Physical Sciences and Mathematics Commons^™

Sequence-Specific Inhibition Of A Nonspecific Protease, Leigh Logsdon, Adam Urbach

Adam R Urbach

A nonspecific exopeptidase, aminopeptidase N (APN), is inhibited sequence-specifically by a synthetic host, cucurbit[7]uril (Q7), which binds with high affinity and specificity to N-terminal phenylalanine (Phe) and 4-(aminomethyl)phenylalanine (AMPhe) and prevents their removal from the peptide. Liquid chromatography experiments demonstrated that in the presence of excess Q7, APN quantitatively converts the pentapeptides Thr-Gly-Ala-X-Met into the dipeptides X-Met (X = Phe, AMPhe). The resulting Q7-bound products are completely stable to proteolytic digestion for at least 24 h. Structure–activity studies revealed a direct correlation between the extent of protection of an N-terminal amino acid and its affinity for Q7. Therefore, Q7 provides …

Effects Of The Number And Placement Of Positive Charges On Viologen–Cucurbit[N]Uril Interactions, Gretchen Vincil, Adam Urbach

Adam R Urbach

Recent developments in the synthesis and applications of the cucurbit[n]uril family of synthetic hosts has led to an increasing interest in the detailed studies of their interactions with a wide variety of guests. This paper describes a quantitative study of the effects of the number and placement of positive charges on the binding of viologen guests to cucurbit[7]uril and cucurbit[8]uril. A series of viologen derivatives with one to four charges was characterised by isothermal titration calorimetry, 1H NMR spectroscopy and mass spectrometry to determine the stoichiometry, affinity and mode of binding. These data show that stoichiometry can be controlled by …

Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach

Adam R Urbach

This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity …

Supramolecular Chemistry: A Capstone Course, Adam Urbach, Christopher Pursell, John Spence

Adam R Urbach

A fourth-year capstone course offers students an opportunity to integrate topics covered in the core disciplinary courses, to learn an advanced interdisciplinary topic, and to approach unfamiliar problems and literature. This article describes a fourth-year capstone course designed to incorporate components of faculty lectures, student seminars, and original, hands-on research projects in order to cover the topic of supramolecular chemistry in one semester with unusual depth. This approach should be applicable to other advanced topics in chemistry.

Benzobis(Imidazolium)–Cucurbit[8]Uril Complexes For Binding And Sensing Aromatic Compounds In Aqueous Solution, Frank Biedermann, Urs Rauwald, Monika Cziferszky, Kyle Williams, Lauren Gann, Bi Guo, Adam Urbach, Christopher Bielawski, Oren Scherman

Adam R Urbach

The utilities of benzobis(imidazolium) salts (BBIs) as stable and fluorescent components of supramolecular assemblies involving the macrocyclic host, cucurbit[8]uril (CB[8]), are described. CB[8] has the unusual ability to bind tightly and selectively to two different guests in aqueous media, typically methyl viologen (MV) as the first guest, followed by an indole, naphthalene, or catechol-containing second guest. Based on similar size, shape, and charge, tetramethyl benzobis(imidazolium) (MBBI) was identified as a potential alternative to MV that would increase the repertoire of guests for cucurbit[8]uril. Isothermal titration calorimetry (ITC) studies showed that MBBI binds to CB[8] in a 1:1 ratio with an …

Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam Urbach

Adam R Urbach

The synthesis of [2]rotaxanes, each comprising a viologen core threaded through a cucurbit[8]uril (Q8, Figure 1) macrocycle and stoppered by tetraphenylmethane groups, and their binding to second guests as inclusion complexes in organic and aqueous media are described. Stoppering was observed to have little effect on binding. Chemical modification of the threaded guest was used to control solubility and binding characteristics, thus demonstrating a novel approach to making artificial receptors with readily modifiable properties.

Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa Heitmann, Alexander Taylor, P Hart, Adam Urbach

Adam R Urbach

This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), ¹H NMR spectroscopy, and X-ray crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly …

Circular Dichroism Spectroscopy In The Undergraduate Curriculum, Adam Urbach

Adam R Urbach

Circular dichroism spectropolarimetry (CD) is a method of optical spectroscopy that seems in most practical ways like UV−visible spectroscopy. The main difference between the two methods is that CD, instead of measuring the absorbance of light as a function of wavelength, measures the difference in absorbance of left versus right circularly polarized light as a function of wavelength. A CD spectrum is an observation of the structure of a chiral compound; it often serves as a “fingerprint” of the structure of biological molecules such as proteins and nucleic acids. For this reason, CD has been broadly applied in biochemistry and …

Viral Infection Causes A Shift In The Self Peptide Repertoire Presented By Human Mhc Class I Molecules, Charles T. Spencer, Jelena S. Bezbradica, Mireya G. Ramos, Chenoa D. Arico, Stephanie B. Conant, Pavlo Gilchuk, Jennifer J. Gray, Mu Zheng, Xinnan Niu, William Hildebrand, Andrew J. Link, Sebastian Joyce

Chemistry Faculty Research

Purpose

MHC class I presentation of peptides allows T cells to survey the cytoplasmic protein milieu of host cells. During infection, presentation of self peptides is, in part, replaced by presentation of microbial peptides. However, little is known about the self peptides presented during infection, despite the fact that microbial infections alter host cell gene expression patterns and protein metabolism.

Experimental design

The self peptide repertoire presented by HLA-A*01;01, HLA-A*02;01, HLA-B*07;02, HLA-B*35;01, and HLA-B*45;01 (where HLA is human leukocyte antigen) was determined by tandem MS before and after vaccinia virus infection.

Results

We observed a profound alteration in the self …

Flow And Scour Constrainst On Uprooting Of Pioneer Woody Seedlings, Sharon Bywater-Reyes, Andrew C. Wilcox, John C. Stella, Anne Lightbody

Geosciences Faculty Publications

Scour and uprooting during flood events is a major disturbance agent that affects plant mortality rates and subsequent vegetation composition and density, setting the trajectory of physical-biological interactions in rivers. During flood events, riparian plants may be uprooted if they are subjected to hydraulic drag forces greater than their resisting force. We measured the resisting force of woody seedlings established on river bars with in situ lateral pull tests that simulated flood flows with and without substrate scour. We quantified the influence of seedling sizes, species (Populus and Tamarix), water-table depth, and scour depth on resisting force. Seedling …

Comparison Of Microfacet Brdf Model To Modified Beckmann-Kirchhoff Brdf Model For Rough And Smooth Surfaces, Samuel D. Butler, Stephen E. Nauyoks, Michael A. Marciniak

Faculty Publications

A popular class of BRDF models is the microfacet models, where geometric optics is assumed. In contrast, more complex physical optics models may more accurately predict the BRDF, but the calculation is more resource intensive. These seemingly disparate approaches are compared in detail for the rough and smooth surface approximations of the modified Beckmann-Kirchhoff BRDF model, assuming Gaussian surface statistics. An approximation relating standard Fresnel reflection with the semi-rough surface polarization term, Q, is presented for unpolarized light. For rough surfaces, the angular dependence of direction cosine space is shown to be identical to the angular dependence in the microfacet …

The Influence Of The Proximal Amide Hydrogen Bonds And The Proximal Helix Dipole On The Catalytic Activity Of Chloroperoxidase, Armando D. Pardillo

FIU Electronic Theses and Dissertations

Chloroperoxidase (CPO) is a heme-thiolate protein with exceptional versatility and great potential as a biocatalyst. The CPO reactive species, Compound I ( Cpd I) is of particular interest, as well as the Cytochrome P450 (P450) -type monoxygenase catalytic activity, which has significant biotechnological potential. Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH•••S) is a conserved feature of heme-thiolate enzymes. In CPO, the effect of NH•••S bonds is amplified by the dipole moment of the proximal helix. The role of the proximal region has been disputed as to whether it simply protects the axial sulfur, or whether …

Evaluation Of The Snow Thermal Model (Sntherm) Through Continuous In Situ Observations Of Snow’S Physical Properties At The Crest-Safe Field Experiment, José Alberto Infante Corona, Jonathan Muñoz, Tarendra Lakhankar, Peter Romanov, Reza Khanbilvardi

Publications and Research

Snowpack properties like temperature or density are the result of a complex energy and mass balance process in the snowpack that varies temporally and spatially. The Snow Thermal Model (SNTHERM) is a 1-dimensional model, energy and mass balance-driven, that simulates these properties. This article analyzes the simulated snowpack properties using SNTHERM forced with two datasets, namely measured meteorological data at the Cooperative Remote Sensing Science and Technology-Snow Analysis and Field Experiment (CREST-SAFE) site and the National Land Data Assimilation System (NLDAS). The study area is located on the premises of Caribou Municipal Airport at Caribou (ME, USA). The model evaluation …

Dependence Of Electrostatic Field Strength On Voltage Ramp Rates For Spacecraft Materials, Krysta Moser

Senior Theses and Projects

No abstract provided.

Abcc9/Sur2 In The Brain: Implications For Hippocampal Sclerosis Of Aging And A Potential Therapeutic Target, Peter T. Nelson, Gregory A. Jicha, Wang-Xia Wang, Eseosa T. Ighodaro, Sergey C. Artiushin, Colin G. Nichols, David W. Fardo

Sanders-Brown Center on Aging Faculty Publications

The ABCC9 gene and its polypeptide product, SUR2, are increasingly implicated in human neurologic disease, including prevalent diseases of the aged brain. SUR2 proteins are a component of the ATP-sensitive potassium (“K _ATP ”) channel, a metabolic sensor for stress and/or hypoxia that has been shown to change in aging. The K _ATP channel also helps regulate the neurovascular unit. Most brain cell types express SUR2, including neurons, astrocytes, oligodendrocytes, microglia, vascular smooth muscle, pericytes, and endothelial cells. Thus it is not surprising that ABCC9 gene variants are associated with risk for human brain diseases. For example, Cantu syndrome is …

Uncovering Adaptive Versus Acclimatized Alterations In Standard Metabolic Rate In Brown Bullhead (Ameiurus Nebulosus), Tood A. Leadley, Anne Mcleod, Timothy B. Johnson, Daniel D. Heath, Ken G. Drouillard

Great Lakes Institute for Environmental Research Publications

Standard metabolic rates (SMR) were measured in Brown Bullheads collected from two locations of the Detroit River, North America, representative of highly contaminated and uncontaminated areas. Measurements of SMR were completed within 10 d of fish collections (acute trials), for fish held in a common pond environment for 1 year (clearance trials) and for F1 generation fish raised in the pond environment (F1 study). SMRs were significantly higher (26%) in fish from the contaminated area during acute trials. Both populations showed large decreases in SMR (49 to 52 %) following clearance, however, differences between populations were still evident. There were …

A Review Of Structural Patterns And Melting Processes In The Archean Craton Of West Greenland: Evidence For Crustal Growth At Convergent Plate Margins As Opposed To Non-Uniformitarian Models, Ali Polat

Earth & Environmental Sciences Publications

The Archean craton of West Greenland consists of many fault-bounded Eoarchean to Neoarchean tectonic terranes (crustal blocks). These tectonic terranes are composed mainly of tonalite-trondhjemite-granodiorite (TTG) gneisses, granitic gneisses, metavolcanic-dominated supracrustal belts, layered anorthositic complexes, and late- to post-tectonic granites. Rock assemblages and geochemical signatures in these terranes suggest that they represent fragments of dismembered oceanic island arcs, consisting mainly of TTG plutons, tholeiitic to calc-alkaline basalts, boninites, picrites, and cumulate layers of ultramafic rocks, gabbros, leucogabbros and anorthosites, with minor sedimentary rocks. The structural characteristics of the terrane boundaries are consistent with the assembly of these island arcs through …

Effect Of Sm Content On Energy Product Of Rapidly Quenched And Oriented Smco5 Ribbons, Wenyong Zhang, Xingzhong Li, Shah R. Valloppilly

Nebraska Center for Materials and Nanoscience: Faculty Publications

The Sm-content dependence of phase composition, anisotropy, and other magnetic properties of Sm_1+δCo₅ (δ ≤ 0.12) ribbons melt spun at 10 m/s has been studied. The samples consist of hexagonal SmCo₅ grains whose c axes are preferentially aligned along the long direction of the ribbon. The lattice parameter a and the cell volume (V) increase with increasing Sm content δ, whereas c decreases. Sm addition appears to improve the degree of the preferred orientation of the c-axis and to increase the mean grain size, which weakens the effective intergranular exchange …

Wintertime Weather-Climate Variability And Its Links To Early Spring Ice-Out In Maine Lakes, Mussie Beyene, Shaleen Jain

Publications

In recent decades, Maine lakes have recorded their earliest ice-out dates in over a century. In temperate regions, seasonal lake ice-cover is a critical phenomenon linking climate, aquatic ecosystem and society. And the lengthening of the ice-free period due to warmer climate has been linked to increased algal growth and declining lake water quality, warming of water temperatures leading to alterations in aquatic biodiversity, and the shortening of ice-fishing period and other traditional winter activities over lakes. In this study, historical record of eight lakes and six benchmarked meteorological stations in Maine for the period 1950–2010 were analyzed to (1) …

8000 Years Of Environmental Evolution Of Barrier–Lagoon Systems Emplaced In Coastal Embayments (Nw Iberia), Rita González-Villanueva, Marta Pérez-Arlucea, Susana Costas, Roberto Bao, Xose L. Otero, Ronald J. Goble

Department of Earth and Atmospheric Sciences: Faculty Publications

The rocky and indented coast of NW Iberia is characterized by the presence of highly valuable and vulnerable, small and shallow barrier– lagoon systems structurally controlled. The case study was selected to analyse barrier–lagoon evolution based on detailed sedimentary architecture, chronology, geochemical and biological proxies. The main objective is to test the hypothesis of structural control and the significance at regional scale of any highenergy event recorded. This work is also aimed at identifying general patterns and conceptualizing the formation and evolution of this type of coastal systems. The results allowed us to establish a conceptual model of Holocene evolution …

Approaches For Detection Of Unstable Processes: A Comparative Study, Yerriswamy Wooluru, D. R. Swamy, P. Nagesh

Journal of Modern Applied Statistical Methods

A process is stable only when parameters of the distribution of a process or product characteristic remain same over time. Only a stable process has the ability to perform in a predictable manner over time. Statistical analysis of process data usually assume that data are obtained from stable process. In the absence of control charts, the hypothesis of process stability is usually assessed by visual examination of the pattern in the run chart. In this paper appropriate statistical approaches have been adopted to detect instability in the process and compared their performance with the run chart of considerably shorter length …

2015: "Go With The Flow", Paul Nebres '16, Kushagra Gupta '16, Jason Chen '16, Noor Michael '16

Distinguished Student Work

In a famous incident in August 2010, a Chinese traffic jam stretched for over 100 kilometers and stranded drivers took over two weeks to get from one side to the other. Stemming from a routine lane closure for road maintenance, the traffic jam soon spiraled out of control, as cars piling up at the jam greatly outnumbered those leaving the other end. Sadly, in todays overpopulated world, these sorts of nightmare scenarios are only becoming more and more common, from chronic traffic jams in congested Chinese cities to Carmageddon in Los Angeles. For drivers, these extensive traffic jams can be …

Distributions Of Long-Lived Radioactive Nuclei Provided By Star-Forming Environments, Marco Fatuzzo, Fred Adams

Faculty Scholarship

Radioactive nuclei play an important role in planetary evolution by providing an internal heat source, which affects planetary structure and helps facilitate plate tectonics. A minimum level of nuclear activity is thought to be necessary—but not sufficient—for planets to be habitable. Extending previous work that focused on short-lived nuclei, this paper considers the delivery of long-lived radioactive nuclei to circumstellar disks in star forming regions. Although the long-lived nuclear species are always present, their abundances can be enhanced through multiple mechanisms. Most stars form in embedded cluster environments, so that disks can be enriched directly by intercepting ejecta from supernovae …

40ar/39ar Ages Of Lunar Impact Glasses: Relationships Among Ar Diffusivity, Chemical Composition, Shape, And Size, John W. Delano Phd, Nicolle Zellner

Atmospheric and Environmental Science Faculty Scholarship

Lunar impact glasses, which are quenched melts produced during cratering events on the Moon, have the potential to providenot only compositional information about both the local and regional geology of the Moon but also information about the impact flux over time. We present in this paper the results of 73 new 40Ar/39Ar analyses of well-characterized, inclusion-free lunar impact glasses and demonstrate that size, shape, chemical composition, fraction of radiogenic 40Ar retained, and cosmic ray exposure (CRE) ages are important for 40Ar/39Ar investigations of these samples. Specifically, analyses of lunar impact glasses from the Apollo 14, 16, and 17 landing sites …

Measurement Of Interaction Between Antiprotons, Adam Gibson-Even, Shirvel Stanislaus, Donald Koetke, Star Collaboration

Physics and Astronomy Faculty Publications

No abstract provided.

West Coast Deep Sea Crustacean Managed Fishery, Jason R. How, F J. Webster, K. L. Travaille, Kim Nardi, A. V. Harry

WA Marine Stewardship Council report series

This report provides a comprehensive description of the West Coast Deep Sea Crustacean Managed Fishery (WCDSCMF) and contains information relevant to assist the assessment of this fishery against the Marine Stewardship Council (MSC) standard (v1.3) for sustainable fishing.

Searches For Continuous Gravitational Waves From Nine Young Supernova Remnants, J. Aasi, B. P. Abbott, R. Abbott, T. Abbott, M. R. Abernathy, F. Acernese, K. Ackley, Marc Favata, Shaon Ghosh, Rodica Martin

Department of Physics and Astronomy Faculty Scholarship and Creative Works

We describe directed searches for continuous gravitational waves (GWs) in data from the sixth Laser Interferometer Gravitational-wave Observatory (LIGO) science data run. The targets were nine young supernova remnants not associated with pulsars; eight of the remnants are associated with non-pulsing suspected neutron stars. One target's parameters are uncertain enough to warrant two searches, for a total of 10. Each search covered a broad band of frequencies and first and second frequency derivatives for a fixed sky direction. The searches coherently integrated data from the two LIGO interferometers over time spans from 5.3-25.3 days using the matched-filtering -statistic. We found …

Smart Sensing And Mobile Computing, Guihai Chen, Dakshnamoorthy Manivannan, Chen Qian, Fangming Liu, Jinsong Han

Computer Science Faculty Publications

No abstract provided.

Contrails: Causal Inference Using Propensity Scores, Dean S. Barron

Journal of Modern Applied Statistical Methods

Contrails are clouds caused by airplane exhausts, which geologists contend decrease daily temperature ranges on Earth. Following the 2001 World Trade Center attack, cancelled domestic flights triggered the first absence of contrails in decades. Resultant exceptional data capacitated causal inference analysis by propensity score matching. Estimated contrail effect was 6.8981°F.

The Bayes Factor For Case-Control Studies With Misclassified Data, Tzesan Lee

Journal of Modern Applied Statistical Methods

The question of how to test if collected data for a case-control study are misclassified was investigated. A mixed approach was employed to calculate the Bayes factor to assess the validity of the null hypothesis of no-misclassification. A real-world data set on the association between lung cancer and smoking status was used as an example to illustrate the proposed method.