Atmospheric boundary-layer structure observed during a haze event due to forest-fire smoke

During a haze event in Baltimore, U.S.A. from July 6 to 8, 2002, smoke from forest fires in the Québec region (Canada), degraded air quality and impacted upon local climate, decreasing solar radiation and air temperature. The smoke particles in and above the atmospheric boundary layer (ABL) served as a tracer and provided a unique opportunity to investigate the ABL structure, especially entrainment. Elastic backscatter lidar measurements taken during the haze event distinctly reveal the downward sweeps (or wisps) of smoke-laden air from the free atmosphere into the ABL. Visualisations of mechanisms such as dry convection, the entrainment process, detrainment, coherent entrainment structures, and mixing inside the ABL, are presented. Thermals overshooting at the ABL top are shown to create disturbances in the form of gravity waves in the free atmosphere aloft, as evidenced by a corresponding ripple structure at the bottom of the smoke layer. Lidar data, aerosol groundbased measurements and supporting meteorological data are used to link free atmosphere, mixed-layer and ground-level aerosols. During the peak period of the haze event (July 7, 2002), the correlation between time series of elastic backscatter lidar data within the mixed layer and the scattering coefficient from a nephelometer at ground level was found to be high (R ¼ 0.96 for z ¼ 324 m, and R ¼ 0.89 for z ¼ 504 m). Ground-level aerosol concentration was at a maximum about 2 h after the smoke layer intersected with the growing ABL, confirming that the wisps do not initially reach the ground

Aerosol optical characterization by nephelometer and lidar: the Baltimore Supersite experiment during the Canadian forest fire smoke intrusion

[1] High spatial and temporal resolution elastic backscatter lidar data from Baltimore are analyzed with a near-end approach to estimate vertical profiles of the aerosol extinction coefficient. The near-end approach makes use of the (1) aerosol scattering coefficient measured at the surface with a nephelometer (0.530 μm), (2) surface level particle size distribution, and (3) refractive index calculated using Mie theory to estimate the aerosol extinction coefficient boundary condition for the lidar equation. There was a broad range of atmospheric turbidity due to a strong haze event, which occurred because of smoke transport from Canadian forest fires, and led to a wide range of observed atmospheric properties. The index of refraction for aerosols estimated during the entire study period is 1.5–0.47 i, which is typical for soot. The measured surface level aerosol scattering coefficient ranged from σp = 0.002 to σp = 0.541 km−1, and the computed aerosol extinction coefficient spanned values κp = 0.01 to κp = 1.05 km−1. The derived mass concentration and the mass scattering ranges were 3.96–194 μg m−3 and 0.05–3.260 m2g−1, respectively. The aerosol optical properties were dominated by light absorption by soot

Characteristics of PM2.5 Episodes Revealed by Semi-Continuous Measurements at the Baltimore Supersite at Ponca St

Highly time-resolved measurements of PM2.5, its major constituents, particle size distributions (9 nm to 20 μ m), CO, NO/NO2, and O3, and meteorological parameters were made from February through November 2002, at the Baltimore Supersite at Ponca St. using commercial and prototype semi-continuous instruments. The average PM2.5 mass concentration during the study period was 16.9 μ g/m3 and a total of 29 PM2.5 pollution episodes, each in which 24-h averaged PM2.5 mass concentrations exceeded 30.0 μ g/m3 for one or more days, were observed. Herein, 6 of the worst episodes are discussed. During these events, PM2.5 excursions were often largely due to elevations in the concentration of one or two of the major species. In addition, numerous short-term excursions were observed and were generally attributable to local sources. Those in OC, EC, nitrate, CO, and NOx levels were often observed in the morning traffic hours, particularly before breakdown of nocturnal inversions. Moreover, fresh accumulation aerosols from local stationary combustion sources were observed on several occasions, as evidenced by elevations in elemental markers when winds were aligned with sources resulting in PM2.5 increments of ∼ 17 μ g/m3. Overall, the results described herein show that concentrations of PM2.5 and its major constituents vary enormously on time scales ranging from < 1 hr to several days, thus imposing a more highly complex pattern of pollutant exposure than can be captured by 24-hr integrated methods, alone. The data suggest that control of a limited number of local sources might achieve compliance with daily and annual PM2.5 standards

Interactive metagenomic visualization in a Web browser

<p>Abstract</p> <p>Background</p> <p>A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.</p> <p>Results</p> <p>Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.</p> <p>Conclusions</p> <p>Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: <url>http://krona.sourceforge.net</url>.</p

SHRiMP: Accurate Mapping of Short Color-space Reads

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp

Airborne Emissions from 1961 to 2004 of Benzo[a]pyrene from U.S. Vehicles per km of Travel Based on Tunnel Studies

We identified 13 historical measurements of polycyclic aromatic hydrocarbons (PAHs) in U.S. vehicular traffic tunnels that were either directly presented as tailpipe emission factors in μg per vehicle-kilometer or convertible to such a form. Tunnel measurements capture fleet cruise emissions. Emission factors for benzo[a]pyrene (BaP) for a tunnel fleet operating under cruise conditions were highest prior to the 1980s and fell from more than 30-μg per vehicle-km to approximately 2-μg/km in the 1990s, an approximately 15-fold decline. Total annual U.S. (cruise) emissions of BaP dropped by a lesser factor, because total annual km driven increased by a factor of 2.7 during the period. Other PAH compounds measured in tunnels over the 40-year period (e.g., benzo[ghi]perylene, coronene) showed comparable reduction factors in emissions. PAH declines were comparable to those measured in tunnels for carbon monoxide, volatile organic compounds, and particulate organic carbon. The historical PAH “source terms” determined from the data are relevant to quantifying the benefits of emissions control technology and can be used in epidemiological studies evaluating the health effects of exposure, such as those undertaken with breast cancer in New York State

Comparison of bacterial microbiota of the predatory mite Neoseiulus cucumeris (Acari: Phytoseiidae) and its factitious prey Tyrophagus putrescentiae (Acari: Acaridae)

Neoseiulus cucumeris is a predatory mite used for biological control of arthropod pests. Mass-reared predators are fed with factitious prey mites such as Tyrophagus putrescentiae. Although some information on certain endosymbionts of N. cucumeris and T. putrescentiae exists, it is unclear whether both species share bacterial communities. The bacterial communities in populations of predator and prey mites, as well as the occurence of potential acaropathogenic bacteria were analyzed. The comparisons were based on the following groups: (i) N. cucumeris mass-production; (ii) N. cucumeris laboratory population with disease symptoms; (iii) T. putrescentiae pure populations and; (iv) T. putrescentiae from rearing units of N. cucumeris. Only 15% of OTUs were present in all samples from predatory and prey mite populations (core OTUs): the intracellular symbionts Wolbachia, Cardinium, plus other Blattabacterium-like, Solitalea-like, and Bartonella-like symbionts. Environmental bacteria were more abundant in predatory mites, while symbiotic bacteria prevailed in prey mites. Relative numbers of certain bacterial taxa were significantly different between the microbiota of prey mites reared with and without N. cucumeris. No significant differences were found in the bacterial communities of healthy N. cucumeris compared to N. cucumeris showing disease symptoms. We did not identify any confirmed acaropathogenic bacteria among microbiota

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute \u3e 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

The Rowett Institute and SRUC are core funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The Roslin Institute forms part of the Royal (Dick) School of Veterinary Studies, University of Edinburgh. This project was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; BB/N016742/1, BB/N01720X/1), including institute strategic programme and national capability awards to The Roslin Institute (BBSRC: BB/P013759/1, BB/P013732/1, BB/J004235/1, BB/J004243/1); and by the Scottish Government as part of the 2016–2021 commission.Peer reviewedPublisher PD