Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation,
2019
Utah State University
Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal
Chemistry and Biochemistry Faculty Publications
This paper presents the first study of the rotations of rigid molecules in 3 dimensions at the air/water interface, using the femtosecond time resolved sum frequency generation (SFG) technique. For the purpose of this research, the aromatic dye molecule C153 was chosen as an example of a molecule having two functional groups that are SFG active, one being the hydrophilic −−C==O group and the other the hydrophobic −−CF3 group. From polarized SFG measurements, the orientations of the two chromophores with respect to the surface normal were obtained. On combining these results with the known relative orientation of the two …
Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards,
2019
Temple University
Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan
COBRA Preprint Series
The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …
Living, Learning, And Leading At Linfield College,
2019
Linfield College
Living, Learning, And Leading At Linfield College, Kelsey Bruce
Student Engagement Posters
Kelsey Bruce discusses student engagement at Linfield College with regard to leadership through student/faculty collaborative research with Dr. Megan Bestwick, speech and debate, and the Linfield Residence Life team.
Global Biochemical And Structural Analysis Of The Type Iv Pilus From The Gram-Positive Bacterium Streptococcus Sanguinis,
2019
Imperial College London
Global Biochemical And Structural Analysis Of The Type Iv Pilus From The Gram-Positive Bacterium Streptococcus Sanguinis, Jamie-Lee Berry, Ishwori Gurung, Jan Haug Anonsen, Ingrid Spielman, Elliot Harper, Alexander M. J. Hall, Vivianne J. Goosens, Claire Raynaud, Michael Koomey, Nicolas Biais, Steve Matthews, Vladimir Pelicic
Publications and Research
Type IV pili (Tfp) are functionally versatile filaments, widespread in prokaryotes, that belong to a large class of filamentous nanomachines known as type IV filaments (Tff). Although Tfp have been extensively studied in several Gram-negative pathogens where they function as key virulence factors, many aspects of their biology remain poorly understood. Here, we performed a global biochemical and structural analysis of Tfp in a recently emerged Gram-positive model, Streptococcus sanguinis. In particular, we focused on the five pilins and pilin-like proteins involved in Tfp biology in S. sanguinis. We found that the two major pilins, PilE1 and PilE2, (i) follow …
Molecular Relatedness Of Two Distinct Type Iv Crispr-Associated (Cas) Proteins,
2019
Utah State University
Molecular Relatedness Of Two Distinct Type Iv Crispr-Associated (Cas) Proteins, Matt Armbrust
Research on Capitol Hill
CRISPR-Cas systems are prokaryotic adaptive immune systems. Bacteria use CRISPR systems as a defense against foreign nucleic acid invasion such as phage infection.
Total Reflection X-Ray Fluorescence,
2019
Loyola University Chicago
Total Reflection X-Ray Fluorescence, Martina Schmeling
Chemistry: Faculty Publications and Other Works
Total reflection X-ray fluorescence (TXRF) spectrometry is a non-destructive and surface sensitive multi-element analytical method based on energy dispersive X-ray fluorescence spectrometry with detection limits in the lower picogram range. It utilizes the total reflection of the primary X-ray beam at or below the critical angle of incidence. At this angle, the fluorescence intensity is substantially enhanced for samples present as small granular residue or as thin homogenous layer deposited at the surface of a thick substrate. Generally, two types of application exist: micro- and trace-analysis as well as surface and thin-layer analysis. For micro- and traceanalysis, a small amount …
Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa,
2019
University of Nebraska at Omaha
Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid
UNO Student Research and Creative Activity Fair
Pathogenic bacteria, such as the gram-negative bacterium Pseudomonas aeruginosa, are becoming resistant to our current arsenal of antibiotics at an alarming rate. P. aeruginosa is a leading cause of nosocomial acquired infections and is a primary co-morbidity in patients with compromised immune systems. One potential source of new antibiotic agents is antimicrobial peptides. Antimicrobial peptides (AMPs) are small proteins, and some have shown a high degree of efficacy and broad-spectrum activity against both Gram-positive and Gram-negative bacteria. An experimental AMP that has been developed by Dr. Wang at UNMC, DASamp2, has shown to be effective against virulent bacteria, including P. …
Large Scale Dynamical Model Of Macrophage/Hiv Interactions,
2019
University of Nebraska at Omaha
Large Scale Dynamical Model Of Macrophage/Hiv Interactions, Matthew M. Froid
UNO Student Research and Creative Activity Fair
Properties emerge from the dynamics of large-scale molecular networks that are not discernible at the individual gene or protein level. Mathematical models - such as probabilistic Boolean networks - of molecular systems offer a deeper insight into how these emergent properties arise. Here, we introduce a non-linear, deterministic Boolean model of protein, gene, and chemical interactions in human macrophage cells during HIV infection. Our model is composed of 713 nodes with 1583 interactions between nodes and is responsive to 38 different inputs including signaling molecules, bacteria, viruses, and HIV viral particles. Additionally, the model accurately simulates the dynamics of over …
Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals,
2019
Wilfrid Laurier University
Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov
Biology Faculty Publications
The electron transport systems in mitochondria of many organisms contain alternative respiratory enzymes distinct from those of the canonical respiratory system depicted in textbooks. Two of these enzymes, the alternative NADH dehydrogenase and the alternative oxidase, were of interest to a limited circle of researchers until they were envisioned as gene therapy tools for mitochondrial disease treatment. Recently, these enzymes were discovered in several animals. Here, we analyse the functioning of alternative NADH dehydrogenases and oxidases in different organisms. We propose that both enzymes ensure bioenergetic and metabolic flexibility during environmental transitions or other conditions which may compromise the operation …
Total Synthesis Of Anticancer Agent Deoxypodophyllotoxin And Antiviral F4-4 Demonstrating The Utility Of The Intramolecular Styryl Diels-Alder (Isda) Reaction,
2019
Brigham Young University
Total Synthesis Of Anticancer Agent Deoxypodophyllotoxin And Antiviral F4-4 Demonstrating The Utility Of The Intramolecular Styryl Diels-Alder (Isda) Reaction, Diana Isabel Saavedra Nova
Theses and Dissertations
The intramolecular styryl Diels – Alder (ISDA) reaction is a rare and unique [4+2] cycloaddition with potential in the syntheses of polycycles. Its utility is based on the formation of two rings and one stereocenter in a single step, making it an efficient method for the construction of lignan-type natural product targets. Detailed mechanistic studies with complex esters and the application to natural product synthesis has been limited due to drawbacks including the loss of aromaticity, producing slow reactivity, a potentially problematic thermal [1,3]-hydrogen shift, and electronic mismatch related to the substituents on the aryl functional groups. In this research, …
Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic,
2019
University of Nebraska - Lincoln
Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic, Abigale Miller
Honors Program: Senior Projects (Public)
Naloxone is a life-saving drug with the ability to reverse an opioid overdose. As the opioid epidemic’s death toll rises, we can turn to Naloxone as a tool to combat the crisis. The epidemic, born of corruption, has a wide reach among the people of the United States, with especially firm grasps on middle-aged people, sufferers of chronic pain, white Americans and those living in the eastern portion of the country. Naloxone’s elegant design saves lives by effectively competing for a position on an opioid biding receptor in the brain to almost instantly end an overdose and restore normal breathing. …
Advanced Selection Methodologies For Dnazymes In Sensing And Healthcare Applications,
2019
Guru Jambheshwar University of Science and Technology
Advanced Selection Methodologies For Dnazymes In Sensing And Healthcare Applications, Sandeep Kumar, Shikha Jain, Neeraj Dilbaghi, Amrik Singh Ahluwalia, Ashraf Aly Hassan, Ki-Hyun Kim
Department of Civil and Environmental Engineering: Faculty Publications
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes …
Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase,
2019
University of Cambridge
Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder
Chemistry and Biochemistry Faculty Publications
Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (ßleaving group obs-Enz=-0.33) than the uncatalyzed reaction (ßleaving group obs=-1.81). This situation is diminished when cationic active site groups are exchanged for alanine. …
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis,
2019
Southern Methodist University
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …
Student-Faculty Collaborative Research Grant Report,
2019
Linfield College
Student-Faculty Collaborative Research Grant Report, Megan Bestwick
Post-Grant Reports
Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect …
A New Multivariate Optical Computing Microelement And Miniature Sensor For Spectroscopic Chemical Sensing In Harsh Environments: Design, Fabrication, And Testing,
2019
University of South Carolina
A New Multivariate Optical Computing Microelement And Miniature Sensor For Spectroscopic Chemical Sensing In Harsh Environments: Design, Fabrication, And Testing, Christopher M. Jones, Bin Dai, Jimmy Price, Jian Li, Megan Pearl, Bill Soltmann, Michael L. Myrick
Faculty Publications
Multivariate optical computing (MOC) is a compressed sensing technique with the ability to provide accurate spectroscopic compositional analysis in a variety of different applications to multiple industries. Indeed, recent developments have demonstrated the successful deployment of MOC sensors in downhole/well-logging environments to interrogate the composition of hydrocarbon and other chemical constituents in oil and gas reservoirs. However, new challenges have necessitated sensors that operate at high temperatures and pressures (up to 230 °C and 138 MPa) as well as even smaller areas that require the miniaturization of their physical footprint. To this end, this paper details the design, fabrication, and …
Transition State Analysis Of The Reaction Catalyzed By The Phosphotriesterase From Sphingiobium Sp. Tcm1,
2019
Texas A&M University
Transition State Analysis Of The Reaction Catalyzed By The Phosphotriesterase From Sphingiobium Sp. Tcm1, Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge, Frank M. Raushel
Chemistry and Biochemistry Faculty Publications
Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic …
Exposure Characterization Of Haloacetic Acids In Humans For Exposure And Risk Assessment Applications: An Exploratory Study,
2019
Indiana University Fairbanks
Exposure Characterization Of Haloacetic Acids In Humans For Exposure And Risk Assessment Applications: An Exploratory Study, Shahid Parvez, Jeffrey L. Ashby, Susana Y. Kimura, Susan D. Richardson
Faculty Publications
Disinfected water is the major source of haloacetic acids (HAAs) in humans, but their inter- and intra-individual variability for exposure and risk assessment applications is under-researched. Thus, we measured HAAs in cross-sectional and longitudinal urine and water specimens from 17 individuals. Five regulated HAAs—mono-, di-, and trichloroacetic acid (MCAA, DCAA, and TCAA) and mono- and dibromoacetic acid (MBAA and DBAA)—and one unregulated HAA—bromochloroacetic acid (BCAA)—were measured. Urinary DCAA, MBAA, DBAA, and BCAA levels were always below the limits of detection (LOD). Measured levels and interindividual variability of urinary MCAA were higher than urinary TCAA. Longitudinal urinary specimens showed MCAA levels …
Interaction And Regulation Between Lipid Mediator Phosphatidic Acid And Circadian Clock Regulators,
2019
University of Missouri–St. Louis
Interaction And Regulation Between Lipid Mediator Phosphatidic Acid And Circadian Clock Regulators, Sang-Chul Kim, Sang-Chul Kim, Dmitri Nusinow, Maria Sorkin, Maria Sorkin, Jose Pruneda-Paz, Xuemin Wang, Xuemin Wang
Biology Department Faculty Works
Circadian clocks play important roles in regulating cellular metabolism, but the reciprocal effect that metabolism has on the clock is largely unknown in plants. Here we show that the central glycerolipid metabolite and lipid mediator phosphatidic acid (PA) interacts with and modulates the function of the core clock regulators LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) in Arabidopsis thaliana. PA reduced the ability of LHY and CCA1 to bind the promoter of their target gene TIMING OF CAB EXPRESSION1. Increased PA accumulation and inhibition of PA-producing enzymes had opposite effects on circadian clock outputs. Diurnal change in levels …
Analysis Of Oxygen-18 Labeled Phosphate To Study Positional Isotope Experiments Using Lc-Qtof-Ms,
2019
Cleveland State University
Analysis Of Oxygen-18 Labeled Phosphate To Study Positional Isotope Experiments Using Lc-Qtof-Ms, Sujatha Chilakala, Iteen Cheng, Ireen Lee, Yan Xu
Chemistry Faculty Publications
A method is proposed in this paper for the determination of oxygen-18 labeled phosphate so that positional isotope experiments using sensitive and rapid liquid chromatography–QTOF–mass spectrometry (LC-QTOF-MS) experiments can be carried out. The positional isotope exchange technique is a useful tool in understanding the mechanisms and kinetics of many enzyme-catalyzed reactions. Detection of the positions and concentration of these exchanged isotopes is the key. Gas chromatography–mass spectrometry (GC-MS) and nuclear magnetic resonance imaging are commonly used analytical techniques for measurement of 18O/16O, 31P and 15N isotope enrichment. Since these techniques either require a time-consuming derivatization …
