Transformation scenarios towards multifunctional landscapes: A multi-criteria land-use allocation model applied to Jambi Province, Indonesia.

In tropical regions, shifting from forests and traditional agroforestry to intensive plantations generates conflicts between human welfare (farmers' demands and societal needs) and environmental protection. Achieving sustainability in this transformation will inevitably involve trade-offs between multiple ecological and socioeconomic functions. To address these trade-offs, our study used a new methodological approach allowing the identification of transformation scenarios, including theoretical landscape compositions that satisfy multiple ecological functions (i.e., structural complexity, microclimatic conditions, organic carbon in plant biomass, soil organic carbon and nutrient leaching losses), and farmers needs (i.e., labor and input requirements, total income to land, and return to land and labor) while accounting for the uncertain provision of these functions and having an actual potential for adoption by farmers. We combined a robust, multi-objective optimization approach with an iterative search algorithm allowing the identification of ecological and socioeconomic functions that best explain current land-use decisions. The model then optimized the theoretical land-use composition that satisfied multiple ecological and socioeconomic functions. Between these ends, we simulated transformation scenarios reflecting the transition from current land-use composition towards a normative multifunctional optimum. These transformation scenarios involve increasing the number of optimized socioeconomic or ecological functions, leading to higher functional richness (i.e., number of functions). We applied this method to smallholder farms in the Jambi Province, Indonesia, where traditional rubber agroforestry, rubber plantations, and oil palm plantations are the main land-use systems. Given the currently practiced land-use systems, our study revealed short-term returns to land as the principal factor in explaining current land-use decisions. Fostering an alternative composition that satisfies additional socioeconomic functions would require minor changes ("low-hanging fruits"). However, satisfying even a single ecological indicator (e.g., reduction of nutrient leaching losses) would demand substantial changes in the current land-use composition ("moonshot"). This would inevitably lead to a profit decline, underscoring the need for incentives if the societal goal is to establish multifunctional agricultural landscapes. With many oil palm plantations nearing the end of their production cycles in the Jambi province, there is a unique window of opportunity to transform agricultural landscapes.

FULL-MDS: Fluorescent Universal Lipid Labeling for Microfluidic Diffusional Sizing.

Microfluidic diffusional sizing (MDS) is a recent and powerful method for determining the hydrodynamic sizes and interactions of biomolecules and nanoparticles. A major benefit of MDS is that it can report the size of a fluorescently labeled target even in mixtures with complex, unpurified samples. However, a limitation of MDS is that the target itself has to be purified and covalently labeled with a fluorescent dye. Such covalent labeling is not suitable for crude extracts such as native nanodiscs directly obtained from cellular membranes. In this study, we introduce fluorescent universal lipid labeling for MDS (FULL-MDS) as a sparse, noncovalent labeling method for determining particle size. We first demonstrate that the inexpensive and well-characterized fluorophore, Nile blue, spontaneously partitions into lipid nanoparticles without disrupting their structure. We then highlight the key advantage of FULL-MDS by showing that it yields robust size information on lipid nanoparticles in crude cell extracts that are not amenable to other sizing methods. Furthermore, even for synthetic nanodiscs, FULL-MDS is faster, cheaper, and simpler than existing labeling schemes.

Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation.

Affinity maturation is a powerful technique in antibody engineering for the in vitro evolution of antigen binding interactions. Key to the success of this process is the expansion of sequence and combinatorial diversity to increase the structural repertoire from which superior binding variants may be selected. However, conventional strategies are often restrictive and only focus on small regions of the antibody at a time. In this study, we used a method that combined antibody chain shuffling and a staggered-extension process to produce unbiased libraries, which recombined beneficial mutations from all six complementarity-determining regions (CDRs) in the affinity maturation of an inhibitory antibody to Arginase 2 (ARG2). We made use of the vast display capacity of ribosome display to accommodate the sequence space required for the diverse library builds. Further diversity was introduced through pool maturation to optimize seven leads of interest simultaneously. This resulted in antibodies with substantial improvements in binding properties and inhibition potency. The extensive sequence changes resulting from this approach were translated into striking structural changes for parent and affinity-matured antibodies bound to ARG2, with a large reorientation of the binding paratope facilitating increases in contact surface and shape complementarity to the antigen. The considerable gains in therapeutic properties seen from extensive sequence and structural evolution of the parent ARG2 inhibitory antibody clearly illustrate the advantages of the unbiased approach developed, which was key to the identification of high-affinity antibodies with the desired inhibitory potency and specificity.

Disentangling climatic and anthropogenic contributions to nonlinear dynamics of alpine grassland productivity on the Qinghai-Tibetan Plateau.

Alpine grasslands on the Qinghai-Tibetan Plateau are sensitive and vulnerable to climate change and human activities. Climate warming and overgrazing have already caused degradation in a large fraction of alpine grasslands on this plateau. However, it remains unclear how human activities (mainly livestock grazing) regulates vegetation dynamics under climate change. Here, alpine grassland productivity (substituted with the normalized difference vegetation index, NDVI) is hypothesized to vary in a nonlinear trajectory to follow climate fluctuations and human disturbances. With generalized additive mixed modelling (GAMM) and residual-trend (RESTREND) analysis together, both magnitude and direction of climatic (in terms of temperature, precipitation, and radiation) and anthropogenic impacts on NDVI variation were examined across alpine meadows, steppes, and desert-steppes on the Qinghai-Tibetan Plateau. The results revealed that accelerating warming and greening, respectively, took place in 76.2% and 78.8% of alpine grasslands on the Qinghai-Tibetan Plateau. The relative importance of temperature, precipitation, and radiation impacts was comparable, between 20.4% and 24.8%, and combined to explain 66.2% of NDVI variance at the pixel scale. The human influence was strengthening and weakening, respectively, in 15.5% and 14.3% of grassland pixels, being slightly larger than any sole climatic variable across the entire plateau. Anthropogenic and climatic factors can be in opposite ways to affect alpine grasslands, even within the same grassland type, likely regulated by plant community assembly and species functional traits. Therefore, the underlying mechanisms of how plant functional diversity regulates nonlinear ecosystem response to climatic and anthropogenic stresses should be carefully explored in the future.

Impacts of grazing exclusion on productivity partitioning along regional plant diversity and climatic gradients in Tibetan alpine grasslands.

The biodiversity-productivity relationship is critical for better predicting ecosystem responses to climate change and human disturbance. However, it remains unclear about the effects of climate change, land use shifts, plant diversity, and their interactions on productivity partitioning above- and below-ground components in alpine grasslands on the Tibetan Plateau. To answer this question, we conducted field surveys at 33 grazed vs. fenced paired sites that are distributed across the alpine meadow, steppe, and desert-steppe zones on the northern Tibetan Plateau in early August of 2010-2013. Generalized additive models (GAMs) showed that aboveground net primary productivity (ANPP) linearly increased with growing season precipitation (GSP) while belowground net primary productivity (BNPP) decreased with growing season temperature (GST). Compared to grazed sites, short-term fencing did not alter the patterns of ANPP along climatic gradients but tended to decrease BNPP at moderate precipitation levels of 200 mm < GSP <450 mm. We also found that ANPP and BNPP linearly increased with species richness, ANPP decreased with Shannon diversity index, and BNPP did not correlate with the Shannon diversity index. Fencing did not alter the relationships between productivity components and plant diversity indices. Generalized additive mixed models furtherly confirmed that the interaction of localized plant diversity and climatic condition nonlinearly regulated productivity partitioning of alpine grasslands in this area. Finally, structural equation models (SEMs) revealed the direction and strength of causal links between biotic and abiotic variables within alpine grassland ecosystems. ANPP was controlled directly by GSP (0.53) and indirectly via species richness (0.41) and Shannon index (-0.12). In contrast, BNPP was influenced directly by GST (-0.43) and indirectly by GSP via species richness (0.05) and Shannon index (-0.02). Therefore, we recommend using a joint approach of GAMs and SEMs for better understanding mechanisms behind the relationship between biodiversity and ecosystem function under climate change and human disturbance.

Preparation of Asymmetric Liposomes Using a Phosphatidylserine Decarboxylase.

Lipid asymmetries between the outer and inner leaflet of the lipid bilayer exist in nearly all biological membranes. Although living cells spend great effort to adjust and maintain these asymmetries, little is known about the biophysical phenomena within asymmetric membranes and their role in cellular function. One reason for this lack of insight into such a fundamental membrane property is the fact that the majority of model-membrane studies have been performed on symmetric membranes. Our aim is to overcome this problem by employing a targeted, enzymatic reaction to prepare asymmetric liposomes with phosphatidylserine (PS) primarily in the inner leaflet. To achieve this goal, we use a recombinant version of a water soluble PS decarboxylase from Plasmodium knowlesi, which selectively decarboxylates PS in the outer leaflet, converting it to phosphatidylethanolamine. The extent of decarboxylation is quantified using high-performance thin-layer chromatography, and the local concentration of anionic PS in the outer leaflet is monitored in terms of the ζ potential. Starting, for example, with 21 mol % 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine sodium salt, the assay leads to liposomes with 21 mol % in the inner and 6 mol % PS in the outer leaflet. This asymmetry persists virtually unchanged for at least 4 days at 20°C and at least 2 days at 40°C. The use of a highly specific enzyme carries the advantage that a minor component such as PS can be adjusted without affecting or being affected by the other lipid species present in the model membrane. The phenomena governing the residual outside PS content are addressed but warrant further study.

Engineering Asymmetric Lipid Vesicles: Accurate and Convenient Control of the Outer Leaflet Lipid Composition.

The asymmetric distribution of lipids between the two bilayer leaflets represents a typical feature of biological membranes. The loss of this asymmetry, for example the exposure of negatively charged lipids on the extracellular membrane leaflet of mammalian cells, is involved in apoptosis and occurs in tumor cells. Thus, the controlled production of asymmetric liposomes helps to better understand such crucial cellular processes. Here, we present an approach that allows us to design asymmetric model-membrane experiments on a rational basis and predict the fraction of exchanged lipid. In addition, we developed a label-free and nondestructive assay to quantify the asymmetric uptake of negatively charged lipids in terms of the zeta potential. This significantly enhances the applicability, impact, and predictive power of model membranes.

Vesicle Leakage Reflects the Target Selectivity of Antimicrobial Lipopeptides from Bacillus subtilis.

Cyclic lipopeptides act against a variety of plant pathogens and are thus highly efficient crop-protection agents. Some pesticides contain Bacillus subtilis strains that produce lipopeptide families, such as surfactins (SF), iturins (IT), and fengycins (FE). The antimicrobial activity of these peptides is mainly mediated by permeabilizing cellular membranes. We used a fluorescence-lifetime based leakage assay to examine the effect of individual lipid components in model membranes on lipopeptide activity. Leakage induction by FE was strongly inhibited by cholesterol (CHOL) as well as by phosphatidylethanolamine (PE) and -glycerol (PG) lipids. Already moderate amounts of CHOL increased the tolerable FE content in membranes by an order of magnitude to 0.5 FE per PC + CHOL. This indicates reduced FE-lipid demixing and aggregation, which is known to be required for membrane permeabilization and explains the strong inhibition by CHOL. Ergosterol (ERG) had a weak antagonistic effect. This confirms results of microbiological tests and agrees with the fungicidal activity and selectivity of FE. SF is known to be much less selective in its antimicrobial action. In line with this, liposome leakage by SF was little affected by sterols and PE. Interestingly, PG increased SF activity and changed its leakage mechanism toward all-or-none, suggesting more specific, larger, and/or longer-lived defect structures. This may be because of the reduced energetic cost of locally accumulating anionic SF in an anionic lipid matrix. IT was found largely inactive in our assays. B. subtilis QST713 produces the lipopeptides in a ratio of 6 mol SF: 37 mol FE: 57 mol IT. Leakage induced by this native mixture was inhibited by CHOL and PE, but unaffected by ERG and by PG in the absence of PE. Note that fungi contain anionic lipids, but little PE. Hence, our data explain the strong, fungicidal activity and selectivity of B. subtilis QST713 lipopeptides.

Amyloid precursor protein dimerization and synaptogenic function depend on copper binding to the growth factor-like domain.

Accumulating evidence suggests that the copper-binding amyloid precursor protein (APP) has an essential synaptic function. APP synaptogenic function depends on trans-directed dimerization of the extracellular E1 domain encompassing a growth factor-like domain (GFLD) and a copper-binding domain (CuBD). Here we report the 1.75 Å crystal structure of the GFLD in complex with a copper ion bound with high affinity to an extended hairpin loop at the dimerization interface. In coimmunoprecipitation assays copper binding promotes APP interaction, whereas mutations in the copper-binding sites of either the GFLD or CuBD result in a drastic reduction in APP cis-orientated dimerization. We show that copper is essential and sufficient to induce trans-directed dimerization of purified APP. Furthermore, a mixed culture assay of primary neurons with HEK293 cells expressing different APP mutants revealed that APP potently promotes synaptogenesis depending on copper binding to the GFLD. Together, these findings demonstrate that copper binding to the GFLD of APP is required for APP cis-/trans-directed dimerization and APP synaptogenic function. Thus, neuronal activity or disease-associated changes in copper homeostasis likely go along with altered APP synaptic function.

Preparation of ready-to-use small unilamellar phospholipid vesicles by ultrasonication with a beaker resonator.

Lipid vesicles are widely used as models to investigate the interactions of proteins, peptides, and small molecules with lipid bilayers. We present a sonication procedure for the preparation of well-defined and ready-to-use small unilamellar vesicles composed of phospholipids with the aid of a beaker resonator. This indirect but efficient sonication method does not require subsequent centrifugation or other purification steps, which distinguishes it from established sonication procedures. Vesicles produced by this method reveal a unimodal size distribution and are unilamellar, as demonstrated by dynamic light scattering and (31)P nuclear magnetic resonance spectroscopy, respectively.

Incapacity of work after arthroscopic Bankart repair.

BACKGROUND AND INTRODUCTION: The incapacity with respect to work following anterior-inferior shoulder dislocation and subsequent Bankart repair has not been previously examined. The objective of this study was to examine a patient's incapacity according to the classification by the REFA Association. The recovery time was measured and the outcome of patients with heavy workload was compared to those with lower workloads. MATERIALS AND METHODS: A total of 74 patients who underwent isolated arthroscopic Bankart repair fulfilled the inclusion criteria. The Constant-Murley Score, UCLA Shoulder Score and ROWE Score for Shoulder Instability were recorded for clinical assessment. The mean follow-up time was 43.1 months (SD ± 17.4; 24-110 months) with a mean age of 34.7 years (SD ± 12.6). Workload was classified as per the REFA Association classification system. Postoperative duration of a patient's incapacity with respect to work and other subjective ratings were provided by the patients themselves. RESULTS: The mean incapacity of work was 2.73 months (95 % CI 1.19-5.36). The incapacity of work was 2.06 months (95 % CI 1.55-2.68) in the group with low physical strains at work (REFA 0-1) and 3.40 months (95 % CI 2.70-4.24) in the group with heavy workload (REFA 2-4/p = 0.005). Overall, the mean Constant-Murley Score was 87.7 (SD ± 13.5). The average UCLA Shoulder Score summed up to 31.9 (SD ± 3.87) and the mean ROWE Score was 87.6 (SD ± 21.7). 13 (17.5 %) patients had problems to compete in their jobs. Three patients had to change the job postoperatively. CONCLUSION: In this study, a relationship between the time of incapacity of work and the workload was observed; patients with low physical strains returned significantly earlier to work after arthroscopic Bankart repair (p = 0.005). In general, the clinical results as measured in the Constant/UCLA/Rowe score were comparable to other studies.

Polar interactions trump hydrophobicity in stabilizing the self-inserting membrane protein Mistic.

Canonical integral membrane proteins are attached to lipid bilayers through hydrophobic transmembrane helices, whose topogenesis requires sophisticated insertion machineries. By contrast, membrane proteins that, for evolutionary or functional reasons, cannot rely on these machineries need to resort to driving forces other than hydrophobicity. A striking example is the self-inserting Bacillus subtilis protein Mistic, which is involved in biofilm formation and has found application as a fusion tag supporting the recombinant production and bilayer insertion of other membrane proteins. Although this unusual protein contains numerous polar and charged residues and lacks characteristic membrane-interaction motifs, it is tightly bound to membranes in vivo and membrane-mimetic systems in vitro. Therefore, we set out to quantify the contributions from polar and nonpolar interactions to the coupled folding and insertion of Mistic. To this end, we defined conditions under which the protein can be unfolded completely and reversibly from various detergent micelles by urea in a two-state equilibrium and where the unfolded state is independent of the detergent used for solubilizing the folded state. This enabled equilibrium unfolding experiments previously used for soluble and ß-barrel membrane proteins, revealing that polar interactions with ionic and zwitterionic headgroups and, presumably, the interfacial dipole potential stabilize the protein much more efficiently than nonpolar interactions with the micelle core. These findings unveil the forces that allow a protein to tightly interact with a membrane-mimetic environment without major hydrophobic contributions and rationalize the differential suitability of detergents for the extraction and solubilization of Mistic-tagged membrane proteins.

Real-time monitoring of membrane-protein reconstitution by isothermal titration calorimetry.

Phase diagrams offer a wealth of thermodynamic information on aqueous mixtures of bilayer-forming lipids and micelle-forming detergents, providing a straightforward means of monitoring and adjusting the supramolecular state of such systems. However, equilibrium phase diagrams are of very limited use for the reconstitution of membrane proteins because of the occurrence of irreversible, unproductive processes such as aggregation and precipitation that compete with productive reconstitution. Here, we exemplify this by dissecting the effects of the K(+) channel KcsA on the process of bilayer self-assembly in a mixture of Escherichia coli polar lipid extract and the nonionic detergent octyl-ß-d-glucopyranoside. Even at starting concentrations in the low micromolar range, KcsA has a tremendous impact on the supramolecular organization of the system, shifting the critical lipid/detergent ratios at the onset and completion of vesicle formation by more than 2-fold. Thus, equilibrium phase diagrams obtained for protein-free lipid/detergent mixtures would be misleading when used to guide the reconstitution process. To address this issue, we demonstrate that, even under such nonequilibrium conditions, high-sensitivity isothermal titration calorimetry can be exploited to monitor the progress of membrane-protein reconstitution in real time, in a noninvasive manner, and at high resolution to yield functional proteoliposomes with a narrow size distribution for further downstream applications.

Microfluidic Diffusional Sizing (MDS) Measurements of Secretory Neutralizing Antibody Affinity Against SARS-CoV-2.

SARS-CoV-2 has rampantly spread around the globe and continues to cause unprecedented loss through ongoing waves of (re)infection. Increasing our understanding of the protection against infection with SARS-CoV-2 is critical to ending the pandemic. Serological assays have been widely used to assess immune responses, but secretory antibodies, the essential first line of defense, have been studied to only a limited extent. Of particular interest and importance are neutralizing antibodies, which block the binding of the spike protein of SARS-CoV-2 to the human receptor angiotensin-converting enzyme-2 (ACE2) and thus are essential for immune defense. Here, we employed Microfluidic Diffusional Sizing (MDS), an immobilization-free technology, to characterize neutralizing antibody affinity to SARS-CoV-2 spike receptor-binding domain (RBD) and spike trimer in saliva. Affinity measurement was obtained through a contrived sample and buffer using recombinant SARS-CoV-2 RBD and monoclonal antibody. Limited saliva samples demonstrated that MDS applies to saliva neutralizing antibody measurement. The ability to disrupt a complex of ACE2-Fc and spike trimer is shown. Using a quantitative assay on the patient sample, we determined the affinity and binding site concentration of the neutralizing antibodies.

α-Synuclein Oligomers Displace Monomeric α-Synuclein from Lipid Membranes.

Parkinson's disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder linked to the accumulation of α-synuclein (αS) protein aggregates in the nervous system. While αS binding to membranes in its monomeric state is correlated to its physiological role, αS oligomerization and subsequent aberrant interactions with lipid bilayers have emerged as key steps in PD-associated neurotoxicity. However, little is known of the mechanisms that govern the interactions of oligomeric αS (OαS) with lipid membranes and the factors that modulate such interactions. This is in large part due to experimental challenges underlying studies of OαS-membrane interactions due to their dynamic and transient nature. Here, we address this challenge by using a suite of microfluidics-based assays that enable in-solution quantification of OαS-membrane interactions. We find that OαS bind more strongly to highly curved, rather than flat, lipid membranes. By comparing the membrane-binding properties of OαS and monomeric αS (MαS), we further demonstrate that OαS bind to membranes with up to 150-fold higher affinity than their monomeric counterparts. Moreover, OαS compete with and displace bound MαS from the membrane surface, suggesting that disruption to the functional binding of MαS to membranes may provide an additional toxicity mechanism in PD. These findings present a binding mechanism of oligomers to model membranes, which can potentially be targeted to inhibit the progression of PD.

Effects of plant diversity on productivity strengthen over time due to trait-dependent shifts in species overyielding.

Plant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems.

The mechanism of denaturation and the unfolded state of the α-helical membrane-associated protein Mistic.

In vitro protein-folding studies using chemical denaturants such as urea are indispensible in elucidating the forces and mechanisms determining the stability, structure, and dynamics of water-soluble proteins. By contrast, α-helical membrane-associated proteins largely evade such approaches because they are resilient to extensive unfolding. We have used optical and NMR spectroscopy to provide an atomistic-level dissection of the effects of urea on the structure and dynamics of the α-helical membrane-associated protein Mistic as well as its interactions with detergent and solvent molecules. In the presence of the zwitterionic detergent lauryl dimethylamine oxide, increasing concentrations of urea result in a complex sequence of conformational changes that go beyond simple two-state unfolding. Exploiting this finding, we report the first high-resolution structural models of the urea denaturation process of an α-helical membrane-associated protein and its completely unfolded state, which contains almost no regular secondary structure but nevertheless retains a topology close to that of the folded state.

Automated circular dichroism spectroscopy for medium-throughput analysis of protein conformation.

Circular dichroism (CD) spectroscopy is a powerful method for monitoring conformational changes of biomolecules. For peptides and proteins, it is highly sensitive to changes in secondary structure, which may be caused by alterations in amino acid composition or solution conditions (e.g., temperature, pH, salts, detergents, denaturants, and excipients), post-translational modifications, self-association, or ligand binding. The assets of CD spectroscopy are that the signal is directly linked to structure, the analyte is measured without labels and in solution, the technique requires low sample amounts, and data analysis is straightforward. However, CD spectroscopy has remained a low-throughput method because it imposes high requirements on the optical quality of sample cells and thus cannot be performed in microplate-reader format. Here, we introduce an automated CD spectrometer equipped with a low-birefringence flow-through cell that is coupled to a three-axis robotic liquid-handling system. This enables unattended CD measurements on up to 384 samples, including sample transfer from 96-well plates into the flow-through cell, data acquisition, and cell cleaning. We show that the accuracy, precision, and reproducibility afforded by the new instrument are excellent and exemplify how the advantages offered by automated CD spectroscopy can be exploited to quantify protein stability by titration with chemical denaturants.

Protocol to determine antibody affinity and concentration in complex solutions using microfluidic antibody affinity profiling.

Conventional methods of measuring affinity are limited by artificial immobilization, large sample volumes, and homogeneous solutions. This protocol describes microfluidic antibody affinity profiling on complex human samples in solution to obtain a fingerprint reflecting both affinity and active concentration of the target protein. To illustrate the protocol, we analyze the antibody response in SARS-CoV-2 omicron-naïve samples against different SARS-CoV-2 variants of concern. However, the protocol and the technology are amenable to a broad spectrum of biomedical questions. For complete details on the use and execution of this protocol, please refer to Emmenegger et al. (2022),1 Schneider et al. (2022),2 and Fiedler et al. (2022).3.

Both COVID-19 infection and vaccination induce high-affinity cross-clade responses to SARS-CoV-2 variants.

The B.1.1.529 (omicron) variant has rapidly supplanted most other SARS-CoV-2 variants. Using microfluidics-based antibody affinity profiling (MAAP), we have characterized affinity and IgG concentration in the plasma of 39 individuals with multiple trajectories of SARS-CoV-2 infection and/or vaccination. Antibody affinity was similar against the wild-type, delta, and omicron variants (K A ranges: 122 ± 155, 159 ± 148, 211 ± 307 µM-1, respectively), indicating a surprisingly broad and mature cross-clade immune response. Postinfectious and vaccinated subjects showed different IgG profiles, with IgG3 (p-value = 0.002) against spike being more prominent in the former group. Lastly, we found that the ELISA titers correlated linearly with measured concentrations (R = 0.72) but not with affinity (R = 0.29). These findings suggest that the wild-type and delta spike induce a polyclonal immune response capable of binding the omicron spike with similar affinity. Changes in titers were primarily driven by antibody concentration, suggesting that B-cell expansion, rather than affinity maturation, dominated the response after infection or vaccination.