Browse Articles

Proteasomes accumulate in the plant apoplast where they participate in microbe-associated molecular pattern (MAMP)-triggered pathogen defense

Abstract Akin to mammalian extracellular fluids, the plant apoplastic fluid (APF) contains a unique collection of proteins, RNAs, and vesicles that drive many physiological processes ranging from cell wall assembly to defense against environmental challenges. Using an improved method to enrich for the Arabidopsis APF, we better define its composition and discover that the APF harbors active proteasomes though microscopic detection, proteasome-specific activity and immunological assays, and mass spectrometry showing selective enrichment of the core protease. Functional analysis of extracellular (ex)-proteasomes reveals that they help promote basal pathogen defense through proteolytic release of microbe-associated molecular patterns (MAMPs) such as flg22 from bacterial flagellin that induce protective reactive-oxygen-species (ROS) bursts. Flagellin-triggered ROS is also strongly suppressed by the enigmatic Pseudomonas syringae virulence effector syringolin-A that blocks ex-proteasome activity. Collectively, we provide a deep catalog of apoplast proteins and evidence that ex-proteasomes participate in the evolving arms race between pathogens and their plant hosts.

Gait impairment associated with neuroimaging biomarkers in Alzheimer’s disease

Isolating non-adiabatically enhanced ground state quantum beats through two-dimensional electronic spectroscopy

Resonant vibrational–electronic (vibronic) couplings in donor–acceptor systems may play a crucial role in driving non-adiabatic internal conversion reported in natural photosynthesis, organic photovoltaic polymers, and singlet exciton fission. Quantum beats arising from impulsive excitation are often employed as spectroscopic reporters of the specific vibrational modes driving this process. However, distinguishing these promoter modes from spectator modes, which do not participate in vibronic mixing and simply accompany ultrafast internal conversion, remains a challenge. This is so because vibrational quantum beats arising from uncoupled monomers can modulate pump–probe transients by themselves. In this paper, we show that vibronic mixing induces quantum beats whose amplitude is anisotropic with respect to the polarization of the light. We propose a readily implementable polarization-controlled two-dimensional electronic spectroscopy experiment to uniquely identify signatures of excited state vibronic resonance using ground state quantum beats by discriminating against vibrational motions (and corresponding quantum beats) that are simply spectators. Through analytical expressions and simulation of two-dimensional electronic spectra, we show that the resulting 2D spectra are expected to exhibit distinct spectral lineshapes with a strong temperature dependence that arises solely due to the excited state vibronic mixing. Our findings suggest an interesting experiment to decipher the presence of excited state vibronic resonances.

Failure to replicate a superiority effect in crowding

Allosteric modulation and direct activation of glycine receptors by a tricyclic sulfonamide

Ionic association and Wien effect in 2D confined electrolytes

Recent experimental advances in nanofluidics have allowed to explore ion transport across molecular-scale pores, in particular, for iontronic applications. Two-dimensional nanochannels—in which a single molecular layer of electrolyte is confined between solid walls—constitute a unique platform to investigate fluid and ion transport in extreme confinement, highlighting unconventional transport properties. In this work, we study ionic association in 2D nanochannels, and its consequences on non-linear ionic transport, using both molecular dynamics simulations and analytical theory. We show that under sufficient confinement, ions assemble into pairs or larger clusters in a process analogous to a Kosterlitz–Thouless transition, here modified by the dielectric confinement. We further show that the breaking of pairs results in an electric-field dependent conduction, a mechanism usually known as the second Wien effect. However the 2D nature of the system results in non-universal, temperature-dependent, scaling of the conductivity with electric field, leading to ionic coulomb blockade in some regimes. A 2D generalization of the Onsager theory fully accounts for the non-linear transport. These results suggest ways to exploit electrostatic interactions between ions to build new nanofluidic devices.

Elliptical ejecta of asteroid Dimorphos is due to its surface curvature

Finite element analysis for pullout resistance and progressive failure of strip anchors in strain softening marine soils

Decoherence dynamics in molecular qubits: Exponential, Gaussian and beyond

In this work, we examine how the structure of system–bath interactions can determine commonly encountered temporal decoherence patterns, such as Gaussian and exponential decay, in molecular and other qubits coupled to a thermal bosonic bath. The analysis, based on a pure dephasing picture that admits analytical treatment, shows that decoherence, in general, is neither purely Gaussian nor exponential but rather the exponential of oscillatory functions, with periods determined by the bath’s frequencies. For initially unentangled qubit-bath states, Gaussian decay is always present at early times. It becomes increasingly dominant with increasing temperature, qubit–bath interaction strength, and bath correlation time. Initial system–bath entanglement that arises due to displacement in the position of the bath states preserves the Gaussian decay. By contrast, strict exponential decay arises only in very specific models that we isolate. However, it becomes dominant for times longer than the bath correlation time or for early times when there is initial entanglement due to momentum displacement of the bath states. For molecular electronic decoherence, the long-time exponential regime plays a limited role as it emerges after most coherence is lost. Thus, the Gaussian decay provides a more suitable (albeit imperfect) model of such decoherence. Furthermore, we discuss the connection between electronic decoherence dynamics and electronic spectroscopic line shape theory, where Gaussian spectral peaks correspond to Gaussian coherence decay and Lorentzian peaks correspond to exponential coherence decay. We find that Gaussian spectral peaks, usually associated with inhomogeneous broadening, can emerge from the entangling unitary system–bath dynamics even when there is no inhomogeneity in the initial conditions.

The DYT6 dystonia causative protein THAP1 is responsible for proteasome activity via PSMB5 transcriptional regulation

Abstract The proteasome plays a pivotal role in protein degradation, and its impairment is associated with various pathological conditions, including neurodegenerative diseases. It is well understood that Nrf1 coordinates the induction of all proteasome genes in response to proteasome dysfunction. However, the molecular mechanism regulating the basal expression of the proteasome remains unclear. Here we identify the transcription factor THAP1, the causative gene of DYT6 dystonia, as a regulator of proteasome activity through a genome-wide genetic screen. We demonstrated that THAP1 directly regulates the expression of the PSMB5 gene, which encodes the central protease subunit β5. Depletion of THAP1 disrupts proteasome assembly, leading to reduced proteasome activity and the accumulation of ubiquitinated proteins. These findings uncover a regulatory mechanism for the proteasome and suggest a potential role for proteasome dysfunction in the pathogenesis of dystonia.

Changes in long-term life expectancy and years of life lost following the Great East Japan Earthquake in Fukushima Prefecture

Abstract Prolonged evacuation after disasters increases the risks of diseases and challenges in healthcare access. This study aimed to analyze changes in life expectancy (LE) and years of life lost (YLL) in Fukushima Prefecture after the Great East Japan Earthquake. LE and YLL were calculated based on a dataset of 276,314 deaths in Fukushima Prefecture from January 2006 to December 2018 and were aggregated and compared in three time periods: 2006–2010, 2012–2015, and 2016–2018. LE and YLL were obtained using a life table method, focusing on four major causes of death: heart diseases, cerebrovascular diseases, pneumonia, and cancers. The overall LE for both males and females in Fukushima prefecture showed an increasing trend in all three periods. Notably, in 2012–2015, the increase in LE and YLL due to cancer was greater in areas with evacuation zones compared to those without evacuation zones. In contrast, in 2016–2018, a notable decrease in YLL due to cerebrovascular diseases for both males and females and due to heart diseases for males was observed in areas with evacuation zones compared to areas without. LE continued to rise in Fukushima Prefecture despite the significant long-term impact of the disaster on the population. Post-disaster changes in LE and YLL differed between areas with and without evacuation zones, suggesting that implementation of effective measures and policies in the region contributed to a successful recovery. This study may be crucial for evaluating future health measures and conditions in Fukushima Prefecture.

Photoelectron–remnant interaction effect on remnant wavefunction in low-kinetic energy electron detachment events

Low-kinetic energy photoelectron detachment experiments have revealed the unexpected dependence of transition intensities on photon energy, which is hypothesized to result from time-dependent coupling between low-kinetic energy photoelectrons and the remnant molecule. This study explores how the kinetic energy and detachment axis of the photoelectron influence the interaction and modify the final remnant electronic structure. Using real-time simulations on several model systems (H2, NO, N2, and C2 hydrocarbons), this study demonstrates that electron–remnant interactions are strongly dependent on the detachment orientation, electron kinetic energy, and remnant electronic structure. The results reveal that higher kinetic energies lead to significant nonadiabatic transitions, while lower kinetic energies yield more adiabatic behavior. While generally lower kinetic energies show prolonged electron–remnant interactions, the extent of temporal and spatial interactions does not necessarily vary linearly with the kinetic energy, and the final remnant electronic structure is found to be very sensitive to the exact nature of the photoelectron–remnant interactions. In addition, the point charge model employed for the photoelectron provides a useful approach for the deconvolution of more complete simulations to provide deeper insights into the specific photoelectron–remnant interactions that determine the eventual remnant wavefunction. The findings underscore the importance of considering both temporal and spatial electron dynamics in understanding low-kinetic energy photodetachment processes and provide a foundation for a further exploration of electron–molecule interactions in the low-energy regime.

Model-constrained deep learning for online fault diagnosis in Li-ion batteries over stochastic conditions

Fairness identification of large language models in recommendation

Erratum: “Modeling of collision-induced excitation and quenching of atomic nitrogen” [J. Chem. Phys. 161, 014104 (2024)]

Morphology of ejecta features from the impact on asteroid Dimorphos

Abstract Hypervelocity impacts play a significant role in the evolution of asteroids, causing material to be ejected and partially reaccreted. However, the dynamics and evolution of ejected material in a binary asteroid system have never been observed directly. Observations of Double Asteroid Redirection Test (DART) impact on asteroid Dimorphos have revealed features on a scale of thousands of kilometers, including curved ejecta streams and a tail bifurcation originating from the Didymos system. Here we show that these features result naturally from the dynamical interaction of the ejecta with the binary system and solar radiation pressure. These mechanisms may be used to constrain the orbit of a secondary body, or to investigate the binary nature of an asteroid. Also, they may reveal breakup or fission events in active asteroids, and help determine the asteroid’s properties following an impact event. In the case of DART, our findings suggest that Dimorphos is a very weak, rubble-pile asteroid, with an ejecta mass estimated to be in the range of (1.1-5.5)×107 kg.

The superoxide dismutase mimetic TEMPOL modulates nicotine-induced hyperlocomotor activity and nicotine-taking behavior in male rats

On the entanglement of chromophore and solvent orbitals

Among various types of chromophore–solvent interactions, the entanglement of chromophore and solvent orbitals, when significant, can cause the chromophore frontier orbitals to spread over to nearby solvent molecules, introducing partial charge-transfer character to the lowest excitations of the chromophore and lowering the excitation energies. While highly intuitive, the physical details of such orbital entanglement effects on the excitation energies of chromophores have yet to be fully explored. Here, using two well-known biochromophores (oxyluciferin and p-hydroxybenzyledene imidazolinone) as examples, we show that the chromophore–solvent orbital entanglements can be elucidated using two quantum mechanical embedding schemes: density matrix embedding theory and absolutely localized molecular orbitals. However, there remains a great challenge to incorporate the orbital entanglement effect in combined quantum mechanical molecular mechanical (QM/MM) calculations, and we hope that our findings will stimulate the development of new methods in that direction.

Evaluation of Cas13d as a tool for genetic interaction mapping

Abstract Mapping genetic interactions (GIs) is crucial for understanding genetic network complexity. In this study, we investigate the utility of Cas13d, a CRISPR system targeting RNA, for GI mapping and compare it to Cas9 and Cas12a, two DNA nucleases commonly used for GI mapping. We find that Cas13d induces faster target gene perturbation and generates more uniform cell populations with double perturbations than Cas9 or Cas12a. We then encounter Cas13d gRNA-gRNA interference when concatenating gRNAs targeting different genes into one gRNA array, which we overcome by a dual promoter gRNA expression strategy. Moreover, by concatenating three gRNAs targeting the same gene into one array, we are able to maximize the Cas13d-mediated knockdown effects. Combining these strategies enhances proliferation phenotypes while reducing library size and facilitates reproducible quantification of GIs in oncogenic signaling pathways. Our study highlights the potential of Cas13d for GI mapping, promising advancements in understanding therapeutically relevant drug response pathways.

Goos–Hänchen shift of inelastically scattered spin-wave beams and cascade nonlinear magnon processes

Abstract We study, using micromagnetic simulations, the inelastic scattering of spin-wave beams on edge-localized spin-wave modes in a thin ferromagnetic film. In the splitting and confluence processes, the new spin-wave beams are generated with frequencies shifted by the edge-mode frequency. We report that inelastically scattered spin-wave beams in both processes not only change their direction of propagation but also undergo lateral shifts along the interface, analogous to the Goos–Hänchen effect known in optics. These shifts of inelastically scattered beams, for a few special cases described in the paper, can be in the range of several wavelengths, which is larger than the Goos–Hänchen shift of elastically reflected beam. Unexpectedly, at selected frequencies, we found a significant increase in the value of the lateral shifts of the scattered spin-wave beams formed in the confluence process. We show that this effect is associated with the cascading nonlinear processes taking place at the edge of the film and involving the primary edge spin wave. Our results make an important contribution to the understanding of the nonlinear nature of spin waves and provide a way to exploit it in signal processing with magnons.