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Articles 1 - 30 of 44
Full-Text Articles in Entire DC Network
Solvation Free Energy In Governing Equations For Dna Hybridization, Protein–Ligand Binding, And Protein Folding, Caroline Harmon, Austin Bui, Jasmin M. Espejo, Marc Gancayco, Jennifer M. Le, Juan Rangel, Daryl K. Eggers
Solvation Free Energy In Governing Equations For Dna Hybridization, Protein–Ligand Binding, And Protein Folding, Caroline Harmon, Austin Bui, Jasmin M. Espejo, Marc Gancayco, Jennifer M. Le, Juan Rangel, Daryl K. Eggers
Faculty Research, Scholarly, and Creative Activity
This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one of 10 base pairs in length, are measured and characterized by isothermal titration calorimetry (ITC) as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔGS) is large and unfavorable. The duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔG …
Genetic Algorithm For Automated Parameterization Of Network Hamiltonian Models Of Amyloid Fibril Formation, Gianmarc Grazioli, Andy Tao, Inika Bhatia, Patrick Regan
Genetic Algorithm For Automated Parameterization Of Network Hamiltonian Models Of Amyloid Fibril Formation, Gianmarc Grazioli, Andy Tao, Inika Bhatia, Patrick Regan
Faculty Research, Scholarly, and Creative Activity
The time scales of long-time atomistic molecular dynamics simulations are typically reported in microseconds, while the time scales for experiments studying the kinetics of amyloid fibril formation are typically reported in minutes or hours. This time scale deficit of roughly 9 orders of magnitude presents a major challenge in the design of computer simulation methods for studying protein aggregation events. Coarse-grained molecular simulations offer a computationally tractable path forward for exploring the molecular mechanism driving the formation of these structures, which are implicated in diseases such as Alzheimer’s, Parkinson’s, and type-II diabetes. Network Hamiltonian models of aggregation are centered around …
Dual Effect Of Secondary Solutes On Binding Equilibria: Contributions From Solute–Reactant Interactions And Solute–Water Interactions, Daryl Eggers, Jennifer M. Le, Nhi T. Nham, Duc N. Pham, Bria M. Castellano
Dual Effect Of Secondary Solutes On Binding Equilibria: Contributions From Solute–Reactant Interactions And Solute–Water Interactions, Daryl Eggers, Jennifer M. Le, Nhi T. Nham, Duc N. Pham, Bria M. Castellano
Faculty Research, Scholarly, and Creative Activity
This study examines the role of water in binding equilibria with a special focus on secondary solutes (cosolutes) that influence the equilibrium but are not constituents of the final product. Using a thermodynamic framework that includes an explicit term for the release of water molecules upon binding, this investigation reveals how solutes may alter equilibria by changing the activity of the reactants, reflected in ΔG°(obs), and by changing the chemical potential of the solvent, reflected in ΔGS. The framework is applied to four experimental binding systems that differ in the degree of electrostatic contributions. The model …
Quantum Diamonds At The Beach: Chemical Insights Into Silica Growth On Nanoscale Diamond Using Multimodal Characterization And Simulation, Perla J. Sandoval, Karen Lopez, Andres Arreola, Anida Len, Nedah Basravi, Pomaikaimaikalani Yamaguchi, Rina Kawamura, Camron X. Stokes, Cynthia Melendrez, Davida Simpson, Sang Jun Lee, Charles James Titus, Virginia Altoe, Sami Sainio, Dennis Nordlund, Kent Irwin, Abraham Wolcott
Quantum Diamonds At The Beach: Chemical Insights Into Silica Growth On Nanoscale Diamond Using Multimodal Characterization And Simulation, Perla J. Sandoval, Karen Lopez, Andres Arreola, Anida Len, Nedah Basravi, Pomaikaimaikalani Yamaguchi, Rina Kawamura, Camron X. Stokes, Cynthia Melendrez, Davida Simpson, Sang Jun Lee, Charles James Titus, Virginia Altoe, Sami Sainio, Dennis Nordlund, Kent Irwin, Abraham Wolcott
Faculty Research, Scholarly, and Creative Activity
Surface chemistry of materials that host quantum bits such as diamond is an important avenue of exploration as quantum computation and quantum sensing platforms mature. Interfacing diamond in general and nanoscale diamond (ND) in particular with silica is a potential route to integrate room temperature quantum bits into photonic devices, fiber optics, cells, or tissues with flexible functionalization chemistry. While silica growth on ND cores has been used successfully for quantum sensing and biolabeling, the surface mechanism to initiate growth was unknown. This report describes the surface chemistry responsible for silica bond formation on diamond and uses X-ray absorption spectroscopy …
Characterization Of Essential Eggshell Proteins From Aedes Aegypti Mosquitoes, Jun Isoe, Carter J. Simington, Max E. Oscherwitz, Alyssa J. Peterson, Alberto A. Rascón, Brooke B. Massani, Roger L. Miesfeld, Michael A. Riehle
Characterization Of Essential Eggshell Proteins From Aedes Aegypti Mosquitoes, Jun Isoe, Carter J. Simington, Max E. Oscherwitz, Alyssa J. Peterson, Alberto A. Rascón, Brooke B. Massani, Roger L. Miesfeld, Michael A. Riehle
Faculty Research, Scholarly, and Creative Activity
Background: Up to 40% of the world population live in areas where mosquitoes capable of transmitting the dengue virus, including Aedes aegypti, coexist with humans. Understanding how mosquito egg development and oviposition are regulated at the molecular level may provide new insights into novel mosquito control strategies. Previously, we identified a protein named eggshell organizing factor 1 (EOF1) that when knocked down with RNA interference (RNAi) resulted in non-melanized and fragile eggs that did not contain viable embryos. Results: In this current study, we performed a comprehensive RNAi screen of putative A. aegypti eggshell proteins to identify additional proteins that …
Dissimilar-At-Boron N-Bodipys: From Light-Harvesting Multichromophoric Arrays To Cpl-Bright Chiral-At-Boron Bodipys, César Ray, Edurne Avellanal-Zaballa, Mónica Muñoz-Úbeda, Jessica Colligan, Florencio Moreno, Gilles Muller, Iván López-Montero, Jorge Bañuelos, Beatriz L. Maroto, Santiago De La Moya
Dissimilar-At-Boron N-Bodipys: From Light-Harvesting Multichromophoric Arrays To Cpl-Bright Chiral-At-Boron Bodipys, César Ray, Edurne Avellanal-Zaballa, Mónica Muñoz-Úbeda, Jessica Colligan, Florencio Moreno, Gilles Muller, Iván López-Montero, Jorge Bañuelos, Beatriz L. Maroto, Santiago De La Moya
Faculty Research, Scholarly, and Creative Activity
We report a workable and easy approach for the direct post-multifunctionalization of common BODIPYs (F-BODIPYs) with minimal interference to the starting photophysical behavior. It entails the easy transformation of an F-BODIPY into the corresponding N-BODIPY by using a dissimilarly-N,N′-disubstituted bis(sulfonamide), which is easily obtained from ethane-1,2-diamine. This approach is exemplified by the rapid synthesis of a selected battery of unprecedented dissimilar-at-boron N-BODIPYs, which are rationally designed to act as efficient multichromophoric arrays for light harvesting by excitation energy transfer, as specific bioprobes for fluorescent imaging, or as efficient chiroptical dyes exhibiting visible circular dichroism and circularly polarized luminescence. Noticeably, this …
Model Binding Experiments With Cucurbit[7]Uril And P-Sulfonatocalix[4]Arene Support Use Of Explicit Solvation Term In Governing Equation For Binding Equilibria, Daryl Eggers, Adam Brewer, Kimberly J. Cacatian, L. Allison Camat, Dominic Castagnoli, Nina Chuang, Lillian N. Chung, Thanh Do, Emily Huynh, Thanayuth Jenpichitkulchai, Anoop Kaur, Frank Le, Roy Ong, Duc Pham, Kevin Shao
Model Binding Experiments With Cucurbit[7]Uril And P-Sulfonatocalix[4]Arene Support Use Of Explicit Solvation Term In Governing Equation For Binding Equilibria, Daryl Eggers, Adam Brewer, Kimberly J. Cacatian, L. Allison Camat, Dominic Castagnoli, Nina Chuang, Lillian N. Chung, Thanh Do, Emily Huynh, Thanayuth Jenpichitkulchai, Anoop Kaur, Frank Le, Roy Ong, Duc Pham, Kevin Shao
Faculty Research, Scholarly, and Creative Activity
The thermodynamics of model host–guest-binding reactions is examined in depth using isothermal titration calorimetry. In conflict with classical thermodynamics, the results indicate that the equilibrium-binding quotient, K, is not a constant for all pairings. This outcome is predicted by an equation for binding equilibria that includes an explicit term for the change in solvation free energy that accompanies the formation of a binary complex. Application of this framework to the experimentally observed concentration dependence of K allows one to obtain the energetic contribution of the solvent, a linked equilibrium denoted here as ΔGH2O. The estimated values of ΔGH2O are large …
First Application Of Markov Chain Monte Carlo-Based Bayesian Data Analysis To The Doppler-Shift Attenuation Method, L. J. Sun, C. Fry, B. Davids, Nicholas Esker, C. Wrede, For Full Author List, See Comments Below
First Application Of Markov Chain Monte Carlo-Based Bayesian Data Analysis To The Doppler-Shift Attenuation Method, L. J. Sun, C. Fry, B. Davids, Nicholas Esker, C. Wrede, For Full Author List, See Comments Below
Faculty Research, Scholarly, and Creative Activity
Motivated primarily by the large uncertainties in the thermonuclear rate of the 30P(p,γ)31S reaction that limit our understanding of classical novae, we carried out lifetime measurements of 31S excited states using the Doppler Shift Lifetimes (DSL2) facility at the TRIUMF Isotope Separator and Accelerator (ISAC-II) facility. The 31S excited states were populated by the 3He(32S,α)31S reaction. The deexcitation γ rays were detected by a clover-type high-purity germanium detector in coincidence with the α particles detected by a silicon detector telescope. We have applied modern Markov chain Monte Carlo-based Bayesian statistical …
Foregrounding The Code: Computational Chemistry Instructional Activities Using A Highly Readable Fluid Simulation Code, Gianmarc Grazioli, Adam Ingwerson, David Santiago, Patrick Regan, Hee Kun Cho
Foregrounding The Code: Computational Chemistry Instructional Activities Using A Highly Readable Fluid Simulation Code, Gianmarc Grazioli, Adam Ingwerson, David Santiago, Patrick Regan, Hee Kun Cho
Faculty Research, Scholarly, and Creative Activity
Computational chemistry instructional activities are often based around students running chemical simulations via a graphical user interface (GUI). GUI-based activities offer many advantages, as they enable students to run chemical simulations with a few mouse clicks. Although these activities are excellent for introducing students to the capabilities of chemical simulations, the disadvantage is that the students’ experience is not representative of how professional computational chemists work. Just as it is important that students in an organic chemistry instructional lab gain hands-on experience with equipment commonly used by professional organic chemists, students of computational chemistry must gain hands-on experience with coding, …
The Differing Effects Of A Dual Acting Regulator On Sirt1, Yujin Hur, Johnson Huynh, Emily Leong, Reena Dosanjh, Annemarie F. Charvat, My H. Vu, Zain Alam, Yue Tong Lee, Christiane C. Cabreros, Emma C. Carroll, Greg L. Hura, Ningkun Wang
The Differing Effects Of A Dual Acting Regulator On Sirt1, Yujin Hur, Johnson Huynh, Emily Leong, Reena Dosanjh, Annemarie F. Charvat, My H. Vu, Zain Alam, Yue Tong Lee, Christiane C. Cabreros, Emma C. Carroll, Greg L. Hura, Ningkun Wang
Faculty Research, Scholarly, and Creative Activity
SIRT1 is an NAD+-dependent protein deacetylase that has been shown to play a significant role in many biological pathways, such as insulin secretion, tumor formation, lipid metabolism, and neurodegeneration. There is great interest in understanding the regulation of SIRT1 to better understand SIRT1-related diseases and to better design therapeutic approaches that target SIRT1. There are many known protein and small molecule activators and inhibitors of SIRT1. One well-studied SIRT1 regulator, resveratrol, has historically been regarded as a SIRT1 activator, however, recent studies have shown that it can also act as an inhibitor depending on the identity of the peptide substrate. …
Metal-Ligand Interactions In A Redox Active Ligand System. Electrochemistry And Spectroscopy Of [M(Dipyvd)2]N+ (M=Zn, Ni, N=0, 1, 2), Connor Fleming, Son Vu, David J.R. Brook, Stefano Agrestini, Eric Pellegrin, Jeffrey Daros
Metal-Ligand Interactions In A Redox Active Ligand System. Electrochemistry And Spectroscopy Of [M(Dipyvd)2]N+ (M=Zn, Ni, N=0, 1, 2), Connor Fleming, Son Vu, David J.R. Brook, Stefano Agrestini, Eric Pellegrin, Jeffrey Daros
Faculty Research, Scholarly, and Creative Activity
Reaction of nickel and zinc triflates with the tridentate leucoverdazyl 1-isopropyl-3,5-di (2′-pyridyl)-6-oxo-2H-tetrazine (dipyvdH) and triethylamine resulted in the neutral coordination compounds M(dipyvd)2 (M = Ni,Zn). In acetonitrile, both compounds undergo two one electron oxidation processes, Zn (dipyvd)2 at −0.28 V and −0.12 V and Ni(dipyvd)2 at −0.32 V and −0.15 V vs ferrocene/ferricenium. Oxidations are ligand based resulting in an intermediate mixed valence species and a cationic bis(verdazyl) compound respectively. Oxidation of the ligand changes a localized, antiaromatic, non-planar 8π electron anion to a planar, delocalized 7π electron radical. The change in ligand structure results in an increase in the …
Steric Effect On Benzyl Ether Olefines Under Sadmet Polymerization, Su Hu
Steric Effect On Benzyl Ether Olefines Under Sadmet Polymerization, Su Hu
Master's Theses
Acyclic diene metathesis (ADMET) polymerization, a type of olefin cross metathesis, is a step-growth and condensation polymerization that can be used to synthesize hydrocarbon polymers with diverse functional groups. Traditional ADMET with symmetric α,ω-dienes is not selective and can only form homopolymers or statistical copolymers. Changing to monomers with acrylate functional groups allows selective reactivity to form block and alternating polymers. In this project, we want to explore other functional groups that result in selective reactivity to form advanced polymer architectures via what we have termed selective acyclic diene metathesis (SADMET) polymerization. Developing new functionalized monomers for SADMET polymerization allows …
Prediction And Confirmation Of A Switch-Like Region Within The N-Terminal Domain Of Hsirt1, Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig, Ningkun Wang
Prediction And Confirmation Of A Switch-Like Region Within The N-Terminal Domain Of Hsirt1, Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig, Ningkun Wang
Faculty Research, Scholarly, and Creative Activity
Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch- like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important …
Science, Physiology, And Nutrition For The Nonscientist, Judi S. Morrill
Science, Physiology, And Nutrition For The Nonscientist, Judi S. Morrill
Open Educational Resources
A wonderful blend of physiology, nutrition, biochemistry, genetics, biology, evolution, chemistry--what we all need to know as informed citizens. A basic knowledge of the life sciences and how our bodies work--to promote our own good health, especially as we're bombarded with misleading advertisements, soundbites, and the like. DNA fingerprinting, calorie requirements, dietary advice, genetic engineering (including gene editing with CRISPR cas9)--all in an easy-to understand book.
Nav1.1 Is Essential For Proprioceptive Signaling And Motor Behaviors, Cyrrus M. Espino, Cheyanne M. Lewis, Serena Ortiz, Miloni S. Dalal, Snigdha Garlapalli, Kaylee M. Wells, Darik A. O'Neil, Katherine A. Wilkinson, Theanne N. Griffith
Nav1.1 Is Essential For Proprioceptive Signaling And Motor Behaviors, Cyrrus M. Espino, Cheyanne M. Lewis, Serena Ortiz, Miloni S. Dalal, Snigdha Garlapalli, Kaylee M. Wells, Darik A. O'Neil, Katherine A. Wilkinson, Theanne N. Griffith
Faculty Research, Scholarly, and Creative Activity
The voltage-gated sodium channel (NaV), NaV1.1, is well-studied in the central nervous system; conversely, its contribution to peripheral sensory neuron function is more enigmatic. Here, we identify a new role for NaV1.1 in mammalian proprioception. RNAscope analysis and in vitro patch-clamp recordings in genetically identified mouse proprioceptors show ubiquitous channel expression and significant contributions to intrinsic excitability. Notably, genetic deletion of NaV1.1 in sensory neurons caused profound and visible motor coordination deficits in conditional knockout mice of both sexes, similar to conditional Piezo2-knockout animals, suggesting that this channel is a major contributor to sensory proprioceptive transmission. Ex vivo muscle afferent …
Exploration Of Novel Nickel Metal Organic Decomposition Inks, Ivy Tran
Exploration Of Novel Nickel Metal Organic Decomposition Inks, Ivy Tran
Master's Theses
In the growing and ever-evolving world of technology, the prospect of printable and flexible electronics has become prominent. Printable metal inks are of significant interest as they can be used to fabricate metal films efficiently, with greener materials, at lower-cost, and with low-waste as compared to conventional metal film deposition techniques. They also allow the utilization of a wider range of materials, giving way to flexible technologies in the future. Here, we introduce the formulation of novel nickel-precursor based liquid organometallic decomposing (MOD) inks that sinter at relatively low temperatures and thermally decompose into a conductive layer. In this work, …
Novel Thermally Decomposable Cobalt Materials, Yu-Jui Chang
Novel Thermally Decomposable Cobalt Materials, Yu-Jui Chang
Master's Theses
Developing suitable material precursors of reduced metal films plays an important role inflexible electronics. We introduce a relatively low-temperature sintering liquid material that may be used to pattern a conductive layer. The liquid material is made of oxidized metal carboxylate salts along with liquid amines or carboxylic acids. When heated above ca. 220 C, this material spontaneously decomposes into reduced metal and various gas-phase products. Inideal (albeit not this) cases, this yields an adherent, electrically conducting perfect metal mirror.Such materials, inks if you will, conserve metal and plate only where deposited, thus meeting an important ecological goal of metal conservation. …
Sorting Phenomena And Chirality Transfer In Fluoride-Bridged Macrocyclic Rare Earth Complexes, Katarzyna Ślepokura, Trevor A. Cabreros, Gilles Muller, Jerzy Lisowski
Sorting Phenomena And Chirality Transfer In Fluoride-Bridged Macrocyclic Rare Earth Complexes, Katarzyna Ślepokura, Trevor A. Cabreros, Gilles Muller, Jerzy Lisowski
Faculty Research, Scholarly, and Creative Activity
The reaction of fluoride anions with mononuclear lanthanide(III) and yttrium(III) hexaaza-macrocyclic complexes results in the formation of dinuclear fluoride-bridged complexes. As indicated by X-ray crystal structures, in these complexes two metal ions bound by the macrocycles are linked by two or three bridging fluoride anions, depending on the type of the macrocycle. In the case of the chiral hexaaza-macrocycle L1 derived from trans-1,2-diaminocyclohexane, the formation of these μ2-fluorido dinuclear complexes is accompanied by enantiomeric self-recognition of macrocyclic units. In contrast, this kind of recognition is not observed in the case of complexes of the chiral macrocycle L2 derived from 1,2-diphenylethylenediamine. …
Neural Upscaling From Residue-Level Protein Structure Networks To Atomistic Structures, Vy T. Duong, Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, Carter T. Butts
Neural Upscaling From Residue-Level Protein Structure Networks To Atomistic Structures, Vy T. Duong, Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, Carter T. Butts
Faculty Research, Scholarly, and Creative Activity
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly com-pressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from …
Silica Hydride: A Separation Material Every Analyst Should Know About, Joseph J. Pesek, Maria T. Matyska
Silica Hydride: A Separation Material Every Analyst Should Know About, Joseph J. Pesek, Maria T. Matyska
Faculty Research, Scholarly, and Creative Activity
This review describes the development, special features and applications of silica hydridebased stationary phases for HPLC. The unique surface of this material is in contrast to ordinary, standard silica, which is the material most frequently used in modern HPLC stationary phases. The standard silica surface contains mainly silanol (Si-OH) groups, while the silica hydride surface is instead composed of silicon-hydrogen groups, which is much more stable, less reactive and delivers different chromatographic and chemical characteristics. Other aspects of this material are described for each of the different bonded moieties available commercially. Some applications for each of these column types are …
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Faculty Research, Scholarly, and Creative Activity
Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.
Realities Of Nutrition, Judi S. Morrill
Realities Of Nutrition, Judi S. Morrill
Open Educational Resources
What Is Nutrition Reality? Is it in the advertising claims that a food is natural or supplies instant energy? Is it in the myriad of dietary supplements? Is it in the diet plans for instant weight loss and glowing health? The only way to find out is to learn the basic principles of nutrition science, so you can be your own nutrition expert. Here is the true introduction to nutrition that you will read with pleasure and real understanding. It will free you from dependence on popular sources of information - often misinformation - so you can distinguish illusion from …
Network Hamiltonian Models Reveal Pathways To Amyloid Fibril Formation, Yue Yu, Gianmarc Grazioli, Megha H. Unhelkar, Rachel W. Martin, Carter T. Butts
Network Hamiltonian Models Reveal Pathways To Amyloid Fibril Formation, Yue Yu, Gianmarc Grazioli, Megha H. Unhelkar, Rachel W. Martin, Carter T. Butts
Faculty Research, Scholarly, and Creative Activity
Amyloid fibril formation is central to the etiology of a wide range of serious human diseases, such as Alzheimer’s disease and prion diseases. Despite an ever growing collection of amyloid fibril structures found in the Protein Data Bank (PDB) and numerous clinical trials, therapeutic strategies remain elusive. One contributing factor to the lack of progress on this challenging problem is incomplete understanding of the mechanisms by which these locally ordered protein aggregates self-assemble in solution. Many current models of amyloid deposition diseases posit that the most toxic species are oligomers that form either along the pathway to forming fibrils or …
Lc-Ms/Ms Method Development For The Quantitation Of Methylmalonic Acid Using Aqueous Normal Phase Chromatography, Daniel Joseph Biocini
Lc-Ms/Ms Method Development For The Quantitation Of Methylmalonic Acid Using Aqueous Normal Phase Chromatography, Daniel Joseph Biocini
Master's Theses
The aim of the study was to develop a quantitative assay for methylmalonic acid (MMA), an important biomarker for clinical diagnosis of vitamin B12 (B12) deficiency. The techniques of liquid chromatography and tandem mass spectrometry (LC-MS/MS) are used for separation and quantitation of MMA, as well as its endogenous isomer succinic acid. The MS/MS method was developed using an infusion set-up and manual tuning experiments. Relevant transitions were detected for the two analytes and MMA-d3, then a preliminary MS/MS method was developed. The preliminary LC method was further optimized. Various gradients, mobile phases (MPs), and additive combinations were used across …
Identification Of The New Isotope 244Md, J. L. Pore, J. M. Gates, R. Orford, C. M. Campbell, R. M. Clark, H. L. Crawford, N. E. Esker, P. Fallon, J. A. Gooding, J. T. Kwarsick, A. O. Macchiavelli, C. Morse, D. Rudolph, A. Såmark-Roth, C. Santamaria, R. S. Shah, M. A. Stoyer
Identification Of The New Isotope 244Md, J. L. Pore, J. M. Gates, R. Orford, C. M. Campbell, R. M. Clark, H. L. Crawford, N. E. Esker, P. Fallon, J. A. Gooding, J. T. Kwarsick, A. O. Macchiavelli, C. Morse, D. Rudolph, A. Såmark-Roth, C. Santamaria, R. S. Shah, M. A. Stoyer
Faculty Research, Scholarly, and Creative Activity
In an experiment performed at Lawrence Berkeley National Laboratory's 88-inch cyclotron, the isotope Md244 was produced in the Bi209(Ar40,5n) reaction. Decay properties of Md244 were measured at the focal plane of the Berkeley Gas-filled Separator, and the mass number assignment of A=244 was confirmed with the apparatus for the identification of nuclide A. The isotope Md244 is reported to have one, possibly two, α-decaying states with α energies of 8.66(2) and 8.31(2) MeV and half-lives of 0.4-0.1+0.4 and ∼6 s, respectively. Additionally, first evidence of the α decay of Bk236 was observed and is reported.
Evaluation Of Silica Hydride Based Amide Stationary Phase For High Performance Liquid Chromatography And Aqueous Normal Phase Separations, Emma Tardiff
Master's Theses
With many modern chromatographic advancements, silica hydride based columns (also known commercially as Type-C) represent yet another evolutionary step in stationary phase development. Type-C silica hydride columns have the ability to retain both polar and nonpolar analytes and have the ability to behave in either RP or ANP modes of separation depending on mobile phase composition. A consequence of this increased stability is that Type-C columns can be used over a wide range of mobile phase compositions, from purely aqueous to purely nonpolar organic solvents, and any combination of the two. While the retention behavior of Type-C columns depends highly …
Global H-Ns Counter-Silencing By Luxr Activates Quorum Sensing Gene Expression, Ryan R. Chaparian, Minh L.N. Tran, Laura C. Miller Conrad, Douglas B. Rusch, Julia C. Van Kessel
Global H-Ns Counter-Silencing By Luxr Activates Quorum Sensing Gene Expression, Ryan R. Chaparian, Minh L.N. Tran, Laura C. Miller Conrad, Douglas B. Rusch, Julia C. Van Kessel
Faculty Research, Scholarly, and Creative Activity
Bacteria coordinate cellular behaviors using a cell-cell communication system termed quorum sensing. In Vibrio harveyi, the master quorum sensing transcription factor LuxR directly regulates >100 genes in response to changes in population density. Here, we show that LuxR derepresses quorum sensing loci by competing with H-NS, a global transcriptional repressor that oligomerizes on DNA to form filaments and bridges. We first identified H-NS as a repressor of bioluminescence gene expression, for which LuxR is a required activator. In an hns deletion strain, LuxR is no longer necessary for transcription activation of the bioluminescence genes, suggesting that the primary role of …
Synthesis And Study Of Verdazyl Stable Free Radical Substituted Oligothiophenes For Magnetoresistive And Spintronic Properties, Amir Shakouri Mansouri
Synthesis And Study Of Verdazyl Stable Free Radical Substituted Oligothiophenes For Magnetoresistive And Spintronic Properties, Amir Shakouri Mansouri
Master's Theses
Interest in spin polarizing materials and their application in electronic devices in the field of spintronics has been steadily growing in recent years. The development of wholly organic spin polarizing materials has been of particular interest due to the material flexibility, solution processing, synthetic modifiability, and longer spin lifetimes of organics compared to inorganic analogs. One class of organic compounds with significant room for exploration is polyconjugated π systems coupled with stable radicals. We have explored the synthesis of oligothiophenes substituted with verdazyl stable free radicals with differing thiophene chain lengths, through a series of halogenation, borylation, and palladium catalyzed …
Synthesis And Evaluation Of Novel Silica Hydride-Based Stationary Phases For Bioanalytical Applications, Seiichiro Watanabe
Synthesis And Evaluation Of Novel Silica Hydride-Based Stationary Phases For Bioanalytical Applications, Seiichiro Watanabe
Master's Theses
Most HPLC columns are packed with silanol (Si-OH)-rich type-B silica that often participates in undesired electrostatic interactions with sample solutes and produces a poor analyte peak shape. These silanols are also known to facilitate the surface hydration required for HILIC mode to retain polar analytes. However, the hydrated surface composition can easily fluctuate, which results in poor reproducibility and requires a lengthy equilibration step. In this study, four novel stationary phases have been developed by using the TYPE-C™ silica material, in which up to 95% of the surface silanols have been replaced with Si-H group. One of the advantages of …
Computational Models Exploring The Role Of Flexibility In Binding Tat Peptide To Tar Rna, Thanh Quoc Le
Computational Models Exploring The Role Of Flexibility In Binding Tat Peptide To Tar Rna, Thanh Quoc Le
Master's Theses
Viral-encoded regulatory proteins interacting with RNA target sequences control the gene expression of lentiviruses, notably the human immunodeficiency virus (HIV) and bovine immunodeficiency virus (BIV). The latter provides a simpler interaction model between the viral trans-activator protein (Tat) and trans-activation response RNA element (TAR), including Tat peptides binding to TAR RNA fragments. This model may offer insights into clinical approaches for treatment, initially through theoretical consideration of the role of peptide flexibility in binding as evidenced by literature-based binding assays and NMR. It has more recently been suggested that DNA-protein binding may also be enhanced by increases in conformational entropy. …