Prevalence of Chlamydophila psittaci in wild birds—potential risk for domestic poultry, pet birds, and public health?

To determine the prevalence of Chlamydophila psittaci in wild birds, cloacal swabs from 527 songbirds, 442 waterfowl, 84 feral pigeons, and 38 cormorants were examined by Chlamydiaceae-specific real-time polymerase chain reaction (PCR) and ArrayTube microarray assays for chlamydial species determination and genotyping of C. psittaci. Inconclusive cases were further characterized by conventional PCR methods targeting the chlamydial outer membrane protein A, 16S, 23S, and intergenic spacer genes followed by sequencing of the PCR product. Swabs of 19 water birds (tufted ducks and pochards), 12 pigeons, and one songbird were tested positive by the Chlamydiaceae-specific real-time PCR. While C. psittaci genotypes B (n = 5) and E (n = 1) were identified in feral pigeons (n = 9), the genotype could not be identified in the remaining three cases. Sequence data of Chlamydiaceae-positive cases (n = 23; 19 waterfowl, three pigeons, one songbird) indicated the presence of nonclassified chlamydial agents (n = 20) and C. psittaci (n = 3) by 16S rRNA PCR and sequencing. In conclusion, C. psittaci was not detected in waterfowl and songbirds, but C. psittaci proved prevalent in urban feral pigeons, where it poses a significant risk for human

Mesoscale Numerical Investigations of Air Traffic Emissions over the North Atlantic during SONEX Flight 8: A Case Study

Chemical data from flight 8 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) exhibited signatures consistent with aircraft emissions, stratospheric air, and surface-based pollution. These signatures are examined in detail, focussing on the broad aircraft emission signatures that are several hundred kilometers in length. A mesoscale meteorological model provides high resolution wind data that are used to calculate backward trajectories arriving at locations along the flight track. These trajectories are compared to aircraft locations in the North Atlantic Flight Corridor over a 27-33 hour period. Time series of flight level NO and the number of trajectory/aircraft encounters within the NAFC show excellent agreement. Trajectories arriving within the stratospheric and surface-based pollution regions are found to experience very few aircraft encounters. Conversely, there are many trajectory/aircraft encounters within the two chemical signatures corresponding to aircraft emissions. Even many detailed fluctuations of NO within the two aircraft signature regions correspond to similar fluctuations in aircraft encountered during the previous 27-33 hours. Results indicate that high resolution meteorological modeling, when coupled with detailed aircraft location data, is useful for understanding chemical signatures from aircraft emissions at scales of several hundred kilometers

Apportioning sources of organic matter in streambed sediments: An integrated molecular and compound-specific stable isotope approach

We present a novel application for quantitatively apportioning sources of organic matter in streambed sediments via a coupled molecular and compound-specific isotope analysis (CSIA) of long-chain leaf wax n-alkane biomarkers using a Bayesian mixing model. Leaf wax extracts of 13 plant species were collected from across two environments (aquatic and terrestrial) and four plant functional types (trees, herbaceous perennials, and C3 and C4 graminoids) from the agricultural River Wensum catchment, UK. Seven isotopic (δ13C27, δ13C29, δ13C31, δ13C27–31, δ2H27, δ2H29, and δ2H27–29) and two n-alkane ratio (average chain length (ACL), carbon preference index (CPI)) fingerprints were derived, which successfully differentiated 93% of individual plant specimens by plant functional type. The δ2H values were the strongest discriminators of plants originating from different functional groups, with trees (δ2H27–29 = − 208‰ to − 164‰) and C3 graminoids (δ2H27–29 = − 259‰ to − 221‰) providing the largest contrasts. The δ13C values provided strong discrimination between C3 (δ13C27–31 = − 37.5‰ to − 33.8‰) and C4 (δ13C27–31 = − 23.5‰ to − 23.1‰) plants, but neither δ13C nor δ2H values could uniquely differentiate aquatic and terrestrial species, emphasizing a stronger plant physiological/biochemical rather than environmental control over isotopic differences. ACL and CPI complemented isotopic discrimination, with significantly longer chain lengths recorded for trees and terrestrial plants compared with herbaceous perennials and aquatic species, respectively. Application of a comprehensive Bayesian mixing model for 18 streambed sediments collected between September 2013 and March 2014 revealed considerable temporal variability in the apportionment of organic matter sources. Median organic matter contributions ranged from 22% to 52% for trees, 29% to 50% for herbaceous perennials, 17% to 34% for C3 graminoids and 3% to 7% for C4 graminoids. The results presented here clearly demonstrate the effectiveness of an integrated molecular and stable isotope analysis for quantitatively apportioning, with uncertainty, plant-specific organic matter contributions to streambed sediments via a Bayesian mixing model approach

Atmospheric Chemical Transport Based on High Resolution Model- Derived Winds: A Case Study

Flight 10 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) extended southwest of Lajes, Azores. A variety of chemical signatures were encountered. These signatures are examined in detail, relating them to meteorological data from a high resolution numerical model having horizontal grid spacing of 30 and 90 km and 26 vertical levels. The meteorological output at hourly intervals is used to create backward trajectories from the locations of the chemical signatures. Four major categories of chemical signatures are discussed-stratospheric, lightning, continental pollution, and a transition layer. The strong stratospheric signal is encountered just south of the Azores in a region of depressed tropopause height. Three chemical signatures at different altitudes in the upper troposphere are attributed to lightning. Backward trajectories arriving at locations of these signatures are related to locations of cloud-to-ground lightning. Results show that the trajectories pass through regions of lightning 1-2 days earlier over the eastern Gulf of Mexico and off the southeast coast of the United States. The lowest leg of the flight exhibits a chemical signature consistent with continental pollution. Trajectories arriving at this signature are found to pass over the highly populated Northeast Corridor of the United States. Surface based pollution apparently is lofted to the altitudes of the trajectories by convective clouds along the East Coast that did not contain lightning. Finally, a chemical transition layer is described. Its chemical signature is intermediate to those of lightning and continental pollution. Trajectories arriving in this layer pass between the trajectories of the lightning and pollution signatures. Thus, they probably are impacted by both sources

Early anthropogenic impact on Western Central African rainforests 2,600 y ago

A potential human footprint on Western Central African rainforests before the Common Era has become the focus of an ongoing controversy. Between 3,000 y ago and 2,000 y ago, regional pollen sequences indicate a replacement of mature rainforests by a forest–savannah mosaic including pioneer trees. Although some studies suggested an anthropogenic influence on this forest fragmentation, current interpretations based on pollen data attribute the ‘‘rainforest crisis’’ to climate change toward a drier, more seasonal climate. A rigorous test of this hypothesis, however, requires climate proxies independent of vegetation changes. Here we resolve this controversy through a continuous 10,500-y record of both vegetation and hydrological changes from Lake Barombi in Southwest Cameroon based on changes in carbon and hydrogen isotope compositions of plant waxes. δ¹³C-inferred vegetation changes confirm a prominent and abrupt appearance of C4 plants in the Lake Barombi catchment, at 2,600 calendar years before AD 1950 (cal y BP), followed by an equally sudden return to rainforest vegetation at 2,020 cal y BP. δD values from the same plant wax compounds, however, show no simultaneous hydrological change. Based on the combination of these data with a comprehensive regional archaeological database we provide evidence that humans triggered the rainforest fragmentation 2,600 y ago. Our findings suggest that technological developments, including agricultural practices and iron metallurgy, possibly related to the large-scale Bantu expansion, significantly impacted the ecosystems before the Common Era

HO_x chemistry during INTEX-A 2004: Observation, model calculation, and comparison with previous studies

OH and HO_2 were measured with the Airborne Tropospheric Hydrogen Oxides Sensor (ATHOS) as part of a large measurement suite from the NASA DC-8 aircraft during the Intercontinental Chemical Transport Experiment-A (INTEX-A). This mission, which was conducted mainly over North America and the western Atlantic Ocean in summer 2004, was an excellent test of atmospheric oxidation chemistry. The HOx results from INTEX-A are compared to those from previous campaigns and to results for other related measurements from INTEX-A. Throughout the troposphere, observed OH was generally 0.95 of modeled OH; below 8 km, observed HO_2 was generally 1.20 of modeled HO_2. This observed-to-modeled comparison is similar to that for TRACE-P, another midlatitude study for which the median observed-to-modeled ratio was 1.08 for OH and 1.34 for HO_2, and to that for PEM-TB, a tropical study for which the median observed-to-modeled ratio was 1.17 for OH and 0.97 for HO_2. HO_2 behavior above 8 km was markedly different. The observed-to-modeled HO_2 ratio increased from ∼1.2 at 8 km to ∼3 at 11 km with the observed-to-modeled ratio correlating with NO. Above 8 km, the observed-to-modeled HO_2 and observed NO were both considerably greater than observations from previous campaigns. In addition, the observed-to-modeled HO_2/OH, which is sensitive to cycling reactions between OH and HO_2, increased from ∼1.5 at 8 km to almost 3.5 at 11 km. These discrepancies suggest a large unknown HO_x source and additional reactants that cycle HO_x from OH to HO_2. In the continental planetary boundary layer, the observed-to-modeled OH ratio increased from 1 when isoprene was less than 0.1 ppbv to over 4 when isoprene was greater than 2 ppbv, suggesting that forests throughout the United States are emitting unknown HO_x sources. Progress in resolving these discrepancies requires a focused research activity devoted to further examination of possible unknown OH sinks and HO_x sources

HOx Observation and Model Comparison During INTEX-A 2004

OH and HO2 were measured with the Airborne Tropospheric Hydrogen Oxides Sensor (ATHOS) as part of a large measurement suite from the NASA DC-8 aircraft during the Intercontinental Chemical Transport Experiment - A (INTEX-A). This mission, which was conducted mainly over North America and the western Atlantic Ocean in summer 2004, was an excellent test of atmospheric oxidation chemistry. Throughout the troposphere, observed OH was generally 0.60 of the modeled OH; below 8 km, observed HO2 was generally 0.78 of modeled HO2. If the over-prediction of tropospheric OH is not due to an instrument calibration error, then it implied less global tropospheric oxidation capacity and longer lifetimes for gases like methane and methyl chloroform than currently thought. This discrepancy falls well outside uncertainties in both the OH measurement and rate coefficients for known reactions and points to a large unknown OH loss. If the modeled OH is forced to agree with observed values by introducing of an undefined OH loss that removed HOx (HOx=OH+HO2), the observed and modeled HO2 and HO2/OH ratios are largely reconciled within the measurement uncertainty. HO2 behavior above 8 km was markedly different. The observed-to-modeled ratio correlating with NO. The observed-to-modeled HO2 ratio increased from approximately 1 at 8 km to more than approximately 2.5 at 11 km with the observed-to-modeled ratio correlating with NO. The observed-to-modeled HO2 and NO were both considerably greater than observations from previous campaigns. In addition, the observed-to-modeled HO2/OH, which is sensitive to cycling reactions between OH and HO2, increased from approximately 1.2 at 8 km to almost 4 above 11 km. In contrast to the lower atmosphere, these discrepancies above 8 km suggest a large unknown HOx source and additional reactants that cycle HOx from OH to HO2. In the continental planetary boundary layer, the OH observed-to-modeled ratio increased from 0.6 when isoprene was less than 0.1 ppbv to over 3 when isoprene was greater than 2 ppbv, suggesting that forests throughout the United States are emitting unknown HOx sources. Progress in resolving these discrepancies requires further examinations of possible unknown OH sinks and HOx sources and a focused research activity devoted to ascertaining the accuracy of the OH and HO2 measurements

Direct Measurements of the Convective Recycling of the Upper Troposphere

We present a statistical representation of the aggregate effects of deep convection on the chemistry and dynamics of the Upper Troposphere (UT) based on direct aircraft observations of the chemical composition of the UT over the Eastern United States and Canada during summer. These measurements provide new and unique observational constraints on the chemistry occurring downwind of convection and the rate at which air in the UT is recycled, previously only the province of model analyses. These results provide quantitative measures that can be used to evaluate global climate and chemistry models

Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk

BACKGROUND: Cytochrome P450 (CYP) enzymes have the potential to affect colorectal cancer (CRC) risk by determining the genotoxic impact of exogenous carcinogens and levels of sex hormones. METHODS: To investigate if common variants of CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1 and CYP19A1 influence CRC risk we genotyped 2,575 CRC cases and 2,707 controls for 20 single nucleotide polymorphisms (SNPs) that have not previously been shown to have functional consequence within these genes. RESULTS: There was a suggestion of increased risk, albeit insignificant after correction for multiple testing, of CRC for individuals homozygous for CYP1B1 rs162558 and heterozygous for CYP1A2 rs2069522 (odds ratio [OR] = 1.36, 95% confidence interval [CI]: 1.03-1.80 and OR = 1.34, 95% CI: 1.00-1.79 respectively). CONCLUSION: This study provides some support for polymorphic variation in CYP1A2 and CYP1B1 playing a role in CRC susceptibility