26 results on '"Holder AJ"'
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2. An Amino Acid Substitution in Elongation Factor EF-G1A Alters the Antibiotic Susceptibility of Pseudomonas aeruginosa LasR-Null Mutants.
- Author
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Abisado-Duque RG, Townsend KA, Mckee BM, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen M, and Chandler JR
- Subjects
- Humans, Amino Acid Substitution, Trans-Activators genetics, Trans-Activators metabolism, Bacterial Proteins metabolism, Mutation, Tobramycin pharmacology, Tobramycin metabolism, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents metabolism, Quorum Sensing, Pseudomonas aeruginosa, Pseudomonas Infections microbiology
- Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum-sensing system to increase resistance to the aminoglycoside antibiotic tobramycin. Paradoxically, lasR -null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism that permits the emergence of lasR -null mutants under tobramycin selection. We hypothesized that some other genetic mutations that emerge in these isolates might modulate the effects of lasR -null mutations on antibiotic resistance. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. In some of these isolates, inactivating lasR further increased resistance, compared with decreasing resistance of the wild-type ancestor. These strain-dependent effects were due to a G61A nucleotide polymorphism in the fusA1 gene encoding amino acid substitution A21T in the translation elongation factor EF-G1A. The EF-G1A mutational effects required the MexXY efflux pump and the MexXY regulator ArmZ. The fusA1 mutation also modulated Δ lasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results identify a gene mutation that can reverse the direction of the antibiotic selection of lasR mutants, a phenomenon known as sign epistasis, and provide a possible explanation for the emergence of lasR -null mutants in clinical isolates. IMPORTANCE One of the most common mutations in Pseudomonas aeruginosa clinical isolates is in the quorum sensing lasR gene. In laboratory strains, lasR disruption decreases resistance to the clinical antibiotic tobramycin. To understand how lasR mutations emerge in tobramycin-treated patients, we mutated lasR in highly tobramycin-resistant laboratory strains and determined the effects on resistance. Disrupting lasR enhanced the resistance of some strains. These strains had a single amino acid substitution in the translation factor EF-G1A. The EF-G1A mutation reversed the selective effects of tobramycin on lasR mutants. These results illustrate how adaptive mutations can lead to the emergence of new traits in a population and are relevant to understanding how genetic diversity contributes to the progression of disease during chronic infections., Competing Interests: The authors declare no conflict of interest.
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- 2023
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3. Tobramycin adaptation alters the antibiotic susceptibility of Pseudomonas aeruginosa quorum sensing-null mutants.
- Author
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Abisado-Duquea RG, McKee BM, Townsend KA, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen MT, and Chandler JR
- Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum sensing system to increase resistance to the aminioglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism allowing the lasR-null mutants to persist under tobramycin selection. We hypothesized that the effects of inactivating lasR on tobramycin resistance might be dependent on the presence or absence of other gene mutations in that strain, a phenomenon known as epistasis. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. We show that the effects of ΔlasR on tobramycin resistance are strain dependent. The effects can be attributed to a point mutation in the gene encoding the translation elongation factor fusA1 (G61A nucleotide substitution), which confers a strong selective advantage to lasR-null PA14 under tobramycin selection. This fusA1 G61A mutation results in increased activity of the MexXY efflux pump and expression of the mexXY regulator ArmZ. The fusA1 mutation can also modulate ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results demonstrate the importance of epistatic gene interactions on antibiotic susceptibility of lasR-null mutants. These results support of the idea that gene interactions might play a significant role in the evolution of quorum sensing in P. aeruginosa.
- Published
- 2023
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4. Substantial yield reduction in sweet potato due to tropospheric ozone, the dose-response function.
- Author
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Holder AJ and Hayes F
- Subjects
- Chlorophyll, Plant Leaves chemistry, Air Pollutants analysis, Air Pollutants toxicity, Ipomoea batatas, Ozone analysis
- Abstract
Impacts of tropospheric ozone on sweet potato (Ipomoea batatas) are poorly understood despite being a staple food grown in locations deemed at risk from ozone pollution. Three varieties of sweet potato were exposed to ozone treatments (peaks of: 30 (Low), 80 (Medium), and 110 (High) ppb) using heated solardomes. Weekly measurements of stomatal conductance (gs) and chlorophyll content (CI) were used to determine physiological responses, along with final yield. gs and CI were reduced with increasing ozone exposure, but effects were partially masked due to elevated leaf senescence and turnover. Yield for the Erato orange and Murasaki varieties was reduced by ∼40% and ∼50% (Medium and High ozone treatments, respectively, vs Low) whereas Beauregard yield was reduced by 58% in both. The DO
3 SE (Deposition of Ozone for Stomatal Exchange) model was parameterized for gs in response to light, temperature, vapour pressure deficit and soil water potential. Clear responses of gs to the environmental parameters were found. Yield reductions were correlated with both concentration based AOT40 (accumulated ozone above a threshold of 40 ppb) and flux based POD6 (accumulated stomatal flux of ozone above a threshold of 6 nmol m- 2 s- 1 ) metrics (R2 0.66 p = 0.01; and R2 0.44 p = 0.05, respectively). A critical level estimate of a POD6 of 3 (mmol m-2 Projected Leaf Area-1 ) was obtained using the relationship. This study showed that sweet potato yield was reduced by ozone pollution, and that stomatal conductance and chlorophyll content were also affected. Results from this study can improve model predictions of ozone impacts on sweet potato together with associated ozone risk assessments for tropical countries., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)- Published
- 2022
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5. Soil & Water Assessment Tool (SWAT) simulated hydrological impacts of land use change from temperate grassland to energy crops: A case study in western UK.
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Holder AJ, Rowe R, McNamara NP, Donnison IS, and McCalmont JP
- Abstract
When considering the large-scale deployment of bioenergy crops, it is important to understand the implication for ecosystem hydrological processes and the influences of crop type and location. Based on the potential for future land use change (LUC), the 10,280 km
2 West Wales Water Framework Directive River Basin District (UK) was selected as a typical grassland dominated district, and the Soil & Water Assessment Tool (SWAT) hydrology model with a geographic information systems interface was used to investigate implications for different bioenergy deployment scenarios. The study area was delineated into 855 sub-basins and 7,108 hydrological response units based on rivers, soil type, land use, and slope. Changes in hydrological components for two bioenergy crops ( Miscanthus and short rotation coppice, SRC) planted on 50% (2,192 km2 ) or 25% (1,096 km2 ) of existing improved pasture are quantified. Across the study area as a whole, only surface run-off with SRC planted at the 50% level was significantly impacted, where it was reduced by up to 23% (during April). However, results varied spatially and a comparison of annual means for each sub-basin and scenario revealed surface run-off was significantly decreased and baseflow significantly increased (by a maximum of 40%) with both Miscanthus and SRC. Evapotranspiration was significantly increased with SRC (at both planting levels) and water yield was significantly reduced with SRC (at the 50% level) by up to 5%. Effects on streamflow were limited, varying between -5% and +5% change (compared to baseline) in the majority of sub-basins. The results suggest that for mesic temperate grasslands, adverse effects from the drying of soil and alterations to streamflow may not arise, and with surface run-off reduced and baseflow increased, there could, depending on crop location, be potential benefits for flood and erosion mitigation., (© 2019 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd.)- Published
- 2019
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6. Measured and modelled effect of land-use change from temperate grassland to Miscanthus on soil carbon stocks after 12 years.
- Author
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Holder AJ, Clifton-Brown J, Rowe R, Robson P, Elias D, Dondini M, McNamara NP, Donnison IS, and McCalmont JP
- Abstract
Soil organic carbon (SOC) is an important carbon pool susceptible to land-use change (LUC). There are concerns that converting grasslands into the C
4 bioenergy crop Miscanthus (to meet demands for renewable energy) could negatively impact SOC, resulting in reductions of greenhouse gas mitigation benefits gained from using Miscanthus as a fuel. This work addresses these concerns by sampling soils (0-30 cm) from a site 12 years (T12 ) after conversion from marginal agricultural grassland into Miscanthus x giganteus and four other novel Miscanthus hybrids. Soil samples were analysed for changes in below-ground biomass, SOC and Miscanthus contribution to SOC (using a13 C natural abundance approach). Findings are compared to ECOSSE soil carbon model results (run for a LUC from grassland to Miscanthus scenario and continued grassland counterfactual), and wider implications are considered in the context of life cycle assessments based on the heating value of the dry matter (DM) feedstock. The mean T12 SOC stock at the site was 8 (±1 standard error) Mg C/ha lower than baseline time zero stocks (T0 ), with assessment of the five individual hybrids showing that while all had lower SOC stock than at T0 the difference was only significant for a single hybrid. Over the longer term, new Miscanthus C4 carbon replaces pre-existing C3 carbon, though not at a high enough rate to completely offset losses by the end of year 12. At the end of simulated crop lifetime (15 years), the difference in SOC stocks between the two scenarios was 4 Mg C/ha (5 g CO2 -eq/MJ). Including modelled LUC-induced SOC loss, along with carbon costs relating to soil nitrous oxide emissions, doubled the greenhouse gas intensity of Miscanthus to give a total global warming potential of 10 g CO2 -eq/MJ (180 kg CO2 -eq/Mg DM)., (© 2019 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd.)- Published
- 2019
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7. Soil N 2 O emissions with different reduced tillage methods during the establishment of Miscanthus in temperate grassland.
- Author
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Holder AJ, McCalmont JP, Rowe R, McNamara NP, Elias D, and Donnison IS
- Abstract
An increase in renewable energy and the planting of perennial bioenergy crops is expected in order to meet global greenhouse gas (GHG) targets. Nitrous oxide (N
2 O) is a potent greenhouse gas, and this paper addresses a knowledge gap concerning soil N2 O emissions over the possible "hot spot" of land use conversion from established pasture to the biofuel crop Miscanthus . The work aims to quantify the impacts of this land use change on N2 O fluxes using three different cultivation methods. Three replicates of four treatments were established: Miscanthus x giganteus (Mxg) planted without tillage; Mxg planted with light tillage; a novel seed-based Miscanthus hybrid planted with light tillage under bio-degradable mulch film; and a control of uncultivated established grass pasture with sheep grazing. Soil N2 O fluxes were recorded every 2 weeks using static chambers starting from preconversion in April 2016 and continuing until the end of October 2017. Monthly soil samples were also taken and analysed for nitrate and ammonium. There was no significant difference in N2 O emissions between the different cultivation methods. However, in comparison with the uncultivated pasture, N2 O emissions from the cultivated Miscanthus plots were 550%-819% higher in the first year (April to December 2016) and 469%-485% higher in the second year (January to October 2017). When added to an estimated carbon cost for production over a 10 year crop lifetime (including crop management, harvest, and transportation), the measured N2 O conversion cost of 4.13 Mg CO2 -eq./ha represents a 44% increase in emission compared to the base case. This paper clearly shows the need to incorporate N2 O fluxes during Miscanthus establishment into assessments of GHG balances and life cycle analysis and provides vital knowledge needed for this process. This work therefore also helps to support policy decisions regarding the costs and benefits of land use change to Miscanthus .- Published
- 2019
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8. Breakdown of a defensive symbiosis, but not endogenous defences, at elevated temperatures.
- Author
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Doremus MR, Smith AH, Kim KL, Holder AJ, Russell JA, and Oliver KM
- Subjects
- Animals, Aphids genetics, Aphids parasitology, Bacteriophages physiology, Enterobacteriaceae genetics, Enterobacteriaceae pathogenicity, Enterobacteriaceae virology, Genotype, Temperature, Aphids microbiology, Bacteriophages genetics, Ecosystem, Symbiosis genetics
- Abstract
Environmental factors, including temperature, can have large effects on species interactions, including mutualisms and antagonisms. Most insect species are infected with heritable bacterial symbionts with many protecting their hosts from natural enemies. However, many symbionts or their products are thermally sensitive; hence, their effectiveness may vary across a range of temperatures. In the pea aphid, Acyrthosiphon pisum, the bacterial symbiont Hamiltonella defensa and its associated APSE bacteriophages confer resistance to this aphid's dominant parasitoid, Aphidius ervi. Here, we investigate the effects of temperature on both endogenous and symbiont-based protection against this parasitoid. We also explored the defensive properties of the X-type symbiont, a bacterium hypothesized to shape aphid defence when co-occurring with H. defensa. We show that H. defensa protection fails at higher temperatures, although some aphid genotype and H. defensa strain combinations are more robust than others at moderately warmer temperatures. We also found that a single X-type strain neither defended against parasitism by A. ervi nor rescued lost H. defensa protection at higher temperatures. In contrast, endogenous aphid resistance was effective across temperatures, revealing that these distinct defensive modes are not equally robust to changing environments. Through a survey of field-collected pea aphids, we found a negative correlation between H. defensa frequencies and average daily temperatures across North American locales, fitting expectations for reduced symbiont benefits under warm climates. Based on these findings, we propose that rising global temperatures could promote the widespread breakdown of defensive mutualisms, a prospect with implications for both human and ecosystem health., (© 2017 John Wiley & Sons Ltd.)
- Published
- 2018
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9. Control of collagen gel mechanical properties through manipulation of gelation conditions near the sol-gel transition.
- Author
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Holder AJ, Badiei N, Hawkins K, Wright C, Williams PR, and Curtis DJ
- Abstract
The ability to control the mechanical properties of cell culture environments is known to influence cell morphology, motility, invasion and differentiation. The present work shows that it is possible to control the mechanical properties of collagen gels by manipulating gelation conditions near the sol gel transition. This manipulation is accomplished by performing gelation in two stages at different temperatures. The mechanical properties of the gel are found to be strongly dependent on the duration and temperature of the first stage. In the second stage the system is quickly depleted of free collagen which self assembles into a highly branched network characteristic of gelation at the higher temperature (37 °C). An important aspect of the present work is the use of advanced rheometric techniques to assess the transition point between viscoelastic liquid and viscoelastic solid behaviour which occurs upon establishment of a sample spanning network at the gel point. The gel time at the stage I temperature is found to indicate the minimum time that the gelling collagen sample must spend under stage I conditions before the two stage gelation procedure generates an enhancement of mechanical properties. Further, the Fractional Maxwell Model is found to provide an excellent description of the time-dependent mechanical properties of the mature collagen gels.
- Published
- 2018
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10. Ilko Dacowo: The practice of iatrogenic tooth enucleation.
- Author
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Holder AJ
- Subjects
- Humans, Iatrogenic Disease, Tooth Extraction
- Published
- 2016
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11. Redox non-innocence of thioether crowns: elucidation of the electronic structure of the mononuclear Pd(III) complexes [Pd([9]aneS3)2]3+ and [Pd([18]aneS6)]3+.
- Author
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Stephen E, Blake AJ, Carter E, Collison D, Davies ES, Edge R, Lewis W, Murphy DM, Wilson C, Gould RO, Holder AJ, McMaster J, and Schröder M
- Abstract
The Pd(II) complexes [Pd([9]aneS(3))(2)](PF(6))(2)·2MeCN (1) ([9]aneS(3) = 1,4,7-trithiacyclononane) and [Pd([18]aneS(6))](PF(6))(2) (2) ([18]aneS(6) = 1,4,7,10,13,16-hexathiacyclooctadecane) can be oxidized electrochemically or chemically oxidized with 70% HClO(4) to [Pd([9]aneS(3))(2)](3+) and [Pd([18]aneS(6))](3+), respectively. These centers have been characterized by single crystal X-ray diffraction, and by UV/vis and multifrequency electron paramagnetic resonance (EPR) spectroscopies. The single crystal X-ray structures of [Pd(III)([9]aneS(3))(2)](ClO(4))(6)·(H(3)O)(3)·(H(2)O)(4) (3) at 150 K and [Pd([18]aneS(6))](ClO(4))(6)·(H(5)O(2))(3) (4) at 90 K reveal distorted octahedral geometries with Pd-S distances of 2.3695(8), 2.3692(8), 2.5356(9) and 2.3490(6), 2.3454(5), 2.5474(6) Å, respectively, consistent with Jahn-Teller distortion at a low-spin d(7) Pd(III) center. The Pd(II) compound [Pd([9]aneS(3))(2)](PF(6))(2) shows a one-electron oxidation process in MeCN (0.2 M NBu(4)PF(6), 293 K) at E(1/2) = +0.57 V vs. Fc(+)/Fc assigned to a formal Pd(III)/Pd(II) couple. Multifrequency (Q-, X-, S-, and L-band) EPR spectroscopic analysis of [Pd([9]aneS(3))(2)](3+) and [Pd([18]aneS(6))](3+) gives g(iso) = 2.024, |A(iso(Pd))| = 18.9 × 10(-4) cm(-1); g(xx) = 2.046, g(yy) = 2.041, g(zz) = 2.004; |A(xx(Pd))| = 24 × 10(-4) cm(-1), |A(yy(Pd))| = 22 × 10(-4) cm(-1), |A(zz(Pd))| = 14 × 10(-4) cm(-1), |a(xx(H))| = 4 × 10(-4) cm(-1), |a(yy(H))| = 5 × 10(-4) cm(-1), |a(zz(H))| = 5.5 × 10(-4) cm(-1) for [Pd([9]aneS(3))(2)](3+), and g(iso) = 2.015, |A(iso(Pd))| = 18.8× 10(-4) cm(-1); g(xx) = 2.048 g(yy) = 2.036, g(zz) = 1.998; |a(xx(H))| = 5, |a(yy(H))| = 5, |a(zz(H))| = 6 × 10(-4) cm(-1); |A(xx(Pd))| = 23× 10(-4) cm(-1), |A(yy(Pd))| = 22 × 10(-4) cm(-1), |A(zz(Pd))| = 4 × 10(-4) cm(-1) for [Pd([18]aneS(6))](3+). Both [Pd([9]aneS(3))(2)](3+) and [Pd([18]aneS(6))](3+) exhibit five-line superhyperfine splitting in the g(zz) region in their frozen solution EPR spectra. Double resonance spectroscopic measurements, supported by density functional theory (DFT) calculations, permit assignment of this superhyperfine to through-bond coupling involving four (1)H centers of the macrocyclic ring. Analysis of the spin Hamiltonian parameters for the singly occupied molecular orbital (SOMO) in these complexes gives about 20.4% and 25% Pd character in [Pd([9]aneS(3))(2)](3+) and [Pd([18]aneS(6))](3+), respectively, consistent with the compositions calculated from scalar relativistic DFT calculations.
- Published
- 2012
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12. A quantum mechanical quantitative structure-property relationship study of the melting point of a variety of organosilicons.
- Author
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Liu Y and Holder AJ
- Subjects
- Freezing, Molecular Structure, Quantitative Structure-Activity Relationship, Transition Temperature, Models, Chemical, Quantum Theory, Silanes chemistry, Siloxanes chemistry
- Abstract
We have developed quantitative structure-property relationship (QSPR) models that correlate the melting points of chain and cyclic silanes and siloxanes with their molecular structures. A comprehensive correlation was derived for a variety of molecules, but the quality of the comprehensive model was modest at best. This provided the impetus for the development of two additional models focused on silanes and siloxanes, respectively. Statistical analyses confirm the robustness of the refined models, and the chemical interpretation of the descriptors was consistent with effects expected for melting., (Copyright © 2011 Elsevier Inc. All rights reserved.)
- Published
- 2011
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13. A quantum mechanical study of methacrylate free-radical polymerizations.
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Miller MD and Holder AJ
- Subjects
- Computer Simulation, Models, Chemical, Quantitative Structure-Activity Relationship, Quantum Theory, Thermodynamics, Free Radicals chemistry, Methacrylates chemistry, Polymerization
- Abstract
Theoretical calculations at the semiempirical and ab initio levels of theory have been completed for a series of methacrylate compounds reported in the literature as measured by pulsed-laser initiated polymerization in conjunction with size-exclusion chromatography (PLP-SEC). Modeling includes calculation of the Gibb's free energies (ΔG(‡)) and activation energies (E(a)). These results were then compared to experimental results. Semiempirical ΔG(‡) using AM1-CI calculations successfully predicted relative activation energies (R(2) = 0.89). HF and DFT methods more accurately predicted absolute activation energies, but the relative values were less reliable. Accurate quantitative structure property relationship (QSAR) models for propagation rate coefficients, k(p), were developed using AM1-CI and DFT. The semiempirical model included two charge descriptors, partial negatively charged surface area (PNSA), and minimum net atomic charge for oxygen (R(2) = 0.959). The DFT information, which included two quantum chemical descriptors (1-electron reactivity index for carbon and point charge component of the molecular dipole) calculated from the ground state structure, had improved statistics (R(2) = 0.979). A second DFT model is reported for 10 hydrocarbon methacrylate structures based on the 1-electron reactivity index for carbon (R(2) = 0.979). Theoretical results were also analyzed to provide an explanation for the unexpectedly large experimental k(p) values observed in the case of larger methacrylate monomers.
- Published
- 2010
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14. A quantum mechanical quantitative structure-activity relationship study of the flexural modulus of C, H, O, N-containing polymers.
- Author
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Holder AJ and Liu Y
- Subjects
- Elastic Modulus, Mechanical Phenomena, Pliability, Quantitative Structure-Activity Relationship, Static Electricity, Materials Testing methods, Models, Chemical, Polymers chemistry
- Abstract
Objective: The result of this research was to develop a quantum mechanically based QSAR model for polymer flexural modulus from structural features of small oligomers of the polymers. The final model was to have both explanatory power and be a reasonably accurate screening tool for new materials., Methods: A quantitative structure-activity relationship (QSAR) was developed using the CODESSA program from quantum mechanical information provided by the AM1 semiempirical method, as implemented in AMPAC., Results: A four-descriptor correlation equation with R(2)=0.91, also satisfying our other statistical criteria. A tetramer was determined to be a sufficient simulator for the polymer chain. The descriptors in the model show that rigidity of the monomer, electrostatic interactions and branching are the most important contributors to the flexural modulus value for a particular system., Significance: The QSAR model we have developed here is conceptually satisfying for flexural, and provides an easily usable tool for rational biomaterials design., (Copyright 2010 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2010
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15. Quantum mechanical quantitative structure-activity relationships to avoid mutagenicity.
- Author
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Holder AJ and Ye L
- Subjects
- Carbon chemistry, Composite Resins chemistry, Ethylene Oxide chemistry, Forecasting, Halogens chemistry, Humans, Hydroxides chemistry, Materials Testing, Molecular Conformation, Regression Analysis, Dental Materials chemistry, Epoxy Compounds chemistry, Models, Chemical, Mutagens chemistry, Quantitative Structure-Activity Relationship
- Abstract
Objective: The purpose of this work is to develop a quantum mechanically based quantitative structure-activity relationship (QMQSAR or QSAR hereafter) adequate to predict and explain Ames TA100-derived mutagenicities for a number of organic molecules., Methods: A set of 35 structurally similar molecules with epoxide (oxirane) functionalities and systematic, reliable experimental data were selected to construct a QSAR model. The SAM1 quantum mechanical method was used to perform conformational analysis and properties calculations. This QM information was used to compute a variety of descriptors. From this a two-descriptor regression model was constructed., Results: The two descriptors are ESP-HACA-1/TMSA and HOMO-LUMO energy gap. Statistical results for the model: R(2)=0.857, R(adj)(2)=0.818,R(cv)(2)=0.848,s(2)=0.0618. The variance inflation factor and significance for both descriptors were 1.082 and <0.001, respectively. The descriptors are related to transport across a membrane and to reactivity., Significance: The model we have presented here facilitates design of non-mutagenic monomers that may be useful for dental restorative composites. The model also serves as a screening tool for rating the mutagenicity of new candidate materials.
- Published
- 2009
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16. A semi-empirical computational model for the inhibition of porcine cholesterol esterase.
- Author
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Code JE, Perko KE, Yourtee DM, Holder AJ, and Kostoryz E
- Subjects
- Animals, Models, Molecular, Molecular Conformation, Quantitative Structure-Activity Relationship, Quantum Theory, Sterol Esterase metabolism, Computer Simulation, Sterol Esterase antagonists & inhibitors, Swine
- Abstract
Cholesterol esterase significantly contributes to cell membrane structure. It also facilitates transfer of cholesterol and phospholipids across membranes. Inhibition of this enzyme by a number of xenobiotics has been reported. This research sought to confirm if a widely used methacrylate monomer, bisphenol A dimethacrylate, inhibits porcine cholesterol esterase since this and other methacrylates are known to leach from various biomaterial preparations. A quantum mechanically developed computational chemistry model is presented. Specific chemical information linking potential mechanisms of cholesterol esterase inhibition to chemical structure is shown. Model chemical descriptors identified the importance of maximum oxygen valency and molecular shape/size to cholesterol esterase inhibition. A porcine cholesterol esterase inhibition mechanism is inherent in bisphenol A dimethacrylate which mimics chemical properties of reported cholesterol esterase inhibitors. This predictive semiempirical quantum mechanical model can be used to design new cholesterol esterase non-inhibitors for biocompatible biomaterials used in an aqueous environment.
- Published
- 2007
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17. Quantum-Mechanical QSPR Models for Polymerization Volume Change of Epoxides and Methacrylates Based on Mercury Dilatometry Results.
- Author
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Miller MD, Holder AJ, Kilway KV, Giese GJ, Finley JE, Travis DM, Iwai BT, and Eick JD
- Abstract
Polymerization volume change (PVC) was measured systematically using mercury dilatometry for 41 epoxide and methacrylate monomers with quartz filler. Quantitative structure property relationship (QSPR) models were developed based on this previously unreported data to gain insight in the data collection method for future models. Successful models included only data from those samples which polymerized to hardness. The most significant descriptors in these models related to monomer reactivity. In contrast, PVC data collected under experimental conditions which maximized monomer conversion resulted in descriptors describing size and branching, indicating conversion must be considered for future PVC measurements. A Rule of Mixtures (ROM) correction term improved correlations of the dilatometer data with varying quartz content, and an adjustment for conversion may similarly enable inclusion of data which had not polymerize to hardness.
- Published
- 2006
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18. An application of the QM-QSAR method to predict and rationalize lipophilicity of simple monomers.
- Author
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Holder AJ, Ye L, Yourtee DM, Agarwal A, Eick JD, and Chappelow CC
- Subjects
- Databases, Factual, Dental Materials toxicity, Materials Testing, Models, Chemical, Molecular Structure, Quantitative Structure-Activity Relationship, Quantum Theory, Solubility, Dental Materials chemistry, Lipids chemistry, Octanols chemistry
- Abstract
Objectives: The goal of this study is to develop a model used to predict octanol/water partition coefficients (log P(o/w)) values for a variety of potential dental materials. In this way, a primary consideration for potential toxicity and a rough estimate of solubility in various environments can be obtained., Method: The AM1 semiempirical quantum mechanical method (in AMPAC) was used to compute chemical data for all compounds in the study. CODESSA then imported the chemical information from AMPAC and computed a large set of informational descriptors. A quantitative structure activity relationship (QSAR) model was derived correlating experimental results from a training set of molecules with certain of the descriptors computed above., Results: A training set of 92 molecules was used to derive the QSAR model and three descriptors were obtained: the molecular surface area, the total dipole moment of the molecule, and FPSA-3 (fractional atom charge weighted partial positive surface area). Various quality indicators were also computed and all fell within acceptable ranges: R(2)=0.945; adjusted R(2)=0.943; R(cv)(2)=0.940; variance inflation factors (VIF) for the descriptors above are 1.116, 1.044, and 1.162, respectively., Significance: This QSAR model can be used to accurately and rapidly predict log P(o/w) values for a wide variety of small organic molecules, including potential dental monomers.
- Published
- 2005
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19. Quantum mechanical structure-activity relationship analyses for skin sensitization.
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Miller MD, Yourtee DM, Glaros AG, Chappelow CC, Eick JD, and Holder AJ
- Subjects
- Risk Assessment, Hypersensitivity immunology, Models, Immunological, Quantitative Structure-Activity Relationship, Quantum Theory, Skin immunology
- Abstract
Allergic contact dermatitis (ACD) results in inflammation of the skin due to sensitization of the immunologic system to a particular substance. The sensitization process is limited by the compound's ability to both permeate and react with proteins in the integumentary system. Currently, only in vivo animal tests such as the local lymph node assay (LLNA) are recognized by regulatory authorities for risk assessment of ACD. A quantitative structure-activity relationship has been developed to predict relative potency, which allows for the prediction of relative sensitization potentials. The experimental values used in this study include EC3 values (the concentration at which the stimulation index equals 3) from LLNA tests. The predictions in this model enable categorization of the compounds into three groups on the basis of risk of sensitization and enable screening of candidate molecules using rapid SAM1 semiempirical calculations prior to animal testing. The model may also be used to reduce the number of animals subjected to testing by providing estimated concentrations required for useful data of risk assessment. The effect of averaging available literature values on predictive ability is also investigated. The model includes halogenated compounds, aromatic compounds, alcohols, aldehydes, and ketones. The computational investigation resulted in a two-descriptor model that is consistent with the assumed mechanism for sensitization.
- Published
- 2005
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20. Rational design of dental materials using computational chemistry.
- Author
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Holder AJ and Kilway KV
- Subjects
- Combinatorial Chemistry Techniques, Drug Design, Informatics, Models, Chemical, Molecular Structure, Quantitative Structure-Activity Relationship, Quantum Theory, Dental Materials chemistry
- Abstract
One of our primary research emphases is the rational design of biomaterials. In this effort we apply a combination of theoretical and experimental approaches, both of which contribute directly to the completion of such a project. Computational chemistry has achieved routine status in modern chemical investigations, and the state-of-the-art is briefly summarized. In such a difficult endeavor as the systematic development of biomaterials, computational chemistry is a natural partner for traditional chemists. Herein, we describe several successful applications of this synergy to the design of dental biomaterials. These include reactivity modeling, sensitization, and density. We also report preliminary progress of polymerization volume change experiments on epoxides that have been specifically designed to provide standardized results for computational analysis.
- Published
- 2005
- Full Text
- View/download PDF
21. Chain melting temperature estimation for phosphatidyl cholines by quantum mechanically derived quantitative structure property relationships.
- Author
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Holder AJ, Yourtee DM, White DA, Glaros AG, and Smith R
- Subjects
- Calorimetry, Differential Scanning, Chemical Phenomena, Chemistry, Physical, Models, Chemical, Molecular Conformation, Phosphatidylcholines chemistry, Quantitative Structure-Activity Relationship, Temperature
- Abstract
Geometries for 62 phosphatidylcholines (PC) were optimized using the AM1 semiempirical quantum mechanical method. Results obtained from these calculations were used to calculate 463 descriptors for each molecule. Quantitative Structure Property Relationships (QSPR) were developed from these descriptors to predict chain melting temperatures (Tm) for the 41 PCs in the training set. After screening each QSPR for statistical validity, the Tm values predicted by each statistically valid QSPR were compared to corresponding Tm values extracted from the literature. The most predictive, chemically meaningful QSPR provided Tm values which agreed with literature values to within experimental error. This QSPR was used to predict Tm values for the remaining 21 PCs to provide external validation for the model. These values also agreed with literature values to within experimental error. The descriptor developed by the final QSPR was the second order average information content, a topological information-theoretical descriptor.
- Published
- 2003
- Full Text
- View/download PDF
22. Remarkable structures of cyclotri(deoxycholate) and cyclotetra(24-norcholate) acetate esters.
- Author
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Dias JR, Pascal RA Jr, Morrill J, Holder AJ, Gao H, and Barnes C
- Subjects
- Acetates chemistry, Biocompatible Materials chemical synthesis, Cholates chemical synthesis, Crystallography, X-Ray, Esters chemical synthesis, Models, Molecular, Molecular Structure, Biocompatible Materials chemistry, Cholates chemistry, Esters chemistry
- Abstract
X-ray crystallographic determinations and AM1 calculations have defined the solid-state and gas-phase structures of cyclotri(deoxycholate) and cyclotetra(24-norcholate). The latter cyclotetramer is one of the largest open macrocycles ever subjected to crystallography.
- Published
- 2002
- Full Text
- View/download PDF
23. Quantum mechanical quantitative structure activity relationships to avoid mutagenicity in dental monomers.
- Author
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Yourtee D, Holder AJ, Smith R, Morrill JA, Kostoryz E, Brockmann W, Glaros A, Chappelow C, and Eick D
- Subjects
- Dose-Response Relationship, Drug, Methacrylates chemistry, Models, Chemical, Mutagenicity Tests, Quantum Theory, Software, Structure-Activity Relationship, Dental Enamel chemistry, Mutagens
- Abstract
The objective of this study was to identify through quantum mechanical quantitative structure activity relationships (Q-QSARs) chemical structures in dental monomers that influence their mutagenicity. AMPAC, a semiempirical computer program that provides quantum mechanical information for chemical structures, was applied to three series of reference chemicals: a set of methacrylates, a set of aromatic and a set of aliphatic epoxy compounds. QSAR models were developed using this chemical information together with mutagenicity data (Salmonella TA 100, Ames Test). CODESSA, a QSAR program that calculates quantum chemical descriptors from information generated by AMPAC and statistically matches these descriptors with observed biological properties was used. QSARs were developed which had r2 values exceeding 0.90 for each study series. These QSARs were used to accurately predict the mutagenicity of BISGMA. a monomer commonly used in dentistry, and two epoxy monomers with developing use in dentistry, GY-281 and UVR-6105. The Q-QSAR quantum mechanical descriptors correctly predicted the level of mutagenicity for all three compounds. The descriptors in the correlation equation pointed to components of structure that may contribute to mutagenesis. The QSARs also provided 'dose windows' for testing mutagenicity, circumventing the need for extensive dose exploration in the laboratory. The Q-QSAR method promises an approach for biomaterials scientists to predict and avoid mutagenicity from the chemicals used in new biomaterial designs.
- Published
- 2001
- Full Text
- View/download PDF
24. Semiempirical and ab initio conformational analysis of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane with application of GIAO-SCF methods to NMR spectrum interpretation.
- Author
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Harris CD, Holder AJ, Eick JD, Chappelow CC, and Stansbury JW
- Subjects
- Magnetic Resonance Spectroscopy methods, Models, Molecular, Molecular Conformation, Spiro Compounds analysis, Spiro Compounds chemistry
- Abstract
The GIAO-SCF method for calculating isotropic nuclear magnetic shielding values has been utilized to explain certain features in the 1H-NMR spectrum of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane. Population distributions of the low-energy conformers based on their ab initio energies were used to produce weighting factors for the individual calculated shielding values to calculate the weighted average of the shielding values for a complete set of conformers. The differences in 1H chemical shifts between the hydrogens of the two methyl groups and between the axial and equatorial hydrogens in 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane were shown to be due to energy differences between the chair and boat orientations of the six-membered ring and contribution from a twist-boat conformation. Results suggest a hypothesis that intramolecular differences in chemical shift might be calculated to a greater degree of accuracy than chemical shifts calculated relative to a standard.
- Published
- 2000
- Full Text
- View/download PDF
25. Evaluation of quantitative structure property relationships necessary for enantioresolution with lambda- and sulfobutylether lambda-carrageenan in capillary electrophoresis.
- Author
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Beck GM, Neau SH, Holder AJ, and Hemenway JN
- Subjects
- Adrenergic beta-Antagonists chemistry, Adrenergic beta-Antagonists isolation & purification, Ethers chemistry, Quantitative Structure-Activity Relationship, Stereoisomerism, Tryptophan analogs & derivatives, Tryptophan chemistry, Tryptophan isolation & purification, Carrageenan chemistry, Electrophoresis, Capillary methods
- Abstract
Lambda-carrageenan, a linear, high molecular weight sulfated polysaccharide, was successfully employed in both its native and sulfobutyl derivatized form as a chiral selector in capillary electrophoresis for the separation of enantiomers of basic pharmaceutical compounds. In order to characterize the chiral selectivity properties of this chiral selector, various structurally related racemic compounds were analyzed for enantiomeric interactions using capillary electrophoresis. The results of these studies were then rationalized and analyzed utilizing a general quantitative structure-property relationship (QSPR) evaluation in order to predict critical analyte structural requirements for successful enantiomeric separation. Important structural components of the analytes were found to include the aromatic content, the type of substitution on the aromatic ring, presence of a primary or secondary protonated amine, and an overall positive charge to the molecule., (Copyright 2000 Wiley-Liss, Inc.)
- Published
- 2000
- Full Text
- View/download PDF
26. A semiempirical computational investigation of the antipsoriatic drug anthralin.
- Author
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Holder AJ and Upadrashta SM
- Subjects
- Anthralin therapeutic use, Molecular Structure, Anthralin chemistry, Psoriasis drug therapy
- Abstract
A series of computational studies was carried out, by using the highly successful Austin Model 1 (AM1) semiempirical method, to illuminate more completely the fundamental, molecular-level forces that affect the function and utility of the antipsoriatic drug anthralin. First, examination of the keto-enol tautomeric equilibrium by AM1 showed that the keto tautomer of the drug is 9.5 kcal/mol more stable than the enol form. Strong electrostatic forces involving the hydrogens on the hydroxy groups (a partial charge of +0.25 in both forms) and the keto oxygen (a partial charge of -0.40) apparently overcome the effects of the increased aromatic stabilization present in the enol form. Second, AM1 was applied to the degradation products of anthralin, 1,8-dihydroxy-9,10-anthraquinone, 1,8,1',8'-tetrahydroxy-10,10'-dianthrone, and a further oxidized form of the dimer. These molecules have been implicated in some of the unpleasant side effects of anthralin. Third, AM1 was used to predict the preferred site of ionization of anthralin.
- Published
- 1992
- Full Text
- View/download PDF
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