculty Publications

Measurement and imaging modes of scanning probe microscopy (SPM) have been routinely applied for characterizing systems of nanoparticles; however the evolution of fabrication methods to prepare arrangements of nanoparticles remains a challenge. Reproducible fabrication of surface structures which integrate nanoparticles within ultra-small patterns will require innovative approaches to achieve high throughput and precision. Strategies for nanoscale lithography have been introduced for preparing defined arrangements of nanoparticles on surfaces based on physical or chemical interactions. For example, physisorption was employed for attaching nanoparticles based on colloidal lithography and site-directed assembly. Microfabricated atomic force microscope (AFM) tips with capillary channels have been …

The Spectroscopic And Computational Exploration Of Sulfur Hydrogen Bonding, Andrew Yoonkeun Lee

Honors Projects

Hydrogen bonds are a subset of non-covalent interactions that occur between X-H — Y, in which X and Y are the very electronegative atoms. In our research, we examine the more unconventional hydrogen bond-like interactions of thiol (SH) containing molecules using vapor-phase infrared (IR) spectroscopy and ab initio computational chemistry. When the SH hydrogen bond donor complexes to a hydrogen bond acceptor, a red shift of the SH stretching mode emerges. An anharmonic oscillator local mode model is applied to the ethanethiol-trimethylamine dimer, and we determine that any IR evidence of dimerization in our experiment is likely obscured by the …

Conformational Studies Of Glucose Transporter 1 (Glut1) As An Anticancer Drug Target, Suliman Almahmoud, Xiaofang Wang, Jonathan L. Vennerstrom, Haizhen A. Zhong

Chemistry Faculty Publications

Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand binding, we ran systemic molecular docking studies for different conformations of GLUT1 using known …

Adaptable Xerogel-Layered Amperometric Biosensor Platforms On Wire Electrodes For Clinically Relevant Measurements, Lillian B. Hughes, Najwa Labban, Grace E. Conway, Julie A. Pollock, Michael C. Leopold

Chemistry Faculty Publications

Biosensing strategies that employ readily adaptable materials for different analytes, can be miniaturized into needle electrode form, and function in bodily fluids represent a significant step toward the development of clinically relevant in vitro and in vivo sensors. In this work, a general scheme for 1st generation amperometric biosensors involving layer-by-layer electrode modification with enzyme-doped xerogels, electrochemically-deposited polymer, and polyurethane semi-permeable membranes is shown to achieve these goals. With minor modifications to these materials, sensors representing potential point-of-care medical tools are demonstrated to be sensitive and selective for a number of conditions. The potential for bedside measurements or continuous monitoring …

Photoelectrochemical Catalysis Of Hydrogen Peroxide With Tellurium Containing Chromophores, James Eliott Lohman

Dissertations and Theses

Growing concerns over climate change and demand for energy worldwide have made development and implementation of alternative energy sources more necessary than ever. Many of the leading energy alternatives suffer from inconsistent energy production due to fluctuations in availability of natural resources, and the current methods of addressing the issue have tremendous ecological and social ramifications of their own. While fuels like hydrogen gas are providing some promise of relief, the scope of infrastructure changes necessary for implementation and the implicit hazards of the use of such fuels complicate their application as an immediate solution. However, hydrogen peroxide carries far …

Interfacial Amino Acids Support Spa47 Oligomerization And Shigella Type Three Secretion System Activation, Hannah J. Demler, Heather B. Case, Yalemi Morales, Abram R. Bernard, Sean J. Johnson, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Like many Gram-negative pathogens, Shigella rely on a type three secretion system (T3SS) for injection of effector proteins directly into eukaryotic host cells to initiate and sustain infection. Protein secretion through the needle-like type three secretion apparatus (T3SA) requires ATP hydrolysis by the T3SS ATPase Spa47, making it a likely target for in vivo regulation of T3SS activity and an attractive target for small molecule therapeutics against shigellosis. Here, we developed a model of an activated Spa47 homo-hexamer, identifying two distinct regions at each protomer interface that we hypothesized to provide intermolecular interactions supportingSpa47 oligomerization and enzymatic activation. Mutational analysis …

Forty Years Of Progress In The Study Of The Hydrogen Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The author looks back at developments over the last few decades concerning the H–bond. The list of atoms involved as proton donor and acceptor has broadened dramatically, including most electronegative atoms and even metals. The factors that control the transfer of the proton across the H–bond have been elucidated and show the importance of even minor changes in its geometry. Small stretches can shut down the transfer entirely, and certain bends can force a proton to transfer against a pK gradient. Along with the recognition that a CH..O interaction can represent a true H–bond, and one with strength comparable to …

Natural Kinds And Ceteris Paratis Generalizations: In Praise Of Hunches, W. Christropher Boyd, Richard N. Boyd

Chemistry Faculty Publications

According to stereotypical logical empiricist conceptions, scientific findings are approximately true (or perhaps true ceteris paribus) law-like generalizations used to predict natural phenomena. They are deployed using topic-neutral, generally reliable inferential principles like deductive or statistical inferences. Natural kinds are the kinds in such generalizations. Chemical examples show that such conceptions are seriously incomplete. Some important chemical generalizations are true often enough, even though not usually true, and they are applied using esoteric topic- and discipline-specific inference rules. Their important methodological role is to underwrite often-enough reliable, often socially implemented, scientifically informed guessing about chemical phenomena. Some chemical natural …

Protocol Measuring Horizontal Gene Transfer From Algae To Non-Photosynthetic Organisms, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Horizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild-type E. coli (recipient). This novel protocol can be used to measure HGT frequency for …

Improving Protein Analysis By Desorption Electrospray Ionization (Desi-Ms), Elahe Honarvar

Dissertations

Electrospray ionization mass spectrometry (ESI-MS) is one of the most well-known and versatile techniques for analyzing a broad range of molecules and it has become one of the leading techniques to study biomolecules, such as proteins. ESI-MS can accurately determine the molecular weight of proteins and provide information about their peptide sequence, post-translational modifications as well as their interaction with other molecules.

During ESI-MS analysis, by spraying a sample of proteins, prepared in form of a solution, charged droplets are produced using an electric field. As the solvent molecules gradually evaporate from these droplets, freely hovering bare protein ions remain. …

The Transformative Possibilities Of The Microbiota And Mycobiota For Health, Disease, Aging, And Technological Innovation, Lucas Jones, Jessica Kumar, Adil Mistry, Thriveen Sankar Chittoor Mana, George Perry, Prakash Reddy, Mark Obrenovich

Chemistry Faculty Research & Creative Works

The gut microbiota is extremely important for the health of the host across its lifespan. Recent studies have elucidated connections between the gut microbiota and neurological disease and disorders such as depression, anxiety, Alzheimer's disease (AD), autism, and a host of other brain illnesses. Dysbiosis of the normal gut flora can have negative consequences for humans, especially throughout key periods during our lifespan as the gut microbes change with age in both phenotype and number of bacterial species. Neurologic diseases, mental disorders, and euthymic states are influenced by alterations in the metabolites produced by gut microbial milieu. We introduce a …

Facile And Label-Free Electrochemical Biosensors For Microrna Detection Based On Dna Origami Nanostructures, Shuo Han, Wenyan Liu, Shuo Yang, Risheng Wang

Chemistry Faculty Research & Creative Works

MicroRNAs (miRNAs) have emerged as the promising molecular biomarkers for early diagnosis and enhanced understanding of the molecular pathogenesis of cancers as well as certain diseases. Here, a facile, label-free, and amplification-free electrochemical biosensor was developed to detect miRNA by using DNA origami nanostructure-supported DNA probes, with methylene blue (MB) serving as the hybridization redox indicator, for the first time. Specifically, the use of cross-shaped DNA origami nanostructures containing multiple single-stranded DNA probes at preselected locations on each DNA nanostructure could increase the accessibility and the recognition efficiency of the probes (due to the rational controlled density of DNA probes). …

Ultrasensitive And Highly Selective Ni₃Te₂ As A Nonenzymatic Glucose Sensor At Extremely Low Working Potential, Bahareh Golrokh Amin, Umanga De Silva, Jahangir Masud, Manashi Nath

Chemistry Faculty Research & Creative Works

Developing Nonenzymatic glucose biosensors has recently been at the center of attention owing to their potential application in implantable and continuous glucose monitoring systems. In this article, nickel telluride nanostructure with the generic formula of Ni₃Te₂ has been reported as a highly efficient electrocatalyst for glucose oxidation, functional at a low operating potential. Ni₃Te₂ nanostructures were prepared by two synthesis methods, direct electrodeposition on the electrode and hydrothermal method. The electrodeposited Ni₃Te₂ exhibited a wide linear range of response corresponding to glucose oxidation exhibiting a high sensitivity of 41.615 mA cm …

Surface-Enhanced Raman Detection Of Glucose On Several Novel Substrates For Biosensing Applications, Laila Saad Alqarni

Dissertations

The small normal Raman cross-section of glucose is considered to be a major challenge for its detection by Surface Enhanced Raman Spectroscopy (SERS) for medical applications. These applications include blood glucose level monitoring of diabetic patients and evaluation of patients with other medical conditions, since glucose is a marker for many human diseases. This dissertation focuses on Surface-Enhanced Raman Scattering primarily for the detection of glucose. Some experiments also are carried out for the detection of the corresponding enzyme glucose oxidase that is used in electrochemical glucose sensors and in biofuel cells. This project explores the possibility of utilizing Surface …

Chemical Approaches For Nanofabrication Based On Colloidal Lithography With Organosilanes, Nanoparticles And Nickel Films: The Role Of Water In Directing Surface Self-Assembly, Neepa Malsi Kumari Kuruppu Arachchige

LSU Doctoral Dissertations

The capabilities for accomplishing fundamental surface studies with molecular systems are demonstrated in this dissertation using measurement and imaging modes of scanning probe microscopy. Model systems were chosen for investigations of surface self-assembly mechanisms, with an emphasis on understanding the role of interfacial water in surface reactivity. A key strategy for molecular level studies was to prepare nanostructures using protocols with colloidal lithography and scanning probe-based lithography (SPL). Nanofabricated samples were characterized ex situ with contact and tapping-mode atomic force microscopy (AFM) after key reaction steps, providing direct views of changes in surface morphology at the nanoscale. Magnetic sample modulation …

Understanding How Map Kinases Influence Endothelial Nitric-Oxide Synthase Activity, Xzaviar Solone

Master of Science in Integrative Biology Theses

Mitogen activated protein kinases (MAPK) p38 and ERK have both been reported to bind endothelial nitric oxide synthase (eNOS) with submicromolar affinity via proposed interactions with a pentabasic non-canonical MAPK binding sequence in the autoinhibitory insertion of eNOS. The neuronal isoform, which lacks the pentabasic motif, did not bind either MAPK significantly. In the present study, the pentabasic motif was validated using predictive modeling programming, and eNOS phosphorylation by MAPKs (P38, ERK and JNK) was examined using in vitro kinase assays and immunoblotting. JNK phosphorylation at Ser¹¹⁴ contrasts with ERK, which phosphorylated Ser⁶⁰⁰, and p38, which phosphorylated …

Rebecca Roesner And Advancing Diversity In The Chemical Sciences, Ryan Denham

Interviews for WGLT

Rebecca Roesner, chair and professor of chemistry at Illinois Wesleyan University, has earned the Stanley C. Israel Regional Award for Advancing Diversity in the Chemical Sciences for her work furthering diversity and inclusivity. Professor Roesner spoke about the award, and her part in helping to promote diversity in the sciences with Ryan Denham from WGLT Radio.

Effects Of Polyamine Binding On The Stability Of Dna I-Motif Structures, Michael M. Molnar, Shelby C. Liddell, Randy M. Wadkins

Faculty and Student Publications

B-form DNA can adopt alternative structures under conditions such as superhelical duress. Alternative DNA structures are favored when there is asymmetric distribution of guanosine and cytosine on complimentary DNA strands. A guanosine-rich strand can form a four-stranded structure known as a quadruplex (G4). The complimentary cytosine-rich strand can utilize intercalating cytosine−cytosine base pairing to form a four-stranded structure known as the i-motif (iM). Both secondary structures are energetically uphill from double-strand DNA (dsDNA), meaning that additional factors are needed for their formation. Most iMs require slightly acidic conditions for structure stabilization. However, crowding agents such as polyethylene glycols and dextrans …

The Development Of Silica Hydride Stationary Phases For High-Performance Liquid Chromatography From Conception To Commercialization, Maria Matyska-Pesek, Joseph Pesek

Faculty Publications, Chemistry

The development of a stationary phase material for high-performance liquid chromatography based on a surface of silica hydride as opposed to silanols on ordinary silica is discussed including synthetic approaches, characterization, and applications. There are several synthetic approaches available to create a silica hydride surface. Modification of the Si–H moiety on the silica surface can be accomplished through the use of a hydrosilation reaction. Both the intermediate silica hydride and the material modified with an organic moiety can be characterized by a number of spectroscopic as well as a variety of other methods. Further insights into the retention mechanism are …

Growth Factors In The Human Body: A Conceptual Update, Estefania Alexandre, Debasish Bandyopadhyay

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

Growth factors are found in most of the organisms including insects, humans, plants, etc. The name ‘growth factors’ became known when the substances were active in stimulating the growth of cells and tissues. Growth factors are regulatory species (signaling molecules mainly proteins) that are generated by the body which function in binding to receptors on the cell surface and are required to stimulate the growth in living responsive cells by triggering cellular proliferation and/or cellular differentiation pathways, as well as by regulating gene transcription in the nucleus. They are quite versatile by promoting cell growth and act in a paracrine, …

Expanding The Toolbox With Site-Specific Methods Of Bioconjugation, Tiauna S. Howard

Seton Hall University Dissertations and Theses (ETDs)

Bioconjugation is an important tool for studying complex biological systems, with site-specificity being the major challenge. Reactions based on amino acid derived organocatalysts have been widely used in organic synthesis, particularly for the asymmetric synthesis of small molecules but this concept has not been vastly explored on biomolecules. To combat these limitations, two chemical strategies are developed to effectively attach synthetic molecules site specifically to proteins. First, a protein modification technique based on conjugation at a non-native functional handle, an aldehyde or ketone, is developed. This functional handle is chemically introduced onto the biomolecules before undergoing the organocatalyzed aldol reaction, …

Electrophilic Oligodeoxynucleotide Synthesis Using Dm-Dmoc For Amino Protection, Shahien Shahsavari, Dhananjani N. A. M. Eriyagama, Bhaskar Halami, Vagarshak Begoyan, Marina Tanasova, Jinsen Chen, Shiyue Fang

Department of Chemistry Publications

Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within …

Fluorescence Of Naphthol As-Mx Is Readily Detectable In Dioxane Mixtures, Evan D. Kindl, Kevin E. Koschnitzke, James A. Blauwkamp, Sean M. Mccann, Veronica R. Moorman

Chemistry & Biochemistry Publications

Numerous enzymes have been demonstrated to be active in non-aqueous solutions, yet the utility of phosphatases under such conditions has been difficult to determine. Here, we demonstrate the ability to fluorescently detect naphthol AS‑MX in high percentages 1,4-dioxane with a fluorescence differential compared with naphthol AS‑MX phosphate. While intensities and maximum fluorescence wavelengths changed depending on solvent conditions, these results demonstrate this system’s potential for testing phosphatase activity in high amounts of dioxane.

Concentration-Dependent Magnetic Properties Of Mnxnio1-X Novel Inverted Core-Shell Nanoparticles, Md Nazmul Alam

Graduate Theses/Dissertations

The doping concentration (Mn concentration) dependent magnetic properties of NiO@NixMn1-xO novel inverted core-shell magnetic nanoparticles are of great interest of this present research. Primarily, we investigated the oxidation state of Ni from size-dependent four NiO NPs samples, and then studied the variation in the magnetic properties of Mn concentration-dependent NiO@NixMn1-xO CNPs. The NiO nanoparticles were synthesized using a thermal decomposition method. The XRD data indicates that the crystal structure (rock salt) remains fixed in all NiO samples and XPS data shows the oxidation state of size-dependent NiO nanoparticles is 2+. The hydrothermal epitaxy method was used to incorporate Mn in …

Ni-Catalyzed Cross-Electrophile Coupling For The Synthesis Of Skipped Polyenes, Catherine P. Mcgeough, Alexandra E. Strom, Timothy F. Jamison

Chemistry: Faculty Publications

Skipped polyenes featuring high (E)-selectivity and varying methyl substitution patterns are synthesized using a nickel-catalyzed cross-coupling reaction between allyl trifluoroacetates and vinyl bromides. The utility of this cross-electrophile coupling is showcased in part by the synthesis of the RST fragment of the marine ladder polyether, maitotoxin. Construction of this fragment is particularly challenging due to the alternating methyl substitution pattern.

Phantoms In Science: Nietzsche's Nonobjectivity On Planck's Quanta, Donald Richard Dickerson Iii

Undergraduate Theses

What does Maxwell Planck's concept of phantomness suggest about the epistemological basis of science and how might a Nietzschean critique reveal solution to the weaknesses revealed? With his solution to Kirchoff's equation, Maxwell Planck launched the paradigm of quantum physics. This same solution undermined much of current understandings of science versus pseudoscience. Using Nietzsche's perspectivism and other philosophical critiques, Planck's answer to blackbody radiation is used to highlight the troubles with phantom problems in science and how to try to direct science towards a more holistic and complete scientific approach.