Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.

Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.

Aged layered double hydroxide nanosheet-polyvinyl alcohol dispersions for enhanced gas barrier coating performance.

Whilst applying a coating layer to a polymer film is a routine approach to enhance the gas barrier properties of the film, it is counter-intuitive to consider that the gas barrier performance of the film would improve by ageing the coating dispersion for weeks before application. Herein, we report that the oxygen barrier performance of a 12 µm PET film coated with a dispersion of inorganic nanosheets in polyvinyl alcohol can be significantly enhanced by ageing this coating dispersion for up to 8 weeks before application. We found up to a 37-fold decrease in the oxygen transmission rate (OTR) of the PET coated film using aged dispersions of [Mg0.66Al0.33(OH)2](NO3)0.33 layered double hydroxide nanosheets (Mg2Al-LDH NS) in polyvinyl alcohol (PVA) compared to the film coated with an equivalent freshly prepared LDH/PVA dispersion. A limiting OTR value of 0.31 cc m-2 day-1 was achieved using the PET film coated with a 3 week aged LDH NS/PVA dispersion. X-ray diffraction experiments show that the degree of in plane alignment of LDH NS on the PET film surface increased significantly from 70.6 ± 0.6 to 86.7 ± 0.6 (%) (100% represents complete alignment of LDH NS platelets on the film surface) for the 4 week aged dispersion compared to the freshly prepared layer. We postulate that when the Mg2Al-LDH NS are aged in PVA the coiled PVA aggregates start to unwrap and attach onto the Mg2Al-LDH NS through hydrogen bonding and eventually form a hydrogen bonded ordered network that facilitates the alignment of nanosheet dispersions during the coating process. Our results suggest that the ageing of inorganic nanosheet dispersions in PVA or other potential hydrogen bonding adhesive systems could be a general approach to improve the alignment of the nanosheets on the polymer film surface once applied and thus improve their performance characteristics for barrier coating applications.

Preparing Lamellae from Vitreous Biological Samples using a Dual-Beam Scanning Electron Microscope for Cryo-Electron Tomography.

Presented here is a protocol for preparing cryo-lamellae from plunge-frozen grids of Plasmodium falciparum-infected human erythrocytes, which could easily be adapted for other biological samples. The basic principles for preparing samples, milling, and viewing lamellae are common to all instruments and the protocol can be followed as a general guide to on-grid cryo-lamella preparation for cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). Electron microscopy grids supporting the cells are plunge-frozen into liquid nitrogen-cooled liquid ethane using a manual or automated plunge freezer, then screened on a light microscope equipped with a cryo-stage. Frozen grids are transferred into a cryo-scanning electron microscope equipped with a focused ion beam (cryoFIB-SEM). Grids are routinely sputter coated prior to milling, which aids dispersal of charge build-up during milling. Alternatively, an e-beam rotary coater can be used to apply a layer of carbon-platinum to the grids, the exact thickness of which can be more precisely controlled. Once inside the cryoFIB-SEM an additional coating of an organoplatinum compound is applied to the surface of the grid via a gas injection system (GIS). This layer protects the front edge of the lamella as it is milled, the integrity of which is critical for achieving uniformly thin lamellae. Regions of interest are identified via SEM and milling is carried out in a step-wise fashion, reducing the current of the ion beam as the lamella reaches electron transparency, in order to avoid excessive heat generation. A grid with multiple lamellae is then transferred to a transmission electron microscope (TEM) under cryogenic conditions for tilt-series acquisition. A robust and contamination-free workflow for lamella preparation is an essential step for downstream techniques, including cellular cryoEM, cryoET, and sub-tomogram averaging. Development of these techniques, especially for lift-out and milling of high-pressure frozen samples, is of high-priority in the field.

Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress.

Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.

SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging.

Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, investigation of the SARS-CoV-2 infection in the native cellular context is scarce, and there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Our results reveal at the whole cell level profound cytopathic effects of SARS-CoV-2 infection, exemplified by a large amount of heterogeneous vesicles in the cytoplasm for RNA synthesis and virus assembly, formation of membrane tunnels through which viruses exit, and drastic cytoplasm invasion into nucleus. Furthermore, cryoET of cell lamellae reveals how viral RNAs are transported from double-membrane vesicles where they are synthesized to viral assembly sites; how viral spikes and RNPs assist in virus assembly and budding; and how fully assembled virus particles exit the cell, thus stablishing a model of SARS-CoV-2 genome replication, virus assembly and egress pathways.

A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction.

MicroED has recently emerged as a powerful method for the analysis of biological structures at atomic resolution. This technique has been largely limited to protein nanocrystals which grow either as needles or plates measuring only a few hundred nanometers in thickness. Furthermore, traditional microED data processing uses established X-ray crystallography software that is not optimized for handling compound effects that are unique to electron diffraction data. Here, we present an integrated workflow for microED, from sample preparation by cryo-focused ion beam milling, through data collection with a standard Ceta-D detector, to data processing using the DIALS software suite, thus enabling routine atomic structure determination of protein crystals of any size and shape using microED. We demonstrate the effectiveness of the workflow by determining the structure of proteinase K to 2.0 Å resolution and show the advantage of using protein crystal lamellae over nanocrystals.

Biotransformation of Silver Released from Nanoparticle Coated Titanium Implants Revealed in Regenerating Bone.

Antimicrobial silver nanoparticle coatings have attracted interest for reducing prosthetic joint infection. However, few studies report in vivo investigations of the biotransformation of silver nanoparticles within the regenerating tissue and its impact on bone formation. We present a longitudinal investigation of the osseointegration of silver nanoparticle-coated additive manufactured titanium implants in rat tibial defects. Correlative imaging at different time points using nanoscale secondary ion mass spectrometry, transmission electron microscopy (TEM), histomorphometry, and 3D X-ray microcomputed tomography provided quantitative insight from the nano- to macroscales. The quality and quantity of newly formed bone is comparable between the uncoated and silver coated implants. The newly formed bone demonstrates a trabecular morphology with bone being located at the implant surface, and at a distance, at two weeks. Nanoscale elemental mapping of the bone-implant interface showed that silver was present primarily in the osseous tissue and colocalized with sulfur. TEM revealed silver sulfide nanoparticles in the newly regenerated bone, presenting strong evidence that the previously in vitro observed biotransformation of silver to silver sulfide occurs in vivo.

Room-Temperature Routes Toward the Creation of Zinc Oxide Films from Molecular Precursors.

The fabrication of "flexible" electronics on plastic substrates with low melting points requires the development of thin-film deposition techniques that operate at low temperatures. This is easily achieved with vacuum- or solution-processed molecular or polymeric semiconductors, but oxide materials remain a significant challenge. Here, we show that zinc oxide (ZnO) can be prepared using only room-temperature processes, with the molecular thin-film precursor zinc phthalocyanine (ZnPc), followed by UV-light treatment in vacuum to elicit degradation of the organic components and transformation of the deposited film to the oxide material. The degradation mechanism was assessed by studying the influence of the atmosphere during the reaction: it was particularly sensitive to the oxygen pressure in the chamber and optimal degradation conditions were established as 3 mbar with 40% oxygen in nitrogen. The morphology of the film remained relatively unchanged during the reaction, but a detailed analysis of its composition using both scanning transmission electron microscopy and secondary ion mass spectrometry revealed that a 40 nm thick layer containing ZnO results from the 100 nm thick precursor after complete reaction. Our methodology represents a simple route for the fabrication of oxides and multilayer structures that can be easily integrated into current molecular thin-film growth setups, without the need for a high-temperature step.