Carbonate clumped isotope geochemistry has primarily focused on mass spectrometric determination of m/z 47 CO2 for geothermometry, but theoretical calculations and recent experiments indicate paired analysis of the m/z 47 (13C18O16O) and m/z 48 (12C18O18O) isotopologues (referred to as Δ47 and Δ48) can be used to study non-equilibrium isotope fractionations and refine temperature estimates. We utilize 5,448 Δ47 and 3,400 Δ48 replicate measurements of carbonate samples and standards, and 183 Δ47 and 195 Δ48 replicate measurements of gas standards from 2015 to 2021 from a multi-year and multi-instrument data set to constrain Δ47 and Δ48 values for 27 samples and standards, including Devils Hole cave calcite, and study equilibrium Δ47-Δ48, Δ47-temperature, and Δ48-temperature relationships. We compare results to previously published findings and calculate equilibrium regressions based on data from multiple laboratories. We report acid digestion fractionation factors, Δ*63-47 and Δ*64-48, and account for their dependence on the initial clumped isotope values of the mineral.

Transgene introgression is a major concern associated with transgenic plant-based vaccines. Agroinfiltration can be used to selectively transform nonreproductive organs and avoid introgression. Here, we introduce a new vaccine modality in which Staphylococcal enterotoxin B (SEB) genes are agroinfiltrated into radishes (Raphanw sativus L.), resulting in transient expression and accumulation of SEB in planta. This approach can simultaneously express multiple antigens in a single leaf. Furthermore, the potential of high-throughput vaccine production was demonstrated by simultaneously agroinfiltrating multiple radish leaves using a multichannel pipette. The expression of SEB was detectable in two leaf cell types (epidermal and guard cells) in agroinfiltrated leaves. ICR mice intranasally immunized with homogenized leaves agroinfiltrated with SEB elicited detectable antibody to SEB and displayed protection against SEB-induced interferon-gamma (IFN-γ) production. The concept of encapsulating antigens in leaves rather than purifying them for immunization may facilitate rapid vaccine production during an epidemic disease.

Rationale

Clumped isotope geochemistry examines the pairing or clumping of heavy isotopes in molecules and provides information about the thermodynamic and kinetic controls on their formation. The first clumped isotope measurements of carbonate minerals were first published 15 years ago, and since then, interlaboratory offsets have been observed, and laboratory and community practices for measurement, data analysis, and instrumentation have evolved. Here we briefly review historical and recent developments for measurements, share Tripati Lab practices for four different instrument configurations, test a recently published proposal for carbonate-based standardization on multiple instruments using multi-year data sets, and report values for 21 different carbonate standards that allow for recalculations of previously published data sets.

Methods

We examine data from 4628 standard measurements on Thermo MAT 253 and Nu Perspective IS mass spectrometers, using a common acid bath (90°C) and small-sample (70°C) individual reaction vessels. Each configuration was investigated by treating some standards as anchors (working standards) and the remainder as unknowns (consistency standards).

Results

We show that different acid digestion systems and mass spectrometer models yield indistinguishable results when instrument drift is well characterized. For linearity correction, mixed gas-and-carbonate standardization or carbonate-only standardization yields similar results. No difference is observed in the use of three or eight working standards for the construction of transfer functions.

Conclusions

We show that all configurations yield similar results if instrument drift is robustly characterized and validate a recent proposal for carbonate-based standardization using large multiyear data sets. Δ₄₇ values are reported for 21 carbonate standards on both the absolute reference frame (ARF; also refered to as the Carbon Dioxide Equilibrated Scale or CDES) and the new InterCarb-Carbon Dioxide Equilibrium Scale (I-CDES) reference frame, facilitating intercomparison of data from a diversity of labs and instrument configurations and restandardization of a broad range of sample sets between 2006, when the first carbonate measurements were published, and the present.

Elemental ratios in biogenic marine calcium carbonates are widely used in geobiology, environmental science, and paleoenvironmental reconstructions. It is generally accepted that the elemental abundance of biogenic marine carbonates reflects a combination of the abundance of that ion in seawater, the physical properties of seawater, the mineralogy of the biomineral, and the pathways and mechanisms of biomineralization. Here we report measurements of a suite of nine elemental ratios (Li/Ca, B/Ca, Na/Ca, Mg/Ca, Zn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and U/Ca) in 18 species of benthic marine invertebrates spanning a range of biogenic carbonate polymorph mineralogies (low-Mg calcite, high-Mg calcite, aragonite, mixed mineralogy) and of phyla (including Mollusca, Echinodermata, Arthropoda, Annelida, Cnidaria, Chlorophyta, and Rhodophyta) cultured at a single temperature (25°C) and a range of pCO₂ treatments (ca. 409, 606, 903, and 2856 ppm). This dataset was used to explore various controls over elemental partitioning in biogenic marine carbonates, including species-level and biomineralization-pathway-level controls, the influence of internal pH regulation compared to external pH changes, and biocalcification responses to changes in seawater carbonate chemistry. The dataset also enables exploration of broad scale phylogenetic patterns of elemental partitioning across calcifying species, exhibiting high phylogenetic signals estimated from both uni- and multivariate analyses of the elemental ratio data (univariate: λ = 0-0.889; multivariate: λ = 0.895-0.99). Comparing partial R ² values returned from non-phylogenetic and phylogenetic regression analyses echo the importance of and show that phylogeny explains the elemental ratio data 1.4-59 times better than mineralogy in five out of nine of the elements analyzed. Therefore, the strong associations between biomineral elemental chemistry and species relatedness suggests mechanistic controls over element incorporation rooted in the evolution of biomineralization mechanisms.

The Cedars is an area in Northern California with a chain of highly alkaline springs resulting from CO2-charged meteorological water interacting with a peridotite body. Serpentinization resulting from this interaction at depth leads to the sequestration of various carbonate minerals into veins accompanied by a release of Ca2+ and OH– enriched water to the surface, creating an environment which promotes rapid precipitation of CaCO3 at surface springs. This environment enables us to apply the recently developed Δ47-Δ48 dual clumped isotope analysis to probe kinetic isotope effects (KIEs) and timescales of CO2 transformation in a region with the potential for geological CO2 sequestration. We analyzed CaCO3 recovered from various localities and identified significant kinetic fractionations associated with CO2 absorption in a majority of samples, characterized by enrichment in Δ47 values and depletion in Δ48 values relative to equilibrium. Surface floes exhibited the largest KIEs (ΔΔ47: 0.163‰, ΔΔ48: −0.761‰). Surface floe samples begin to precipitate out of solution within the first hour of CO2 absorption, and the dissolved inorganic carbon (DIC) pool requires a residence time of >100 h to achieve isotopic equilibria. The Δ48/Δ47 slope of samples from the Cedars (−3.223 ± 0.519) is within the range of published theoretical values designed to constrain CO2 hydrolysis-related kinetic fractionation (−1.724 to −8.330). The Δ47/δ18O slope (−0.009 ± 0.001) and Δ47/δ13C slope (−0.009 ± 0.001) are roughly consistent with literature values reported from a peridotite in Oman of −0.006 ± 0.002 and −0.005 ± 0.002, respectively. The consistency of slopes in the multi-isotope space suggests the Δ47-Δ48 dual carbonate clumped isotope framework can be applied to study CO2-absorption processes in applied systems, including sites of interest for geological sequestration.

Background

While vaccines have established utility against COVID-19, phase 3 efficacy studies have generally not comprehensively evaluated protection provided by previous infection or hybrid immunity (previous infection plus vaccination). Individual patient data from US government-supported harmonized vaccine trials provide an unprecedented sample population to address this issue. We characterized the protective efficacy of previous SARS-CoV-2 infection and hybrid immunity against COVID-19 early in the pandemic over three-to six-month follow-up and compared with vaccine-associated protection.

Methods

In this post-hoc cross-protocol analysis of the Moderna, AstraZeneca, Janssen, and Novavax COVID-19 vaccine clinical trials, we allocated participants into four groups based on previous-infection status at enrolment and treatment: no previous infection/placebo; previous infection/placebo; no previous infection/vaccine; and previous infection/vaccine. The main outcome was RT-PCR-confirmed COVID-19 >7-15 days (per original protocols) after final study injection. We calculated crude and adjusted efficacy measures.

Findings

Previous infection/placebo participants had a 92% decreased risk of future COVID-19 compared to no previous infection/placebo participants (overall hazard ratio [HR] ratio: 0.08; 95% CI: 0.05-0.13). Among single-dose Janssen participants, hybrid immunity conferred greater protection than vaccine alone (HR: 0.03; 95% CI: 0.01-0.10). Too few infections were observed to draw statistical inferences comparing hybrid immunity to vaccine alone for other trials. Vaccination, previous infection, and hybrid immunity all provided near-complete protection against severe disease.

Interpretation

Previous infection, any hybrid immunity, and two-dose vaccination all provided substantial protection against symptomatic and severe COVID-19 through the early Delta period. Thus, as a surrogate for natural infection, vaccination remains the safest approach to protection.

Funding

National Institutes of Health.