Enhanced detection of antigen-specific T cells by a multiplexed AIM assay.

Broadly applicable methods to identify and characterize antigen-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T cells are key to immunology research, including studies of vaccine responses and immunity to infectious diseases. We developed a multiplexed activation-induced marker (AIM) assay that presents several advantages compared to single pairs of AIMs. The simultaneous measurement of four AIMs (CD69, 4-1BB, OX40, and CD40L) creates six AIM pairs that define CD4 <sup>+</sup> T cell populations with partial and variable overlap. When combined in an AND/OR Boolean gating strategy for analysis, this approach enhances CD4 <sup>+</sup> T cell detection compared to any single AIM pair, while CD8 <sup>+</sup> T cells are dominated by CD69/4-1BB co-expression. Supervised and unsupervised clustering analyses show differential expression of the AIMs in defined T helper lineages and that multiplexing mitigates phenotypic biases. Paired and unpaired comparisons of responses to infections (HIV and cytomegalovirus [CMV]) and vaccination (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) validate the robustness and versatility of the method

Spontaneous HIV expression during suppressive ART is associated with the magnitude and function of HIV-specific CD4+ and CD8+ T cells.

Spontaneous transcription and translation of HIV can persist during suppressive antiretroviral therapy (ART). The quantity, phenotype, and biological relevance of this spontaneously "active" reservoir remain unclear. Using multiplexed single-cell RNAflow-fluorescence in situ hybridization (FISH), we detect active HIV transcription in 14/18 people with HIV on suppressive ART, with a median of 28/million CD4 <sup>+</sup> T cells. While these cells predominantly exhibit abortive transcription, p24-expressing cells are evident in 39% of participants. Phenotypically diverse, active reservoirs are enriched in central memory T cells and CCR6- and activation-marker-expressing cells. The magnitude of the active reservoir positively correlates with total HIV-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T cell responses and with multiple HIV-specific T cell clusters identified by unsupervised analysis. These associations are particularly strong with p24-expressing active reservoir cells. Single-cell vDNA sequencing shows that active reservoirs are largely dominated by defective proviruses. Our data suggest that these reservoirs maintain HIV-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T responses during suppressive ART

Coupling evolutionary dynamics of fungal effectors and functional genomics : towards understanding mechanisms of Venturia inaequalis virulence and identifying durable resistance genes in apple

During infection, pathogens secrete small secreted proteins (SSPs), called effectors, that promote disease. Plant receptors encoded by resistance R genes might recognize such effectors (also called avirulence factors AVRs), resulting in plant immunity. Pathogens evade recognition thanks to the emergence of virulent alleles present in populations. It has been demonstrated that avirulent effectors are crucial for the pathogen infection cycle and that their loss-of-function may induce a substantial fitness cost. This kind of effector is expected to be under purifying selective pressure. Here, we aim at identifying the effector repertoire of Venturia inaequalis, the agent of apple scab, assessing its evolutionary dynamics and studying the role of candidate effectors in virulence. We sequenced de novo 90 strains, collected on apple and on their wild relatives and differing in their host range or virulence to study allelic polymorphism at 880 putative effector loci. The top-20 hits for highly conserved sequences were selected as candidates for further functional analyses. In planta gene expression showed a significant induction of these conserved SSP at the early stage of plant infection. Their functions were investigated using targeted deletion mutants. Remarkably, loss of two conserved SSPs resulted in reduced aggressiveness without any alteration in growth in vitro. GFP-tagged protein and heterologous expression were used to assess their sub-cellular localization in infected apple leaves. Involvement of theses SSP in the modulation of host defence was also investigated using an apple full-transcript microarray. Highly conserved effectors will be used to screen for novel R genes in Malus genotypes characterized for their high resistance to scab. This combined knowledge should enable us to understand strategies used by the pathogen to overcome defences in apple and consequently to build more durable resistance towards apple scab

Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity.

Plasma RNAemia, delayed antibody responses and inflammation predict COVID-19 outcomes, but the mechanisms underlying these immunovirological patterns are poorly understood. We profile 782 longitudinal plasma samples from 318 hospitalized patients with COVID-19. Integrated analysis using k-means reveals four patient clusters in a discovery cohort: mechanically ventilated critically-ill cases are subdivided into good prognosis and high-fatality clusters (reproduced in a validation cohort), while non-critical survivors segregate into high and low early antibody responders. Only the high-fatality cluster is enriched for transcriptomic signatures associated with COVID-19 severity, and each cluster has distinct RBD-specific antibody elicitation kinetics. Both critical and non-critical clusters with delayed antibody responses exhibit sustained IFN signatures, which negatively correlate with contemporaneous RBD-specific IgG levels and absolute SARS-CoV-2-specific B and CD4 <sup>+</sup> T cell frequencies. These data suggest that the "Interferon paradox" previously described in murine LCMV models is operative in COVID-19, with excessive IFN signaling delaying development of adaptive virus-specific immunity

Socio-economic assessement of farmers' vulnerability as water users subject to global change stressors in the hard rock area of southern India. The SHIVA ANR project

International audienceDemand for vulnerability assessments is growing in policy-making circles, to support the choice of appropriate measures and policies to reduce the vulnerability of water users and resources. Through the SHIVA ANR project, we are seeking a method to assess and map the vulnerability of farmers in southern India to both climate and socioeconomic changes, and secondly, to assess the costs and benefits associated with trends farmers' vulnerability in the medium and long-term. The project is focusing on southern India 's hard rock area, as in the geological context, both surface and ground water resources are naturally limited. We are also focusing on farming populations as these are the main water users in the area and rely exclusively on groundwater. The area covers southern India's semi-arid zone, where the rainfall gradient ranges from 600 mm to 1100 mm. Vulnerability is expected to vary according to local climatic conditions but also the socioeconomic characteristics of farming households. The SHIVA research team has been divided into six thematic groups in order to address the different scientific issues : downscaling the regional climate scenario, farm area projections, vulnerability assessments and quantification, vulnerability mapping, hydrological modelling and upscaling, and vulnerability impact assessements. Our approach is multidisciplinary to cater for for numerous inherent themes, and integrated to cater for vulnerability as a dynamic and multidimensional concept. The project 's first results after 10 months of research are presented below

Using agroecological zones to promote European collaboration in organic farming research.

Agro-ecological and other spatial information can be used to improve our understanding of organic farming research issues, inform the application of research from one area to another, and support collaboration and prioritisation within regional research programmes. Of the 25 organic farming research priorities identified by the IFOAM EU Group in 2004, 15 were related to regional differences in agroecological conditions. The other priorities were potentially affected by spatial differences in political, institutional and socio-economic conditions. In relation to agro-ecological data, the capacity to identify i) general agro-ecological areas and ii) areas with specific agro-ecological advantage or stress seems particularly useful. The use of a geographic information system (GIS) to integrate spatial data to identify and display such areas is illustrated with two examples

Links between early pollen development and aperture pattern in monocots

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