Biology subjects

Deckers, T.

Publications and source records attributed to Deckers, T..

4 recordsLinked to original sources

bioRxiv2026

Bulk and single-cell transcriptomics reveal elevated endogenous retrovirus expression linked to immunopathology in severe COVID-19.

SARS-CoV-2 infection triggers expression of endogenous retroviruses (ERVs), but whether this persists during COVID-19 and contributes to disease severity has not been well characterized. In this study, we analyzed bulk and single-cell RNA-sequencing datasets from multiple cohorts of severe COVID-19 patients to investigate the role of ERVs in COVID-19 immunopathology. We identified 33 differentially expressed proviral ERV loci in severe COVID-19 compared with healthy individuals (severe COVID-19 signature ERVs). ERV activation was associated with dysregulation of ERV epigenetic regulators, and their expression strongly correlated with key inflammatory pathways implicated in severe COVID-19, including neutrophil degranulation, interleukin signaling, and inflammasome activation. Anakinra treatment reversed activation of signature ERVs. Six signature ERVs were specific to intensive care unit (ICU) admission and significantly correlated with hospital-free days at day 45 (HFD-45). At the single-cell level, signature ERVs were significantly upregulated in erythroid-like and erythroid precursor cells and macrophages of patients with severe disease. Within these cells, we found evidence of ERV-associated differences in inflammatory gene expression, whereby cells expressing signature ERVs showed heightened expression of innate immune genes compared with cells not expressing these ERVs. Together, our study unmasked specific ERV loci activated in severe COVID-19 that are linked to immunopathology.

immunology↗

bioRxiv2026

Honey bee (Apis mellifera) gut microbiome associations with viruses and pesticides across Canadian agroecosystems

The honey bee (Apis mellifera) gut microbiome plays a central role in host health, yet its variation across agricultural landscapes remains poorly resolved. This study investigates how major environmental stressors, particularly pesticide exposure and RNA virus loadings, shape the honey bee gut microbiome in a large-scale field study conducted across Canada, spanning diverse agroecosystems from British Columbia to Quebec. We identify consistent associations between specific bacterial taxa and major RNA viruses, including enrichment of Serratia marcescens with SBV and depletion of Bombella intestini with BQCV. Pesticide exposure is likewise linked to reproducible shifts in key microbial taxa. Together, these findings reveal that interacting stressors jointly shape the bee gut microbiome and enable prediction of microbiome responses in agroecosystems. HighlightsDistinct associations identified between gut bacteria and major bee RNA viruses (BQCV, SBV, LSV, IAPV) Pesticide exposure is linked to reproducible shifts in key microbial taxa Combined virus-pesticide effects form coordinated clusters that predict microbiome variation and specific bacterial responses Integrated modeling demonstrates that environmental stressors can jointly explain microbiome structure beyond crop effects Graphical abstractSchematic overview of potential links between pesticide exposure and RNA virus infection and their effects on the bee gut bacterial community. Solid arrows indicate associations supported by the present study, whereas dashed arrows indicate hypothesized or unresolved interactions. Associations between the presence of specific bee RNA viruses (left) or pesticide residues (right) and changes in the relative abundance of particular gut taxa (pink {uparrow}, increased; blue {downarrow}, decreased). The pesticide subtype is indicated by the icon in the cell (leaf - herbicide, hyphae - fungicide and insect - insecticide). Several bacterial taxa showed reproducible associations with specific viral or pesticide variables, including Bombella intestini, Serratia marcescens, Melissococcus plutonius, Paenibacillus alvei, Apibacter sp. wkB309, and Gilliamella sp. A7. Abbreviations: BQCV Black queen cell virus; LSV, Lake Sinai virus; SBV, Sacbrood virus; IAPV, Israeli acute paralysis virus. (p/n/b) indicate the sample matrix in which the pesticide was detected, namely pollen, nectar, and bee tissue, respectively. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/731697v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@cb92a4org.highwire.dtl.DTLVardef@1087045org.highwire.dtl.DTLVardef@102cabforg.highwire.dtl.DTLVardef@4ce2f1_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Imaging biological macromolecules in their native state with single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography (cryo-ET) requires optimized approaches for the preparation and vitrification of biological samples. Here, we describe EasyGrid, a versatile technology enabling systematic, tailored and advanced sample preparation for cellular and structural biology. This automated, standalone platform combines in-line plasma treatment, microfluidic dispensing, blot-less sample spreading, jet-based vitrification and on-the-fly grid quality control using light interferometry to streamline cryo-EM sample optimization. With EasyGrid, we optimized grid preparation for different purified macromolecular complexes and subsequently determined their structure with cryo-EM. We also demonstrated how the platform allows better vitrification of large, mammalian cells compared to standard plunge-freezing. Automated sample preparation with EasyGrid establishes an advanced, high-throughput platform for both single-particle cryo-EM and cellular cryo-ET sample preparation.

molecular biology↗

bioRxiv2019

Compaction dynamics during progenitor cell self-assembly reveal granular mechanics

We study the self-assembly dynamics of human progenitor cells in agarose micro-wells that are used for production of chondrogenic organoids. Using image analysis on time-lapse microscopy, we estimate the aggregate area in function of time for a large number of aggregates. In control conditions, the aggregate radius follows an exponential relaxation that is consistent with the dewetting dynamics of a liquid film. Introducing Y-27632 Rho kinase inhibitor, the compatibility with the liquid model is lost, and slowed down relaxation dynamics are observed. We demonstrate that these aggregates behave as granular piles undergoing compaction, with a density relaxation that follows a stretched exponential. Using simulations with an individual cell-based model, we construct a phase diagram of cell aggregates that suggests that the aggregate in presence of Rho kinase inhibitor approaches the glass transition.

biophysics↗