The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes

BACKGROUND: Many drugs of natural origin are hydrophobic and can pass through cell membranes. Hydrophobic molecules must be susceptible to active efflux systems if they are to be maintained at lower concentrations in cells than in their environment. Multi-drug resistance (MDR), often mediated by intrinsic membrane proteins that couple energy to drug efflux, provides this function. All eukaryotic genomes encode several gene families capable of encoding MDR functions, among which the ABC transporters are the largest. The number of candidate MDR genes means that study of the drug-resistance properties of an organism cannot be effectively carried out without taking a genomic perspective. RESULTS: We have annotated sequences for all 60 ABC transporters from the Caenorhabditis elegans genome, and performed a phylogenetic analysis of these along with the 49 human, 30 yeast, and 57 fly ABC transporters currently available in GenBank. Classification according to a unified nomenclature is presented. Comparison between genomes reveals much gene duplication and loss, and surprisingly little orthology among analogous genes. Proteins capable of conferring MDR are found in several distinct subfamilies and are likely to have arisen independently multiple times. CONCLUSIONS: ABC transporter evolution fits a pattern expected from a process termed 'dynamic-coherence'. This is an unusual result for such a highly conserved gene family as this one, present in all domains of cellular life. Mechanistically, this may result from the broad substrate specificity of some ABC proteins, which both reduces selection against gene loss, and leads to the facile sorting of functions among paralogs following gene duplication

Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences

India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia

Unimolecular decomposition kinetics of the stabilised Criegee intermediates CH₂OO and CD₂OO

Decomposition kinetics of stabilised CH2OO and CD2OO Criegee intermediates have been investigated as a function of temperature (450–650 K) and pressure (2–350 Torr) using flash photolysis coupled with time-resolved cavity-enhanced broadband UV absorption spectroscopy. Decomposition of CD2OO was observed to be faster than CH2OO under equivalent conditions. Production of OH radicals following CH2OO decomposition was also monitored using flash photolysis with laser-induced fluorescence (LIF), with results indicating direct production of OH in the v = 0 and v = 1 states in low yields. Master equation calculations performed using the Master Equation Solver for Multi-Energy well Reactions (MESMER) enabled fitting of the barriers for the decomposition of CH2OO and CD2OO to the experimental data. Parameterisations of the decomposition rate coefficients, calculated by MESMER, are provided for use in atmospheric models and implications of the results are discussed. For CH2OO, the MESMER fits require an increase in the calculated barrier height from 78.2 kJ mol−1 to 81.8 kJ mol−1 using a temperature-dependent exponential down model for collisional energy transfer with 〈ΔE〉down = 32.6(T/298 K)1.7 cm−1 in He. The low- and high-pressure limit rate coefficients are k1,0 = 3.2 × 10−4(T/298)−5.81exp(−12 770/T) cm3 s−1 and k1,∞ = 1.4 × 1013(T/298)0.06exp(−10 010/T) s−1, with median uncertainty of ∼12% over the range of experimental conditions used here. Extrapolation to atmospheric conditions yields k1(298 K, 760 Torr) = 1.1+1.5−1.1 × 10−3 s−1. For CD2OO, MESMER calculations result in 〈ΔE〉down = 39.6(T/298 K)1.3 cm−1 in He and a small decrease in the calculated barrier to decomposition from 81.0 kJ mol−1 to 80.1 kJ mol−1. The fitted rate coefficients for CD2OO are k2,0 = 5.2 × 10−5(T/298)−5.28exp(−11 610/T) cm3 s−1 and k2,∞ = 1.2 × 1013(T/298)0.06exp(−9800/T) s−1, with overall error of ∼6% over the present range of temperature and pressure. The extrapolated k2(298 K, 760 Torr) = 5.5+9.2−5.5 × 10−3 s−1. The master equation calculations for CH2OO indicate decomposition yields of 63.7% for H2 + CO2, 36.0% for H2O + CO and 0.3% for OH + HCO with no significant dependence on temperature between 400 and 1200 K or pressure between 1 and 3000 Torr

The impact of the third O-2 addition reaction network on ignition delay times of neo-pentane

We studied the oxidation of neo-pentane by combining experiments, theoretical calculations, and mechanistic developments to elucidate the impact of the 3rd O 2 addition reaction network on ignition delay time predictions. The experiments are based on photoionization mass spectrometry in jet-stirred and time-resolved flow reactors allowing for sensitive detection of the keto-hydroperoxide (KHP) and keto-dihydroperoxide (KDHP) intermediates. With neo-pentane exhibiting a unique symmetric molecular structure, which consequently results only in single KHP and KDHP isomers, theoretical calculations of ionization and fragment appearance energies and of absolute photoionization cross sections enabled the unambiguous identification and quantification of the KHP intermediate. Its temperature and time-resolved profiles together with calculated and experimentally observed KHP-to-KDHP signal ratios were compared to simulation results based on a newly developed mechanism that describes the 3rd O-2 addition reaction network. A satisfactory agreement has been observed between the experimental data points and the simulation results, thus adding confidence to the model's overall performance. Finally, this mechanism was used to predict ignition delay times reported previously in shock tube and rapid compression machine experiments (J. Bugler et al., Combust. Flame 163 (2016) 138-156). While the model accurately reproduces the experimental data, simulations with and without the 3rd O-2 addition reaction network included reveal only a negligible effect on the predicted ignition delay times at 10 and 20 atm. According to model calculations, low temperatures and high pressures promote the importance of the 3rd O-2 addition reactions. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.Peer reviewe

Time-resolved measurements of product formation in the low-temperature (550-675 K) oxidation of neopentane : a probe to investigate chain-branching mechanism

Product formation, in particular ketohydroperoxide formation and decomposition, were investigated in time-resolved, Cl-atom initiated neopentane oxidation experiments in the temperature range 550-675 K using a photoionization time-of-flight mass spectrometer. Ionization light was provided either by Advanced Light Source tunable synchrotron radiation or similar to 10.2 eV fixed energy radiation from a H-2-discharge lamp. Experiments were performed both at 1-2 atm pressure using a high-pressure reactor and also at similar to 9 Torr pressure employing a low-pressure reactor for comparison. Because of the highly symmetric structure of neopentane, ketohydroperoxide signal can be attributed to a 3-hydroperoxy-2,2-dimethylpropanal isomer, i.e. from a gamma-ketohydroperoxide (gamma-KHP). The photoionization spectra of the gamma-KHP measured at low-and high pressures and varying oxygen concentrations agree well with each other, further supporting they originate from the single isomer. Measurements performed in this work also suggest that the "Korcek" mechanism may play an important role in the decomposition of 3-hydroperoxy-2,2-dimethylpropanal, especially at lower temperatures. However, at higher temperatures where gamma-KHP decomposition to hydroxyl radical and oxy-radical dominates, oxidation of the oxy-radical yields a new important channel leading to acetone, carbon monoxide, and OH radical. Starting from the initial neopentyl + O-2 reaction, this channel releases altogether three OH radicals. A strongly temperature-dependent reaction product is observed at m/z = 100, likely attributable to 2,2-dimethylpropanedial.Peer reviewe

Seasonality of Formic Acid (HCOOH) in London during the ClearfLo Campaign

Following measurements in the winter of 2012, formic acid (HCOOH) and nitric acid (HNO3) were measured using a chemical ionization mass spectrometer (CIMS) during the Summer Clean Air for London (ClearfLo) campaign in London, 2012. Consequently, the seasonal dependence of formic acid sources could be better understood. A mean formic acid concentration of 1.3 ppb and a maximum of 12.7 ppb was measured which is significantly greater than that measured during the winter campaign (0.63 ppb and 6.7 ppb, respectively). Daily calibrations of formic acid during the summer campaign gave sensitivities of 1.2 ion counts s-1 parts per trillion (ppt) by volume-1 and a limit of detection of 34 ppt. During the summer campaign, there was no correlation between formic acid and anthropogenic emissions such as NOx and CO or peaks associated with the rush hour as was identified in the winter. Rather, peaks in formic acid were observed that correlated with solar irradiance. Analysis using a photochemical trajectory model has been conducted to determine the source of this formic acid. The contribution of formic acid formation through ozonolysis of alkenes is important but the secondary production from biogenic VOCs could be the most dominant source of formic acid at this measurement site during the summer

Direct kinetic measurements and theoretical predictions of an isoprene-derived Criegee intermediate

Isoprene has the highest emission into Earth’s atmosphere of any nonmethane hydrocarbon. Atmospheric processing of alkenes, including isoprene, via ozonolysis leads to the formation of zwitterionic reactive intermediates, known as Criegee intermediates (CIs). Direct studies have revealed that reactions involving simple CIs can significantly impact the tropospheric oxidizing capacity, enhance particulate formation, and degrade local air quality. Methyl vinyl ketone oxide (MVK-oxide) is a four-carbon, asymmetric, resonance-stabilized CI, produced with 21 to 23% yield from isoprene ozonolysis, yet its reactivity has not been directly studied. We present direct kinetic measurements of MVK-oxide reactions with key atmospheric species using absorption spectroscopy. Direct UV-Vis absorption spectra from two independent flow cell experiments overlap with the molecular beam UV-Vis-depletion spectra reported recently [M. F. Vansco, B. Marchetti, M. I. Lester, J. Chem. Phys. 149, 44309 (2018)] but suggest different conformer distributions under jet-cooled and thermal conditions. Comparison of the experimental lifetime herein with theory indicates only the syn-conformers are observed; anti-conformers are calculated to be removed much more rapidly via unimolecular decay. We observe experimentally and predict theoretically fast reaction of syn-MVK-oxide with SO₂ and formic acid, similar to smaller alkyl-substituted CIs, and by contrast, slow removal in the presence of water. We determine products through complementary multiplexed photoionization mass spectrometry, observing SO₃ and identifying organic hydroperoxide formation from reaction with SO₂ and formic acid, respectively. The tropospheric implications of these reactions are evaluated using a global chemistry and transport model

Direct kinetic measurements and theoretical predictions of an isoprene-derived Criegee intermediate

Isoprene has the highest emission into Earth’s atmosphere of any nonmethane hydrocarbon. Atmospheric processing of alkenes, including isoprene, via ozonolysis leads to the formation of zwitterionic reactive intermediates, known as Criegee intermediates (CIs). Direct studies have revealed that reactions involving simple CIs can significantly impact the tropospheric oxidizing capacity, enhance particulate formation, and degrade local air quality. Methyl vinyl ketone oxide (MVK-oxide) is a four-carbon, asymmetric, resonance-stabilized CI, produced with 21 to 23% yield from isoprene ozonolysis, yet its reactivity has not been directly studied. We present direct kinetic measurements of MVK-oxide reactions with key atmospheric species using absorption spectroscopy. Direct UV-Vis absorption spectra from two independent flow cell experiments overlap with the molecular beam UV-Vis-depletion spectra reported recently [M. F. Vansco, B. Marchetti, M. I. Lester, J. Chem. Phys. 149, 44309 (2018)] but suggest different conformer distributions under jet-cooled and thermal conditions. Comparison of the experimental lifetime herein with theory indicates only the syn-conformers are observed; anti-conformers are calculated to be removed much more rapidly via unimolecular decay. We observe experimentally and predict theoretically fast reaction of syn-MVK-oxide with SO₂ and formic acid, similar to smaller alkyl-substituted CIs, and by contrast, slow removal in the presence of water. We determine products through complementary multiplexed photoionization mass spectrometry, observing SO₃ and identifying organic hydroperoxide formation from reaction with SO₂ and formic acid, respectively. The tropospheric implications of these reactions are evaluated using a global chemistry and transport model