Rate constants for the reaction of NO and HO2 with peroxy radicals formed from the reaction of OH, Cl or NO3 with alkenes, dienes and α,β-unsaturated carbonyls

Rate constants for the gas-phase reaction of NO and HO2 radicals with 33 peroxy radicals are presented. The peroxy radicals are derived from the addition of either OH, Cl, or NO3 radicals, followed by addition of O2, to a series of alkenes: tetrachloroethene, ethene, 2,3-dimethyl but-2-ene, butadiene, 2,3,4,5-tetramethyl hexa-2,4-diene, 1,1,2,3,4,4-hexachlorobutadiene, but-1-ene-3-one (methyl vinyl ketone) and 2,3-dimethylpen-2-ene-4-one. The rate constants were predicted using a correlation between the singly occupied molecular orbital (SOMO) energy of the peroxy radical and the logarithm of the rate constant for reaction with NO or HO2. A discussion of the accuracy of the method and the trends in the reactivity of the titled peroxy radicals is given. Peroxy radicals derived from halogenated alkenes have larger values of rate constants for reaction with NO relative to reaction with HO2, indicating that they are more likely to react with NO, rather than HO2, in the atmosphere. The reverse is true for peroxy radicals derived from alkylated alkenes

Kinetics and mechanism of the reaction between atomic chlorine and dimethyl selenide; comparison with the reaction between atomic chlorine and dimethyl sulfide

Dimethyl selenide is the most abundant gaseous selenium species in marine environments. In this work, the value of the rate coefficient for the gas-phase reaction between dimethyl selenide and Cl atoms has been determined for the first time. The value of the second-order rate coefficient obtained was (5.0±1.4)×10–10 cm3 molecule–1 s–1. The very fast nature of the reaction means that, when estimating the lifetime of dimethyl selenide in the atmosphere, loss due to reaction with Cl atoms should be considered along with loss due to reaction with O3 and with OH and NO3 radicals. Analysis of the available kinetic data suggests that at 760 Torr the dominant reaction pathway for the reaction of Cl atoms with dimethyl selenide will be the addition of Cl to the Se atom forming an adduct of the type CH3Se(Cl)CH3. Theoretical calculations, at the B3LYP/6-311++G(2df,p)//B3LYP/6-311++G(d,p) level of theory, show that at 298 K the value of rH for the formation of the adduct is –111.4 kJ mol–1. This value may be compared to –97.0 kJ mol–1, the value calculated for rH for the formation of the analogous sulfur adduct, CH3S(Cl)CH3, following the reaction between Cl atoms and dimethyl sulfide. Variational RRKM theory was used to predict the thermal decomposition rates of the two adducts back to starting materials. The estimated rate constant for the decomposition of the selenium adduct to the reactants is 5×10–5 s–1, compared to 0.02 s–1 in the case of the sulfur adduct. However, our calculations suggest that the CH3Se(Cl)CH3 adduct, which is initially formed highly excited, will not be stabilised under atmospheric conditions, but rather will decompose to yield CH3SeCl and CH3, a process that is calculated to be exothermic with respect to the initial reactants by 5.8 kJ mol–1. The formation of CH3SCl and CH3 from the sulfur adduct, on the other hand, is endothermic by 20.8 kJ mol–1 with respect to the initial reactants, and is thus not expected to occur

Changes to DPPC domain structure in the presence of carbon nanoparticles

DPPC (dipalmitoylphosphatidylcholine) is a disaturated lipid capable of forming closely packed monolayers at the air–liquid interface of the lung and allows the surface tension within the alveoli to reduce to almost zero and thus prevent alveolar collapse. Carbon nanoparticles are formed in natural and man-made combustion events, including diesel engines, and are capable of reaching the alveolar epithelium during breathing. In this work, we have used Brewster angle microscopy and neutron reflectivity to study the effect of differing concentrations of carbon nanoparticles on the structure of DPPC monolayer as the monolayer is subject to compression and expansion. The results show that the inclusion of carbon nanoparticles within a DPPC monolayer affects the formation and structure of the lipid domains. The domains lose their circular structure and show a crenated structure as well as a reduction in overall size of the domains. This change in structure is also evident following expansion of the lipid monolayer, suggesting that some carbon nanoparticles may remain associated with the monolayer. This observation could have an important implication regarding the removal of nanosized airborne pollutants from the human lung

Hydrogen bonded complexes between nitrogen dioxide, nitric acid, nitrous acid and water with SiH3OH and Si(OH)4

The inter-conversion of nitrogen oxides and oxy acids on silica surfaces is of major atmospheric importance. As a preliminary step towards rationalising experimental observations, and understanding the mechanisms behind such reactions we have looked at the binding energies of NO2, N2O4, HNO3, HONO and H2O with simple proxies of a silica surface, namely SiH3OH and Si(OH)4 units. The geometries of these molecular clusters were optimised at both HF/6-311+G(d) and B3LYP/6-311+G(d) level of theory. The SCF energies of the species were determined at the HF/6-311++G(3df,2pd) and B3LYP/6-311++G(3df,2pd) level. The values indicate that nitric acid is by far the most strongly bound species, in agreement with experimental observations. It was also found that the dimer N2O4 is significantly more strongly bound to the Si(OH)4 and SiH3OH units than NO2 itself. The vibrational frequencies calculated for the hydrogen-bonded complexes are compared to the experimentally observed frequencies of the adsorbed species where possible

Proton transfer and tautomerism in 2-aminopurine–thymine and pyrrolocytosine–guanine base pairs

Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitively are not clear. To address this question ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T an alternative, stable, tautomer base pair was located in the first electronically excited state, however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations

The differential effects of low birth weight and Western diet consumption upon early life hepatic fibrosis development in guinea pig

Key points: Postnatal intake of a high saturated fat/high sugar diet, the Western diet (WD), is a risk factor for liver fibrosis. Recently, adverse in utero conditions resulting in low birth weight (LBW) have also been associated with postnatal fibrosis development. We demonstrate that suboptimal in utero conditions resulting in LBW are associated with changes in hepatic profibrotic genes in conjunction with minimal liver fibrosis in young non-overweight adult guinea pigs. Our results also indicate that WD promotes liver steatosis, enhanced expression of hepatic genes and proteins of the proinflammatory, profibrotic, cell death and collagen deposition pathways in conjunction with mild hepatic fibrosis. Our data highlight that pathways responsible for the initiation of a profibrotic state and ultimately hepatic fibrosis appear different depending upon the insult, an in utero-induced LBW outcome or a postnatal WD exposure. Postnatal intake of an energy dense diet, the Western diet (WD), is a strong risk factor for liver fibrosis. Recently, adverse in utero conditions resulting in low birth weight (LBW) have also been associated with postnatal fibrosis development. We assessed the independent and possible synergistic effects of placental insufficiency-induced LBW and postnatal WD consumption on liver fibrosis in early adulthood, with a specific focus on changes in inflammation and apoptosis pathways in association with fibrogenesis. Male LBW (uterine artery ablation) and normal birth weight (NBW) guinea pig pups were fed either a control diet (CD) or WD from weaning to 150 days. Significant steatosis, mild lobular inflammation, apoptosis and mild stage 1 fibrosis (perisinusoidal or portal) were evident in WD-fed offspring (NBW/WD and LBW/WD). In LBW/CD versus NBW/CD offspring, increased transforming growth factor-beta 1 and matrix metallopeptidase mRNA and sma- and Mad-related protein 4 (SMAD4) were present in conjunction with minimal stage 1 portal fibrosis. Further, connective tissue growth factor mRNA was increased and miR-146a expression decreased in LBW offspring, irrespective of diet. Independent of birth weight, WD-fed offspring exhibited increased expression of fibrotic genes as well as elevated inflammatory and apoptotic markers. Moreover, the augmented expression of collagen, type III, alpha 1 and tumor necrosis factor-alpha was associated with increased recruitment of RNA polymerase II and enhanced histone acetylation (K9) to their respective promoters. These data support a role for both LBW and postnatal WD as factors contributing to hepatic fibrosis development in offspring through distinct pathways

Why do models overestimate surface ozone in the Southeast United States

Ozone pollution in the Southeast US involves complex chemistry driven by emissions of anthropogenic nitrogen oxide radicals (NOx  ≡  NO + NO2) and biogenic isoprene. Model estimates of surface ozone concentrations tend to be biased high in the region and this is of concern for designing effective emission control strategies to meet air quality standards. We use detailed chemical observations from the SEAC4RS aircraft campaign in August and September 2013, interpreted with the GEOS-Chem chemical transport model at 0.25°  ×  0.3125° horizontal resolution, to better understand the factors controlling surface ozone in the Southeast US. We find that the National Emission Inventory (NEI) for NOx from the US Environmental Protection Agency (EPA) is too high. This finding is based on SEAC4RS observations of NOx and its oxidation products, surface network observations of nitrate wet deposition fluxes, and OMI satellite observations of tropospheric NO2 columns. Our results indicate that NEI NOx emissions from mobile and industrial sources must be reduced by 30–60 %, dependent on the assumption of the contribution by soil NOx emissions. Upper-tropospheric NO2 from lightning makes a large contribution to satellite observations of tropospheric NO2 that must be accounted for when using these data to estimate surface NOx emissions. We find that only half of isoprene oxidation proceeds by the high-NOx pathway to produce ozone; this fraction is only moderately sensitive to changes in NOx emissions because isoprene and NOx emissions are spatially segregated. GEOS-Chem with reduced NOx emissions provides an unbiased simulation of ozone observations from the aircraft and reproduces the observed ozone production efficiency in the boundary layer as derived from a regression of ozone and NOx oxidation products. However, the model is still biased high by 6 ± 14 ppb relative to observed surface ozone in the Southeast US. Ozonesondes launched during midday hours show a 7 ppb ozone decrease from 1.5 km to the surface that GEOS-Chem does not capture. This bias may reflect a combination of excessive vertical mixing and net ozone production in the model boundary layer

Mutations in Nonessential eIF3k and eIF3l Genes Confer Lifespan Extension and Enhanced Resistance to ER Stress in Caenorhabditis elegans

The translation initiation factor eIF3 is a multi-subunit protein complex that coordinates the assembly of the 43S pre-initiation complex in eukaryotes. Prior studies have demonstrated that not all subunits of eIF3 are essential for the initiation of translation, suggesting that some subunits may serve regulatory roles. Here, we show that loss-of-function mutations in the genes encoding the conserved eIF3k and eIF3l subunits of the translation initiation complex eIF3 result in a 40% extension in lifespan and enhanced resistance to endoplasmic reticulum (ER) stress in Caenorhabditis elegans. In contrast to previously described mutations in genes encoding translation initiation components that confer lifespan extension in C. elegans, loss-of-function mutations in eif-3.K or eif-3.L are viable, and mutants show normal rates of growth and development, and have wild-type levels of bulk protein synthesis. Lifespan extension resulting from EIF-3.K or EIF-3.L deficiency is suppressed by a mutation in the Forkhead family transcription factor DAF-16. Mutations in eif-3.K or eif-3.L also confer enhanced resistance to ER stress, independent of IRE-1-XBP-1, ATF-6, and PEK-1, and independent of DAF-16. Our data suggest a pivotal functional role for conserved eIF3k and eIF3l accessory subunits of eIF3 in the regulation of cellular and organismal responses to ER stress and agingNational Institutes of Health (U.S.) (Grant R01-GM084477)National Institutes of Health (U.S.) (Pre-Doctoral Training Grant T32GM007287

Intratumor Heterogeneity of the Estrogen Receptor and the Long-term Risk of Fatal Breast Cancer.

Background:Breast cancer patients with estrogen receptor (ER)-positive disease have a continuous long-term risk for fatal breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal breast cancer. Methods:The STO-3 trial enrolled 1780 postmenopausal lymph node-negative breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao's quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term breast cancer-specific survival analyses by intra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics. Results:A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P = .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] = 1.98, 95% confidence interval [CI] = 1.31 to 3.00; luminal A subtype tumors: HR = 2.43, 95% CI = 1.18 to 4.99). Conclusions:Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors

Does Type of Tumor Histology Impact Survival among Patients with Stage IIIB/IV Non-Small Cell Lung Cancer Treated with First-Line Doublet Chemotherapy?

Chemotherapy regimens may have differential efficacy by histology in nonsmall cell lung cancer (NSCLC). We examined the impact of histology on survival of patients (N = 2,644) with stage IIIB/IV NSCLC who received first-line cisplatin/carboplatin plus gemcitabine (C/C+G) and cisplatin/carboplatin plus a taxane (C/C+T) identified retrospectively in the SEER cancer registry (1997–2002). Patients with squamous and nonsquamous cell carcinoma survived 8.5 months and 8.1 months, respectively (P = .018). No statistically significant difference was observed in survival between C/C+G and C/C+T in both histologies. Adjusting for clinical and demographic characteristics, the effect of treatment regimen on survival did not differ by histology (P for interaction = .257). There was no statistically significant difference in hazard of death by histology in both groups. These results contrast the predictive role of histology and improved survival outcomes observed for cisplatin-pemetrexed regimens in advanced nonsquamous NSCLC