A pan-influenza antibody inhibiting neuraminidase via receptor mimicry.

Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.

Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.

Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.

Direct assessment of the acidity of individual surface hydroxyls.

The state of deprotonation/protonation of surfaces has far-ranging implications in chemistry, from acid-base catalysis1 and the electrocatalytic and photocatalytic splitting of water2, to the behaviour of minerals3 and biochemistry4. An entity's acidity is described by its proton affinity and its acid dissociation constant pKa (the negative logarithm of the equilibrium constant of the proton transfer reaction in solution). The acidity of individual sites is difficult to assess for solids, compared with molecules. For mineral surfaces, the acidity is estimated by semi-empirical concepts, such as bond-order valence sums5, and increasingly modelled with first-principles molecular dynamics simulations6,7. At present, such predictions cannot be tested-experimental measures, such as the point of zero charge8, integrate over the whole surface or, in some cases, individual crystal facets9. Here we assess the acidity of individual hydroxyl groups on In2O3(111)-a model oxide with four different types of surface oxygen atom. We probe the strength of their hydrogen bonds with the tip of a non-contact atomic force microscope and find quantitative agreement with density functional theory calculations. By relating the results to known proton affinities of gas-phase molecules, we determine the proton affinity of the different surface sites of In2O3 with atomic precision. Measurements on hydroxylated titanium dioxide and zirconium oxide extend our method to other oxides.

Broad sarbecovirus neutralization by a human monoclonal antibody.

The recent emergence of SARS-CoV-2 variants of concern1-10 and the recurrent spillovers of coronaviruses11,12 into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.

A perspective on potential antibody-dependent enhancement of SARS-CoV-2.

Antibody-dependent enhancement (ADE) of disease is a general concern for the development of vaccines and antibody therapies because the mechanisms that underlie antibody protection against any virus have a theoretical potential to amplify the infection or trigger harmful immunopathology. This possibility requires careful consideration at this critical point in the pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we review observations relevant to the risks of ADE of disease, and their potential implications for SARS-CoV-2 infection. At present, there are no known clinical findings, immunological assays or biomarkers that can differentiate any severe viral infection from immune-enhanced disease, whether by measuring antibodies, T cells or intrinsic host responses. In vitro systems and animal models do not predict the risk of ADE of disease, in part because protective and potentially detrimental antibody-mediated mechanisms are the same and designing animal models depends on understanding how antiviral host responses may become harmful in humans. The implications of our lack of knowledge are twofold. First, comprehensive studies are urgently needed to define clinical correlates of protective immunity against SARS-CoV-2. Second, because ADE of disease cannot be reliably predicted after either vaccination or treatment with antibodies-regardless of what virus is the causative agent-it will be essential to depend on careful analysis of safety in humans as immune interventions for COVID-19 move forward.

Structural and Functional Impacts of ER Coactivator Sequential Recruitment.

Nuclear receptors recruit multiple coactivators sequentially to activate transcription. This "ordered" recruitment allows different coactivator activities to engage the nuclear receptor complex at different steps of transcription. Estrogen receptor (ER) recruits steroid receptor coactivator-3 (SRC-3) primary coactivator and secondary coactivators, p300/CBP and CARM1. CARM1 recruitment lags behind the binding of SRC-3 and p300 to ER. Combining cryo-electron microscopy (cryo-EM) structure analysis and biochemical approaches, we demonstrate that there is a close crosstalk between early- and late-recruited coactivators. The sequential recruitment of CARM1 not only adds a protein arginine methyltransferase activity to the ER-coactivator complex, it also alters the structural organization of the pre-existing ERE/ERα/SRC-3/p300 complex. It induces a p300 conformational change and significantly increases p300 HAT activity on histone H3K18 residues, which, in turn, promotes CARM1 methylation activity on H3R17 residues to enhance transcriptional activity. This study reveals a structural role for a coactivator sequential recruitment and biochemical process in ER-mediated transcription.

Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures.

Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in Toxoplasma gondii, an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite's long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.

A phase 1 study in healthy volunteers to investigate the safety, tolerability, and pharmacokinetics of VIR-2482: a monoclonal antibody for the prevention of severe influenza A illness.

The objective of this study was to evaluate the safety, tolerability, pharmacokinetics (PK), and immunogenicity of VIR-2482 in healthy adult subjects. A phase 1, first-in-human, randomized, double-blind, placebo-controlled dose-escalation study was conducted. One hundred participants were allocated to four cohorts (60 mg, 300 mg, 1,200 mg, and 1,800 mg). In each cohort, participants were randomized in a 4:1 ratio (active:placebo) to receive either VIR-2482 or volume-matched placebo by gluteal intramuscular injection. Participants remained at the investigative site under observation for 48 h, and adverse events (AEs) were collected for 56 days. PK and immunogenicity were measured up to 52 weeks post-dose. VIR-2482 was well tolerated at all doses studied. The overall incidence of AEs was comparable between VIR-2482 (68.8%) and placebo (85.0%). Nineteen VIR-2482 (23.8%) and six placebo (30.0%) recipients had Grade 1 or 2 AEs that were considered to be related to the study intervention. There were no treatment-related serious AEs. Injection-site reactions (ISRs) were reported in six (7.5%) VIR-2482 recipients, while no such reactions were reported among the placebo recipients. All ISRs were Grade 1, and there was no relationship with the dose. Median VIR-2482 serum elimination half-life ranged from 56.7 to 70.6 days across cohorts. The serum area under the curve and Cmax were dose-proportional. Nasopharyngeal VIR-2482 concentrations were approximately 2%-5% of serum levels and were less than dose-proportional. The incidence of immunogenicity across all cohorts was 1.3%. Overall, the safety, tolerability, and pharmacokinetic profile of VIR-2482 at doses up to 1,800 mg supported its further investigation as a long-acting antibody for the prevention of influenza A illness. This study has been registered at ClinicalTrials.gov under identifier NCT04033406.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Ultracompact wavefront characterization of femtosecond 3D printed microlenses using double-frequency Ronchi interferometry.

3D printed microoptics have become important tools for miniature endoscopy, novel CMOS-based on-chip sensors, OCT-fibers, among others. Until now, only image quality and spot diagrams were available for optical characterization. Here, we introduce Ronchi interferometry as ultracompact and quick quantitative analysis method for measuring the wavefront aberrations after propagating coherent light through the 3D printed miniature optics. We compare surface shapes by 3D confocal microscopy with optical characterizations by Ronchi interferograms. Phase retrieval gives us the transversal wave front aberration map, which indicates that the aberrations of our microlenses that have been printed with a Nanoscribe GT or Quantum X printer exhibit RMS wavefront aberrations as small as λ/20, Strehl ratios larger than 0.91, and near-diffraction limited modulation transfer functions. Our method will be crucial for future developments of 3D printed microoptics, as the method is ultracompact, ultra-stable, and very fast regarding measurement and evaluation. It could fit directly into a 3D printer and allows for in-situ measurements right after printing as well as fast iterations for improving the shape of the optical surface.

Expression of versican isoforms V0/V1 by pancreatic cancer associated fibroblasts increases fibroblast proliferation.

BACKGROUND: Versican is a large extracellular matrix (ECM) proteoglycan with four isoforms V0-3. Elevated V0/V1 levels in breast cancer and glioma regulate cell migration and proliferation, but the role of versican in pancreatic ductal adenocarcinoma (PDAC) remains unclear. METHODS: In this study, we evaluated the expression levels of versican isoforms, as well as their cellular source and interacting partners, in vivo, in human and mouse primary and metastatic PDAC tumours and in vitro, in pancreatic tumour cells and fibroblasts using immunostaining, confocal microscopy and qPCR techniques. We also investigated the effect of versican expression on fibroblast proliferation and migration using genetic and pharmacological approaches. RESULTS: We found that versican V0/V1 is highly expressed by cancer-associated fibroblasts (CAFs) in mouse and human primary and metastatic PDAC tumours. Our data also show that exposing fibroblasts to tumour-conditioned media upregulates V0 and V1 expressions, while Verbascoside (a CD44 inhibitor) downregulates V0/V1 expression. Importantly, V0/V1 knockdown significantly inhibits fibroblast proliferation. Mechanistically, we found that inhibiting hyaluronan synthesis does not affect versican co-localisation with CD44 in fibroblasts. CONCLUSION: CAFs express high levels of versican V0/V1 in primary and liver metastatic PDAC tumours and versican V0/V1 supports fibroblast proliferation.

Nightmares in Swiss elite athletes: Associated factors.

Nightmares, defined as extremely dysphoric dreams, can cause significant distress in everyday life if they occur frequently. Their aetiology is based on a disposition-stress model. As elite athletes often experience high stress levels, the present study investigated factors that might be associated with nightmare frequency in a large cohort of 2297 Swiss elite athletes (1066 women, 1231 men) with a mean age of 22.05 ± 7.53 years. In total, about 6% of the athletes reported frequent nightmares (once a week or more often). We found that well-established factors like female gender and general stress levels were related to nightmare frequency. To a smaller extent, the number of training hours, lost training days due to illness, and having early training sessions were also associated with nightmare frequency. Sport discipline was not related to nightmare frequency. An unexpected finding was the association between late alcohol intake 4 hr prior to bedtime and nightmare frequency. Our findings support the idea that stress related to practicing sports might affect nightmare frequency. Future research should study whether inventions designed for athletes suffering from frequent nightmares are beneficial for them and might even improve their athletic performance.

Interaction of surface cations of cleaved mica with water in vapor and liquid forms.

Natural minerals contain ions that become hydrated when they come into contact with water in vapor and liquid forms. Muscovite mica - a common phyllosilicate with perfect cleavage planes - is an ideal system to investigate the details of ion hydration. The cleaved mica surface is decorated by an array of K+ ions that can be easily exchanged with other ions or protons when immersed in an aqueous solution. Despite the vast interest in the atomic-scale hydration processes of these K+ ions, experimental data under controlled conditions have remained elusive. Here, atomically resolved non-contact atomic force microscopy (nc-AFM) is combined with X-ray photoelectron spectroscopy (XPS) to investigate the cation hydration upon dosing water vapor at 100 K in ultra-high vacuum (UHV). The cleaved surface is further exposed to ultra-clean liquid water at room temperature, which promotes ion mobility and partial ion-to-proton substitution. The results offer the first direct experimental views of the interaction of water with muscovite mica under UHV. The findings are in line with previous theoretical predictions.

NH3 adsorption and competition with H2O on a hydroxylated aluminosilicate surface.

The interaction between ammonia (NH3) and (alumino)silicates is of fundamental and applied importance, yet the specifics of NH3 adsorption on silicate surfaces remain largely unexplored, mainly because of experimental challenges related to their electrically insulating nature. An example of this knowledge gap is evident in the context of ice nucleation on silicate dust, wherein the role of NH3 for ice nucleation remains debated. This study explores the fundamentals of the interaction between NH3 and microcline feldspar (KAlSi3O8), a common aluminosilicate with outstanding ice nucleation abilities. Atomically resolved non-contact atomic force microscopy, x-ray photoelectron spectroscopy, and density functional theory-based calculations elucidate the adsorption geometry of NH3 on the lowest-energy surface of microcline, the (001) facet, and its interplay with surface hydroxyls and molecular water. NH3 and H2O are found to adsorb molecularly in the same adsorption sites, creating H-bonds with the proximate surface silanol (Si-OH) and aluminol (Al-OH) groups. Despite the closely matched adsorption energies of the two molecules, NH3 readily yields to replacement by H2O, challenging the notion that ice nucleation on microcline proceeds via the creation of an ordered H2O layer atop pre-adsorbed NH3 molecules.

Phospho-RNA sequencing with circAID-p-seq.

Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3' end. Unfortunately, current library preparation protocols rely only on a 3' hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3' phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3'-phospho RNA molecules.

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks.

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.

CO-Induced Dimer Decay Responsible for Gem-Dicarbonyl Formation on a Model Single-Atom Catalyst.

The ability to coordinate multiple reactants at the same active site is important for the wide-spread applicability of single-atom catalysis. Model catalysts are ideal to investigate the link between active site geometry and reactant binding, because the structure of single-crystal surfaces can be precisely determined, the adsorbates imaged by scanning tunneling microscopy (STM), and direct comparisons made to density functional theory. In this study, we follow the evolution of Rh1 adatoms and minority Rh2 dimers on Fe3O4(001) during exposure to CO using time-lapse STM at room temperature. CO adsorption at Rh1 sites results exclusively in stable Rh1CO monocarbonyls, because the Rh atom adapts its coordination to create a stable pseudo-square planar environment. Rh1(CO)2 gem-dicarbonyl species are also observed, but these form exclusively through the breakup of Rh2 dimers via an unstable Rh2(CO)3 intermediate. Overall, our results illustrate how minority species invisible to area-averaging spectra can play an important role in catalytic systems, and show that the decomposition of dimers or small clusters can be an avenue to produce reactive, metastable configurations in single-atom catalysis.

Potent broadly neutralizing antibody VIR-3434 controls hepatitis B and D virus infection and reduces HBsAg in humanized mice.

BACKGROUND & AIMS: Chronic hepatitis B is a global public health problem, and coinfection with hepatitis delta virus (HDV) worsens disease outcome. Here, we describe a hepatitis B virus (HBV) surface antigen (HBsAg)-targeting monoclonal antibody (mAb) with the potential to treat chronic hepatitis B and chronic hepatitis D. METHODS: HBsAg-specific mAbs were isolated from memory B cells of HBV vaccinated individuals. In vitro neutralization was determined against HBV and HDV enveloped with HBsAg representing eight HBV genotypes. Human liver-chimeric mice were treated twice weekly with a candidate mAb starting 3 weeks post HBV inoculation (spreading phase) or during stable HBV or HBV/HDV coinfection (chronic phase). RESULTS: From a panel of human anti-HBs mAbs, VIR-3434 was selected and engineered for pre-clinical development. VIR-3434 targets a conserved, conformational epitope within the antigenic loop of HBsAg and neutralized HBV and HDV infection with higher potency than hepatitis B immunoglobulins in vitro. Neutralization was pan-genotypic against strains representative of HBV genotypes A-H. In the spreading phase of HBV infection in human liver-chimeric mice, a parental mAb of VIR-3434 (HBC34) prevented HBV dissemination and the increase in intrahepatic HBV RNA and covalently closed circular DNA. In the chronic phase of HBV infection or co-infection with HDV, HBC34 treatment decreased circulating HBsAg by >1 log and HDV RNA by >2 logs. CONCLUSIONS: The potently neutralizing anti-HBs mAb VIR-3434 reduces circulating HBsAg and HBV/HDV viremia in human liver-chimeric mice. VIR-3434 is currently in clinical development for treatment of patients with chronic hepatitis B or D. IMPACT AND IMPLICATIONS: Chronic infection with hepatitis B virus and co-infection with hepatitis D virus place approximately 290 million individuals worldwide at risk of severe liver disease and cancer. Available treatments result in low rates of functional cure or require lifelong therapy that does not eliminate the risk of liver disease. We isolated and characterized a potent human antibody that neutralizes hepatitis B and D viruses and reduces infection in a mouse model. This antibody could provide a new treatment for patients with chronic hepatitis B and D.

Measurement of atom resolvability in cryo-EM maps with Q-scores.

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.