We introduce a general design to construct fluorescence-switching probes. Upon the interaction of the ligand with the protein, the crowded surroundings restrict the bond rotation of the fluorescent molecular rotor to trigger a strong fluorescence signal, which is reduced upon the addition of a competitive ligand or after protein degradation.

Quantitative detection of trace amounts of a biomarker in protein rich human blood plasma using fluorescent probes is a great challenge as the real signal is usually obscured by nonspecific fluorescence. This problem occurs because most of the fluorescent dyes bind very tightly with blood proteins to produce a large fluorescence increase, resulting in overestimation of the biomarker concentrations and false positive diagnosis. In this paper, we report that biotinylated fluorescent probes encapsulated in avidin protein can generate very specific fluorescence in blood serum by blocking out nonspecific dye-protein interactions. We applied our novel probe design to detect two different types of biomolecules, hydrogen sulfide and nitroreductase. Our Avidin conjugated probes achieved quantitative analyte detection in blood serum; whereas concentrations were overestimated up to 320-fold when bare fluorescent probes were employed. As compared to conventional approaches where fluorescent probes are encapsulated into polymers and nanoparticles, our simple approach successfully overcomes many key issues such as dye leakage, long preparation steps, inconsistent dye-host ratios, difficulty in constructing in situ in a complex medium, and limited application to detect only small metabolites.

Despite the promising improvements made recently on fluorescence probes for the detection of enzymes and reactive small molecules, two fundamental problems remain: weaker fluorescence of many dyes in aqueous buffers and strong nonspecific signals in samples containing high protein levels. In this paper, we introduce a novel fluorescent probe encapsulated in protein cavity (FPEPC) concept as demonstrated by SNAP-tag protein and three environment-sensitive fluorescence probes to overcome these two problems. The probes were constructed by following the current probe design for enzymes and reactive small molecules but with an additional benzylguanine moiety for selective SNAP-tag conjugation. The SNAP-tag conjugated probes achieved quantitative nitroreductase and hydrogen sulfide detection in blood plasma, whereas analyte concentrations were overestimated up to 700-fold when bare fluorescent probes were employed for detection. Furthermore, detection sensitivity was increased dramatically, as our probes displayed 390-fold fluorescence enhancement upon SNAP-tag conjugation, in stark contrast to the weak fluorescence of the free probes in aqueous solutions. Compared with the conventional approaches where fluorescent probes are encapsulated into polymers and nanoparticles, our simple and general approach successfully overcame many key issues such as dye leakage, long preparation steps, inconsistent dye-host ratios, difficulty in constructing in situ in a complex medium, and limited application to detect only small metabolites.

The shallow Nice submarine slope is notorious for the 1979 tsunamigenic landslide that caused eight casualties and severe infrastructural damage. Many previous studies have tackled the question whether earthquake shaking would lead to slope failure and a repetition of the deadly scenario in the region. The answers are controversial. In this study, we assess for the first time the factor of safety using peak ground accelerations (PGAs) from synthetic accelerograms from a simulated offshore Mw 6.3 earthquake at a distance of 25km from the slope. Based on cone penetration tests (CPTu) and multichannel seismic reflection data, a coarser grained sediment layer was identified. In an innovative geotechnical approach based on uniform cyclic and arbitrary triaxial loading tests, we show that the sandy silt on the Nice submarine slope will fail under certain ground motion conditions. The uniform cyclic triaxial tests indicate that liquefaction failure is likely to occur in Nice slope sediments in the case of a Mw 6.3 earthquake 25km away. A potential future submarine landslide could have a slide volume (7.7 × 10 6 m 3 ) similar to the 1979 event.Arbitrary loading tests reveal post-loading pore water pressure rise, which might explain post-earthquake slope failures observed in the field. This study shows that some of the earlier studies offshore Nice may have overestimated the slope stability because they underestimated potential PGAs on the shallow marine slope deposits.

This paper aims to understand the hydrothermal sites near the Yonaguni Knoll IV in the Okinawa Trough, and to develop new techniques to study fluid flow patterns for hydrothermal systems and their impact on ore deposits on the seafloor. Hydraulic parameters are important for hydrothermal system studies, but in-situ measurements of fluid migration rates are difficult. Hydrothermal fluids can reach several hundred degrees Celsius, temperatures high enough to perturb hydrothermal fields and pore water migration patterns. Using in-situ temperature data as constraints, we model and synthesize 1-D and 3-D cylindrical hydrothermal models to fit the spatial variations of observed temperature fields. The 1-D modeling uses Péclet number analysis along the conduit. We also construct a 3-D cylindrical model to estimate the temperature and fluid velocity fields using a finite element software. All domains are set to be porous to allow the fluid to flow. The simulation is run until it reaches a semi steadystate solution, allowing both the temperature and velocity fields to stabilize. Results show the dimension of the thermal anomaly zone is likely controlled by advective heat transfer along the vent due to upward fluid flow. We estimate a Péclet number of-1.6, and the vertical fluid flow velocities at these sites are high, approximately 10-6 m s-1 , that is, about 100 m yr-1. This is a spatially averaged estimate over tens to hundreds of meters and does not take into account finer-scale venting, which may be very heterogeneous. The results of this work may help estimate the quantity of metal elements transported through pore fluid migration at modern hydrothermal sites.

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<p>Earthquakes are a main trigger of subaqueous landslides and surficial sediment remobilization at ocean margins and lake basins. If the earthquake loading is insufficient to lead to sediment failure, the subsequent dewatering and inherent compaction may enhance the shear strength of sedimentary slopes, a process termed „seismic strengthening“, which is believed to be especially relevant for the upper 10s of meters. This mechanism has been suggested to explain the observed paucity of submarine landslides on active margins when compared to the short recurrence of strong earthquakes in such settings. However, only few field studies were dedicated on this topic and little is known about which settings are especially prone to seismic strengthening.</p><p>Here, we present geotechnical data from diatom-rich sedimentary slopes in Chilean lakes and at the Japan Trench margin. We use the overburden-normalized undrained shear strength as an indicator of consolidation state. In Chile, this data is derived from in-situ dynamic cone penetrometer measurements, whereas the Japan data is obtained by lab vane shear tests on sediment cores. Both settings show extremely elevated shear strength of about ~5-10 times higher than expected for normally-consolidated sediment in the upper meters of a sequence. Significant overconsolidation is confirmed by one-dimensional compression tests, providing overconsolidation ratios of ~2-8 (Chilean lakes) and 4-9 (Japan Trench). For each setting, the shear strength profiles of sites with different sedimentation rates show very similar trends when they are normalized over the sediment age instead of over overburden stress. As older sediments experienced more earthquakes, this apparent age-dependency may form a new argument supporting the hypothesis of seismic strengthening. Following previous lab experiments on mixtures of diatoms and clayey-silt, we postulate that a high susceptibility to seismic strengthening in both settings is caused by the abundance of diatom frustules which are typically characterized by a high particle interlocking and surface roughness. On the Japan Trench margin, biogenic opal forms ~15% in dry weight, and given the hollow structure of diatom frustules, we infer that diatoms take up a considerable space in the in-situ sediment texture. We conclude that seismically active margins with diatom-rich sediments have a reduced susceptibility to submarine landslide hazards.</p>

A method for the simultaneous determination of nine strain coefficients, both shear and tensile, of crystalline bilayers is proposed and realized. The X-ray diffraction peak intensities along 2 (vertical) and (horizontal) scans relative to the plane of incidence of three Bragg reflections whose atomic planes are not parallel to each other can be used to obtain shear and tensile strain coefficients. The theoretical considerations and experimental examples for single-crystal GeSi/Si overlayers are reported. It is also demonstrated that, for GeSi/Si, the shear and tensile strain coefficients of the Si substrate tend to vanish when the GeSi layer is thicker than 40 nm.