Global model simulations of air pollution during the 2003 European heat wave

Three global Chemistry Transport Models - MOZART, MOCAGE, and TM5 - as well as MOZART coupled to the IFS meteorological model including assimilation of ozone (O-3) and carbon monoxide (CO) satellite column retrievals, have been compared to surface measurements and MOZAIC vertical profiles in the troposphere over Western/Central Europe for summer 2003. The models reproduce the meteorological features and enhancement of pollution during the period 2-14 August, but not fully the ozone and CO mixing ratios measured during that episode. Modified normalised mean biases are around -25% (except similar to 5% for MOCAGE) in the case of ozone and from -80% to -30% for CO in the boundary layer above Frankfurt. The coupling and assimilation of CO columns from MOPITT overcomes some of the deficiencies in the treatment of transport, chemistry and emissions in MOZART, reducing the negative biases to around 20%. The high reactivity and small dry deposition velocities in MOCAGE seem to be responsible for the overestimation of O-3 in this model. Results from sensitivity simulations indicate that an increase of the horizontal resolution to around 1 degrees x1 degrees and potential uncertainties in European anthropogenic emissions or in long-range transport of pollution cannot completely account for the underestimation of CO and O-3 found for most models. A process-oriented TM5 sensitivity simulation where soil wetness was reduced results in a decrease in dry deposition fluxes and a subsequent ozone increase larger than the ozone changes due to the previous sensitivity runs. However this latest simulation still underestimates ozone during the heat wave and overestimates it outside that period. Most probably, a combination of the mentioned factors together with underrepresented biogenic emissions in the models, uncertainties in the modelling of vertical/horizontal transport processes in the proximity of the boundary layer as well as limitations of the chemistry schemes are responsible for the underestimation of ozone (overestimation in the case of MOCAGE) and CO found in the models during this extreme pollution event

Fluorescence correlation spectroscopy of the binding of nucleotide excision repair protein XPC-hHr23B with DNA substrates

The interaction of the nucleotide excision repair (NER) protein dimeric complex XPC-hHR23B, which is implicated in the DNA damage recognition step, with three Cy3.5 labeled 90-bp double-stranded DNA substrates (unmodified, with a central unpaired region, and cholesterol modified) and a 90-mer single-strand DNA was investigated in solution by fluorescence correlation spectroscopy. Autocorrelation functions obtained in the presence of an excess of protein show larger diffusion times (τ d) than for free DNA, indicating the presence of DNA-protein bound complexes. The fraction of DNA bound (θ), as a way to describe the percentage of protein bound to DNA, was directly estimated from FCS data. A significantly stronger binding capability for the cholesterol modified substrate (78% DNA bound) than for other double-stranded DNA substrates was observed, while the lowest affinity was found for the single-stranded DNA (27%). This is in accordance with a damage recognition role of the XPC protein. The similar affinity of XPC for undamaged and 'bubble' DNA sub

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil

Gas Accretion and Star Formation Rates

Cosmological numerical simulations of galaxy evolution show that accretion of metal-poor gas from the cosmic web drives the star formation in galaxy disks. Unfortunately, the observational support for this theoretical prediction is still indirect, and modeling and analysis are required to identify hints as actual signs of star-formation feeding from metal-poor gas accretion. Thus, a meticulous interpretation of the observations is crucial, and this observational review begins with a simple theoretical description of the physical process and the key ingredients it involves, including the properties of the accreted gas and of the star-formation that it induces. A number of observations pointing out the connection between metal-poor gas accretion and star-formation are analyzed, specifically, the short gas consumption time-scale compared to the age of the stellar populations, the fundamental metallicity relationship, the relationship between disk morphology and gas metallicity, the existence of metallicity drops in starbursts of star-forming galaxies, the so-called G dwarf problem, the existence of a minimum metallicity for the star-forming gas in the local universe, the origin of the alpha-enhanced gas forming stars in the local universe, the metallicity of the quiescent BCDs, and the direct measurements of gas accretion onto galaxies. A final section discusses intrinsic difficulties to obtain direct observational evidence, and points out alternative observational pathways to further consolidate the current ideas.Comment: Invited review to appear in Gas Accretion onto Galaxies, Astrophysics and Space Science Library, eds. A. J. Fox & R. Dav\'e, to be published by Springe

An analysis of the morphology and submarine landslide potential of the upper and middle continental slope offshore Fraser Island, Queensland, Australia

This study presents an investigation into the geomorphological, sedimentological and geotechnical properties of submarine landslides present on the continental slope offshore Fraser Island. An extensive range of previously undiscovered features including marginal plateaus, linear rills, ridges and gullies, canyon systems, as well as slides and slumps were identified. Gravity cores (5.65 m and 3.64 m long) taken in the ‘Upper Slope Slide’ (25 km2 in area, 200-300 m thick), and the ‘Middle Slope Slide’ (11 km2 in area, 100-150 m thick) indicate the slide scars contain drapes of Pleistocene to Recent hemipelagic mud. Shorter gravity cores (1.33 m and 0.43 m long) taken adjacent to both slides terminated in stiff muds of upper Pliocene to lower Pleistocene age (Upper Slope Slide), and upper Miocene to lower Pliocene age (Middle Slope Slide). This unique pattern shows that the sediment is being accumulated and protected inside the slide hollows, while being actively removed from the exposed adjacent slopes, most likely by abrasion. Biostratigraphic ages determined for the basal material demonstrate that the seafloor surfaces at both sites are effectively erosional unconformities. The basal, stiff sediments on the upper slope was deposited between 2 and 2.5 Ma BP; this material was scoured and then buried beneath a 1 m thick sediment drape at 0.45 Ma BP. Sediments exposed on the seafloor adjacent to the Middle Slope Slide were dated at around 6-8.5 Ma BP. This indicates that the smooth upper continental slope developed its morphology by the late-mid Pleistocene, while the middle slope is a Post-Pliocene feature. It is thought that Pliocene-Pleistocene geological events including fluctuations in the intensity of surface and abyssal ocean currents are responsible for re-sculpting the continental slope’s morphology and have a) increased abrasion and erosion of the middle and upper slope; while b) suppressed sediment delivery

Global model simulations of air pollution during the 2003 European heat wave

Three global Chemistry Transport Models – MOZART, MOCAGE, and TM5 – as well as MOZART coupled to the IFS meteorological model including assimilation of ozone (O<sub>3</sub>) and carbon monoxide (CO) satellite column retrievals, have been compared to surface measurements and MOZAIC vertical profiles in the troposphere over Western/Central Europe for summer 2003. The models reproduce the meteorological features and enhancement of pollution during the period 2–14 August, but not fully the ozone and CO mixing ratios measured during that episode. Modified normalised mean biases are around −25% (except ~5% for MOCAGE) in the case of ozone and from −80% to −30% for CO in the boundary layer above Frankfurt. The coupling and assimilation of CO columns from MOPITT overcomes some of the deficiencies in the treatment of transport, chemistry and emissions in MOZART, reducing the negative biases to around 20%. The high reactivity and small dry deposition velocities in MOCAGE seem to be responsible for the overestimation of O<sub>3</sub> in this model. Results from sensitivity simulations indicate that an increase of the horizontal resolution to around 1°×1° and potential uncertainties in European anthropogenic emissions or in long-range transport of pollution cannot completely account for the underestimation of CO and O<sub>3</sub> found for most models. A process-oriented TM5 sensitivity simulation where soil wetness was reduced results in a decrease in dry deposition fluxes and a subsequent ozone increase larger than the ozone changes due to the previous sensitivity runs. However this latest simulation still underestimates ozone during the heat wave and overestimates it outside that period. Most probably, a combination of the mentioned factors together with underrepresented biogenic emissions in the models, uncertainties in the modelling of vertical/horizontal transport processes in the proximity of the boundary layer as well as limitations of the chemistry schemes are responsible for the underestimation of ozone (overestimation in the case of MOCAGE) and CO found in the models during this extreme pollution event

Neil3-dependent base excision repair regulates lipid metabolism and prevents atherosclerosis in Apoe-deficient mice

Increasing evidence suggests that oxidative DNA damage accumulates in atherosclerosis. Recently, we showed that a genetic variant in the human DNA repair enzyme NEIL3 was associated with increased risk of myocardial infarction. Here, we explored the role of Neil3/NEIL3 in atherogenesis by both clinical and experimental approaches. Human carotid plaques revealed increased NEIL3 mRNA expression which significantly correlated with mRNA levels of the macrophage marker CD68. Apoe−/−Neil3−/− mice on high-fat diet showed accelerated plaque formation as compared to Apoe−/− mice, reflecting an atherogenic lipid profile, increased hepatic triglyceride levels and attenuated macrophage cholesterol efflux capacity. Apoe−/−Neil3−/− mice showed marked alterations in several pathways affecting hepatic lipid metabolism, but no genotypic alterations in genome integrity or genome-wide accumulation of oxidative DNA damage. These results suggest a novel role for the DNA glycosylase Neil3 in atherogenesis in balancing lipid metabolism and macrophage function, potentially independently of genome-wide canonical base excision repair of oxidative DNA damage

A dualistic model of primary anal canal adenocarcinoma with distinct cellular origins, etiologies, inflammatory microenvironments and mutational signatures: implications for personalised medicine.

Primary adenocarcinoma of the anal canal is a rare and aggressive gastrointestinal disease with unclear pathogenesis. Because of its rarity, no clear clinical practice guideline has been defined and a targeted therapeutic armamentarium has yet to be developed. The present article aimed at addressing this information gap by in-depth characterising the anal glandular neoplasms at the histologic, immunologic, genomic and epidemiologic levels. In this multi-institutional study, we first examined the histological features displayed by each collected tumour (n = 74) and analysed their etiological relationship with human papillomavirus (HPV) infection. The intratumoural immune cell subsets (CD4, CD8, Foxp3), the expression of immune checkpoints (PD-1, PD-L1), the defect in mismatch repair proteins and the mutation analysis of multiple clinically relevant genes in the gastrointestinal cancer setting were also determined. Finally, the prognostic significance of each clinicopathological variable was assessed. Phenotypic analysis revealed two region-specific subtypes of anal canal adenocarcinoma. The significant differences in the HPV status, density of tumour-infiltrating lymphocytes, expression of immune checkpoints and mutational profile of several targetable genes further supported the separation of these latter neoplasms into two distinct entities. Importantly, anal gland/transitional-type cancers, which poorly respond to standard treatments, displayed less mutations in downstream effectors of the EGFR signalling pathway (i.e., KRAS and NRAS) and demonstrated a significantly higher expression of the immune inhibitory ligand-receptor pair PD-1/PD-L1 compared to their counterparts arising from the colorectal mucosa. Taken together, the findings reported in the present article reveal, for the first time, that glandular neoplasms of the anal canal arise by HPV-dependent or independent pathways. These etiological differences leads to both individual immune profiles and mutational landscapes that can be targeted for therapeutic benefits

The rise and fall of methanotrophy following a deepwater oil-well blowout

The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea1. Most of the methane released was thought to have been consumed by marine microbes between July and August 20102, 3. Here, we report spatially extensive measurements of methane concentrations and oxidation rates in the nine months following the spill. We show that although gas-rich deepwater plumes were a short-lived feature, water column concentrations of methane remained above background levels throughout the rest of the year. Rates of microbial methane oxidation peaked in the deepwater plumes in May and early June, coincident with a rapid rise in the abundance of known and new methane-oxidizing microbes. At this time, rates of methane oxidation reached up to 5,900 nmol l−1 d−1—the highest rates documented in the global pelagic ocean before the blowout4. Rates of methane oxidation fell to less than 50 nmol l−1 d−1 in late June, and continued to decline throughout the remainder of the year. We suggest the precipitous drop in methane consumption in late June, despite the persistence of methane in the water column, underscores the important role that physiological and environmental factors play in constraining the activity of methane-oxidizing bacteria in the Gulf of Mexico

Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments

During these last 15 years, drug discovery strategies have essentially focused on identifying small molecules able to inhibit catalytic sites. However, other mechanisms could be targeted. Protein-protein interactions play crucial roles in a number of biological processes, and, as such, their disruption or stabilization is becoming an area of intense activity. Along the same line, inhibition of protein-membrane could be of major importance in several disease indications. Despite the many challenges associated with the development of such classes of interaction modulators, there has been considerable success in the recent years. Importantly, through the existence of protein hot-spots and the presence of druggable pockets at the macromolecular interfaces or in their vicinities, it has been possible to find small molecule effectors using a variety of screening techniques, including combined virtual ligand-in vitro screening strategy. Indeed such in silico-in vitro protocols emerge as the method of choice to facilitate our quest of novel drug-like compounds or of mechanistic probes aiming at facilitating the understanding of molecular reactions involved in the Health and Disease process. In this review, we comment recent successes of combined in silico-in vitro screening methods applied to modulating macromolecular interactions with a special emphasis on protein-membrane interactions