Physical Coupling Mechanisms Research Articles

Structural basis of mRNA decay by the human exosome-ribosome supercomplex.

The interplay between translation and mRNA decay is widespread in human cells1-3. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largelyby the cytoplasmic exosome4-9, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. 10-16). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear7,17,18. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.

Coupling Analysis between the Transonic Buffeting Flow and a Heaving Supercritical Airfoil Based on Dynamic Mode Decomposition

The coupling between a transonic buffeting flow and a supercritical airfoil with harmonic heave motion was studied. A parametric space of the heave frequency and amplitude was investigated using a verified fluid–structural interaction framework. The spatial-temporal flow pattern around the transonic airfoil was studied using dynamic mode decomposition (DMD) to unveil the physical coupling mechanism. The results show three types of flow responses under the heave motion: (I) A buffet frequency response with a λ-shape shock wave structure and recirculation zone at the shock foot. The aerodynamic performance was alike the scenario in the flow past the stationary airfoil. (II) A transitional response with a weakened shock and enhanced boundary layer. The aerodynamic performance deteriorated sharply at f=fbuffet and recovered after the frequency was past the buffet frequency. The flow pattern was characterized by a double-shock structure that interacted with the enhanced boundary layer. (III) A heave frequency response with the dominant heave motion. The variance in the aerodynamic loading increased significantly at f>fbuffet and there were higher heave amplitudes in this stage. The driving motion of the airfoil transferred the energy of the buffet mode to the boundary layer with a more even energy balance according to the energy contribution analysis of the DMD modes.

Airglow-imager based observation of possible influences of subtropical mesospheric gravity waves on F-region ionosphere over Jammu & Kashmir, India

As a joint research collaboration between the National Atmospheric Research Laboratory (NARL), and the University of Kashmir (KU), NARL installed an all-sky airglow CCD imager (with centre wavelengths of 630 nm, 557.7 nm [2 nm band widths] and 840 nm [150 nm wide band with blocking notch at 866 nm to avoid the contamination of molecular oxygen emissions]) in the University campus in Srinagar (75°E, 34°N, geographic), Jammu and Kashmir, India (western Himalayan region). To understand the upper atmospheric dynamics and ionospheric electrodynamics and their associated physical coupling mechanisms, the imager observes airglow emissions of OH molecules (~ 85 km height; 840 nm) and atomic oxygen occurring at the heights of ~ 97 km (557.7 nm) and ~ 250 km (630 nm). Airglow observations in Kashmir commenced in the night of August 11, 2017 and the present work reports on the characteristics of first-time observation of Medium Scale Travelling Ionospheric Disturbances (MSTIDs with horizontal wavelengths of ~ 100–300 km) over Kashmir region during 20:30—22:30 IST (Indian standard time) on August 15, 2017 (India independence day). Initially, the phase front of MSTIDs was aligned along the north-west and south-east direction and moved at ~ 57 m/s towards the south-west direction and finally the westward direction by aligning along the meridian before they disappeared. Along with SAMI-3 ionospheric model simulations, simultaneous multiwavelength airglow observations indicate that secondary gravity waves generated due to dissipation of upward propagating mesospheric gravity waves in the heights of ~ 85–95 km would have contributed to the generation of MSTIDs in the F region ionospheric plasma through electrodynamical coupling between the E and F region (Perkins instability) ionosphere.

Efficient mate finding in planktonic copepods swimming in turbulence.

Zooplankton live in dynamic environments where turbulence may challenge their limited swimming abilities. How this interferes with fundamental behavioral processes remains elusive. We reconstruct simultaneously the trajectories of flow tracers and calanoid copepods and we quantify their ability to find mates when ambient flow imposes physical constrains on their motion and impairs their olfactory orientation. We show that copepods achieve high encounter rates in turbulence due to the contribution of advection and vigorous swimming. Males further convert encounters within the perception radius to contacts and then to mating via directed motion toward nearby organisms within the short time frame of the encounter. Inertial effects do not result in preferential concentration, reducing the geometric collision kernel to the clearance rate, which we model accurately by superposing turbulent velocity and organism motion. This behavioral and physical coupling mechanism may account for the ability of copepods to reproduce in turbulent environments.

Thermo-magneto-elastoplastic coupling model of metal magnetic memory testing method for ferromagnetic materials

Metal magnetic memory (MMM) testing (also known as micro-magnetic testing) is a new non-destructive electromagnetic testing method that can diagnose ferromagnetic materials at an early stage by measuring the MMM signal directly on the material surface. Previous experiments have shown that many factors affect MMM signals, in particular, the temperature, the elastoplastic state, and the complex environmental magnetic field. However, the fact that there have been only a few studies of either how these factors affect the signals or the physical coupling mechanisms among them seriously limits the industrial applications of MMM testing. In this paper, a nonlinear constitutive relation for a ferromagnetic material considering the influences of temperature and elastoplastic state is established under a weak magnetic field and is used to establish a nonlinear thermo-magneto-elastoplastic coupling model of MMM testing. Comparing with experimental data verifies that the proposed theoretical model can accurately describe the thermo-magneto-elastoplastic coupling influence on MMM signals. The proposed theoretical model can predict the MMM signals in a complex environment and so is expected to provide a theoretical basis for improving the degree of quantification in MMM testing.

Non‐invasive piezoelectric detection of heartbeat rate and blood pressure

A non-invasive piezoelectric-based sheet sensor is utilised for the deliberate measurement of heartbeat rate and blood pressure. It may consist of a single sheet to capture various temporal signals or it can be formed as an array of small piezoelectric sensors to capture the temporal and spatial cardiac signals over the chest to give an added spatial granularity on top of the localised temporal signal. The mechanical activity of the heart will cause the piezoelectric sheet to deform, and thus produce a voltage signal. To count the heartbeat rate, a mechanical model has been developed using the corresponding electric waveform; a compression ratio is defined due to the delay as a result of the physical coupling mechanism. Validation of the obtained results has been performed using conventional techniques and apparatus. The quantitative assessment shows low errors when compared with other conventional meters.

Photomechanical Responses in Drosophila Photoreceptors

Phototransduction in Drosophila microvillar photoreceptor cells is mediated by a G protein-activated phospholipase C (PLC). PLC hydrolyzes the minor membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP(2)), leading by an unknown mechanism to activation of the prototypical transient receptor potential (TRP) and TRP-like (TRPL) channels. We found that light exposure evoked rapid PLC-mediated contractions of the photoreceptor cells and modulated the activity of mechanosensitive channels introduced into photoreceptor cells. Furthermore, photoreceptor light responses were facilitated by membrane stretch and were inhibited by amphipaths, which alter lipid bilayer properties. These results indicate that, by cleaving PIP(2), PLC generates rapid physical changes in the lipid bilayer that lead to contractions of the microvilli, and suggest that the resultant mechanical forces contribute to gating the light-sensitive channels.

Variations on Sun’s role in climate change

It is good that Physics Today reported on the work of Nicola Scafetta and Bruce West. They have done by far the best work in relating solar variability to terrestrial climate, bringing sophistication and rigor to a field dominated mostly by unsupportable positions that the Sun’s effect is negligible on the one hand, or is responsible for nearly all observed global warming on the other. That solar variability has appreciable coupling to Earth’s climate becomes obvious when an observer notes the imprint of the Schwabe sunspot cycle on the climate temperature record. 1 1. N. Scafetta, B. J. West, Geophys. Res. Lett. 32, L18713 (2005), fig. 2. https://doi.org/10.1029/2005GL023849 The identical scaleless noise spectra for solar and terrestrial climate fluctuations provide additional support for coupling and for regarding the Earth–Sun network as a complex system. Unfortunately, the Intergovernmental Panel on Climate Change clings to its position that solar variability effects are negligible, to the detriment of its credibility. Given known solar variability, the IPCC position can be rationalized only if the so-called hockey-stick global temperature reconstruction, 2 2. M. E. Mann, P. D. Jones, Geophys. Res. Lett. 30, 1820 (2003). https://doi.org/10.1029/2003GL017814 which shows little natural variation, is valid. However, that reconstruction is at odds with natural history and has been shown to be statistically flawed; 3 3. E. J. Wegman, D. W. Scott, Y. H. Said, Ad Hoc Committee Report on the “Hockey Stick” Global Climate Reconstruction, Committee on Energy and Commerce, US House of Representatives, Washington, DC (2006), available at http://www.climateaudit.org/pdf/others/07142006_Wegman_Report.pdf. more recent reconstructions 4,5 4. A. Moberg et al. , Nature 433, 613 (2005). https://doi.org/10.1038/nature03265 5. C. Loehle, Energy Environ. 18, 1049 (2007). https://doi.org/10.1260/095830507782616797 show much more natural variation. The fact that general circulation models do not give appreciable Sun–Earth coupling merely shows that they are leaving out essential physics—by no means their only serious shortcoming. Unfortunately, the phenomenological approach of Scafetta and West only informs us of the magnitude of the climatic impact of solar variability. It does not shed light on the actual physical mechanisms, so it points to the need for more research on physical coupling mechanisms between those interacting complex systems. It is also unfortunate that Physics Today chose to feature this work as an Opinion, rather than giving it the fullfledged article status it deserves. The readership should be informed in more detail about this important work.REFERENCESSection:ChooseTop of pageREFERENCES <<1. N. Scafetta, B. J. West, Geophys. Res. Lett. 32, L18713 (2005), fig. 2. https://doi.org/10.1029/2005GL023849 , Google ScholarCrossref, ISI2. M. E. Mann, P. D. Jones, Geophys. Res. Lett. 30, 1820 (2003). https://doi.org/10.1029/2003GL017814 , Google ScholarCrossref, ISI3. E. J. Wegman, D. W. Scott, Y. H. Said, Ad Hoc Committee Report on the “Hockey Stick” Global Climate Reconstruction, Committee on Energy and Commerce, US House of Representatives, Washington, DC (2006), available at http://www.climateaudit.org/pdf/others/07142006_Wegman_Report.pdf. Google Scholar4. A. Moberg et al. , Nature 433, 613 (2005). https://doi.org/10.1038/nature03265 , Google ScholarCrossref, ISI5. C. Loehle, Energy Environ. 18, 1049 (2007). https://doi.org/10.1260/095830507782616797 , Google ScholarCrossref© 2008 American Institute of Physics.

A coupled tire structure/acoustic cavity model

The dynamic characteristic of the tires is a key factor in the road-induced interior noise in passenger vehicles. The tire acoustic cavity is a very important factor in the tire dynamics and it must be considered in analyses. This paper describes a closed form analytical model for tire-wheel structures. In order to incorporate the dynamics of the cavity on the tire response, the tire acoustic-structure coupled problem is solved simultaneously. The tire is modeled as an annular cylindrical shell where only the outside shell is flexible, i.e. tire sidewalls and wheel are assumed rigid. From the analytical solution of the eigenproblems, both the tire structure and cavity acoustic responses are expanded in terms of their eigenfunctions. The main objective of the model is to have an efficient tool to investigate the physical coupling mechanisms between the acoustic cavity and the tire structure without the need of complicated numerical model such as finite elements. The result shows that the proposed model captures the main mechanisms of the effect of the tire air acoustic on the tire dynamics.

Capacitative Ca(2+) entry in vascular endothelial cells is mediated via pathways sensitive to 2 aminoethoxydiphenyl borate and xestospongin C.

1. Agonists increase endothelial cell intracellular Ca(2+), in part, by capacitative entry, which is triggered by the filling state of intracellular Ca(2+) stores. It has been suggested that depletion of endoplasmic reticulum (ER) Ca(2+) stores either leads to a physical coupling between the ER and a plasma membrane channel, or results in production of an intracellular messenger which affects the gating of membrane channels. As an axis involving the IP(3) receptor has been implicated in a physical coupling mechanism the aim of this study was to examine the effects of the putative IP(3) receptor antagonists/modulators, 2 aminoethoxydiphenyl borate (2APB) and xestospongin C, on endothelial cell Ca(2+) entry. 2. Studies were conducted in fura 2 loaded cultured bovine aortic endothelial cells and endothelial cells isolated from rat heart. 3. 2APB (30 - 300 microM) inhibited Ca(2+) entry induced by both agonists (ATP 1 microM, bradykinin 0.1 microM) and receptor-independent mechanisms (thapsigargin 1 microM, ionomycin 0.5 and 5 microM). 2APB did not diminish endothelial cell ATP-induced production of IP(3) nor effect in vitro binding of [(3)H]-IP(3) to an adrenal cortex binding protein. Capacitative Ca(2+) entry was also blocked by disruption of the actin cytoskeleton with cytochalasin (100 nM) while the initial Ca(2+) release phase was unaffected. 4. Similarly to 2APB, xestospongin C (3 - 10 microM) inhibited ATP-induced Ca(2+) release and capacitative Ca(2+) entry. Further, xestospongin C inhibited capacitative Ca(2+) entry induced by thapsigargin (1 microM) and ionomycin (0.5 microM). 5. The data are consistent with a mechanism of capacitative Ca(2+) entry in vascular endothelial cells which requires (a) IP(3) receptor binding and/or an event distal to the activation of the ER receptor and (b) a spatial relationship, dictated by the cytoskeleton, between Ca(2+) release and entry pathways.

Thermodynamics of Symport and Antiport Catalyzed by Cloned or Native Transporters

Thermodynamic measurements are required to confirm whether cloned transport-associated proteins in a membrane truly constitute a functional transport system. Symport or antiport, catalyzed by native systems or by cloned proteins in membranes, can lead to steady-state intracellular accumulation of solute when the electrochemical potentials of activator ion and solute are energetically coupled. Secondary active transport can occur if an appropriate physical coupling mechanism exists in the membrane. Driving forces for secondary active transport are ultimately established by primary active transport or respiration. Steep steady-state gradients of solute can be maintained when the ion:solute coupling ratio is greater than one and/or when coupling includes an electrical component. Although the steady-state accumulation of substrate is independent of the exact physical mechanism of transport, non-equilibrium and equilibrium transport kinetics aid in interpreting the rate, direction (symport versus antiport) and control of ion-coupled flux across a membrane. In some cases, the activator ion's chemical gradient alone is energetically adequate to maintain steady-state intracellular accumulation of solute, as demonstrated in invertebrate epithelial cells. To interpret accumulation ratios accurately, it is necessary to measure the intracellular activity coefficients for ions. For example, liquid ion-exchange microelectrode measurements demonstrate that over 30% of intracellular Na+ can be sequestered in epithelial cells.

Solar activity and Indian weather/climate

The literature on influences of solar activity on the Indian weather and climate is reviewed since the discovery of sunspot cycle. Fluctuations in solar activity are undoubtedly a factor affecting weather and climate. Although the results of some of the studies are conflicting, Indian weather and climate is, in general, inversely related to sunspots. However, the areal extent of floods in India seems to expand and contract in phase with the Hale double sunspot cycle, suggesting that the flood rhythm is in some manner controlled by long-term solar activity related to solar magnetic effects. All the evidences of solar influences on weather and climate may have practical implications in improving long-range forecasting of weather and climate, once the physical coupling mechanisms and their modification by other factors are clearly understood. Some of the promising plausible physical mechanisms for explaining solar effects on weather and climate are also discussed.

Initiation of non-tropical thunderstorms by solar activity

Correlative evidence accumulating since 1926 suggests that there must be some physical coupling mechanism between solar activity and thunderstorm occurrence in middle to high latitudes. Such a link may be provided by alteration of atmospheric electric parameters through the influence of cosmic ray decreases and/or high-energy solar protons associated with active solar events. Galactic cosmic ray decreases tend to enhance the electric field at low heights. The protons produce excess ionization near and above 20km, greatly increasing the atmospheric conductivity and possibly lowering the height of the electrosphere. Consequent effects near the solar proton cut-off latitude also lead to an enhancement of the atmospheric electric field near the surface. If appropriate meteorological conditions (warm moist air with updrafts) exist or develop during a solar event, the atmospheric electric field enhancement may be sufficient to trigger thunderstorm development. The suggested mechanism appears plausible enough to warrant a co-ordinated experimental effort involving satellite balloon and ground-based measurements of the possible forcing functions (solar protons and cosmic rays) and the responding atmospheric electrical and ionic species' characteristics.

EMP Coupling Through Cable Shields

Recent research in electromagnetic coupling between the interior and exterior of coaxial cables is described. Both tubular shields and shields with apertures are discussed with reference to the physical coupling mechanisms and their mathematical representations in terms of transmission-line models.

EMP coupling through cable shields

Recent research in electromagnetic coupling between the interior and exterior of coaxial cables is described. Both tubular shields and shields with apertures are discussed with reference to the physical coupling mechanisms and their mathematical representations in terms of transmission-line models.