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

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