Genetic identification of unique immunological responses in mice infected with virulent and attenuated Francisella tularensis

Francisella tularensis is a category A select agent based on its infectivity and virulence but disease mechanisms in infection remain poorly understood. Murine pulmonary models of infection were therefore employed to assess and compare dissemination and pathology and to elucidate the host immune response to infection with the highly virulent Type A F. tularensis strain Schu4 versus the less virulent Type B live vaccine strain (LVS). We found that dissemination and pathology in the spleen was significantly greater in mice infected with F. tularensis Schu4 compared to mice infected with F. tularensis LVS. Using gene expression rofiling to compare the response to infection with the two F. tularensis strains, we found that there were significant differences in the expression of genes involved in the apoptosis pathway, antigen processing and presentation pathways, and inflammatory response pathways in mice infected with Schu4 when compared to LVS. These transcriptional differences coincided with marked differences in dissemination and severity of organ lesions in mice infected with the Schu4 and LVS strains. Therefore, these findings indicate that altered apoptosis, antigen presentation and production of inflammatory mediators explain the differences in pathogenicity of F. tularensis Schu4 and LVS

Molecular composition of organic aerosols in central Amazonia: An ultra-high-resolution mass spectrometry study

The Amazon Basin plays key role in atmospheric chemistry, biodiversity and climate change. In this study we applied nanoelectrospray (nanoESI) ultra-high-resolution mass spectrometry (UHRMS) for the analysis of the organic fraction of PM2.5 aerosol samples collected during dry and wet seasons at a site in central Amazonia receiving background air masses, biomass burning and urban pollution. Comprehensive mass spectral data evaluation methods (e.g. Kendrick mass defect, Van Krevelen diagrams, carbon oxidation state and aromaticity equivalent) were used to identify compound classes and mass distributions of the detected species. Nitrogen-and/or sulfur-containing organic species contributed up to 60% of the total identified number of formulae. A large number of molecular formulae in organic aerosol (OA) were attributed to later-generation nitrogen-and sulfur-containing oxidation products, suggesting that OA composition is affected by biomass burning and other, potentially anthropogenic, sources. Isoprene-derived organosulfate (IEPOX-OS) was found to be the most dominant ion in most of the analysed samples and strongly followed the concentration trends of the gas-phase anthropogenic tracers confirming its mixed anthropogenic-biogenic origin. The presence of oxidised aromatic and nitro-aromatic compounds in the samples suggested a strong influence from biomass burning especially during the dry period. Aerosol samples from the dry period and under enhanced biomass burning conditions contained a large number of molecules with high carbon oxidation state and an increased number of aromatic compounds compared to that from the wet period. The results of this work demonstrate that the studied site is influenced not only by biogenic emissions from the forest but also by biomass burning and potentially other anthropogenic emissions from the neighbouring urban environments. © 2016 Author(s)

Instrumentation and measurement strategy for the NOAA SENEX aircraft campaign as part of the Southeast Atmosphere Study 2013

Natural emissions of ozone-and-aerosol-precursor gases such as isoprene and monoterpenes are high in the southeastern US. In addition, anthropogenic emissions are significant in the southeastern US and summertime photochemistry is rapid. The NOAA-led SENEX (Southeast Nexus) aircraft campaign was one of the major components of the Southeast Atmosphere Study (SAS) and was focused on studying the interactions between biogenic and anthropogenic emissions to form secondary pollutants. During SENEX, the NOAA WP-3D aircraft conducted 20 research flights between 27 May and 10 July 2013 based out of Smyrna, TN. Here we describe the experimental approach, the science goals and early results of the NOAA SENEX campaign. The aircraft, its capabilities and standard measurements are described. The instrument payload is summarized including detection limits, accuracy, precision and time resolutions for all gas-and-aerosol phase instruments. The inter-comparisons of compounds measured with multiple instruments on the NOAA WP-3D are presented and were all within the stated uncertainties, except two of the three NO2 measurements. The SENEX flights included day- and nighttime flights in the southeastern US as well as flights over areas with intense shale gas extraction (Marcellus, Fayetteville and Haynesville shale). We present one example flight on 16 June 2013, which was a daytime flight over the Atlanta region, where several crosswind transects of plumes from the city and nearby point sources, such as power plants, paper mills and landfills, were flown. The area around Atlanta has large biogenic isoprene emissions, which provided an excellent case for studying the interactions between biogenic and anthropogenic emissions. In this example flight, chemistry in and outside the Atlanta plumes was observed for several hours after emission. The analysis of this flight showcases the strategies implemented to answer some of the main SENEX science questions.</p

Investigation of Photochemistry at High Latitudes: Comparison of model predictions to measurements of short lived species

Recent field campaigns have measured enhanced levels of NOx (NO+NO2) and HOx precursors (i.e., H2O2, CH2O, and HONO) that can not be accounted for by gas phase chemistry alone. Snowpack emission is now considered a source of these species. Therefore, the photochemistry in the polar boundary layer is now believed to be much more complex than initially thought. Field campaigns to Summit, Greenland in the summer of 2003 and the spring of 2004 have obtained the first measurements of peroxy (HO2+RO2) and hydroxyl (OH) radicals in the Artic boundary layer. Measurements were collected with a chemical ionization mass spectrometer (CIMS). A highly constrained (ie., O3, H2O, CH4, CO, j-values, NO, H2O2,CH2O, and HONO) 0-D steady-state model was employed in order to test our current understanding of photochemistry. HO2+RO2 measurements were in excellent agreement with model predictions for both spring and summer. OH measurements were in good agreement with spring model predictions but were a factor of two greater than summer model predictions. The role of snowpack emission is also addressed in a HOx budget performed on the spring campaign. Measurements of nitric acid (HNO3) and pernitric acid (HO2NO2) were obtained with the CIMS during the Antarctic Tropospheric Chemistry Investigation (ANTCI). The linkage between HOx and NOx chemistry is examined through partitioning of reactive nitrogen between HNO3 and HO2NO2. The possible impact of reactive nitrogen partitioning on nitrate ions (NO3-) at coring sites is also investigated.Ph.D.Committee Chair: Dr. Greg Huey; Committee Member: Dr. David Tan; Committee Member: Dr. Paul Wine; Committee Member: Dr. Robert Whetten; Committee Member: Dr. Rodney Webe

Sulfuric acid in the Amazon basin: measurements and evaluation of existing sulfuric acid proxies

Sulfuric acid is a key contributor to new particle formation, though measurements of its gaseous concentrations are difficult to make. Several parameterizations to estimate sulfuric acid exist, all of which were constructed using measurements from the Northern Hemisphere. In this work, we report the first measurements of sulfuric acid from the Amazon basin. These measurements are consistent with concentrations measured in Hyytiälä, Finland, though, unlike Hyytiälä, there is no clear correlation of sulfuric acid with global radiation. There was a minimal difference in sulfuric acid observed between the wet and dry seasons in the Amazon basin. We also test the efficacy of existing proxies to estimate sulfuric acid in this region. Our results suggest that nighttime sulfuric acid production is due to both a stabilized Criegee intermediate pathway and oxidation of SO2 by OH, the latter of which is not currently accounted for in existing proxies. These results also illustrate the drawbacks of the common substitution of radiation for OH concentrations. None of the tested proxies effectively estimate sulfuric acid measurements at night. For estimates at all times of day, a recently published proxy based on data from the boreal forest should be used. If only daytime estimates are needed, several recent proxies that do not include the Criegee pathway are sufficient. More investigation of nighttime sulfuric acid production pathways is necessary to close the gap between measurements and estimates with existing proxies.Institutional support for GoAmazon2014/5 was provided by the Central Office of the Large Scale Biosphere Atmosphere Experiment in Amazonia (LBA), the National Institute of Amazonian Research (INPA), and Amazonas State University (UEA) and the local Research Support Foundation (FAPEAM/GOAMAZON). We also acknowledge support from the Atmospheric Radiation Measurement (ARM) Climate Research Facility, a user facility of the United States Department of Energy, Office of Science, sponsored by the Office of Biological and Environmental Research, and support from the Atmospheric System Research (ASR; grant nos. DE-SC0011122 and DE-SC0019000) program of that office. James N. Smith acknowledges support from a Brazilian Science Mobility Program (Programa Ciência sem Fronteiras) Special Visiting Researcher Scholarship. Roger Seco acknowledges grants RYC2020-029216-I and CEX2018-000794-S funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. The authors would also like to thank Michelia Dam, Hayley Glicker, Adam Thomas, and Jeremy Wakeen, for their contributions to discussions regarding this project.Peer reviewe

Reclassification of Wolbachia persica as Francisella persica comb. nov and emended description of the family Francisellaceae

The taxonomic status of the bacterium Wolbachia persica is described, and based on the evidence presented, transfer of this species to the genus Francisella as Francisella persica comb. nov. is proposed. This reclassification is supported by data generated from genomic comparisons of W. persica ATCC VR-331(T) (=FSC845(T)=DSM 101678(T)) to other near neighbours, including Francisella tularensis subsp. novicida. The full-length 16S rRNA gene sequence of strain ATCC VR-331(T) had 98.5 % nucleotide identity to the cognate gene in F. tularensis, with the highest similarity to subspecies novicida. Phylogenetic trees of full-length 16S rRNA gene, gyrA and recA sequences from species of the genera Wolbachia (class Alphaproteobacteria) and Francisella (class Gammaproteobacteria) indicated that W. persica ATCC VR-331(T) was most closely related to members of the genus Francisella and not Wolbachia. Local collinear blocks within the chromosome of strain ATCC VR-331(T) had considerable similarity with F. tularensis subsp. novicida, but not with any Wolbachia strain. The genomes of strain ATCC VR-331(T) and F. tularensis subsp. novicida Utah 112(T) (=ATCC 15482(T)) contained an average nucleotide identity mean of 88.72 % and median of 89.18 %. Importantly, the genome of strain ATCC VR-331(T) contained one Francisella Pathogenicity Island, similar to F. tularensis subsp. novicida, as well as the Francisella-specific gene fopA1 and F. tularensis-specific genes fopA2 and lpnA (also referred to as tul4). In contrast to the obligate intracellular genus Wolbachia, strain ATCC VR-331(T) and facultative intracellular Francisella can replicate in specialized cell-free media. Collectively, these results demonstrate that Wolbachia persica should be reclassified in the genus Francisella as Francisella persica comb. nov. The type strain of Francisella persica comb. nov. is ATCC VR-331(T) (=FSC845(T)=DSM 101678(T)). An emended description of the family Francisellaceae is also provided

Chemical Production of Oxygenated Volatile Organic Compounds Strongly Enhances Boundary-Layer Oxidation Chemistry and Ozone Production

Photolysis of oxygenated volatile organic compounds (OVOCs) produces a primary source of free radicals, including OH and inorganic and organic peroxy radicals (HO2 and RO2), consequently increasing photochemical ozone production. The amplification of radical cycling through OVOC photolysis provides an important positive feedback mechanism to accelerate ozone production. The large production of OVOCs near the surface helps promote photochemistry in the whole boundary layer. This amplifier effect is most significant in regions with high nitrogen oxides (NOx) and VOC concentrations such as Wangdu, China. Using a 1-D model with comprehensive observations at Wangdu and the Master Chemical Mechanism (MCM), we find that OVOC photolysis is the largest free-radical source in the boundary layer (46%). The condensed chemistry mechanism we used severely underestimates the OVOC amplifier effect in the boundary layer, resulting in a lower ozone production rate sensitivity to NOx emissions. Due to this underestimation, the model-simulated threshold NOx emission value, below which ozone production decreases with NOx emission decrease, is biased low by 24%. The underestimated OVOC amplifier effect in a condensed mechanism implies a low bias in the current 3-D model-estimated efficacy of NOx emission reduction on controlling ozone in polluted urban and suburban regions of China

Secondary organic aerosol formation from ambient air in an oxidation flow reactor in central Amazonia

International audienceSecondary organic aerosol (SOA) formation from ambient air was studied using an oxidation flow reactor (OFR) coupled to an aerosol mass spectrometer (AMS) during both the wet and dry seasons at the Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) field campaign. Measurements were made at two sites down-wind of the city of Manaus, Brazil. Ambient air was oxidized in the OFR using variable concentrations of either OH or O 3 , over ranges from hours to days (O 3) or weeks (OH) of equivalent atmospheric aging. The amount of SOA formed in the OFR ranged from 0 to as much as 10 µg m −3 , depending on the amount of SOA precursor gases in ambient air. Typically, more SOA was formed during nighttime than daytime, and more from OH than from O 3 oxidation. SOA yields of individual organic precursors under OFR conditions were measured by standard addition into ambient air and were confirmed to be consistent with published environmental chamber-derived SOA yields. Positive matrix factoriza-tion of organic aerosol (OA) after OH oxidation showed formation of typical oxidized OA factors and a loss of primary Published by Copernicus Publications on behalf of the European Geosciences Union. 468 B. B. Palm et al.: SOA formation from ambient air in an oxidation flow reactor OA factors as OH aging increased. After OH oxidation in the OFR, the hygroscopicity of the OA increased with increasing elemental O : C up to O : C∼1.0, and then decreased as O : C increased further. Possible reasons for this decrease are discussed. The measured SOA formation was compared to the amount predicted from the concentrations of measured ambient SOA precursors and their SOA yields. While measured ambient precursors were sufficient to explain the amount of SOA formed from O 3 , they could only explain 10–50 % of the SOA formed from OH. This is consistent with previous OFR studies, which showed that typically unmeasured semivolatile and intermediate volatility gases (that tend to lack C=C bonds) are present in ambient air and can explain such additional SOA formation. To investigate the sources of the unmeasured SOA-forming gases during this campaign, multilinear regression analysis was performed between measured SOA formation and the concentration of gas-phase tracers representing different precursor sources. The majority of SOA-forming gases present during both seasons were of biogenic origin. Urban sources also contributed substantially in both seasons, while biomass burning sources were more important during the dry season. This study enables a better understanding of SOA formation in environments with diverse emission sources