Engineered immunogens to elicit antibodies against conserved coronavirus epitopes.

Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employ computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant receptor binding domain. These engineered proteins bind with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interact with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicit sera with broad betacoronavirus reactivity and protect as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.

Identification of CDRH3 loops in the B cell receptor repertoire that can be engaged by candidate immunogens.

A major goal for the development of vaccines against rapidly mutating viruses, such as influenza or HIV, is to elicit antibodies with broad neutralization capacity. However, B cell precursors capable of maturing into broadly neutralizing antibodies (bnAbs) can be rare in the immune repertoire. Due to the stochastic nature of B cell receptor (BCR) rearrangement, a limited number of third heavy chain complementary determining region (CDRH3) sequences are identical between different individuals. Thus, in order to successfully engage broadly neutralizing antibody precursors that rely on their CDRH3 loop for antigen recognition, immunogens must be able to tolerate sequence diversity in the B cell receptor repertoire across an entire vaccinated population. Here, we present a combined experimental and computational approach to identify BCRs in the human repertoire with CDRH3 loops predicted to be engaged by a target immunogen. For a given antibody/antigen pair, deep mutational scanning was first used to measure the effect of CDRH3 loop substitution on binding. BCR sequences, isolated experimentally or generated in silico, were subsequently evaluated to identify CDRH3 loops expected to be bound by the candidate immunogen. We applied this method to characterize two HIV-1 germline-targeting immunogens and found differences in the frequencies with which they are expected to engage target B cells, thus illustrating how this approach can be used to evaluate candidate immunogens towards B cell precursors engagement and to inform immunogen optimization strategies for more effective vaccine design.

Engineered Immunogens to Elicit Antibodies Against Conserved Coronavirus Epitopes.

Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employed computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant RBD. These engineered proteins bound with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interacted with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicited sera with broad betacoronavirus reactivity and protected as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.

A mathematical model for the auxetic response of liquid crystal elastomers.

We develop a mathematical model that builds on the surprising nonlinear mechanical response observed in recent experiments on nematic liquid crystal elastomers. Namely, under uniaxial tensile loads, the material, rather than thinning in the perpendicular directions, becomes thicker in one direction for a sufficiently large strain, while its volume remains unchanged. Motivated by this unusual large-strain auxetic behaviour, we model the material using an Ogden-type strain-energy function and calibrate its parameters to available datasets. We show that Ogden strain-energy functions are particularly suitable for modelling nematic elastomers because of their mathematical simplicity and their clear formulation in terms of the principal stretches, which have a direct kinematic interpretation. This article is part of the theme issue 'The Ogden model of rubber mechanics: Fifty years of impact on nonlinear elasticity'.

Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity.

The non-classical class Ib molecule human leukocyte antigen E (HLA-E) has limited polymorphism and can bind HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we report the isolation of 3H4, a murine HLA-E-VL9-specific IgM antibody that enhances killing of HLA-E-VL9-expressing cells by an NKG2A+ NK cell line. Structural analysis reveal that 3H4 acts by preventing CD94/NKG2A docking on HLA-E-VL9. Upon in vitro maturation, an affinity-optimized IgG form of 3H4 showes enhanced NK killing of HLA-E-VL9-expressing cells. HLA-E-VL9-specific IgM antibodies similar in function to 3H4 are also isolated from naïve B cells of cytomegalovirus (CMV)-negative, healthy humans. Thus, HLA-E-VL9-targeting mouse and human antibodies isolated from the naïve B cell antibody pool have the capacity to enhance NK cell cytotoxicity.

Rapid selection of HIV envelopes that bind to neutralizing antibody B cell lineage members with functional improbable mutations.

Elicitation of broadly neutralizing antibodies (bnAbs) by an HIV vaccine will involve priming the immune system to activate antibody precursors, followed by boosting immunizations to select for antibodies with functional features required for neutralization breadth. The higher the number of acquired mutations necessary for function, the more convoluted are the antibody developmental pathways. HIV bnAbs acquire a large number of somatic mutations, but not all mutations are functionally important. In this study, we identify a minimal subset of mutations sufficient for the function of the naturally occurring V3-glycan bnAb DH270.6. Using antibody library screening, candidate envelope immunogens that interact with DH270.6-like antibodies containing this set of key mutations are identified and selected in vitro. Our results demonstrate that less complex B cell evolutionary pathways than those naturally observed exist for the induction of HIV bnAbs by vaccination, and they establish rational approaches to identify boosting candidate immunogens.

Nematic liquid crystalline elastomers are aeolotropic materials.

Continuum models describing ideal nematic solids are widely used in theoretical studies of liquid crystal elastomers. However, experiments on nematic elastomers show a type of anisotropic response that is not predicted by the ideal models. Therefore, their description requires an additional term coupling elastic and nematic responses, to account for aeolotropic effects. In order to better understand the observed elastic response of liquid crystal elastomers, we analyse theoretically and computationally different stretch and shear deformations. We then compare the elastic moduli in the infinitesimal elastic strain limit obtained from the molecular dynamics simulations with the ones derived theoretically, and show that they are better explained by including nematic order effects within the continuum framework.

A pseudo-anelastic model for stress softening in liquid crystal elastomers.

Liquid crystal elastomers exhibit stress softening with residual strain under cyclic loads. Here, we model this phenomenon by generalizing the classical pseudo-elastic formulation of the Mullins effect in rubber. Specifically, we modify the neoclassical strain-energy density of liquid crystal elastomers, depending on the deformation and the nematic director, by incorporating two continuous variables that account for stress softening and the associated set strain. As the material behaviour is governed by different forms of the strain-energy density on loading and unloading, the model is referred to as pseudo-anelastic. We then analyse qualitatively the mechanical responses of the material under cyclic uniaxial tension, which is easier to reproduce in practice, and further specialize the model in order to calibrate its parameters to recent experimental data at different temperatures. The excellent agreement between the numerical and experimental results confirms the suitability of our approach. Since the pseudo-energy function is controlled by the strain-energy density for the primary deformation, it is valid also for materials under multiaxial loads. Our study is relevant to mechanical damping applications and serves as a motivation for further experimental tests.

Multiplexed GTPase and GEF biosensor imaging enables network connectivity analysis.

Here we generate fluorescence resonance energy transfer biosensors for guanine exchange factors (GEFs) by inserting a fluorescent protein pair in a structural 'hinge' common to many GEFs. Fluorescent biosensors can map the activation of signaling molecules in space and time, but it has not been possible to quantify how different activation events affect one another or contribute to a specific cell behavior. By imaging the GEF biosensors in the same cells as red-shifted biosensors of Rho GTPases, we can apply partial correlation analysis to parse out the extent to which each GEF contributes to the activation of a specific GTPase in regulating cell movement. Through analysis of spontaneous cell protrusion events, we identify when and where the GEF Asef regulates the GTPases Cdc42 and Rac1 to control cell edge dynamics. This approach exemplifies a powerful means to elucidate the real-time connectivity of signal transduction networks.

Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor.

Lattice light-sheet microscopy (LLSM) is valuable for its combination of reduced photobleaching and outstanding spatiotemporal resolution in 3D. Using LLSM to image biosensors in living cells could provide unprecedented visualization of rapid, localized changes in protein conformation or posttranslational modification. However, computational manipulations required for biosensor imaging with LLSM are challenging for many software packages. The calculations require processing large amounts of data even for simple changes such as reorientation of cell renderings or testing the effects of user-selectable settings, and lattice imaging poses unique challenges in thresholding and ratio imaging. We describe here a new software package, named ImageTank, that is specifically designed for practical imaging of biosensors using LLSM. To demonstrate its capabilities, we use a new biosensor to study the rapid 3D dynamics of the small GTPase Rap1 in vesicles and cell protrusions.

Spatiotemporal dynamics of GEF-H1 activation controlled by microtubule- and Src-mediated pathways.

Rho family GTPases are activated with precise spatiotemporal control by guanine nucleotide exchange factors (GEFs). Guanine exchange factor H1 (GEF-H1), a RhoA activator, is thought to act as an integrator of microtubule (MT) and actin dynamics in diverse cell functions. Here we identify a GEF-H1 autoinhibitory sequence and exploit it to produce an activation biosensor to quantitatively probe the relationship between GEF-H1 conformational change, RhoA activity, and edge motion in migrating cells with micrometer- and second-scale resolution. Simultaneous imaging of MT dynamics and GEF-H1 activity revealed that autoinhibited GEF-H1 is localized to MTs, while MT depolymerization subadjacent to the cell cortex promotes GEF-H1 activation in an ~5-µm-wide peripheral band. GEF-H1 is further regulated by Src phosphorylation, activating GEF-H1 in a narrower band ~0-2 µm from the cell edge, in coordination with cell protrusions. This indicates a synergistic intersection between MT dynamics and Src signaling in RhoA activation through GEF-H1.

Likely equilibria of the stochastic Rivlin cube.

The problem of the Rivlin cube is to determine the stability of all homogeneous equilibria of an isotropic incompressible hyperelastic body under equitriaxial dead loads. Here, we consider the stochastic version of this problem where the elastic parameters are random variables following standard probability laws. Uncertainties in these parameters may arise, for example, from inherent data variation between different batches of homogeneous samples, or from different experimental tests. As for the deterministic elastic problem, we consider the following questions: what are the likely equilibria and how does their stability depend on the material constitutive law? In addition, for the stochastic model, the problem is to derive the probability distribution of deformations, given the variability of the parameters. This article is part of the theme issue 'Rivlin's legacy in continuum mechanics and applied mathematics'.

Nonlinear scaling effects in the stiffness of soft cellular structures.

For cellular structures with uniform geometry, cell size and distribution, made from a neo-Hookean material, we demonstrate experimentally that large stretching causes nonlinear scaling effects governed by the microstructural architecture and the large strains at the cell level, which are not predicted by the linear elastic theory. For this purpose, three honeycomb-like structures with uniform square cells in stacked distribution were designed, where the number of cells varied, while the material volume and the ratio between the thickness and the length of the cell walls were fixed. These structures were manufactured from silicone rubber and tested under large uniaxial tension in a bespoke test fixture. Optical strain measurements were used to assess the deformation by capturing both the global displacements of the structure and the local deformations in the form of a strain map. The experimental results showed that, under sufficiently large strains, there was an increase in the stiffness of the structure when the same volume of material was arranged as many small cells compared to when it was organized as fewer larger cells. Finite element simulations confirmed our experimental findings. This study sheds light upon the nonlinear elastic responses of cellular structures in large-strain deformations, which cannot be captured within the linear elasticity framework.

Stochastic isotropic hyperelastic materials: constitutive calibration and model selection.

Biological and synthetic materials often exhibit intrinsic variability in their elastic responses under large strains, owing to microstructural inhomogeneity or when elastic data are extracted from viscoelastic mechanical tests. For these materials, although hyperelastic models calibrated to mean data are useful, stochastic representations accounting also for data dispersion carry extra information about the variability of material properties found in practical applications. We combine finite elasticity and information theories to construct homogeneous isotropic hyperelastic models with random field parameters calibrated to discrete mean values and standard deviations of either the stress-strain function or the nonlinear shear modulus, which is a function of the deformation, estimated from experimental tests. These quantities can take on different values, corresponding to possible outcomes of the experiments. As multiple models can be derived that adequately represent the observed phenomena, we apply Occam's razor by providing an explicit criterion for model selection based on Bayesian statistics. We then employ this criterion to select a model among competing models calibrated to experimental data for rubber and brain tissue under single or multiaxial loads.

How to characterize a nonlinear elastic material? A review on nonlinear constitutive parameters in isotropic finite elasticity.

The mechanical response of a homogeneous isotropic linearly elastic material can be fully characterized by two physical constants, the Young's modulus and the Poisson's ratio, which can be derived by simple tensile experiments. Any other linear elastic parameter can be obtained from these two constants. By contrast, the physical responses of nonlinear elastic materials are generally described by parameters which are scalar functions of the deformation, and their particular choice is not always clear. Here, we review in a unified theoretical framework several nonlinear constitutive parameters, including the stretch modulus, the shear modulus and the Poisson function, that are defined for homogeneous isotropic hyperelastic materials and are measurable under axial or shear experimental tests. These parameters represent changes in the material properties as the deformation progresses, and can be identified with their linear equivalent when the deformations are small. Universal relations between certain of these parameters are further established, and then used to quantify nonlinear elastic responses in several hyperelastic models for rubber, soft tissue and foams. The general parameters identified here can also be viewed as a flexible basis for coupling elastic responses in multi-scale processes, where an open challenge is the transfer of meaningful information between scales.

Comparative effect of ochratoxin A on inflammation and oxidative stress parameters in gut and kidney of piglets.

Ochratoxin A (OTA) is a secondary metabolite produced by fungi of Aspergillus and Penicillium genra. OTA is mainly nephrotoxic but can also cause hepatotoxicity, mutagenicity, teratogenicity, neurotoxicity and immunotoxicity. As recent studies have highlighted the close relationship between gastrointestinal tract and kidney, as principal organs involved in absorption and respective excretion of xenobiotics, the aim of the present study was to analyze the effect of a subchronic exposure (30 days) to 0.05 mg/kg OTA on immune response and oxidative stress parameters at the level of intestine and kidney of young swine. The experiment was realised on twelve crossbred weaned piglets randomly allotted to both control group or toxin group fed 0.050 mg OTA/kg feed. Our results have shown that a subchronic intoxication with a low dose of OTA for 30 days affected the immune response and the anti-oxidant self-defense at gut and kidney level. The gene expression of both markers of signaling pathways involved in inflammation and inflammatory cytokines were affected in a much higher extent in the gut than in the kidney Of OTA intoxicated piglets.

Microstructure-based hyperelastic models for closed-cell solids.

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

The optimal density of cellular solids in axial tension.

For cellular bodies with uniform cell size, wall thickness, and shape, an important question is whether the same volume of material has the same effect when arranged as many small cells or as fewer large cells. To answer this question, for finite element models of periodic structures of Mooney-type material with different structural geometry and subject to large strain deformations, we identify a nonlinear elastic modulus as the ratio between the mean effective stress and the mean effective strain in the solid cell walls, and show that this modulus increases when the thickness of the walls increases, as well as when the number of cells increases while the volume of solid material remains fixed. Since, under the specified conditions, this nonlinear elastic modulus increases also as the corresponding mean stress increases, either the mean modulus or the mean stress can be employed as indicator when the optimum wall thickness or number of cells is sought.

Effects of prophylactic ibuprofen and paracetamol administration on the immunogenicity and reactogenicity of the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugated vaccine (PHiD-CV) co-administered with DTPa-combined vaccines in children: An open-label, randomized, controlled, non-inferiority trial.

Prophylactic paracetamol administration impacts vaccine immune response; this study ( www.clinicaltrials.gov : NCT01235949) is the first to assess PHiD-CV immunogenicity following prophylactic ibuprofen administration. In this phase IV, multicenter, open-label, randomized, controlled, non-inferiority study in Romania (November 2010-December 2012), healthy infants were randomized 3:3:3:1:1:1 to prophylactically receive immediate, delayed or no ibuprofen (IIBU, DIBU, NIBU) or paracetamol (IPARA, DPARA, NPARA) after each of 3 primary doses (PHiD-CV at age 3/4/5 months co-administered with DTPa-HBV-IPV/Hib at 3/5 and DTPa-IPV/Hib at 4 months) or booster dose (PHiD-CV and DTPa-HBV-IPV/Hib; 12-15 months). Non-inferiority of immune response one month post-primary vaccination in terms of percentage of infants with anti-pneumococcal antibody concentrations ≥0.2 µg/mL (primary objective) was demonstrated if the upper limit (UL) of the 98.25% confidence interval of difference between groups (NIBU vs IIBU, NIBU vs DIBU) was <10% for ≥7/10 serotypes. Immunogenicity and reactogenicity/safety were evaluated, including confirmatory analysis of difference in fever incidences post-primary vaccination in IBU or DIBU group compared to NIBU. Of 850 infants randomized, 812 were included in the total vaccinated cohort. Non-inferiority was demonstrated for both comparisons (UL was <10% for 9/10 vaccine serotypes; exceptions: 6B [NIBU], 23F [IIBU]). However, fever incidence post-primary vaccination in the IIBU and DIBU groups did not indicate a statistically significant reduction. Prophylactic administration (immediate or delayed) of paracetamol decreased fever incidence but seemed to reduce immune response to PHiD-CV, except when given only at booster. Twenty-seven serious adverse events were reported for 15 children; all resolved and were not vaccination-related.

γ irradiation induced effects on bismuth active centres and related photoluminescence properties of Bi/Er co-doped optical fibres.

We investigate the effects of γ irradiation on bismuth active centres (BACs) and related photoluminescence properties of bismuth/erbium co-doped silica fibre (BEDF), [Si] ~28, [Ge] ~1.60, [Al] ~0.10, [Er] ~ <0.10 and [Bi] ~0.10 atom%, fabricated by in-situ solution doping and Modified Chemical Vapor Deposition (MCVD). The samples were irradiated at 1 kGy, 5 kGy, 15 kGy, 30 kGy and 50 kGy doses, and dose rate of 5.5 kGy/h, at room temperature. The optical properties of BEDF samples are tested before and after γ irradiation. We found that high dose γ irradiation could significantly influence the formation and composition of BACs and their photoluminescence performance, as important changes in absorption and emission properties associated with the 830 nm pump produces the direct evidence of γ irradiation effects on BAC-Si. We notice that the saturable to unsaturable absorption ratio at pump wavelength could be increased with high dose γ irradiation, indicating that emission and pump efficiency could be increased by γ irradiation. Our experimental results also reveal good radiation survivability of the BEDF under low and moderate γ irradiation. Our investigation suggests the existence of irradiation related processing available for tailoring the photoluminescence properties and performance of bismuth doped/co-doped fibres.