Studying how administration route and dose regulates antibody generation against LNPs for mRNA delivery with single-particle resolution.

Following the recent approval of both siRNA- and mRNA-based therapeutics, nucleic acid therapies are considered a game changer in medicine. Their envisioned widespread use for many therapeutic applications with an array of cellular target sites means that various administration routes will be employed. Concerns exist regarding adverse reactions against the lipid nanoparticles (LNPs) used for mRNA delivery, as PEG coatings on nanoparticles can induce severe antibody-mediated immune reactions, potentially being boosted by the inherently immunogenic nucleic acid cargo. While exhaustive information is available on how physicochemical features of nanoparticles affects immunogenicity, it remains unexplored how the fundamental choice of administration route regulates anti-particle immunity. Here, we directly compared antibody generation against PEGylated mRNA-carrying LNPs administered by the intravenous, intramuscular, or subcutaneous route, using a novel sophisticated assay capable of measuring antibody binding to authentic LNP surfaces with single-particle resolution. Intramuscular injections in mice were found to generate overall low and dose-independent levels of anti-LNP antibodies, while both intravenous and subcutaneous LNP injections generated substantial and highly dose-dependent levels. These findings demonstrate that before LNP-based mRNA medicines can be safely applied to new therapeutic applications, it will be crucial to carefully consider the choice of administration route.

Enhanced Single-Particle Collision Electrochemistry at Polysulfide-Functionalized Microelectrodes for SARS-CoV-2 Detection.

Single-particle collision electrochemistry (SPCE) has shown great promise in biosensing applications due to its high sensitivity, high flux, and fast response. However, a low effective collision frequency and a large number of interfering substances in complex matrices limit its broad application in clinical samples. Herein, a novel and universal SPCE biosensor was proposed to realize sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on the collision and oxidation of single silver nanoparticles (Ag NPs) on polysulfide-functionalized gold ultramicroelectrodes (Ps-Au UMEs). Taking advantage of the strong interaction of the Ag-S bond, collision and oxidation of Ag NPs on the Ps-Au UME surface could be greatly promoted to generate enhanced Faraday currents. Compared with bare Au UMEs, the collision frequency of Ps-Au UMEs was increased by 15-fold, which vastly improved the detection sensitivity and practicability of SPCE in biosensing. By combining magnetic separation, liposome encapsulation release, and DNAzyme-assisted signal amplification, the SPCE biosensor provided a dynamic range of 5 orders of magnitude for spike proteins with a detection limit of 6.78 fg/mL and a detection limit of 21 TCID50/mL for SARS-CoV-2. Furthermore, SARS-CoV-2 detection in nasopharyngeal swab samples of infected patients was successfully conducted, indicating the potential of the SPCE biosensor for use in clinically relevant diagnosis.

Comprehensive analysis of ambient air quality during second lockdown in national capital territory of Delhi.

The lockdown imposed in Delhi, due to the second wave of the COVID-19 pandemic has led to significant gains in air quality. Under the lockdown, restrictions were imposed on movement of people, operation of industrial establishments and hospitality sector amongst others. In the study, Air Quality Index and concentration trends of six pollutants, i.e. PM2.5, PM10, NO2, SO2, CO, and O3 were analysed for National Capital Territory of Delhi, India for three periods in 2021 (pre-lockdown: 15 March to 16 April 2021, lockdown: 17 April to 31 May 2021 and post-lockdown: 01 June to 30 June). Data for corresponding periods in 2018-2020 was also analysed. Lockdown period saw 6 days in satisfactory AQI category as against 0 days in the same category during the pre-lockdown period. Average PM2.5, PM10, NO2 and SO2 concentrations reduced by 22%, 31%, 25% and 28% respectively during lockdown phase as compared to pre-lockdown phase, while O3 was seen to increase. Variation in meteorological parameters and correlation of pollutants has also been examined. The significant improvement arising due to curtailment of certain activities in the lockdown period indicates the importance of local emission control, and helps improve the understanding of the dynamics of air pollution, thus highlighting policy areas to regulatory bodies for effective control of air pollution.

Mechanical tuning of virus-like particles.

HYPOTHESIS: Virus-like particles (VLPs) are promising scaffolds for developing mucosal vaccines. For their optimal performance, in addition to design parameters from an immunological perspective, biophysical properties may need to be considered. EXPERIMENTS: We investigated the mechanical properties of VLPs scaffolded on the coat protein of Acinetobacter phage AP205 using atomic force microscopy and small angle X-ray scattering. FINDINGS: Investigations showed that AP205 VLP is a tough nanoshell of stiffness 93 ± 23 pN/nm and elastic modulus 0.11 GPa. However, its mechanical properties are modulated by attaching muco-inert polyethylene glycol to 46 ± 10 pN/nm and 0.05 GPa. Addition of antigenic peptides derived from SARS-CoV2 spike protein by genetic fusion increased the stiffness to 146 ± 54 pN/nm although the elastic modulus remained unchanged. These results, which are interpreted in terms of shell thickness and coat protein net charge variations, demonstrate that surface conjugation can induce appreciable changes in the biophysical properties of VLP-scaffolded vaccines.

Effect of COVID-19 lockdown on the characterization and mixing state of carbonaceous particles in the urban atmosphere of Liaocheng, the North China Plain

To investigate the effect of COVID-19 control measures on aerosol chemistry, the chemical compositions, mixing states, and formation mechanisms of carbonaceous particles in the urban atmosphere of Liaocheng in the North China Plain (NCP) were compared before and during the pandemic using a single particle aerosol mass spectrometry (SPAMS). The results showed that the concentrations of five air pollutants including PM2.5, PM10, SO2, NO2, and CO decreased by 41.2%-71.5% during the pandemic compared to those before the pandemic, whereas O3 increased by 1.3 times during the pandemic because of the depressed titration of O3 and more favorable meteorological conditions. The count and percentage contribution of carbonaceous particles in the total detected particles were lower during the pandemic than those before the pandemic. The carbonaceous particles were dominated by elemental and organic carbon (ECOC, 35.9%), followed by elemental carbon-aged (EC-aged, 19.6%) and organic carbon-fresh (OCfresh, 13.5%) before the pandemic, while EC-aged (25.3%), ECOC (17.9%), and secondary ions-rich (SEC, 17.8%) became the predominant species during the pandemic. The carbonaceous particle sizes during the pandemic showed a broader distribution than that before the pandemic, due to the condensation and coagulation of carbonaceous particles in the aging processes. The relative aerosol acidity (Rra) was smaller before the pandemic than that during the pandemic, indicating the more acidic particle aerosol during the pandemic closely related to the secondary species and relative humidity (RH). More than 95.0% and 86.0% of carbonaceous particles in the whole period were internally mixed with nitrate and sulfate, implying that most of the carbonaceous particles were associated with secondary oxidation during their formation processes. The diurnal variations of oxalate particles and correlation analyses suggested that oxalate particles before the pandemic were derived from aqueous oxidation driven by RH and liquid water content (LWC), while oxalate particles during the pandemic were originated from O3dominated photochemical oxidation.(c) 2022 Chinese Society of Particuology and Institute of Process Engineering, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

A Facile Method to Coat Nanoparticles with Lipid Bilayer Membrane: Hybrid Silica Nanoparticles Disguised as Biomembrane Vesicles by Particle Penetration of Concentrated Lipid Layers.

Natural membrane vesicles, including extracellular vesicles and enveloped viruses, participate in various events in vivo. To study and manipulate these events, biomembrane-coated nanoparticles inspired by natural membrane vesicles are developed. Herein, an efficient method is presented to prepare organic-inorganic hybrid materials in high yields that can accommodate various lipid compositions and particle sizes. To demonstrate this method, silica nanoparticles are passed through concentrated lipid layers prepared using density gradient centrifugation, followed by purification, to obtain lipid membrane-coated nanoparticles. Various lipids, including neutral, anionic, and cationic lipids, are used to prepare concentrated lipid layers. Single-particle analysis by imaging flow cytometry determines that silica nanoparticles are uniformly coated with a single lipid bilayer. Moreover, cellular uptake of silica nanoparticles is enhanced when covered with a lipid membrane containing cationic lipids. Finally, cell-free protein expression is applied to embed a membrane protein, namely the Spike protein of severe acute respiratory syndrome coronavirus 2, into the coating of the nanoparticles, with the correct orientation. Therefore, this method can be used to develop organic-inorganic hybrid nanomaterials with an inorganic core and a virus-like coating, serving as carriers for targeted delivery of cargos such as proteins, DNA, and drugs.

Recovering mixtures of fast-diffusing states from short single-particle trajectories.

Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.

Optimizing the Sensitivity of Biological Particle Detectors through Atmospheric Particle Analysis According to Climatic Characteristics in South Korea

Biological agents used in biological warfare or bioterrorism are also present in bioaerosols. Prompt identification of a biological weapon and its characteristics is necessary. Herein, we optimized an environmentally adaptive detection algorithm that can better reflect changes in the complex South Korean environment than the current models. The algorithm distinguished between normal and biological particles using a laser-induced fluorescence-based biological particle detector capable of real-time measurements and size classification. We ensured that the algorithm operated with minimal false alarms in any environment by training based on experimental data acquired from an area where rainfall, snow, fog and mist, Asian dust, and water waves on the beach occur. To prevent time and money wastage due to false alarms, the detection performance for each level of sensitivity was examined to enable the selection of multiple sensitivities according to the background, and the appropriate level of sensitivity for the climate was determined. The basic sensitivity was set more conservatively than before, with a 3% alarm rate at 20 agent-containing particles per liter of air (ACPLA) and a 100% alarm rate at 63 ACPLA. The reliability was increased by optimizing five variables. False alarms did not occur in situations where no alarm was unnecessary.

A general controllable release amplification strategy of liposomes for single-particle collision electrochemical biosensing.

As an important component of the COVID-19 mRNA vaccines, liposomes play a key role in the efficient protection and delivery of mRNA to cells. Herein, due to the controllable release amplification strategy of liposomes, a reliable and robust single-particle collision electrochemical (SPCE) biosensor was constructed for H9N2 avian influenza virus (H9N2 AIV) detection by combining liposome encapsulation-release strategy with immunomagnetic separation. The liposomes modified with biotin and loaded with platinum nanoparticles (Pt NPs) were used as signal probes for the first time. Biotin facilitated the coupling of biomolecules (DNA or antibodies) through the specific reaction of biotin-streptavidin. Each liposome can encapsulate multiple Pt NPs, which were ruptured under the presence of 1 × PBST (phosphate buffer saline with 0.05% Tween-20) within 2 min, and the encapsulated Pt NPs were released for SPCE experiment. The combination of immunomagnetic separation not only improved the anti-interference capabilities but also avoided the agglomeration of Pt NPs, enabling the SPCE biosensor to realize ultrasensitive detection of 18.1 fg/mL H9N2 AIV. Furthermore, the reliable SPCE biosensor was successfully applied in specific detection of H9N2 AIV in complex samples (chicken serum, chicken liver and chicken lung), which promoted the universality of SPCE biosensor and its application prospect in early diagnosis of diseases.

The atomic portrait of SARS-CoV-2 as captured by cryo-electron microscopy.

Transmission electron microscopy has historically been indispensable for virology research, as it offers unique insight into virus function. In the past decade, as cryo-electron microscopy (cryo-EM) has matured and become more accessible, we have been able to peer into the structure of viruses at the atomic level and understand how they interact with the host cell, with drugs or with antibodies. Perhaps, there was no time in recent history where cryo-EM was more needed, as SARS-CoV-2 has spread around the globe, causing millions of deaths and almost unquantifiable economic devastation. In this concise review, we aim to mark the most important contributions of cryo-EM to understanding the structure and function of SARS-CoV-2 proteins, from surface spikes to the virus core and from virus-receptor interactions to antibody binding.

An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser.

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera.

During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as ∼2.7 Šfrom a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Šlevel to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics.

Conformational flexibility and structural variability of SARS-CoV2 S protein.

Spike (S) glycoprotein of SARS-CoV2 exists chiefly in two conformations, open and closed. Most previous structural studies on S protein have been conducted at pH 8.0, but knowledge of the conformational propensities under both physiological and endosomal pH conditions is important to inform vaccine development. Our current study employed single-particle cryoelectron microscopy to visualize multiple states of open and closed conformations of S protein at physiological pH 7.4 and near-physiological pH 6.5 and pH 8.0. Propensities of open and closed conformations were found to differ with pH changes, whereby around 68% of S protein exists in open conformation at pH 7.4. Furthermore, we noticed a continuous movement in the N-terminal domain, receptor-binding domain (RBD), S2 domain, and stalk domain of S protein conformations at various pH values. Several key residues involving RBD-neutralizing epitopes are differentially exposed in each conformation. This study will assist in developing novel therapeutic measures against SARS-CoV2.

Molecular Basis for Bordetella pertussis Interference with Complement, Coagulation, Fibrinolytic, and Contact Activation Systems: the Cryo-EM Structure of the Vag8-C1 Inhibitor Complex.

Complement, contact activation, coagulation, and fibrinolysis are serum protein cascades that need strict regulation to maintain human health. Serum glycoprotein, a C1 inhibitor (C1-INH), is a key regulator (inhibitor) of serine proteases of all the above-mentioned pathways. Recently, an autotransporter protein, virulence-associated gene 8 (Vag8), produced by the whooping cough pathogen, Bordetella pertussis, was shown to bind to C1-INH and interfere with its function. Here, we present the structure of the Vag8-C1-INH complex determined using cryo-electron microscopy at a 3.6-Å resolution. The structure shows a unique mechanism of C1-INH inhibition not employed by other pathogens, where Vag8 sequesters the reactive center loop of C1-INH, preventing its interaction with the target proteases.IMPORTANCE The structure of a 10-kDa protein complex is one of the smallest to be determined using cryo-electron microscopy at high resolution. The structure reveals that C1-INH is sequestered in an inactivated state by burial of the reactive center loop in Vag8. By so doing, the bacterium is able to simultaneously perturb the many pathways regulated by C1-INH. Virulence mechanisms such as the one described here assume more importance given the emerging evidence about dysregulation of contact activation, coagulation, and fibrinolysis leading to COVID-19 pneumonia.