Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells.

Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.

Visualization of translation reorganization upon persistent collision stress in mammalian cells.

Aberrantly slow mRNA translation leads to ribosome stalling and subsequent collision with the trailing neighbor. Ribosome collisions have recently been shown to act as stress sensors in the cell, with the ability to trigger stress responses balancing survival and apoptotic cell-fate decisions depending on the stress level. However, we lack a molecular understanding of the reorganization of translation processes over time in mammalian cells exposed to an unresolved collision stress. Here we visualize the effect of a persistent collision stress on translation using in situ cryo electron tomography. We observe that low dose anisomycin collision stress leads to the stabilization of Z-site bound tRNA on elongating 80S ribosomes, as well as to the accumulation of an off-pathway 80S complex possibly resulting from collision splitting events. We visualize collided disomes in situ, occurring on compressed polysomes and revealing a stabilized geometry involving the Z-tRNA and L1 stalk on the stalled ribosome, and eEF2 bound to its collided rotated-2 neighbor. In addition, non-functional post-splitting 60S complexes accumulate in the stressed cells, indicating a limiting Ribosome associated Quality Control clearing rate. Finally, we observe the apparition of tRNA-bound aberrant 40S complexes shifting with the stress timepoint, suggesting a succession of different initiation inhibition mechanisms over time. Altogether, our work visualizes the changes of translation complexes under persistent collision stress in mammalian cells, indicating how perturbations in initiation, elongation and quality control processes contribute to an overall reduced protein synthesis.

Continuous-Variable Entanglement Test in Driven Quantum Contacts.

The standard entanglement test using the Clauser-Horne-Shimony-Holt inequality is known to fail in mesoscopic junctions at finite temperatures. Since this is due to the bidirectional particle flow, a similar failure is expected to occur in an ac-driven contact. We develop a continuous-variable entanglement test suitable for electrons and holes that are created by the ac drive. At low enough temperatures the generalized Bell inequality is violated in junctions with low conductance or a small number of transport channels and with ac voltages which create few electron-hole pairs per cycle. Our ac-entanglement test depends on the total number of electron-hole pairs and on the distribution of probabilities of pair creations similar to the Fano factor.

Quantum phase slips in superconducting wires with weak inhomogeneities.

Quantum phase slips are traditionally considered in diffusive superconducting wires which are assumed homogeneous. We present a definite estimate for the amplitude of phase slips that occur at a weak inhomogeneity in the wire where local resistivity is slightly increased. We model such a weak link as a general coherent conductor and show that the amplitude is dominated by the topological part of the action. We argue that such weak links occur naturally in apparently homogeneous wires and adjust the estimate to that case. The fabrication of an artificial weak link would localize phase slips and facilitate a better control of the phase-slip amplitude.

Effects of metallic contacts on electron transport through graphene.

We report on a first-principles study of the conductance through graphene suspended between Al contacts as a function of junction length, width, and orientation. The charge transfer at the leads and into the freestanding section gives rise to an electron-hole asymmetry in the conductance and in sufficiently long junctions induces two conductance minima at the energies of the Dirac points for suspended and clamped regions, respectively. We obtain the potential profile along a junction caused by doping and provide parameters for effective model calculations of the junction conductance with weakly interacting metallic leads.

Elementary events of electron transfer in a voltage-driven quantum point contact.

We find that the statistics of electron transfer in a coherent quantum point contact driven by an arbitrary time-dependent voltage is composed of elementary events of two kinds: unidirectional one-electron transfers determining the average current and bidirectional two-electron processes contributing to the noise only. This result pertains at vanishing temperature while the extended Keldysh-Green's function formalism in use also enables the systematic calculation of the higher-order current correlators at finite temperatures.