Biology subjects

Wiktor, J.

Publications and source records attributed to Wiktor, J..

3 recordsLinked to original sources

bioRxiv2025

Molecular kinetics dictate population dynamics in CRISPR-based plasmid defense

Understanding and manipulating mobile genetic element (MGE) spread within bacterial communities represents a great challenge with wide-ranging potential benefits. It requires a detailed understanding of spatial effects and cell-to-cell variability in defence systems such as CRISPR-Cas. Here, we report a time-lapse imaging-based assay with simultaneous fluorescent labeling of CRISPR-Cascade complexes and the conjugative plasmid RP4, enabling direct, single-cell-resolution observation of conjugation and CRISPR interference. We find that Cascade, under wild-type-like expression scenarios, provides a nudge towards plasmid clearance rather than full immunity, and can be counteracted by the ParDE plasmid addiction system. These limitations could be overcome by higher Cascade expression, yet by quantifying single-cell variability, we observe a tradeoff between plasmid clearance and cell growth. We synthesize these measurements into a spatially-resolved, agent-based model of plasmid population dynamics. The imaging and analysis techniques used here will facilitate disentanglement of how single-cell molecular events result in community-wide plasmid dynamics.

molecular biology↗

bioRxiv2021

Latitudinal patterns in intertidal ecosystem structure in West Greenland suggest resilience to climate change

Climate change has ecosystem-wide cascading effects. Little is known, however, about the resilience of Arctic marine ecosystems to environmental change. Here we quantify and compare large-scale patterns in rocky intertidal biomass, coverage and zonation in six regions along a north-south gradient of temperature and ice conditions in West Greenland (60-72{degrees}N). We related the level and variation in assemblage composition, biomass and coverage to latitudinal-scale environmental drivers. Across all latitudes, the intertidal assemblage was dominated by a core of stress-tolerant foundation species that constituted >95% of the biomass. Hence, canopy-forming macroalgae, represented by Fucus distichus subsp. evanescens and F. vesiculosus and, up to 69 {degrees}N, also Ascophyllum nodosum, together with Semibalanus balanoides, occupied >70% of the vertical tidal range in all regions. Thus, a similar functional assemblage composition occurred across regions, and no latitudinal depression was observed. The most conspicuous difference in species composition from south to north was that three common species (the macroalgae Ascophyllum nodosum, the amphipod Gammarus setosus and the gastropod Littorina obtusata) disappeared from the mid-intertidal, although at different latitudes. There were no significant relationships between assemblage metrics and air temperature or sea ice coverage as obtained from weather stations and satellites, respectively. Although the mean biomass decreased >50% from south to north, local biomass in excess of 10 000 g ww m-2 was found even at the northernmost site, demonstrating the patchiness of this habitat and the effect of small-scale variation in environmental characteristics. Hence, using the latitudinal gradient in a space-for-time substitution, our results suggest that while climate modification may lead to an overall increase in the intertidal biomass in north Greenland, it is unlikely to drive dramatic functional changes in ecosystem structure in the near future. Our dataset provides an important baseline for future studies to verify these predictions for Greenlands intertidal zone.

ecology↗

bioRxiv2020

RecA mediated homology search finds segregated sister locus in minutes after a double stranded break

Homologous recombination (HR) is essential for the accurate repair of double-stranded DNA breaks (DSBs); it begins when the RecBCD2 complex resects the ends of the DSB into 3' single-stranded DNA (ssDNA) on which a RecA filament assembles. HR depends on the ability of this RecA-ssDNA filament to locate the homologous repair template on the sister chromosome. The mechanism by which the homology is located among vast amounts of heterologous DNA is not yet understood, despite a long history of research. Here, we directly visualize the repair of DSBs in hundreds of individual cells, using high-throughput microfluidics and fluorescence microscopy. We find that in E. coli, DSB repair is completed in 15 minutes without fitness loss. We further show that the search takes less than 10 minutes and is mediated by a thin, highly dynamic RecA filament that stretches throughout the cell. We propose a model in which the architecture of the RecA filament effectively reduces search dimensionality to two dimensions. The model is corroborated by the observation that the search time does not depend on the length of the cell or the amount of DNA, and also predicts a search time that is consistent with our measurement. Since the RecA family proteins are conserved in all organisms, our results also translate to other systems that rely on homologous recombination.

microbiology↗