Comprehensive structure and functional adaptations of the yeast nuclear pore complex.

Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.

Architecture and self-assembly of the jumbo bacteriophage nuclear shell.

Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2-4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.

Acoustic, Phononic, Brillouin Light Scattering and Faraday Wave-Based Frequency Combs: Physical Foundations and Applications.

Frequency combs (FCs)-spectra containing equidistant coherent peaks-have enabled researchers and engineers to measure the frequencies of complex signals with high precision, thereby revolutionising the areas of sensing, metrology and communications and also benefiting the fundamental science. Although mostly optical FCs have found widespread applications thus far, in general FCs can be generated using waves other than light. Here, we review and summarise recent achievements in the emergent field of acoustic frequency combs (AFCs), including phononic FCs and relevant acousto-optical, Brillouin light scattering and Faraday wave-based techniques that have enabled the development of phonon lasers, quantum computers and advanced vibration sensors. In particular, our discussion is centred around potential applications of AFCs in precision measurements in various physical, chemical and biological systems in conditions where using light, and hence optical FCs, faces technical and fundamental limitations, which is, for example, the case in underwater distance measurements and biomedical imaging applications. This review article will also be of interest to readers seeking a discussion of specific theoretical aspects of different classes of AFCs. To that end, we support the mainstream discussion by the results of our original analysis and numerical simulations that can be used to design the spectra of AFCs generated using oscillations of gas bubbles in liquids, vibrations of liquid drops and plasmonic enhancement of Brillouin light scattering in metal nanostructures. We also discuss the application of non-toxic room-temperature liquid-metal alloys in the field of AFC generation.

Understanding Self-Catalyzed Epitaxial Growth of III-V Nanowires toward Controlled Synthesis.

The self-catalyzed growth of III-V nanowires has drawn plenty of attention due to the potential of integration in current Si-based technologies. The homoparticle-assisted vapor-liquid-solid growth mechanism has been demonstrated for self-catalyzed III-V nanowire growth. However, the understandings of the preferred growth sites of these nanowires are still limited, which obstructs the controlled synthesis and the applications of self-catalyzed nanowire arrays. Here, we experimentally demonstrated that thermally created pits could serve as the preferred sites for self-catalyzed InAs nanowire growth. On that basis, we performed a pregrowth annealing strategy to promote the nanowire density by enhancing the pits formation on the substrate surface and enable the nanowire growth on the substrate that was not capable to facilitate the growth. The discovery of the preferred self-catalyzed nanowire growth sites and the pregrowth annealing strategy have shown great potentials for controlled self-catalyzed III-V nanowire array growth with preferred locations and density.

Arithmetic with optical topological charges in stepwise-excited Rb vapor.

We report on experimentally observed addition, subtraction, and cancellation of orbital angular momentum (OAM) in the process of parametric four-wave mixing that results in frequency up- and down-converted emission in Rb vapor. Specific features of OAM transfer from resonant laser fields with different optical topological charges to the spatially and temporally coherent blue light (CBL) have been considered. We have observed the conservation of OAM in nonlinear wave mixing in a wide range of experimental conditions, including a noncollinear geometry of the applied laser beams, and furthermore, that the CBL accumulates the total OAM of the applied laser light. Spectral and power dependences of vortex and plane wavefront blue light beams have been compared.

A reusable unsupported rhenium nanocrystalline catalyst for acceptorless dehydrogenation of alcohols through γ-C-H activation.

Rhenium nanocrystalline particles (Re NPs), of 2 nm size, were prepared from NH4ReO4 under mild conditions in neat alcohol. The unsupported Re NPs convert secondary and benzylic alcohols to ketones and aldehydes, respectively, through catalytic acceptorless dehydrogenation (AD). The oxidant- and acceptor-free neat dehydrogenation of alcohols to obtain dihydrogen gas is a green and atom-economical process for making carbonyl compounds. Secondary aliphatic alcohols give quantitative conversion and yield. Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Re K-edge X-ray absorption near-edge structure (XANES), and X-ray absorption fine structure (EXAFS) data confirmed the characterization of the Re NPs as metallic rhenium with surface oxidation to rhenium(IV) oxide (ReO2). Isotope labeling experiments revealed a novel γ-CH activation mechanism for AD of alcohols.

An intron endonuclease facilitates interference competition between coinfecting viruses.

Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. In this work, we studied intron-encoded homing endonuclease gp210 in bacteriophage ΦPA3 and found that it contributes to viral competition by interfering with the replication of a coinfecting phage, ΦKZ. We show that gp210 targets a specific sequence in ΦKZ, which prevents the assembly of progeny viruses. This work demonstrates how a homing endonuclease can be deployed in interference competition among viruses and provide a relative fitness advantage. Given the ubiquity of homing endonucleases, this selective advantage likely has widespread evolutionary implications in diverse plasmid and viral competition as well as virus-host interactions.

The Molecular Architecture of the Nuclear Basket.

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.

Effects of coupling, bubble size, and spatial arrangement on chaotic dynamics of microbubble cluster in ultrasonic fields.

Microbubble clustering may occur when bubbles become bound to targeted surfaces or are grouped by acoustic radiation forces in medical diagnostic applications. The ability to identify the formation of such clusters from the ultrasound echoes may be of practical use. Nonlinear numerical simulations were performed on clusters of microbubbles modeled by the modified Keller-Miksis equations. Encapsulated bubbles were considered to mimic practical applications but the aim of the study was to examine the effects of inter-bubble spacing and bubble size on the dynamical behavior of the cluster and to see if chaotic or bifurcation characteristics could be helpful in diagnostics. It was found that as microbubbles were clustered closer together, their oscillation amplitude for a given applied ultrasound power was reduced, and for inter-bubble spacing smaller than about ten bubble radii nonlinear subharmonics and ultraharmonics were eliminated. For clustered microbubbles, as for isolated microbubbles, an increase in the applied acoustic power caused bifurcations and transition to chaos. The bifurcations preceding chaotic behavior were identified by Floquet analysis and confirmed to be of the period-doubling type. It was found that as the number of microbubbles in a cluster increased, regularization occurred at lower ultrasound power and more windows of order appeared.

Laser shock-based platform for controllable forming of nanowires.

One-dimensional nanomaterials have attracted a great deal of research interest in the past few decades due to their unique mechanical, electrical, and optical properties. Changing the shape of nanowires (NWs) is both challenging and crucial to change the property and open wide functions of NWs, such as strain engineering, electronic transport, mechanical properties, band structure, and quantum properties, etc. Here we report a scalable strategy to conduct cutting, bending, and periodic straining of NWs by making use of laser shock pressure. Three-dimensional shaping of silver NWs is demonstrated, during which the Ag NWs exhibit very good ductility (strain-to-failure reaches 110%). Meanwhile, the high electrical conductivity of Ag NWs could retain well under controlled laser shock pressure. The microstructure observation indicates that the main deformation mechanism in Ag NWs under dynamic loading is formation of twinning and stacking fault, while dislocation motion and pile-up is less obvious. This method could be applied to semiconductor NWs as well.

A mobile intron facilitates interference competition between co-infecting viruses.

Mobile introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. Here we studied a mobile intron in bacteriophage ΦPA3 and found its homing endonuclease gp210 contributes to viral competition by interfering with the virogenesis of co-infecting phage ΦKZ. We show that gp210 targets a specific sequence in its competitor ΦKZ, preventing the assembly of progeny viruses. This work reports the first demonstration of how a mobile intron can be deployed to engage in interference competition and provide a reproductive advantage. Given the ubiquity of introns, this selective advantage likely has widespread evolutionary implications in nature.

Neural echo state network using oscillations of gas bubbles in water.

In the framework of physical reservoir computing (RC), machine learning algorithms designed for digital computers are executed using analog computerlike nonlinear physical systems that can provide energy-efficient computational power for predicting time-dependent quantities that can be found using nonlinear differential equations. We suggest a bubble-based RC (BRC) system that combines the nonlinearity of an acoustic response of a cluster of oscillating gas bubbles in water with a standard echo state network (ESN) algorithm that is well suited to forecast chaotic time series. We confirm the plausibility of the BRC system by numerically demonstrating its ability to forecast certain chaotic time series similarly to or even more accurately than ESN.

Biomechanical Sensing Using Gas Bubbles Oscillations in Liquids and Adjacent Technologies: Theory and Practical Applications.

Gas bubbles present in liquids underpin many natural phenomena and human-developed technologies that improve the quality of life. Since all living organisms are predominantly made of water, they may also contain bubbles-introduced both naturally and artificially-that can serve as biomechanical sensors operating in hard-to-reach places inside a living body and emitting signals that can be detected by common equipment used in ultrasound and photoacoustic imaging procedures. This kind of biosensor is the focus of the present article, where we critically review the emergent sensing technologies based on acoustically driven oscillations of bubbles in liquids and bodily fluids. This review is intended for a broad biosensing community and transdisciplinary researchers translating novel ideas from theory to experiment and then to practice. To this end, all discussions in this review are written in a language that is accessible to non-experts in specific fields of acoustics, fluid dynamics and acousto-optics.

A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli.

Nucleus-forming jumbo phages establish an intricate subcellular organization, enclosing phage genomes within a proteinaceous shell called the phage nucleus. During infection in Pseudomonas, some jumbo phages assemble a bipolar spindle of tubulin-like PhuZ filaments that positions the phage nucleus at midcell and drives its intracellular rotation. This facilitates the distribution of capsids on its surface for genome packaging. Here we show that the Escherichia coli jumbo phage Goslar assembles a phage nucleus surrounded by an array of PhuZ filaments resembling a vortex instead of a bipolar spindle. Expression of a mutant PhuZ protein strongly reduces Goslar phage nucleus rotation, demonstrating that the PhuZ cytoskeletal vortex is necessary for rotating the phage nucleus. While vortex-like cytoskeletal arrays are important in eukaryotes for cytoplasmic streaming and nucleus alignment, this work identifies a coherent assembly of filaments into a vortex-like structure driving intracellular rotation within the prokaryotic cytoplasm.

Acoustic frequency combs using gas bubble cluster oscillations in liquids: a proof of concept.

We propose a new approach to the generation of acoustic frequency combs (AFC)-signals with spectra containing equidistant coherent peaks. AFCs are essential for a number of sensing and measurement applications, where the established technology of optical frequency combs suffers from fundamental physical limitations. Our proof-of-principle experiments demonstrate that nonlinear oscillations of a gas bubble cluster in water insonated by a low-pressure single-frequency ultrasound wave produce signals with spectra consisting of equally spaced peaks originating from the interaction of the driving ultrasound wave with the response of the bubble cluster at its natural frequency. The so-generated AFC posses essential characteristics of optical frequency combs and thus, similar to their optical counterparts, can be used to measure various physical, chemical and biological quantities.

Spectrally wide acoustic frequency combs generated using oscillations of polydisperse gas bubble clusters in liquids.

Acoustic frequency combs leverage unique properties of the optical frequency comb technology in high-precision measurements and innovative sensing in optically inaccessible environments such as under water, under ground, or inside living organisms. Because acoustic combs with wide spectra would be required for many of these applications but techniques of their generation have not yet been developed, here we propose an approach to the creation of spectrally wide acoustic combs using oscillations of polydisperse gas bubble clusters in liquids. By means of numerical simulations, we demonstrate that clusters consisting of bubbles with precisely controlled sizes can produce wide acoustic spectra composed of equally spaced coherent peaks. We show that under typical experimental conditions, bubble clusters remain stable over time, which is required for a reliable recording of comb signals. We also demonstrate that the spectral composition of combs can be tuned by adjusting the number and size of bubbles in a cluster.

Beamed UV sonoluminescence by aspherical air bubble collapse near liquid-metal microparticles.

Irradiation with UV-C band ultraviolet light is one of the most commonly used ways of disinfecting water contaminated by pathogens such as bacteria and viruses. Sonoluminescence, the emission of light from acoustically-induced collapse of air bubbles in water, is an efficient means of generating UV-C light. However, because a spherical bubble collapsing in the bulk of water creates isotropic radiation, the generated UV-C light fluence is insufficient for disinfection. Here we show, based on detailed theoretical modelling and rigorous simulations, that it should be possible to create a UV light beam from aspherical air bubble collapse near a gallium-based liquid-metal microparticle. The beam is perpendicular to the metal surface and is caused by the interaction of sonoluminescence light with UV plasmon modes of the metal. We estimate that such beams can generate fluences exceeding 10 mJ/cm2, which is sufficient to irreversibly inactivate most common pathogens in water with the turbidity of more than 5 Nephelometric Turbidity Units.

On the definition of Landau constants in amplitude equations away from a critical point.

A weakly nonlinear stability analysis of shear flows based on amplitude expansion is re-examined. While it has been known that the condition required to define the coefficients of the resulting Stuart-Landau series representing the nonlinear temporal evolution of the most amplified Fourier component of a disturbance is not unique, we show that it can be formulated in a flexible generic form that incorporates different conditions used by various authors previously. The new formulation is interpreted from the point of view of low-dimensional projection of a full solution of a problem onto the space spanned by the basic flow vector and the eigenvector of the linearized problem. It is rigorously proven that the generalized condition formulated in this work reduces to a standard solvability condition at the critical point, where the basic flow first becomes unstable with respect to infinitesimal disturbances, and that it results in a well-posed problem for the determination of coefficients of Stuart-Landau series both at the critical point and a finite distance away from it. On a practical side, the generalized condition reported here enables one to choose the projection in such a way that the resulting low-dimensional approximate solution emphasizes specific physical features of interest via selecting the appropriate projection weight matrix without changing the overall asymptotic expansion procedure.

Surface amorphization of NiTi alloy induced by Ultrasonic Nanocrystal Surface Modification for improved mechanical properties.

We report herein the effects of Ultrasonic Nano-crystal Surface Modification (UNSM), a severe surface plastic deformation process, on the microstructure, mechanical (hardness, wear), wettability and biocompatibility properties of NiTi shape memory alloy. Complete surface amorphization of NiTi was achieved by this process, which was confirmed by X-ray diffraction and high-resolution transmission electron microscopy. The wear resistance of the samples after UNSM processing was significantly improved compared with the non-processed samples due to increased surface hardness of the alloy by this process. In addition, cell culture study demonstrated that the biocompatibility of the samples after UNSM processing has not been compromised compared to the non-processed sample. The combination of high wear resistance and good biocompatibility makes UNSM an appealing process for treating alloy-based biomedical devices.

Super-strengthening and stabilizing with carbon nanotube harnessed high density nanotwins in metals by shock loading.

CNTs reinforced metal composites has great potential due to their superior properties, such as light weight, high strength, low thermal expansion and high thermal conductivity. The current strengthening mechanisms of CNT/metal composite mainly rely on CNTs' interaction with dislocations and CNT's intrinsic high strength. Here we demonstrated that laser shock loading the CNT/metal composite results in high density nanotwins, stacking fault, dislocation around the CNT/metal interface. The composites exhibit enhanced strength with excellent stability. The results are interpreted by both molecular dynamics simulation and experiments. It is found the shock wave interaction with CNTs induces a stress field, much higher than the applied shock pressure, surrounding the CNT/metal interface. As a result, nanotwins were nucleated under a shock pressure much lower than the critical values to generate twins in metals. This hybrid unique nanostructure not only enhances the strength, but also stabilize the strength, as the nanotwin boundaries around the CNTs help pin the dislocation movement.