Relationship between ocean velocity and motionally induced electrical signals: 1. in the presence of horizontal velocity gradients

Motionally induced electric fields and electric currents in the ocean depend to first order solely on the vertical dimension. We investigate the significance of two-dimensional (2-D) perturbations that arise in the presence of horizontal velocity gradients. The full electric response is calculated for two schematic geometries that contain horizontal velocity gradients, have a two-layer ocean with a layer of sediment beneath, and are described by four nondimensional parameters. When considered over the realistic ranges of oceanic aspect ratio (the ratio of water depth to the width of velocity), sediment thickness, and sediment conductivity, velocity errors arising from 2-D perturbations are found to be less than a few percent of the dominant one-dimensional (1-D) signal. All errors depend on the aspect ratio to the power of 1.9 (1) for signals induced by the vertical (horizontal) component of the Earth's magnetic field. Depth-uniform velocity errors are proportional to the 1-D sediment conductance ratio, whereas depth-varying velocity errors are independent of sediment thickness or conductivity. Errors are weakly (proportionally) dependent on the jet depth for signals induced by the vertical (horizontal) component of the magnetic field. Two-dimensional perturbations decay away from the forcing region with a half width of 0.2-1 times the 1-D effective water depth. This study extends the first-order theory to the maximum expected aspect ratios for oceanic flow and finds small perturbations with simple dependencies on the nondimensional parameters

Relationship between ocean velocity and motionally induced electrical signals: 2. in the presence of sloping topography

Motionally induced electric fields and electric currents in the ocean depend to first order solely on the vertical dimension. We investigate the significance of two-dimensional (2-D) perturbations that arise in the presence of sloping topography. The full electric response is calculated for a schematic geometry that contains a topographic slope, has a two-layer ocean with a layer of sediment beneath, and is described by five nondimensional parameters. When considered over the realistic ranges of topographic aspect ratio (the ratio of mean water depth to topographic width), topographic relief, sediment thickness, and sediment conductivity, velocity errors arising from 2-D perturbations are found to be less than a few percent of the dominant one-dimensional (1-D) signal. All errors depend on the topographic aspect ratio to the power of 1.9 and have linear dependence on topographic relief and the depth of the surface jet. Depth-uniform velocity errors are roughly proportional to the 1-D sediment conductance ratio, whereas depth-varying velocity errors are independent of sediment thickness or conductivity. Two-dimensional perturbations decay with a half width of 0.2–1 times the 1-D effective water depth. The magnitude of estimated errors is consistent with those found at a measurement location with strong 2-D perturbations. This study extends the first-order theory to the maximum expected aspect ratios for topography and finds small perturbations with simple dependencies. Overall, the 1-D approximation is found to be adequate for interpreting observations at all but the most extreme locations

A vertical-mode decomposition to investigate low-frequency internal motion across the Atlantic at 26° N

Hydrographic data from full-depth moorings maintained by the Rapid/\-MOCHA project and spanning the Atlantic at 26° N are decomposed into vertical modes in order to give a dynamical framework for interpreting the observed fluctuations. Vertical modes at each mooring are fit to pressure perturbations using a Gauss-Markov inversion. Away from boundaries, the vertical structure is almost entirely described by the first baroclinic mode, as confirmed by high correlation between the original signal and reconstructions using only the first baroclinic mode. These first baroclinic motions are also highly coherent with altimetric sea surface height (SSH). Within a Rossby radius (45 km) of the western and eastern boundaries, however, the decomposition contains significant variance at higher modes, and there is a corresponding decrease in the agreement between SSH and either the original signal or the first baroclinic mode reconstruction. Compared to the full transport signal, transport fluctuations described by the first baroclinic mode represent <25 km of the variance within 10 km of the western boundary, in contrast to 60 km at other locations. This decrease occurs within a Rossby radius of the western boundary. At the eastern boundary, a linear combination of many baroclinic modes is required to explain the observed vertical density profile of the seasonal cycle, a result that is consistent with an oceanic response to wind-forcing being trapped to the eastern boundary

hMMS2 serves a redundant role in human PCNA polyubiquitination

<p>Abstract</p> <p>Background</p> <p>In yeast, DNA damage leads to the mono and polyubiquitination of the sliding clamp PCNA. Monoubiquitination of PCNA is controlled by RAD18 (E3 ligase) and RAD6 (E2 conjugating enzyme), while the extension of the monoubiquitinated PCNA into a polyubiquitinated substrate is governed by RAD5, and the heterodimer of UBC13/MMS2. Each modification directs a different branch of the DNA damage tolerance pathway (DDT). While PCNA monoubiquitination leads to error-prone bypass via TLS, biochemical studies have identified MMS2 along with its heteromeric partner UBC13 to govern the error-free repair of DNA lesions by catalyzing the formation of lysine 63-linked polyubiquitin chains (K63-polyUb). Recently, it was shown that PCNA polyubiquitination is conserved in human cells and that this modification is dependent on RAD18, UBC13 and SHPRH. However, the role of hMMS2 in this process was not specifically addressed.</p> <p>Results</p> <p>In this report we show that mammalian cells in which MMS2 was reduced by siRNA-mediated knockdown maintains PCNA polyubiquitination while a knockdown of RAD18 or UBC13 abrogates PCNA ubiquitination. Moreover, the additional knockdown of a UEV1A (MMS2 homolog) does not deplete PCNA polyubiquitination. Finally, mouse embryonic stem cells null for MMS2 with or without the additional depletion of mUEV1A continue to polyubiquitinated PCNA with normal kinetics.</p> <p>Conclusion</p> <p>Our results point to a high level of redundancy in the DDT pathway and suggest the existence of another hMMS2 variant (hMMSv) or complex that can compensate for its loss.</p

Wnt, Hedgehog and Junctional Armadillo/β-Catenin Establish Planar Polarity in the Drosophila Embryo

To generate specialized structures, cells must obtain positional and directional information. In multi-cellular organisms, cells use the non-canonical Wnt or planar cell polarity (PCP) signaling pathway to establish directionality within a cell. In vertebrates, several Wnt molecules have been proposed as permissible polarity signals, but none has been shown to provide a directional cue. While PCP signaling components are conserved from human to fly, no PCP ligands have been reported in Drosophila. Here we report that in the epidermis of the Drosophila embryo two signaling molecules, Hedgehog (Hh) and Wingless (Wg or Wnt1), provide directional cues that induce the proper orientation of Actin-rich structures in the larval cuticle. We further find that proper polarity in the late embryo also involves the asymmetric distribution and phosphorylation of Armadillo (Arm or β-catenin) at the membrane and that interference with this Arm phosphorylation leads to polarity defects. Our results suggest new roles for Hh and Wg as instructive polarizing cues that help establish directionality within a cell sheet, and a new polarity-signaling role for the membrane fraction of the oncoprotein Arm

Nanotools for Neuroscience and Brain Activity Mapping

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function

Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces

Embryogenesis is an extraordinarily robust process, exhibiting the ability to control tissue size and repair patterning defects in the face of environmental and genetic perturbations. The size and shape of a developing tissue is a function of the number and size of its constituent cells as well as their geometric packing. How these cellular properties are coordinated at the tissue level to ensure developmental robustness remains a mystery; understanding this process requires studying multiple concurrent processes that make up morphogenesis, including the spatial patterning of cell fates and apoptosis, as well as cell intercalations. In this work, we develop a computational model that aims to understand aspects of the robust pattern repair mechanisms of the Drosophila embryonic epidermal tissues. Size control in this system has previously been shown to rely on the regulation of apoptosis rather than proliferation; however, to date little work has been done to understand the role of cellular mechanics in this process. We employ a vertex model of an embryonic segment to test hypotheses about the emergence of this size control. Comparing the model to previously published data across wild type and genetic perturbations, we show that passive mechanical forces suffice to explain the observed size control in the posterior (P) compartment of a segment. However, observed asymmetries in cell death frequencies across the segment are demonstrated to require patterning of cellular properties in the model. Finally, we show that distinct forms of mechanical regulation in the model may be distinguished by differences in cell shapes in the P compartment, as quantified through experimentally accessible summary statistics, as well as by the tissue recoil after laser ablation experiments

Using motionally-induced electric signals to indirectly measure ocean velocity: Instrumental and theoretical developments

The motion of conductive sea water through the earth's magnetic field generates electromagnetic (EM) fields through a process called motional induction. Direct measurements of oceanic electric fields can be easily converted to water velocities by application of a first order theory. This technique has been shown to obtain high quality velocities through instrumental advances and an accumulation of experience during the past decades. EM instruments have unique operational considerations and observe, for instance, vertically-averaged horizontal velocity (from stationary sensors) or vertical profiles of horizontal velocity (from expendable probes or autonomous profiling floats). The first order theory describes the dominant electromagnetic response, in which vertically-averaged and vertically-varying horizontal velocities are proportional to electric fields and electric currents, respectively. After discussions of the first order theory and deployment practices, operational capabilities are shown through recently published projects that describe stream-coordinate velocity structure of the Antarctic Circumpolar Current, quickly-evolving overflow events in the Denmark Strait, and time-development of momentum input into the ocean from a hurricane. A detailed analysis of the Gulf Stream at its separation point from the continental slope serves as a case study for interpreting EM measurements, including the incorporation of geophysical knowledge of the sediment. In addition, the first order approximation is tested by the many features at this location that contradict the approximation's underlying assumptions: sharp horizontal velocity gradients, steep topography, and thick and inhomogeneous sediments. Numerical modeling of this location shows that the first order assumption is accurate to a few percent (a few cm s-1) in almost all cases. The errors in depth-varying velocity are <3% (1-3 cm s-1), are substantiated by the direct observations, and can be corrected by iterative methods. Though errors in the depth-uniform velocity are <2 cm s-1 (<10%) at all locations except for the upper continental slope, where apparent but unresolved meander events in water shallower than 500 m can generate depth-uniform errors of order 30%, there are not sufficient observations to confirm these errors directly. Errors in the first order approximation at this location show no non-linear increase due to the joint effect of steep topography and horizontal velocity gradients. Using motional induction in the world's oceans, aside from stationary measurements when depth-uniform ocean currents meander across topography, these results suggest that the first order approximation is accurate to within 1-2 cm s-1 or less in almost all regions of the ocean, an error similar to the instrumental accuracy of EM instruments. © 2011 Elsevier Ltd. All rights reserved