Controls and relationships of soil organic carbon abundance and persistence vary across pedo-climatic regions.

One of the largest uncertainties in the terrestrial carbon cycle is the timing and magnitude of soil organic carbon (SOC) response to climate and vegetation change. This uncertainty prevents models from adequately capturing SOC dynamics and challenges the assessment of management and climate change effects on soils. Reducing these uncertainties requires simultaneous investigation of factors controlling the amount (SOC abundance) and duration (SOC persistence) of stored C. We present a global synthesis of SOC and radiocarbon profiles (nProfile = 597) to assess the timescales of SOC storage. We use a combination of statistical and depth-resolved compartment models to explore key factors controlling the relationships between SOC abundance and persistence across pedo-climatic regions and with soil depth. This allows us to better understand (i) how SOC abundance and persistence covary across pedo-climatic regions and (ii) how the depth dependence of SOC dynamics relates to climatic and mineralogical controls on SOC abundance and persistence. We show that SOC abundance and persistence are differently related; the controls on these relationships differ substantially between major pedo-climatic regions and soil depth. For example, large amounts of persistent SOC can reflect climatic constraints on soils (e.g., in tundra/polar regions) or mineral absorption, reflected in slower decomposition and vertical transport rates. In contrast, lower SOC abundance can be found with lower SOC persistence (e.g., in highly weathered tropical soils) or higher SOC persistence (e.g., in drier and less productive regions). We relate variable patterns of SOC abundance and persistence to differences in the processes constraining plant C input, microbial decomposition, vertical C transport and mineral SOC stabilization potential. This process-oriented grouping of SOC abundance and persistence provides a valuable benchmark for global C models, highlighting that pedo-climatic boundary conditions are crucial for predicting the effects of climate change and soil management on future C abundance and persistence.

Non-structural carbohydrate concentrations in tree organs vary across biomes and leaf habits, but are independent of the fast-slow plant economic spectrum.

Carbohydrate reserves play a vital role in plant survival during periods of negative carbon balance. Under a carbon-limited scenario, we expect a trade-offs between carbon allocation to growth, reserves, and defense. A resulting hypothesis is that carbon allocation to reserves exhibits a coordinated variation with functional traits associated with the 'fast-slow' plant economics spectrum. We tested the relationship between non-structural carbohydrates (NSC) of tree organs and functional traits using 61 angiosperm tree species from temperate and tropical forests with phylogenetic hierarchical Bayesian models. Our results provide evidence that NSC concentrations in stems and branches are decoupled from plant functional traits. while those in roots are weakly coupled with plant functional traits. In contrast, we found that variation between NSC concentrations in leaves and the fast-slow trait spectrum was coordinated, as species with higher leaf NSC had trait values associated with resource conservative species, such as lower SLA, leaf N, and leaf P. We also detected a small effect of leaf habit on the variation of NSC concentrations in branches and roots. Efforts to predict the response of ecosystems to global change will need to integrate a suite of plant traits, such as NSC concentrations in woody organs, that are independent of the 'fast-slow' plant economics spectrum and that capture how species respond to a broad range of global change drivers.

On the importance of time in carbon sequestration in soils and climate change mitigation.

A clear definition of carbon sequestration in soils is necessary to quantify soil's role in climate change mitigation accurately. Don et al. (2023) proposed defining carbon sequestration as "[the] Process of transferring carbon from the atmosphere into the soil through plants or other organisms, which is retained as soil organic carbon resulting in a global carbon stock increase of the soil". In our view, this definition is incomplete because a comprehensive definition of carbon sequestration should explicitly include the time that carbon remains stored in an ecosystem, thus mitigating its contribution to the greenhouse effect.

Carbon sequestration in the subsoil and the time required to stabilize carbon for climate change mitigation.

Soils store large quantities of carbon in the subsoil (below 0.2 m depth) that is generally old and believed to be stabilized over centuries to millennia, which suggests that subsoil carbon sequestration (CS) can be used as a strategy for climate change mitigation. In this article, we review the main biophysical processes that contribute to carbon storage in subsoil and the main mathematical models used to represent these processes. Our guiding objective is to review whether a process understanding of soil carbon movement in the vertical profile can help us to assess carbon storage and persistence at timescales relevant for climate change mitigation. Bioturbation, liquid phase transport, belowground carbon inputs, mineral association, and microbial activity are the main processes contributing to the formation of soil carbon profiles, and these processes are represented in models using the diffusion-advection-reaction paradigm. Based on simulation examples and measurements from carbon and radiocarbon profiles across biomes, we found that advective and diffusive transport may only play a secondary role in the formation of soil carbon profiles. The difference between vertical root inputs and decomposition seems to play a primary role in determining the shape of carbon change with depth. Using the transit time of carbon to assess the timescales of carbon storage of new inputs, we show that only small quantities of new carbon inputs travel through the profile and can be stabilized for time horizons longer than 50 years, implying that activities that promote CS in the subsoil must take into consideration the very small quantities that can be stabilized in the long term.

Making the case for an International Decade of Radiocarbon.

Radiocarbon (14C) is a critical tool for understanding the global carbon cycle. During the Anthropocene, two new processes influenced 14C in atmospheric, land and ocean carbon reservoirs. First, 14C-free carbon derived from fossil fuel burning has diluted 14C, at rates that have accelerated with time. Second, 'bomb' 14C produced by atmospheric nuclear weapon tests in the mid-twentieth century provided a global isotope tracer that is used to constrain rates of air-sea gas exchange, carbon turnover, large-scale atmospheric and ocean transport, and other key C cycle processes. As we write, the 14C/12C ratio of atmospheric CO2 is dropping below pre-industrial levels, and the rate of decline in the future will depend on global fossil fuel use and net exchange of bomb 14C between the atmosphere, ocean and land. This milestone coincides with a rapid increase in 14C measurement capacity worldwide. Leveraging future 14C measurements to understand processes and test models requires coordinated international effort-a 'decade of radiocarbon' with multiple goals: (i) filling observational gaps using archives, (ii) building and sustaining observation networks to increase measurement density across carbon reservoirs, (iii) developing databases, synthesis and modelling tools and (iv) establishing metrics for identifying and verifying changes in carbon sources and sinks. This article is part of the Theo Murphy meeting issue 'Radiocarbon in the Anthropocene'.

A decrease in the age of respired carbon from the terrestrial biosphere and increase in the asymmetry of its distribution.

We provide here a model-based estimate of the transit time of carbon through the terrestrial biosphere, since the time of carbon uptake through photosynthesis until its release through respiration. We explored the consequences of increasing productivity versus increasing respiration rates on the transit time distribution and found that while higher respiration rates induced by higher temperature increase the transit time because older carbon is respired, increases in productivity cause a decline in transit times because more young carbon is available to supply increased metabolism. The combined effect of increases in temperature and productivity results in a decrease in transit times, with the productivity effect dominating over the respiration effect. By using an ensemble of simulation trajectories from the Carbon Data Model Framework (CARDAMOM), we obtained time-dependent transit time distributions incorporating the twentieth century global change. In these simulations, transit time declined over the twentieth century, suggesting an increased productivity effect that augmented the amount of respired young carbon, but also increasing the release of old carbon from high latitudes. The transit time distribution of carbon becomes more asymmetric over time, with more carbon transiting faster through tropical and temperate regions, and older carbon being respired from high latitude regions. This article is part of the Theo Murphy meeting issue 'Radiocarbon in the Anthropocene'.

Relating mineral-organic matter stabilization mechanisms to carbon quality and age distributions using ramped thermal analysis.

Organic carbon (OC) association with soil minerals stabilizes OC on timescales reflecting the strength of mineral-C interactions. We applied ramped thermal oxidation to subsoil B horizons with different mineral-C associations to separate OC according to increasing temperature of oxidation, i.e. thermal activation energy. Generally, OC released at lower temperatures was richer in bioavailable forms like polysaccharides, while OC released at higher temperatures was more aromatic. Organic carbon associated with pedogenic oxides was released at lower temperatures and had a narrow range of 14C content. By contrast, N-rich compounds were released at higher temperatures from samples with 2 : 1 clays and short-range ordered (SRO) amorphous minerals. Temperatures of release overlapped for SRO minerals and crystalline oxides, although the mean age of OC released was older for the SRO. In soils with more mixed mineralogy, the added presence of older OC released at temperatures greater than 450°C from clays resulted in a broader distribution of OC ages within the sample, especially for soils rich in 2 : 1 layer expandable clays such as smectite. While pedogenic setting affects mineral stability and absolute OC age, mineralogy controls the structure of OC age distribution within a sample, which may provide insight into model structures and OC dynamics under changing conditions. This article is part of the Theo Murphy meeting issue 'Radiocarbon in the Anthropocene'.

Increased atmospheric CO2 and the transit time of carbon in terrestrial ecosystems.

The response of terrestrial ecosystems to increased atmospheric CO2 concentrations is controversial and not yet fully understood, with previous large-scale forest manipulation experiments exhibiting contrasting responses. Although there is consensus that increased CO2 has a relevant effect on instantaneous processes such as photosynthesis and transpiration, there are large uncertainties regarding the fate of extra assimilated carbon in ecosystems. Filling this research gap is challenging because tracing the movement of new carbon across ecosystem compartments involves the study of multiple processes occurring over a wide range of timescales, from hours to millennia. We posit that a comprehensive quantification of the effect of increased CO2 must answer two interconnected questions: How much and for how long is newly assimilated carbon stored in ecosystems? Therefore, we propose that the transit time distribution of carbon is the key concept needed to effectively address these questions. Here, we show how the transit time distribution of carbon can be used to assess the fate of newly assimilated carbon and the timescales at which it is cycled in ecosystems. We use as an example a transit time distribution obtained from a tropical forest and show that most of the 60% of fixed carbon is respired in less than 1 year; therefore, we infer that under increased CO2 , most of the new carbon would follow a similar fate unless increased CO2 would cause changes in the rates at which carbon is cycled and transferred among ecosystem compartments. We call for a more frequent adoption of the transit time concept in studies seeking to quantify the ecosystem response to increased CO2 .

The HLA class I immunopeptidomes of AAV capsid proteins.

Introduction: Cellular immune responses against AAV vector capsid represent an obstacle for successful gene therapy. Previous studies have used overlapping peptides spanning the entire capsid sequence to identify T cell epitopes recognized by AAV-specific CD8+ T cells. However, the repertoire of peptides naturally displayed by HLA class I molecules for CD8 T cell recognition is unknown. Methods: Using mRNA transfected monocyte-derived dendritic cells (MDDCs) and MHC-associated peptide proteomics (MAPPs), we identified the HLA class I immunopeptidomes of AAV2, AAV6 and AAV9 capsids. MDDCs were isolated from a panel of healthy donors that have diverse alleles across the US population. mRNA-transfected MDDCs were lysed, the peptide:HLA complexes immunoprecipitated, and peptides eluted and analyzed by mass spectrometry. Results: We identified 65 AAV capsid-derived peptides loaded on HLA class I molecules of mRNA transfected monocyte derived dendritic cells. The HLA class I peptides are distributed along the entire capsid and more than 60% are contained within HLA class II clusters. Most of the peptides are organized as single species, however we identified twelve clusters containing at least 2 peptides of different lengths. Only 9% of the identified peptides have been previously identified as T cell epitopes, demonstrating that the immunogenicity potential for the vast majority of the AAV HLA class I immunopeptidome remains uncharacterized. In contrast, 12 immunogenic epitopes identified before were not found to be naturally processed in our study. Remarkably, 11 naturally presented AAV peptides were highly conserved among the three serotypes analyzed suggesting the possibility of cross-reactive AAV-specific CD8 T cells. Discussion: This work is the first comprehensive study identifying the naturally displayed HLA class I peptides derived from the capsid of AAVs. The results from this study can be used to generate strategies to assess immunogenicity risk and cross-reactivity among serotypes during gene therapies.

Sistema OLGA (Operative Link on Gastritis Assessment) como marcador para cáncer gástrico y displasia en una población colombiana de alto riesgo: estudio multicéntrico

Introducción. En Asia y Europa, el sistema OLGA ha sido útil como marcador de riesgo de cáncer gástrico. Sin embargo, su utilidad en poblaciones de alto riesgo en Colombia aún se desconoce. Objetivo. Establecer si los estadios OLGA se asocian con un mayor riesgo de cáncer y displasia en una población de alto riesgo en Colombia y determinar la capacidad diagnóstica de la escala para evaluar dicho riesgo. Materiales y métodos. Se realizó un estudio multicéntrico con pacientes con cáncer gástrico y displasia (casos), y pacientes con atrofia y metaplasia intestinal (controles), provenientes de tres centros de una zona de alto riesgo de cáncer gástrico en Colombia. Se incluyeron 506 pacientes cuyo estudio endoscópico e histopatológico fue realizado mediante el sistema de Sydney y la estadificación de OLGA propuesta por Rugge. El efecto de cada variable de interés sobre la enfermedad (cáncer gástrico y displasia) se evaluó mediante modelos bivariados y multivariados. Un valor de p menor de 0,05 se consideró estadísticamente significativo. Resultados. Los estadios elevados del sistema OLGA (III-IV) se asociaron con un mayor riesgo de displasia y cáncer gástrico (OR ajustado = 8,71; IC95 % = 5,09-14,9; p=0,001) con una sensibilidad del 54,9 %, especificidad del 89,3 % y una razón de probabilidad positiva de 5,17. Conclusiones. El estadio OLGA es un marcador de riesgo de cáncer gástrico y displasia en la población de estudio. Se recomienda su implementación como estrategia para optimizar el diagnóstico oportuno y el seguimiento de pacientes con mayor riesgo.

Introduction. The OLGA system has been proved to be useful in Asia and Europe as a risk marker of gastric cancer. However, its usefulness in high-risk populations in Colombia is still unknown. Objective. To assess potential associations between the OLGA staging system and an increased risk of gastric cancer and dysplasia in a high-risk Colombian population and to establish diagnostic capacity of the scale to assess the risk. Materials and methods. We carried out a multicenter study including patients with cancer and dysplasia (cases) and patients with atrophy and intestinal metaplasia (controls). A total of 506 patients were recruited from three centers in an area with a high risk population in Colombia. The endoscopic and histopathologic studies were evaluated according to the Sydney system and the OLGA staging system proposed by Rugge. The effect of each variable on the disease (gastric cancer and dysplasia) was evaluated using bivariate and multivariate models. Statistical significance was set considering a p value inferior to 0.05. Results. Advanced stages of the OLGA system (III-IV) were associated with a higher risk of dysplasia and gastric cancer (adjusted OR = 8.71; CI95% = 5.09-14.9; p=0.001), sensitivity=54.9%, specificity=89.3% and positive likelihood ratio=5.17. Conclusions. The OLGA staging system is a risk marker for gastric cancer and dysplasia in the studied population. We recommend its implementation to improve the timely diagnosis and follow-up of patients with the highest cancer risk.

Molecular 14 C evidence for contrasting turnover and temperature sensitivity of soil organic matter components.

Climate projection requires an accurate understanding for soil organic carbon (SOC) decomposition and its response to warming. An emergent view considers that environmental constraints rather than chemical structure alone control SOC turnover and its temperature sensitivity (i.e., Q10 ), but direct long-term evidence is lacking. Here, using compound-specific radiocarbon analysis of soil profiles along a 3300-km grassland transect, we provide direct evidence for the rapid turnover of lignin-derived phenols compared with slower-cycling molecular components of SOC (i.e., long-chain lipids and black carbon). Furthermore, in contrast to the slow-cycling components whose turnover is strongly modulated by mineral association and exhibits low Q10 , lignin turnover is mainly regulated by temperature and has a high Q10 . Such contrasts resemble those between fast-cycling (i.e., light) and mineral-associated slow-cycling fractions from globally distributed soils. Collectively, our results suggest that warming may greatly accelerate the decomposition of lignin, especially in soils with relatively weak mineral associations.

The Operative Link on Gastritis Assessment (OLGA) system as a marker for gastric cancer and dysplasia in a Colombian population at risk: A multicenter study / Sistema OLGA (Operative Link on Gastritis Assessment) como marcador para cáncer gástrico y displasia en una población colombiana de alto riesgo: estudio multicéntrico.

Introduction. The OLGA system has been proved to be useful in Asia and Europe as a risk marker of gastric cancer. However, its usefulness in high-risk populations in Colombia is still unknown. Objective. To assess potential associations between the OLGA staging system and an increased risk of gastric cancer and dysplasia in a high-risk Colombian population and to establish diagnostic capacity of the scale to assess the risk. Materials and methods. We carried out a multicenter study including patients with cancer and dysplasia (cases) and patients with atrophy and intestinal metaplasia (controls). A total of 506 patients were recruited from three centers in an area with a high risk population in Colombia. The endoscopic and histopathologic studies were evaluated according to the Sydney system and the OLGA staging system proposed by Rugge. The effect of each variable on the disease (gastric cancer and dysplasia) was evaluated using bivariate and multivariate models. Statistical significance was set considering a p value inferior to 0.05. Results. Advanced stages of the OLGA system (III-IV) were associated with a higher risk of dysplasia and gastric cancer (adjusted OR = 8.71; CI95% = 5.09-14.9; p=0.001), sensitivity=54.9%, specificity=89.3% and positive likelihood ratio=5.17. Conclusions. The OLGA staging system is a risk marker for gastric cancer and dysplasia in the studied population. We recommend its implementation to improve the timely diagnosis and follow-up of patients with the highest cancer risk.

Introducción. En Asia y Europa, el sistema OLGA ha sido útil como marcador de riesgo de cáncer gástrico. Sin embargo, su utilidad en poblaciones de alto riesgo en Colombia aún se desconoce. Objetivo. Establecer si los estadios OLGA se asocian con un mayor riesgo de cáncer y displasia en una población de alto riesgo en Colombia y determinar la capacidad diagnóstica de la escala para evaluar dicho riesgo.Materiales y métodos. Se realizó un estudio multicéntrico con pacientes con cáncer gástrico y displasia (casos), y pacientes con atrofia y metaplasia intestinal (controles), provenientes de tres centros de una zona de alto riesgo de cáncer gástrico en Colombia. Se incluyeron 506 pacientes cuyo estudio endoscópico e histopatológico fue realizado mediante el sistema de Sydney y la estadificación de OLGA propuesta porRugge. El efecto de cada variable de interés sobre la enfermedad (cáncer gástrico y displasia) se evaluó mediante modelos bivariados y multivariados. Un valor de p menor de 0,05 se consideró estadísticamente significativo.Resultados. Los estadios elevados del sistema OLGA (III-IV) se asociaron con un mayor riesgo de displasia y cáncer gástrico (OR ajustado = 8,71; IC95 % = 5,09-14,9; p=0,001) con una sensibilidad del 54,9 %, especificidad del 89,3 % y una razón de probabilidad positiva de 5,17.Conclusiones. El estadio OLGA es un marcador de riesgo de cáncer gástrico y displasia en la población de estudio. Se recomienda su implementación como estrategia para optimizar el diagnóstico oportuno y el seguimiento de pacientes con mayor riesgo.

Edaphic controls of soil organic carbon in tropical agricultural landscapes.

Predicting soil organic carbon (SOC) is problematic in tropical soils because mechanisms of SOC (de)stabilization are not resolved. We aimed to identify such storage mechanisms in a tropical soil landscape constrained by 100 years of similar soil inputs and agricultural disturbance under the production of sugarcane, a C4 grass and bioenergy feedstock. We measured soil physicochemical parameters, SOC concentration, and SOC dynamics by soil horizon to one meter to identify soil parameters that can predict SOC outcomes. Applying correlative analyses, linear mixed model (LMM) regression, model selection by AICc, and hierarchical clustering we found that slow moving SOC was related to many soil parameters, while the fastest moving SOC was only related to soil surface charge. Our models explained 78-79%, 51-57%, 7-8% of variance in SOC concentration, slow pool decay, and fast pool decay, respectively. Top SOC predictors were roots, the ratio of organo-complexed iron (Fe) to aluminum (Al), water stable aggregates (WSagg), and cation exchange capacity (CEC). Using hierarchical clustering we also assessed SOC predictors across gradients of depth and rainfall with strong reductions in Roots, SOC, and slow pool decay associated with increasing depth, while increased rainfall was associated with increased Clay and WSagg and reduced CEC in surface soils. Increased negative surface charge, water stable aggregation, organo-Fe complexation, and root inputs were key SOC protection mechanisms despite high soil disturbance. Further development of these relationships is expected to improve understanding of SOC storage mechanisms and outcomes in similar tropical agricultural soils globally.

Effect of the high-level trigger for detecting long-lived particles at LHCb.

Long-lived particles (LLPs) show up in many extensions of the Standard Model, but they are challenging to search for with current detectors, due to their very displaced vertices. This study evaluated the ability of the trigger algorithms used in the Large Hadron Collider beauty (LHCb) experiment to detect long-lived particles and attempted to adapt them to enhance the sensitivity of this experiment to undiscovered long-lived particles. A model with a Higgs portal to a dark sector is tested, and the sensitivity reach is discussed. In the LHCb tracking system, the farthest tracking station from the collision point is the scintillating fiber tracker, the SciFi detector. One of the challenges in the track reconstruction is to deal with the large amount of and combinatorics of hits in the LHCb detector. A dedicated algorithm has been developed to cope with the large data output. When fully implemented, this algorithm would greatly increase the available statistics for any long-lived particle search in the forward region and would additionally improve the sensitivity of analyses dealing with Standard Model particles of large lifetime, such as K S 0 or Λ0 hadrons.

Younger carbon dominates global soil carbon efflux.

Soil carbon (C) is comprised of a continuum of organic compounds with distinct ages (i.e., the time a C atom has experienced in soil since the C atom entered soil). The contribution of different age groups to soil C efflux is critical for understanding soil C stability and persistence, but is poorly understood due to the complexity of soil C pool age structure and potential distinct turnover behaviors of age groups. Here, we build upon the quantification of soil C transit times to infer the age of C atoms in soil C efflux (aefflux ) from seven sequential soil layer depths down to 2 m at a global scale, and compare this age with radiocarbon-inferred ages of C retained in corresponding soil layers (asoil ). In the whole 0-2 m soil profile, the mean aefflux is 194 21 1021 (mean with 5%-95% quantiles) year and is just about one-eighth of asoil ( 1476 717 2547 year), demonstrating that younger C dominates soil C efflux. With increasing soil depth, both aefflux and asoil are increased, but their disparities are markedly narrowed. That is, the proportional contribution of relatively younger soil C to efflux is decreased in deeper layers, demonstrating that C inputs (new and young) stay longer in deeper layers. Across the globe, we find large spatial variability of the contribution of soil C age groups to C efflux. Especially, in deep soil layers of cold regions (e.g., boreal forests and tundra), aefflux may be older than asoil , suggesting that older C dominates C efflux only under a limited range of conditions. These results imply that most C inputs may not contribute to long-term soil C storage, particularly in upper layers that hold the majority of new C inputs.

Expression of fatty acid synthase genes and their role in development and arboviral infection of Aedes aegypti.

BACKGROUND: Fatty acids are the building blocks of complex lipids essential for living organisms. In mosquitoes, fatty acids are involved in cell membrane production, energy conservation and expenditure, innate immunity, development and reproduction. Fatty acids are synthesized by a multifunctional enzyme complex called fatty acid synthase (FAS). Several paralogues of FAS were found in the Aedes aegypti mosquito. However, the molecular characteristics and expression of some of these paralogues have not been investigated. METHODS: Genome assemblies of Ae. aegypti were analyzed, and orthologues of human FAS was identified. Phylogenetic analysis and in silico molecular characterization were performed to identify the functional domains of the Ae. aegypti FAS (AaFAS). Quantitative analysis and loss-of-function experiments were performed to determine the significance of different AaFAS transcripts in various stages of development, expression following different diets and the impact of AaFAS on dengue virus, serotype 2 (DENV2) infection and transmission. RESULTS: We identified seven putative FAS genes in the Ae. aegypti genome assembly, based on nucleotide similarity to the FAS proteins (tBLASTn) of humans, other mosquitoes and invertebrates. Bioinformatics and molecular analyses suggested that only five of the AaFAS genes produce mRNA and therefore represent complete gene models. Expression levels of AaFAS varied among developmental stages and between male and female Ae. aegypti. Quantitative analyses revealed that expression of AaFAS1, the putative orthologue of the human FAS, was highest in adult females. Transient knockdown (KD) of AaFAS1 did not induce a complete compensation by other AaFAS genes but limited DENV2 infection of Aag2 cells in culture and the midgut of the mosquito. CONCLUSION: AaFAS1 is the predominant AaFAS in adult mosquitoes. It has the highest amino acid similarity to human FAS and contains all enzymatic domains typical of human FAS. AaFAS1 also facilitated DENV2 replication in both cell culture and in mosquito midguts. Our data suggest that AaFAS1 may play a role in transmission of dengue viruses and could represent a target for intervention strategies.

The HLA class-II immunopeptidomes of AAV capsids proteins.

Introduction: Gene therapies are using Adeno-associated viruses (AAVs) as vectors, but immune responses against the capsids pose challenges to their efficiency and safety. Helper T cell recognition of capsid-derived peptides bound to human leukocyte antigen (HLA) class II molecules is an essential step in the AAV-specific adaptive immunity. Methods: Using MHC-associated peptide proteomics, we identified the HLA-DR and HLA-DQ immunopeptidomes of the capsid proteins of three different AAV serotypes (AAV2, AAV6, and AAV9) from a panel of healthy donors selected to represent a majority of allele usage. Results: The identified sequences span the capsids of all serotypes, with AAV2 having the highest peptide count. For all the serotypes, multiple promiscuous peptides were identified and displayed by both HLA-DR and -DQ. However, despite high sequence homology, there were few identical peptides among AAV2, AAV6, and AAV9 immunopeptidomes, and none were promiscuous. Discussion: Results from this work represent a comprehensive immunopeptidomics research of potential CD4+ T cell epitopes and provide the basis for immunosurveillance efforts for safer and more efficient AAV-based gene therapies.

Simons Observatory: characterizing the Large Aperture Telescope Receiver with radio holography.

We present near-field radio holography measurements of the Simons Observatory Large Aperture Telescope Receiver optics. These measurements demonstrate that radio holography of complex millimeter-wave optical systems comprising cryogenic lenses, filters, and feed horns can provide detailed characterization of wave propagation before deployment. We used the measured amplitude and phase, at 4 K, of the receiver near-field beam pattern to predict two key performance parameters: 1) the amount of scattered light that will spill past the telescope to 300 K and 2) the beam pattern expected from the receiver when fielded on the telescope. These cryogenic measurements informed the removal of a filter, which led to improved optical efficiency and reduced sidelobes at the exit of the receiver. Holography measurements of this system suggest that the spilled power past the telescope mirrors will be less than 1%, and the main beam with its near sidelobes are consistent with the nominal telescope design. This is the first time such parameters have been confirmed in the lab prior to deployment of a new receiver. This approach is broadly applicable to millimeter and submillimeter instruments.

Beyond bulk: Density fractions explain heterogeneity in global soil carbon abundance and persistence.

Understanding the controls on the amount and persistence of soil organic carbon (C) is essential for predicting its sensitivity to global change. The response may depend on whether C is unprotected, isolated within aggregates, or protected from decomposition by mineral associations. Here, we present a global synthesis of the relative influence of environmental factors on soil organic C partitioning among pools, abundance in each pool (mg C g-1  soil), and persistence (as approximated by radiocarbon abundance) in relatively unprotected particulate and protected mineral-bound pools. We show that C within particulate and mineral-associated pools consistently differed from one another in degree of persistence and relationship to environmental factors. Soil depth was the best predictor of C abundance and persistence, though it accounted for more variance in persistence. Persistence of all C pools decreased with increasing mean annual temperature (MAT) throughout the soil profile, whereas persistence increased with increasing wetness index (MAP/PET) in subsurface soils (30-176 cm). The relationship of C abundance (mg C g-1  soil) to climate varied among pools and with depth. Mineral-associated C in surface soils (<30 cm) increased more strongly with increasing wetness index than the free particulate C, but both pools showed attenuated responses to the wetness index at depth. Overall, these relationships suggest a strong influence of climate on soil C properties, and a potential loss of soil C from protected pools in areas with decreasing wetness. Relative persistence and abundance of C pools varied significantly among land cover types and soil parent material lithologies. This variability in each pool's relationship to environmental factors suggests that not all soil organic C is equally vulnerable to global change. Therefore, projections of future soil organic C based on patterns and responses of bulk soil organic C may be misleading.