(Supplementary Table 1) Proportions of methane (C1) to ethane (C2) and the stable isotope composition of methane (d13CCH4) of gas and oil collected by gas bubble sampler during cruise M 114 in the southern Gulf of Mexico

Hydrocarbon seepage is a widespread process at the continental margins of the Gulf of Mexico. We used a multidisciplinary approach, including multibeam mapping and visual seafloor observations with different underwater vehicles to study the extent and character of complex hydrocarbon seepage in the Bay of Campeche, southern Gulf of Mexico. Our observations showed that seafloor asphalt deposits previously only known from the Chapopote Knoll also occur at numerous other knolls and ridges in water depths from 1230 to 3150 m. In particular the deeper sites (Chapopopte and Mictlan knolls) were characterized by asphalt deposits accompanied by extrusion of liquid oil in form of whips or sheets, and in some places (Tsanyao Yang, Mictlan, and Chapopote knolls) by gas emission and the presence of gas hydrates in addition. Molecular and stable carbon isotopic compositions of gaseous hydrocarbons suggest their primarily thermogenic origin. Relatively fresh asphalt structures were settled by chemosynthetic communities including bacterial mats and vestimentiferan tube worms, whereas older flows appeared largely inert and devoid of corals and anemones at the deep sites. The gas hydrates at Tsanyao Yang and Mictlan Knolls were covered by a 5-to-10 cm-thick reaction zone composed of authigenic carbonates, detritus, and microbial mats, and were densely colonized by 1-2 m-long tube worms, bivalves, snails, and shrimps. This study increased knowledge on the occurrences and dimensions of asphalt fields and associated gas hydrates at the Campeche Knolls. The extent of all discovered seepage structure areas indicates that emission of complex hydrocarbons is a widespread, thus important feature of the southern Gulf of Mexico.

Bubble growth by injection of gas into viscous liquids in cylindrical and conical tubes.

The laminar low Mach number flow of a gas in a tube is analyzed for very small and very large values of the inlet-to-wall temperature ratio. When this ratio tends to zero, pressure forces confine the cold gas to a thin core around the axis of the tube. This core is neatly bounded by an ablation front that consumes it at a finite distance from the tube inlet. When the temperature ratio tends to infinity, the temperature of the gas increases smoothly from the wall to the axis of the tube and the shear stress and heat flux are positive at the wall despite the fact that the viscosity and thermal conductivity of the gas scaled with their inlet values tend to zero at the wall.

Pressure measurements of the detachment bubble on the Bolund Island

Pressure measurements on the surface of a 1:230 scale model of Bolund Island are presented. The model is smooth and no boundary layer generation has been considered since the experiment is designed as the simplest possible reference case. Measurement have been taken for a range of Reynolds numbers based on the average undisturbed wind speed U∞ and the maximum height of the island, h [1.7×104, 8.5×104], and for a range of wind directions. Four minutes time series of pressure in more than 400 points have been acquired and analysed to obtain the spatial distribution of both the time average and the variance of the pressure signal. The horizontal extension of the detachment bubble for the different Reynolds numbers and wind directions is identified by isobars and curves of constant value of pressure variance. The applicability of this technique for evaluating the horizontal topology of high turbulence regions associated to detachment bubbles after escarpments in potential wind farm sites is analysed. The results obtained shows that the behaviour of the mean pressure coefficient, Cp, the std. pressure coefficient, Cp, and the skewness of the pressure, Sp can be used to study the bubble over the island to a certain extent. This experiment is part of the set of different analysis on the Bolund test case that is being undertaken within WAUDIT project by the different scientific groups.

Pressure measurements of the detachment bubble on the Bolund Island

Pressure measurements on the surface of a 1:230 scale model of Bolund Island are presented. The model is smooth and no boundary layer generation has been considered since the experiment is designed as the simplest possible reference case. Measurement have been taken for a range of Reynolds numbers based on the average undisturbed wind speed U? and the maximum height of the island, h [1.7×104 , 8.5×104], and for a range of wind directions. Four minutes time series of pressure in more than 400 points have been acquired and analysed to obtain the spatial distribution of both the time average and the variance of the pressure signal. The horizontal extension of the detachment bubble for the different Reynolds numbers and wind directions is identified by isobars and curves of constant value of pressure variance. The applicability of this technique for evaluating the horizontal topology of high turbulence regions associated to detachment bubbles after escarpments in potential wind farm sites is analysed. The results obtained shows that the behaviour of the mean pressure coefficient, Cp, the std. pressure coefficient, C?p, and the skewness of the pressure, Sp can be used to study the bubble over the island to a certain extent. This experiment is part of the set of different analysis on the Bolund test case that is being undertaken within WAUDIT project by the different scientific groups.

Numerical study of ultrasound induced non-linear shape and size bubble oscillations in viscoelastic media

The theoretical study of forced bubble oscillations is motivated by the importance of cavitation bubbles and oscillating encapsulated microbubbles (i.e. contrast agents) in medical sciences. In more details,theoretical studies on bubble dynamics addressing the sound-bubble interaction phenomenon provide the basis for understanding the dynamics of contrast agent microbubbles used in medical diagnosis and of non-linearly oscillating cavitation bubbles in the case of high-intensity ultrasound therapy. Moreover, the inclusion of viscoelasticity is of vital importance for an accurate theoretical analysis since most biological tissues and fluids exhibit non-Newtonian behavior.

RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates

Sequence-selective transcription by bacterial RNA polymerase (RNAP) requires σ factor that participates in both promoter recognition and DNA melting. RNAP lacking σ (core enzyme) will initiate RNA synthesis from duplex ends, nicks, gaps, and single-stranded regions. We have used DNA templates containing short regions of heteroduplex (bubbles) to compare initiation in the presence and absence of various σ factors. Using bubble templates containing the σD-dependent flagellin promoter, with or without its associated upstream promoter (UP) element, we demonstrate that UP element stimulation occurs efficiently even in the absence of σ. This supports a model in which the UP element acts primarily through the α subunit of core enzyme to increase the initial association of RNAP with the promoter. Core and holoenzyme do differ substantially in the template positions chosen for initiation: σD restricts initiation to sites 8–9 nucleotides downstream of the conserved −10 element. Remarkably, σA also has a dramatic effect on start-site selection even though the σA holoenzyme is inactive on the corresponding homoduplexes. The start sites chosen by the σA holoenzyme are located 8 nucleotides downstream of sequences on the nontemplate strand that resemble the conserved −10 hexamer recognized by σA. Thus, σA appears to recognize the −10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, σ also localizes the transcription start site.