Evaluation of NO3- production and organic matter mineralization at each site sampled according to the following: rates of potential O₂ consumption (line with an open circle, nmol O₂ cm^-3 min^-1), potential nitrification (line with a black square, nmol NH4+ cm^-3 min^-1) and relative nitrification (gray bars, % of O₂ consumption; average ± standard error).

<p>Evaluation of NO3- production and organic matter mineralization at each site sampled according to the following: rates of potential O₂ consumption (line with an open circle, nmol O₂ cm^-3 min^-1), potential nitrification (line with a black square, nmol NH4+ cm^-3 min^-1) and relative nitrification (gray bars, % of O₂ consumption; average ± standard error).</p

Influence of algal and microalgal mat on the following processes.

<p>A) Potential nitrification, B) Actual denitrification, C) Potential anammox, D) Potential O₂ consumption, E) Estimated dissimilatory nitrate reduction to ammonium (DNRA). Box and whiskers, min and max. The presence of algal and microalgal mat had a highly significant influence over all studied processes (n = 6; p<0.001, Mann- Whitney U), except for potential O₂ consumption (D), where the difference was significant (n = 6; p<0.05, Mann- Whitney U).</p

Suggested model for the growth and development of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in sediments with high and low mineralization rates.

<p>The sediment is divided into oxic (light gray), oxic/anoxic (middle gray) and anoxic (dark gray) sediment zones. </p

Physico-chemical characteristics of the water column and sediment from the lagoon collection sites from September 2001.

<p>Physico-chemical characteristics of the water column and sediment from the lagoon collection sites from September 2001.</p

Actual denitrification and Dn (white bars) and Dw (shaded bars) rates (μmol N₂ m^-2 h^-1, n = 5, average ± standard error) measured in intact sediment cores of study site lagoons.

<p>Actual denitrification and Dn (white bars) and Dw (shaded bars) rates (μmol N₂ m^-2 h^-1, n = 5, average ± standard error) measured in intact sediment cores of study site lagoons.</p

N cycle anaerobic processes in sediment slurries based on NO3- reduction.

<p>Left axis represents the percentage of N reduction in each process: potential anammox (black bars), potential denitrification (dark gray bars) and estimated DNRA (light gray bars).</p

Data.xlsx

These data represent multiple different nitrogen cycling processes (denitrification, nitrification, dissimilatory nitrate reduction to ammonium) and oxygen consumption in 12 tropical coastal lagoon sediments and processes that may drive nitrogen cycling. The data here were collected in ecosystems with low nitrate concentrations

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban <i>Rattus norvegicus</i> Using Circular DNA Enrichment and Metagenomics

<div><p><i>Rattus norvegicus</i> (<i>R</i>. <i>norvegicus</i>) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from <i>R</i>. <i>norvegicus</i> collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known <i>R</i>. <i>norvegicus</i> Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in <i>R</i>. <i>norvegicus</i> could help identify viruses with pathogenic potential.</p></div

Subset of phylogenetic relationship among the papillomavirus L1 genes and L1 genes from the RnPV3 and RnPV2-variants identified in this study.

<p>The bootstraps values presented were inferred from 1000 bootstrap replicates. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141952#pone.0141952.s002" target="_blank">S2 Fig</a> for a complete tree of 289 L1 genes, the RnPV3 L1 gene and the RnpV2 type variant L1 genes.</p

Challenge with A/Brisbane/59/2007 (H1N1) after immunizations with different doses.

<p>6 to 10 months-old ferrets were immunized twice at two week-intervals with CAF01 adjuvanted and non-adjuvanted influenza vaccine at different dose levels. A third group was left un-vaccinated. All ferrets were challenged with 10⁷ TCID₅₀ of A/Brisbane/59/2007 (H1N1) four weeks after the second immunization (n = 4). <b>A</b>, <b>B</b> and <b>C</b> show the relative amounts of viral RNA found in nasal washes of individual infected animals at peak replication day (day 4), measured by quantitative RT-PCR. <b>D</b>, <b>E</b> and <b>F</b> show hemagglutination inhibition assay serum titers at day 11 using influenza A/Brisbane/59/2007. Values marked with an asterisk are significantly different (*, <i>p</i><0.05; **, <i>p</i><0.01; ***, <i>p</i><0.001), assessed by ANOVA.</p