Modelling concentration heterogeneities in streets using the street-network model MUNICH

Populations in urban areas are exposed to high local concentrations of pollutants, such as nitrogen dioxide and particulate matter, because of unfavourable dispersion conditions and the proximity to traffic. To simulate these concentrations over cities, models like the street-network model MUNICH (Model of Urban Network of Intersecting Canyons and Highways) rely on parameterizations to represent the air flow and the concentrations of pollutants in streets. In the current version, MUNICH v2.0, concentrations are assumed to be homogeneous in each street segment. A new version of MUNICH, where the street volume is discretized, is developed to represent the street gradients and to better estimate peoples' exposure. Three vertical levels are defined in each street segment. A horizontal discretization is also introduced under specific conditions by considering two zones with a parameterization taken from the Operational Street Pollution Model (OSPM). Simulations are performed over two districts of Copenhagen, Denmark, and one district of greater Paris, France. Results show an improvement in the comparison to observations, with higher concentrations at the bottom of the street, closer to traffic, of pollutants emitted by traffic (NOx, black carbon, organic matter). These increases reach up to 60 % for NO2 and 30 % for PM10 in comparison to MUNICH v2.0. The aspect ratio (ratio between building height and street width) influences the extent of the increase of the first-level concentrations compared to the average of the street. The increase is higher for wide streets (low aspect ratio and often higher traffic) by up to 53 % for NOx and 18 % for PM10. Finally, a sensitivity analysis with regard to the influence of the street network highlights the importance of using the model MUNICH with a network rather than with a single street.</p

Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112T and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112T has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B12). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with 13C3-glycerol demonstrated that L. reuteri JCM 1112T could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112T to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri

Commentary on Viewpoint: Human skeletal muscle wasting in hypoxia: a matter of hypoxic dose?: Skeletal muscle wasting in hypoxia; a matter of altitude.

SKELETAL MUSCLE WASTING IN HYPOXIA; A MATTER OF ALTITUDE TO THE EDITOR: D’Hulst and Deldicque (1) argue that the severity of muscle atrophy incurred at high altitude is dependent on the combined effect of duration and degree of hypoxia exposure, or “hypoxic dose” (1). We do see a limitation of this concept, as it implies that someone residing in Leuven (altitude: 28 m) for 10 years would be subjected to a hypoxic dose of 2,454 km·h and incur 5% atrophy. Although the authors wrote that “it is unknown which parameter, altitude, or time spent at altitude is most decisive in the overall metric of hypoxic dose,” our illustration suggests that altitude is the prime determinant. This is further supported by the cut-off point at 4,000 m in a plot of the degree of atrophy vs. altitude (using the data in Table 1), whereas there was no clear relationship with duration of altitude residence. This cut-off point is likely related to the shape of the hemoglobin dissociation curve, where the oxygen tension at 4,000 m is such that physiologically significant arterial hemoglobin desaturation occurs (2). We acknowledge that one cannot entirely dismiss the importance of duration of hypoxic exposure, simply because skeletal muscle atrophy can only be noticed some time after net protein breakdown is initiated. However, muscle atrophy will not continue indefinitely, but will reach a new steady state (how otherwise can Tibetans still have muscle?). Finally, other adaptations than atrophy, such as an increase in hematocrit and capillarization, serve to attenuate muscle tissue hypoxia and atrophy (3) during residence at altitude. REFERENCES 1. D=Hulst G, Deldicque L. Viewpoint: Human skeletal muscle wasting in hypoxia: a matter of hypoxic dose? J Appl Physiol. doi:10.1152/ japplphysiol.00264.2016. 2. Wagner PD, Wagner HE, Groves BM, Cymerman A, Houston CS. Hemoglobin P(50) during a simulated ascent of Mt. Everest, Operation Everest II. High Alt Med Biol 8: 32–42, 2007. doi:10.1089/ham.2006. 1049. 3. Wüst RCI, Jaspers RT, van Heijst AF, Hopman MT, Hoofd LJ, van der Laarse WJ, Degens H. Region-specific adaptations in determinants of rat skeletal muscle oxygenation to chronic hypoxia. Am J Physiol Heart Circ Physiol 297: H364–H374, 2009. doi:10.1152/ajpheart.00272.2009

Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis

BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE). METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable genome

Nunataryuk field campaigns: understanding the origin and fate of terrestrial organic matter in the coastal waters of the Mackenzie Delta region

Climate warming and related drivers of soil thermal change in the Arctic are expected to modify the distribution and dynamics of carbon contained in perennially frozen grounds. Thawing of permafrost in the Mackenzie River watershed of northwestern Canada, coupled with increases in river discharge and coastal erosion, triggers the release of terrestrial organic matter (OMt) from the largest Arctic drainage basin in North America into the Arctic Ocean. While this process is ongoing and its rate is accelerating, the fate of the newly mobilized organic matter as it transits from the watershed through the delta and into the marine system remains poorly understood. In the framework of the European Horizon 2020 Nunataryuk programme, and as part of the Work Package 4 (WP4) Coastal Waters theme, four field expeditions were conducted in the Mackenzie Delta region and southern Beaufort Sea from April to September 2019. The temporal sampling design allowed the survey of ambient conditions in the coastal waters under full ice cover prior to the spring freshet, during ice breakup in summer, and anterior to the freeze-up period in fall. To capture the fluvial–marine transition zone, and with distinct challenges related to shallow waters and changing seasonal and meteorological conditions, the field sampling was conducted in close partnership with members of the communities of Aklavik, Inuvik and Tuktoyaktuk, using several platforms, namely helicopters, snowmobiles, and small boats. Water column profiles of physical and optical variables were measured in situ, while surface water, groundwater, and sediment samples were collected and preserved for the determination of the composition and sources of OMt, including particulate and dissolved organic carbon (POC and DOC), and colored dissolved organic matter (CDOM), as well as a suite of physical, chemical, and biological variables. Here we present an overview of the standardized datasets, including hydrographic profiles, remote sensing reflectance, temperature and salinity, particle absorption, nutrients, dissolved organic carbon, particulate organic carbon, particulate organic nitrogen, CDOM absorption, fluorescent dissolved organic matter intensity, suspended particulate matter, total particulate carbon, total particulate nitrogen, stable water isotopes, radon in water, bacterial abundance, and a string of phytoplankton pigments including total chlorophyll. Datasets and related metadata can be found in Juhls et al. (2021) (https://doi.org/10.1594/PANGAEA.937587).</p