Promiscuous Partitioning of a Covalent Intermediate Common in the Pentein Superfamily

SummaryMany enzymes in the pentein superfamily use a transient covalent intermediate in their catalytic mechanisms. Here we trap and determine the structure of a stable covalent adduct that mimics this intermediate using a mutant dimethylarginine dimethylaminohydrolase and an alternative substrate. The interactions observed between the enzyme and trapped adduct suggest an altered angle of attack between the nucleophiles of the first and second half-reactions of normal catalysis. The stable covalent adduct is also capable of further reaction. Addition of imidazole rescues the original hydrolytic activity. Notably, addition of other amines instead yields substituted arginine products, which arise from partitioning of the intermediate into the evolutionarily related amidinotransferase reaction pathway. The enzyme provides both selectivity and catalysis for the amidinotransferase reaction, underscoring commonalities among the reaction pathways in this mechanistically diverse enzyme superfamily. The promiscuous partitioning of this intermediate may also help to illuminate the evolutionary history of these enzymes

Modeling organic aerosols in a megacity: potential contribution of semi-volatile and intermediate volatility primary organic compounds to secondary organic aerosol formation

It has been established that observed local and regional levels of secondary organic aerosols (SOA) in polluted areas cannot be explained by the oxidation and partitioning of anthropogenic and biogenic VOC precursors, at least using current mechanisms and parameterizations. In this study, the 3-D regional air quality model CHIMERE is applied to estimate the potential contribution to SOA formation of recently identified semi-volatile and intermediate volatility organic precursors (S/IVOC) in and around Mexico City for the MILAGRO field experiment during March 2006. The model has been updated to include explicitly the volatility distribution of primary organic aerosols (POA), their gas-particle partitioning and the gas-phase oxidation of the vapors. Two recently proposed parameterizations, those of Robinson et al. (2007) ("ROB") and Grieshop et al. (2009) ("GRI") are compared and evaluated against surface and aircraft measurements. The 3-D model results are assessed by comparing with the concentrations of OA components from Positive Matrix Factorization of Aerosol Mass Spectrometer (AMS) data, and for the first time also with oxygen-to-carbon ratios derived from high-resolution AMS measurements. The results show a substantial enhancement in predicted SOA concentrations (2–4 times) with respect to the previously published base case without S/IVOCs (Hodzic et al., 2009), both within and downwind of the city leading to much reduced discrepancies with the total OA measurements. Model improvements in OA predictions are associated with the better-captured SOA magnitude and diurnal variability. The predicted production from anthropogenic and biomass burning S/IVOC represents 40–60% of the total measured SOA at the surface during the day and is somewhat larger than that from commonly measured aromatic VOCs, especially at the T1 site at the edge of the city. The SOA production from the continued multi-generation S/IVOC oxidation products continues actively downwind. Similar to aircraft observations, the predicted OA/ΔCO ratio for the ROB case increases from 20–30 μg sm<sup>−3</sup> ppm<sup>−1</sup> up to 60–70 μg sm<sup>−3</sup> ppm<sup>−1</sup> between a fresh and 1-day aged air mass, while the GRI case produces a 30% higher OA growth than observed. The predicted average O/C ratio of total OA for the ROB case is 0.16 at T0, substantially below observed value of 0.5. A much better agreement for O/C ratios and temporal variability (<i>R</i><sup>2</sup>=0.63) is achieved with the updated GRI treatment. Both treatments show a deficiency in regard to POA ageing with a tendency to over-evaporate POA upon dilution of the urban plume suggesting that atmospheric HOA may be less volatile than assumed in these parameterizations. This study highlights the important potential role of S/IVOC chemistry in the SOA budget in this region, and highlights the need for further improvements in available parameterizations. The agreement observed in this study is not sufficient evidence to conclude that S/IVOC are the major missing SOA source in megacity environments. The model is still very underconstrained, and other possible pathways such as formation from very volatile species like glyoxal may explain some of the mass and especially increase the O/C ratio

The Dynamics of Sustained Reentry in a Loop Model with Discrete Gap Junction Resistance

Dynamics of reentry are studied in a one dimensional loop of model cardiac cells with discrete intercellular gap junction resistance ($R$). Each cell is represented by a continuous cable with ionic current given by a modified Beeler-Reuter formulation. For $R$ below a limiting value, propagation is found to change from period-1 to quasi-periodic ($QP$) at a critical loop length ($L_{crit}$) that decreases with $R$. Quasi-periodic reentry exists from $L_{crit}$ to a minimum length ($L_{min}$) that is also shortening with $R$. The decrease of $L_{crit}(R)$ is not a simple scaling, but the bifurcation can still be predicted from the slope of the restitution curve giving the duration of the action potential as a function of the diastolic interval. However, the shape of the restitution curve changes with $R$.Comment: 6 pages, 7 figure

Absence of lattice strain anomalies at the electronic topological transition in zinc at high pressure

High pressure structural distortions of the hexagonal close packed (hcp) element zinc have been a subject of controversy. Earlier experimental results and theory showed a large anomaly in lattice strain with compression in zinc at about 10 GPa which was explained theoretically by a change in Fermi surface topology. Later hydrostatic experiments showed no such anomaly, resulting in a discrepancy between theory and experiment. We have computed the compression and lattice strain of hcp zinc over a wide range of compressions using the linearized augmented plane wave (LAPW) method paying special attention to k-point convergence. We find that the behavior of the lattice strain is strongly dependent on k-point sampling, and with large k-point sets the previously computed anomaly in lattice parameters under compression disappears, in agreement with recent experiments.Comment: 9 pages, 6 figures, Phys. Rev. B (in press

Stochastic virtual tests for fiber composites

We will describe a Virtual Test system for continuous fiber composites. The virtual test draws from a new wave of advanced experiments and theory that address physical, mathematical, and engineering aspects of material definition and failure prediction. The methods go far beyond currently standard tests and conventional FEM analysis to challenge our conception of what can constitute a practicable engineering approach. Emphasis will be given to high temperature ceramic matrix composites with textile reinforcement, which have been the subject material of the National Hypersonic Science Center, Materials and Structures, a joint AFOSR/NASA program. However, thematic topics also address generic fiber composites. Development has been organized as a “pipeline” that links the separate disciplinary efforts of groups housed in seven institutions spread across the United States. The main research steps are: high resolution three-dimensional (3D) imaging of the microstructure, statistical characterization of the microstructure, formulation of a probabilistic generator for creating virtual specimens that replicate the measured statistics, creation of a computational model for a virtual specimen that allows general representation of discrete damage events, calibration of the model using room and high temperature tests, simulation of failure, and model validation. Key new experiments include digital surface image correlation and µm-resolution 3D computed tomography imaging of the microstructure and evolving damage, both executed at temperatures exceeding 1500°C. Conceptual advances include using both geometry and topology to characterize stochastic microstructures. Computational methods include new probabilistic algorithms for generating stochastic virtual specimens and a new Augmented Finite Element Method that yields extreme efficiency in dealing with arbitrary cracking in heterogeneous materials. The challenge of relating variance in engineering properties to stochastic microstructure in a computationally tractable manner, while retaining necessary physical details in models, will be discussed

Lunar and solar FTIR nitric acid measurements at Eureka in winter 2001/2002: comparisons with observations at Thule and Kiruna and with CMAM and SLIMCAT model calculations

For the first time, vertical column measurements of (HNO3) above the Arctic Stratospheric Ozone Observatory (AStrO) at Eureka (80N, 86W), Canada, have been made during polar night using lunar spectra recorded with a Fourier Transform Infrared (FTIR) spectrometer, from October 2001 to March 2002. AStrO is part of the primary Arctic station of the Network for the Detection of Stratospheric Change (NDSC). These measurements were compared with FTIR measurements at two other NDSC Arctic sites: Thule, Greenland (76.5N, 68.8W) and Kiruna, Sweden (67.8N, 20.4E). The measurements were also compared with two atmospheric models: the Canadian Middle Atmosphere Model (CMAM) and SLIMCAT. This is the first time that CMAM HNO3 columns have been compared with observations in the Arctic. Eureka lunar measurements are in good agreement with solar ones made with the same instrument. Eureka and Thule HNO3 columns are consistent within measurement error. Differences among HNO3 columns measured at Kiruna and those measured at Eureka and Thule can be explained on the basis of the available sunlight hours and the polar vortex location. The comparison of CMAM HNO3 columns with Eureka and Kiruna data shows good agreement, considering CMAM small inter-annual variability. The warm 2001/02 winter with almost no Polar Stratospheric Clouds (PSCs) makes the comparison of the warm climate version of CMAM with these observations a good test for CMAM under no PSC conditions. SLIMCAT captures the magnitude of HNO3 columns at Eureka, and the day-to-day variability, but generally reports higher HNO3 columns than the CMAM climatological mean columns

The lipids of the common house cricket,Acheta domesticus L. I. Lipid classes and fatty acid distribution

The lipids of the common house cricket,Acheta domesticus L., have been examined with the following results. The fatty acids associated with the lipid extracts do not change significantly from the third through the eleventh week of the crickets’ postembryonic life. The major fatty acids are linoleic (30–40%), oleic (23–27%), palmitic (24–30%), and stearic acids (7–11%). There are smaller amounts of palmitoleic (3–4%), myristic (∼1%), and linolenic acids (<1%). The fatty acid composition of the cricket lipids reflects but is not identical to the fatty acids of the dietary lipids: linoleic (53%), oleic (24%), palmitic (15%), stearic (3%), myristic (2%), and linolenic acid (2%).The amount of triglycerides present in the crickets increases steadily from the second through the seventh or eighth week of postembryonic life, then drops sharply. Other lipid classes, such as hydrocarbons, simple esters, diglycerides, monoglycerides, sterols, and free fatty acids remain about constant. The composition of the fatty acids associated with the tri‐, di‐, and monoglycerides and the free fatty acid fraction are all about the same. The fatty acids associated with the simple esters are high in stearic acid.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142007/1/lipd0247.pd

Experimental constraints on a dark matter origin for the DAMA annual modulation effect

A claim for evidence of dark matter interactions in the DAMA experiment has been recently reinforced. We employ a new type of germanium detector to conclusively rule out a standard isothermal galactic halo of Weakly Interacting Massive Particles (WIMPs) as the explanation for the annual modulation effect leading to the claim. Bounds are similarly imposed on a suggestion that dark pseudoscalars mightlead to the effect. We describe the sensitivity to light dark matter particles achievable with our device, in particular to Next-to-Minimal Supersymmetric Model candidates.Comment: v4: introduces recent results from arXiv:0807.3279 and arXiv:0807.2926. Sensitivity to pseudoscalars is revised in light of the first. Discussion on the subject adde