Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities

Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by extracting diagnostic molecular species such as fatty acids and nucleic acids from the community and determining which specific molecules have incorporated the isotope. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. Stable isotope probing allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This short review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

A comprehensive investigation of an offshore active fault in the Western Sagami Bay, central Japan

Offshore active faults, especially those in the deep sea, are very difficult to study because of the water and sedimentary cover. To characterize the nature and geometry of offshore active faults, a combination of methods must be employed. Generally, seismic profiling is used to map these faults, but often only fault-related folds rather than fracture planes are imaged. Multi-beam swath bathymetry provides information on the structure and growth history of a fault because movements of an active fault are reflected in the bottom morphology. Submersible and deep-tow surveys allow direct observations of deformations on the seafloor (including fracture zones and microstructures). In the deep sea, linearly aligned cold seep communities provide indirect evidence for active faults and the spatial migration of their activities. The Western Sagami Bay fault (WSBF) in the western Sagami Bay off central Japan is an active fault that has been studied in detail using the above methods. The bottom morphology, fractured breccias directly observed and photographed, seismic profiles, as well as distribution and migration of cold seep communities provide evidence for the nature and geometry of the fault. Focal mechanism solutions of selected earthquakes in the western Sagami Bay during the period from 1900 to 1995 show that the maximum compression trends NW-SE and the minimum stress axis strikes NE-SW, a stress pattern indicating a left-lateral strike-slip fault.

Direct observation of adsorption sites of protein impurities and their effects on step advancement of protein crystals

We measured noninvasively step velocities of elementary two-dimensional (2D) islands on {110} faces of tetragonal lysozyme crystals, under various supersaturations, by laser confocal microscopy combined with differential interference contrast microscopy. We studied the correlation between the effects of protein impurities on the growth of elementary steps and their adsorption sites on a crystal surface, using three kinds of proteins: fluorescent-labeled lysozyme (F-lysozyme), covalently bonded dimers of lysozyme (dimer), and a 18 kDa polypeptide (18 kDa). These three protein impurities suppressed the advancement of the steps. However, they exhibited different supersaturation dependencies of the suppression of the step velocities. To clarify the cause of this difference, we observed in situ the adsorption sites of individual molecules of F-lysozyme and fluorescent-labeled dimer (F-dimer) on the crystal surface by single-molecule visualization. We found that F-lysozyme adsorbed preferentially on steps (i.e., kinks), whereas F-dimer adsorbed randomly on terraces. Taking into account the different adsorption sites of F-lysozyme and F-dimer, we could successfully explain the different effects of the impurities on the step velocities. These observations strongly suggest that 18 kDa also adsorbs randomly on terraces. Seikagaku lysozyme exhibited a complex effect that could not alone be explained by the two major impurities (dimer and 18 kDa) present in Seikagaku lysozyme, indicating that trace amounts of other impurities significantly affect the step advancement.

Direct formation of form I poly(1-butene) single crystals from melt crystallization in ultrathin films

The morphologies and crystalline structures of melt-crystallized ultrathin isotactic poly(1-butene) films have been studied with transmission electron microscopy and electron diffraction. It is demonstrated that a bypass of form II crystallization can be achieved with an increase in its crystallization temperature. Electron microscopy observations show that melt-grown isotactic poly(1-butene) single crystals have a well-shaped hexagonal form, whereas form I crystals converted from form II display the morphologies of their tetragonal precursors. Electron diffraction results indicate that, instead of the twinned hexagonal pattern of the converted form I crystal, the directly formed form I single crystals exhibit an untwinned hexagonal pattern.

Direct Numerical Simulation of a Spatially Evolving Supersonic Turbulent Boundary Layer at Ma=6

Direct numerical simulation is carried out for a spatially evolving supersonic turbulent boundary layer at free-stream Mach number 6. To overcome numerical instability, the seventh-order WENO scheme is used for the convection terms of Navier-Stokes equations, and fine mesh is adopted to minimize numerical dissipation. Compressibilty effects on the near-wall turbulent kinetic energy budget are studied. The cross-stream extended self-similarity and scaling exponents including the near-wall region are studied. In high Mach number flows, the coherence vortex structures are arranged to be smoother and streamwised, and the hair-pin vortices are less likely to occur.

Liquid phase epitaxy growth of AlxGayIn1-x-yPzAs1-zGaAs with direct band gap up to 2.0 eV

III-V pentenary semiconductor AlGaInPAs with a direct band gap of up to 2.0 eV has been grown successfully on GaAs substrates by liquid phase epitaxy;(LPE). With the introduction of the energy bowing parameters of quaternaries, the theoretical calculations agree well with the measured PL peak energy data from pentenary samples.

Synchronous Multi-Scale Observations on Rock Damage and Rupture

This paper reports a multi-scale study on damage evolution process and rupture of gabbro under uniaxial compression with several experimental techniques, including MTS810 testing machine, white digital speckle correlation method, and acoustic emission technique. In particular, the synchronization of the three experimental systems is realized for the study of relationship of deformation and damage at multiple scales. It is found that there are significant correlation between damage evolution at small and large length scales, and rupture at sample scale, especially it displays critical sensitivity at multiple scales and trans-scale fluctuations.

Direct numerical test of the B-G-K model equation by the DSMC method

In the present paper the rarefied gas how caused by the sudden change of the wall temperature and the Rayleigh problem are simulated by the DSMC method which has been validated by experiments both in global flour field and velocity distribution function level. The comparison of the simulated results with the accurate numerical solutions of the B-G-K model equation shows that near equilibrium the BG-K equation with corrected collision frequency can give accurate result but as farther away from equilibrium the B-G-K equation is not accurate. This is for the first time that the error caused by the B-G-K model equation has been revealed.

Direct numerical simulation of transition and turbulence in compressible mixing layer

The three-dimensional compressible Navier-Stokes equations are approximated by a fifth order upwind compact and a sixth order symmetrical compact difference relations combined with three-stage Ronge-Kutta method. The computed results are presented for convective Mach number Mc = 0.8 and Re = 200 with initial data which have equal and opposite oblique waves. From the computed results we can see the variation of coherent structures with time integration and full process of instability, formation of Lambda-vortices, double horseshoe vortices and mushroom structures. The large structures break into small and smaller vortex structures. Finally, the movement of small structure becomes dominant, and flow field turns into turbulence. It is noted that production of small vortex structures is combined with turning of symmetrical structures to unsymmetrical ones. It is shown in the present computation that the flow field turns into turbulence directly from initial instability and there is not vortex pairing in process of transition. It means that for large convective Mach number the transition mechanism for compressible mixing layer differs from that in incompressible mixing layer.

Direct Numerical Simulation of Passive Scalar in Decaying Compressible Turbulence

The passive scalars in the decaying compressible turbulence with the initial Reynolds number (defined by Taylor scale and RMS velocity) Re=72, the initial turbulent Mach numbers (defined by RMS velocity and mean sound speed) Mt=0.2-0.9, and the Schmidt numbers of passive scalar Sc=2-10 are numerically simulated by using a 7th order upwind difference scheme and 8th order group velocity control scheme. The computed results are validated with different numerical methods and different mesh sizes. The Batchelor scaling with k(-1) range is found in scalar spectra. The passive scalar spectra decay faster with the increasing turbulent Mach number. The extended self-similarity (ESS) is found in the passive scalar of compressible turbulence.

An analysis of subgrid-resolved scale interactions with use of results from direct numerical simulations

Subgrid nonlinear interaction and energy transfer are analyzed using direct numerical simulations of isotropic turbulence. Influences of cutoff wave number at different ranges of scale on the energetics and dynamics have been investigated. It is observed that subgrid-subgrid interaction dominates the turbulent dynamics when cut-off wave number locates in the energy-containing range while resolved-subgrid interaction dominates if it is in the dissipation range; By decomposing the subgrid energy transfer and nonlinear interaction into 'forward' and 'backward' groups according to the sign of triadic interaction, we find that individually each group has very large contribution, but the net of them is much smaller, implying that tremendous cancellation happens between these two groups.

Direct Numerical Simulation of Supersonic Turbulent Boundary Layer Flow

Direct numerical simulations of a spatially evolving supersonic flat-plate turbulent boundary layer flow with free Mach number M = 2.25 and Reynolds number Re = 365000/in are performed. The transition process from laminar to turbulent flow is obtained by solving the three-dimensional compressible Navier-Stokes, equations, using high-order accurate difference schemes. The obtained statistical results agree well with the experimental and theoretical data. From the numerical results it can be seen that the transition process under the considered conditions is the process which skips the Tolimien-Schlichting instability and the second instability through the instability of high gradient shear layer and becomes of laminar flow breakdown. This means that the transition process is a bypass-type transition process. The spanwise asymmetry of the disturbance locally upstream imposed is important to induce the bypass-type transition. Furthermore, with increasing the time disturbance frequency the transition will delay. When the time disturbance frequency is large enough, the transition will disappear.

可压剪切层线性稳定性特征直接数值模拟=Direct Simulation of the Linear Instabilities in Compressible Shear Layers

基于伪随机数生成技术促生白噪声扰动,以高精度迎风/对称紧致混合差分算法求解二维/三维非定常可压Navier-Stokes方程,揭示了可压自由剪切层初始剪切过程中扰动的线性演化特征,以及该过程对扰动波数和方向的内在选择性.验证了所用算法的有效性,表明线性理论同数值模拟相结合是可压剪切层研究的合理途径之一.

Arc Root Motions In An Argon-Hydrogen Direct-Current Plasma Torch At Reduced Pressure

Arc root motions in generating dc argon-hydrogen plasma at reduced pressure are optically observed using a high-speed video camera. The time resolved angular position of the arc root attachment point is measured and analysed. The arc root movement is characterized as a chaotic and jumping motion along the circular direction on the anode surface.

Direct Numerical Simulation Of Hypersonic Boundary-Layer Transition Over A Blunt Cone

Direct numerical simulation of transition How over a blunt cone with a freestream Mach number of 6, Reynolds number of 10,000 based on the nose radius, and a 1-deg angle of attack is performed by using a seventh-order weighted essentially nonoscillatory scheme for the convection terms of the Navier-Stokes equations, together with an eighth-order central finite difference scheme for the viscous terms. The wall blow-and-suction perturbations, including random perturbation and multifrequency perturbation, are used to trigger the transition. The maximum amplitude of the wall-normal velocity disturbance is set to 1% of the freestream velocity. The obtained transition locations on the cone surface agree well with each other far both cases. Transition onset is located at about 500 times the nose radius in the leeward section and 750 times the nose radius in the windward section. The frequency spectrum of velocity and pressure fluctuations at different streamwise locations are analyzed and compared with the linear stability theory. The second-mode disturbance wave is deemed to be the dominating disturbance because the growth rate of the second mode is much higher than the first mode. The reason why transition in the leeward section occurs earlier than that in the windward section is analyzed. It is not because of higher local growth rate of disturbance waves in the leeward section, but because the growth start location of the dominating second-mode wave in the leeward section is much earlier than that in the windward section.