Convective injection and photochemical decay of peroxides in the tropical upper troposphere: Methyl iodide as a tracer of marine convection

The convective injection and subsequent fate of the peroxides H2O2 and CH3OOH in the upper troposphere is investigated using aircraft observations from the NASA Pacific Exploratory Mission-Tropics A (PEM-Tropics A) over the South Pacific up to 12 km altitude. Fresh convective outflow is identified by high CH3I concentrations; CH3I is an excellent tracer of marine convection because of its relatively uniform marine boundary layer concentration, relatively well-defined atmospheric lifetime against photolysis, and high sensitivity of measurement. We find that mixing ratios of CH3OOH in convective outflow at 8-12 km altitude are enhanced on average by a factor of 6 relative to background, while mixing ratios of H2O2 are enhanced by less than a factor of 2. The scavenging efficiency of H2O2 in the precipitation associated with deep convection is estimated to be 55-70%. Scavenging of CH3OOH is negligible. Photolysis of convected peroxides is a major source of the HOx radical family (OH + peroxy radicals) in convective outflow. The timescale for decay of the convective enhancement of peroxides in the upper troposphere is determined using CH3I as a chemical clock and is interpreted using photochemical model calculations. Decline of CH3OOH takes place on a timescale of a 1-2 days, but the resulting HOx converts to H2O2, so H2O2 mixing ratios show no decline for ∼5 days following a convective event. The perturbation to HOx at 8-12 km altitude from deep convective injection of peroxides decays on a timescale of 2-3 days for the PEM-Tropics A conditions. Copyright 1999 by the American Geophysical Union

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

BACKGROUND: DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. METHODOLOGY/PRINCIPAL FINDINGS: The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. CONCLUSIONS: The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature

Obscured phylogeny and possible recombinational dormancy in Escherichia coli

<p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide polymorphisms in chromosomes of representative strains to reconstruct the topology of its emergence.</p> <p>Results</p> <p>The phylogeny of <it>E. coli </it>varies according to the segment of chromosome analyzed. Recombination between extant <it>E. coli </it>groups is largely limited to only three intergroup pairings.</p> <p>Conclusions</p> <p>Segment-dependent phylogenies most likely are legacies of a complex recombination history. However, <it>E. coli </it>are now in an epoch in which they no longer broadly share DNA. Using the definition of species as organisms that freely exchange genetic material, this recombinational dormancy could reflect either the end of <it>E. coli </it>as a species, or herald the coalescence of <it>E. coli </it>groups into new species.</p

Exploring perceptions of advertising ethics: an informant-derived approach

Whilst considerable research exists on determining consumer responses to pre-determined statements within numerous ad ethics contexts, our understanding of consumer thoughts regarding ad ethics in general remains lacking. The purpose of our study therefore is to provide a first illustration of an emic and informant-based derivation of perceived ad ethics. The authors use multi-dimensional scaling as an approach enabling the emic, or locally derived deconstruction of perceived ad ethics. Given recent calls to develop our understanding of ad ethics in different cultural contexts, and in particular within the Middle East and North Africa (MENA) region, we use Lebanon—the most ethically charged advertising environment within MENA—as an illustrative context for our study. Results confirm the multi-faceted and pluralistic nature of ad ethics as comprising a number of dimensional themes already salient in the existing literature but in addition, we also find evidence for a bipolar relationship between individual themes. The specific pattern of inductively derived relationships is culturally bound. Implications of the findings are discussed, followed by limitations of the study and recommendations for further research

Experimental Microbial Evolution of Extremophiles

Experimental microbial evolutions (EME) involves studying closely a microbial population after it has been through a large number of generations under controlled conditions (Kussell 2013). Adaptive laboratory evolution (ALE) selects for fitness under experimentally imposed conditions (Bennett and Hughes 2009; Dragosits and Mattanovich 2013). However, experimental evolution studies focusing on the contributions of genetic drift and natural mutation rates to evolution are conducted under non-selective conditions to avoid changes imposed by selection (Hindré et al. 2012). To understand the application of experimental evolutionary methods to extremophiles it is essential to consider the recent growth in this field over the last decade using model non-extremophilic microorganisms. This growth reflects both a greater appreciation of the power of experimental evolution for testing evolutionary hypotheses and, especially recently, the new power of genomic methods for analyzing changes in experimentally evolved lineages. Since many crucial processes are driven by microorganisms in nature, it is essential to understand and appreciate how microbial communities function, particularly with relevance to selection. However, many theories developed to understand microbial ecological patterns focus on the distribution and the structure of diversity within a microbial population comprised of single species (Prosser et al. 2007). Therefore an understanding of the concept of species is needed. A common definition of species using a genetic concept is a group of interbreeding individuals that is isolated from other such groups by barriers of recombination (Prosser et al. 2007). An alternative ecological species concept defines a species as set of individuals that can be considered identical in all relevant ecological traits (Cohan 2001). This is particularly important because of the abundance and deep phylogenetic complexity of microbial communities. Cohan postulated that “bacteria occupy discrete niches and that periodic selection will purge genetic variation within each niche without preventing divergence between the inhabitants of different niches”. The importance of gene exchange mechanisms likely in bacteria and archaea and therefore extremophiles, arises from the fact that their genomes are divided into two distinct parts, the core genome and the accessory genome (Cohan 2001). The core genome consists of genes that are crucial for the functioning of an organism and the accessory genome consists of genes that are capable of adapting to the changing ecosystem through gain and loss of function. Strains that belong to the same species can differ in the composition of accessory genes and therefore their capability to adapt to changing ecosystems (Cohan 2001; Tettelin et al. 2005; Gill et al. 2005). Additional ecological diversity exists in plasmids, transposons and pathogenicity islands as they can be easily shared in a favorable environment but still be absent in the same species found elsewhere (Wertz et al. 2003). This poses a major challenge for studying ALE and community microbial ecology indicating a continued need to develop a fitting theory that connects the fluid nature of microbial communities to their ecology (Wertz et al. 2003; Coleman et al. 2006). Understanding the nature and contribution of different processes that determine the frequencies of genes in any population is the biggest concern in population and evolutionary genetics (Prosser et al. 2007) and it is critical for an understanding of experimental evolution

Global urban environmental change drives adaptation in white clover.

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

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It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate

Convective injection and photochemical decay of peroxides in the tropical upper troposphere: Methyl iodide as a tracer of marine convection

The convective injection and subsequent fate of the peroxides H2O2 and CH3OOH in the upper troposphere is investigated using aircraft observations from the NASA Pacific Exploratory Mission-Tropics A (PEM-Tropics A) over the South Pacific up to 12 km altitude. Fresh convective outflow is identified by high CH3I concentrations; CH3I is an excellent tracer of marine convection because of its relatively uniform marine boundary layer concentration, relatively well-defined atmospheric lifetime against photolysis, and high sensitivity of measurement. We find that mixing ratios of CH3OOH in convective outflow at 8-12 km altitude are enhanced on average by a factor of 6 relative to background, while mixing ratios of H2O2 are enhanced by less than a factor of 2. The scavenging efficiency of H2O2 in the precipitation associated with deep convection is estimated to be 55-70%. Scavenging of CH3OOH is negligible. Photolysis of convected peroxides is a major source of the HOx radical family (OH + peroxy radicals) in convective outflow. The timescale for decay of the convective enhancement of peroxides in the upper troposphere is determined using CH3I as a chemical clock and is interpreted using photochemical model calculations. Decline of CH3OOH takes place on a timescale of a 1-2 days, but the resulting HOx converts to H2O2, so H2O2 mixing ratios show no decline for ∼5 days following a convective event. The perturbation to HOx at 8-12 km altitude from deep convective injection of peroxides decays on a timescale of 2-3 days for the PEM-Tropics A conditions. Copyright 1999 by the American Geophysical Union