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

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

Major bleeding during negative pressure wound/V.A.C.® - therapy for postsurgical deep sternal wound infection - a critical appraisal

Negative-pressure wound therapy, commercially known as vacuum-assisted closure (V.A.C.®) therapy, has become one of the most popular (and efficacious) interim (prior to flap reconstruction) or definite methods of managing deep sternal wound infection. Complications such as profuse bleeding, which may occur during negative-pressure therapy but not necessarily due to it, are often attributed to a single factor and reported as such. However, despite the wealth of clinical experience internationally available, information regarding certain simple considerations is still lacking. Garnering information on all the factors that could possibly influence the outcome has become more difficult due to a (fortunate) decrease in the incidence of deep sternal wound infection. If more insight is to be gained from fewer clinical cases, then various potentially confounding factors should be fully disclosed before complications can be attributed to the technique itself or improvements to negative-pressure wound therapy for deep sternal wound infection can be accepted as evidence-based and the guidelines for its use adapted. The authors propose the adoption of a simple checklist in such cases

Inverse modelling of CH4 emissions for 2010-2011 using different satellite retrieval products from GOSAT and SCIAMACHY

At the beginning of 2009 new space-borne observations of dry-air column-averaged mole fractions of atmospheric methane (XCH$_{4}$) became available from the Thermal And Near infrared Sensor for carbon Observations–Fourier Transform Spectrometer (TANSO-FTS) instrument on board the Greenhouse Gases Observing SATellite (GOSAT). Until April 2012 concurrent methane (CH$_{4}$) retrievals were provided by the SCanning Imaging Absorption spectroMeter for Atmospheric CartograpHY (SCIAMACHY) instrument on board the ENVironmental SATellite (ENVISAT). The GOSAT and SCIAMACHY XCH$_{4}$ retrievals can be compared during the period of overlap. We estimate monthly average CH$_{4}$ emissions between January 2010 and December 2011, using the TM5-4DVAR inverse modelling system. In addition to satellite data, high-accuracy measurements from the Cooperative Air Sampling Network of the National Oceanic and Atmospheric Administration Earth System Research Laboratory (NOAA ESRL) are used, providing strong constraints on the remote surface atmosphere. We discuss five inversion scenarios that make use of different GOSAT and SCIAMACHY XCH$_{4}$ retrieval products, including two sets of GOSAT proxy retrievals processed independently by the Netherlands Institute for Space Research (SRON)/Karlsruhe Institute of Technology (KIT), and the University of Leicester (UL), and the RemoTeC “Full- Physics” (FP) XCH$_{4}$ retrievals available from SRON/KIT. The GOSAT-based inversions show significant reductions in the root mean square (rms) difference between retrieved and modelled XCH$_{4}$, and require much smaller bias corrections compared to the inversion using SCIAMACHY retrievals, reflecting the higher precision and relative accuracy of the GOSAT XCH$_{4}$. Despite the large differences between the GOSAT and SCIAMACHY retrievals, 2-year average emission maps show overall good agreement among all satellitebased inversions, with consistent flux adjustment patterns, particularly across equatorial Africa and North America. Over North America, the satellite inversions result in a significant redistribution of CH$_{4}$ emissions from North-East to South-Central United States. This result is consistent with recent independent studies suggesting a systematic underestimation of CH$_{4}$ emissions from North American fossil fuel sources in bottom-up inventories, likely related to natural gas production facilities. Furthermore, all four satellite inversions yield lower CH$_{4}$ fluxes across the Congo basin compared to the NOAA-only scenario, but higher emissions across tropical East Africa. The GOSAT and SCIAMACHY inversions show similar performance when validated against independent shipboard and aircraft observations, and XCH$_{4}$ retrievals available from the Total Carbon Column Observing Network (TCCON)

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

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

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

Nanomechanical properties of α-synuclein amyloid fibrils: a comparative study by nanoindentation, harmonic force microscopy, and Peakforce QNM

We report on the use of three different atomic force spectroscopy modalities to determine the nanomechanical properties of amyloid fibrils of the human α-synuclein protein. α-Synuclein forms fibrillar nanostructures of approximately 10 nm diameter and lengths ranging from 100 nm to several microns, which have been associated with Parkinson's disease. Atomic force microscopy (AFM) has been used to image the morphology of these protein fibrils deposited on a flat surface. For nanomechanical measurements, we used single-point nanoindentation, in which the AFM tip as the indenter is moved vertically to the fibril surface and back while the force is being recorded. We also used two recently developed AFM surface property mapping techniques: Harmonic force microscopy (HarmoniX) and Peakforce QNM. These modalities allow extraction of mechanical parameters of the surface with a lateral resolution and speed comparable to tapping-mode AFM imaging. Based on this phenomenological study, the elastic moduli of the α-synuclein fibrils determined using these three different modalities are within the range 1.3-2.1 GPa. We discuss the relative merits of these three methods for the determination of the elastic properties of protein fibrils, particularly considering the differences and difficulties of each method