Submarine channels have been important throughout geologic time for feeding globally significant volumes of sediment from land to the deep sea. Modern observations show that submarine channels can be sculpted by supercritical turbidity currents (seafloor sediment flows) that can generate upstream-migrating bedforms with a crescentic planform. In order to accurately interpret supercritical flows and depositional environments in the geologic record, it is important to be able to recognize the depositional signature of crescentic bedforms. Field geologists commonly link scour fills containing massive sands to crescentic bedforms, whereas models of turbidity currents produce deposits dominated by back-stepping beds. Here we reconcile this apparent contradiction by presenting the most detailed study yet that combines direct flow observations, time-lapse seabed mapping, and sediment cores, thus providing the link from flow process to depositional product. These data were collected within the proximal part of a submarine channel on the Squamish Delta, Canada. We demonstrate that bedform migration initially produces back-stepping beds of sand. However, these back-stepping beds are partially eroded by further bedform migration during subsequent flows, resulting in scour fills containing massive sand. As a result, our observations better match the depositional architecture of upstream-migrating bedforms produced by fluvial models, despite the fact that they formed beneath turbidity currents.
Many DNA-modifying enzymes act in a manner that requires communication between two noncontiguous DNA sites. These sites can be brought into contact either by a diffusion-mediated chance interaction between enzymes bound at the two sites, or by active translocation of the intervening DNA by a site-bound enzyme. EcoP15I, a type III restriction enzyme, needs to interact with two recognition sites separated by up to 3,500 bp before it can cleave DNA. Here, we have studied the behavior of EcoP15I, using a novel fast-scan atomic force microscope, which uses a miniaturized cantilever and scan stage to reduce the mechanical response time of the cantilever and to prevent the onset of resonant motion at high scan speeds. With this instrument, we were able to achieve scan rates of up to 10 frames per s under fluid. The improved time resolution allowed us to image EcoP15I in real time at scan rates of 1-3 frames per s. EcoP15I translocated DNA in an ATP-dependent manner, at a rate of 79 ؎ 33 bp/s. The accumulation of supercoiling, as a consequence of movement of EcoP15I along the DNA, could also be observed. EcoP15I bound to its recognition site was also seen to make nonspecific contacts with other DNA sites, thus forming DNA loops and reducing the distance between the two recognition sites. On the basis of our results, we conclude that EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive DNA loop formation and ATPasedriven translocation of the intervening DNA contour.imaging ͉ nucleic acid ͉ restriction-modification enzyme ͉ scanning-probe
In order to fold non-native proteins, chaperonin GroEL undergoes numerous conformational changes and GroES binding in the ATP-dependent reaction cycle. We constructed the real-time three-dimensional-observation system at high resolution using a newly developed fast-scanning atomic force microscope. Using this system, we visualized the GroES binding to and dissociation from individual GroEL with a lifetime of 6 s (k ¼ 0.17 s À1 ).We
Antidunes and their sedimentary structures can be useful in reconstructing paleo-hydraulic conditions, especially for large discharge events. However, three-dimensional (3D) antidunes in sand-sized sediments have not yet been studied extensively, as compared to either two-dimensional (2D) antidunes or antidunes in gravel-sized sediments. In this study, we estimated formative conditions of gravel step-pool morphologies and applied them to the formation of 3D antidunes over a sand bed. Formative conditions are expressed in terms of a relationship between the water discharge per unit width and the bed slope. Flume experiments demonstrated that 3D mound-like antidune configurations and their associated internal sedimentary structures could be preserved. Internal sedimentary structures were characterized by shallow lens-like structures whose bases were erosional. Although gently-dipping concave-upward lamination was dominant, convex-upward lamination was occasionally observed. The dimensions of lenticular lamina-sets can be used to estimate antidune geometry. Thus if 3D antidunes can be interpreted in the stratigraphic record, it is possible to estimate the paleo-hydraulic parameters such as water discharge and bed slope more precisely than previously.
The development of bedforms under unidirectional, oscillatory and combined-flows results from temporal changes in sediment transport, flow and morphological response. In such flows, the bedform characteristics (for example, height, wavelength and shape) change over time, from their initiation to equilibrium with the imposed conditions, even if the flow conditions remain unchanged. These variations in bedform morphology during development are reflected in the sedimentary structures preserved in the rock record. Hence, understanding the time and morphological development in which bedforms evolve to an equilibrium stage is critical for informed reconstruction of the ancient sedimentary record. This article presents results from a laboratory flume study on bedform development and equilibrium development time conducted under purely unidirectional, purely oscillatory and combined-flow conditions, which aimed to test and extend an empirical model developed in past work solely for unidirectional ripples. The present results yield a unified model for bedform development and equilibrium under unidirectional, oscillatory and combined-flows. The experimental results show that the processes of bedform genesis and growth are common to all types of flows, and can be characterized into four stages: (i) incipient bedforms; (ii) growing bedforms; (iii) stabilizing bedforms; and (iv) fully developed bedforms. Furthermore, the development path of bedform; growth exhibits the same general trend for different flow types (for example, unidirectional, oscillatory and combined-flows), bedform size (for example, small versus large ripples), bedform shape (for example, symmetrical or rounded), bedform planform geometry (for example, two-dimensional versus three-dimensional), flow velocities and sediment grain sizes. The equilibrium time for a wide range of bed configurations was determined and found to be inversely proportional to the sediment transport flux occurring for that flow condition.
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