Biology subjects

Timmins, J.

Publications and source records attributed to Timmins, J..

5 recordsLinked to original sources

bioRxiv2026

Deinococcus radiodurans HU: a versatile architect of nucleoid structure and plasticity

Nucleoid-associated proteins are known to compact and organise bacterial genomes, but how their local DNA binding shapes higher-order chromatin architecture remains unclear. Using in vitro and in situ approaches, we investigated how Deinococcus radiodurans HU (DrHU) orchestrates nucleoid organisation. DrHU engages DNA through two synergistic binding modes: high-affinity {beta}-hairpin-mediated stabilisation of DNA loops and low-affinity, multivalent interaction via its N-terminal tail, driving parallel, uniformly spaced DNA alignment. In vitro, DrHU organises supercoiled plasmid DNA into regular 2D lattices of double-spirals, while in situ, UV-C light induces a nucleoid transition from a loose DNA mesh to a blue liquid crystalline phase characterised by DNA swirls. The striking structural similarity and shared inter-filament spacing of these two arrangements suggests that DrHU plays a pivotal role in genome organisation through its versatile binding properties that enable DNA loop stabilisation, protection and DNA bridging, linking molecular interactions to 3D genome ordering and stress-induced remodelling.

microbiology↗

bioRxiv2025

Rapid fluorescence lifetime sensor development of LifeCamp enables transient and baseline absolute calcium measurements

Genetically encoded calcium sensors (GECIs) have been instrumental for studying neuronal activity and intracellular signaling. GECIs are typically fluorescence-intensity sensors that change brightness upon calcium binding. Iterative improvements in GECIs have yielded indicators that report action potential-evoked calcium entry with high sensitivity and temporal resolution, enabling measurement of network activity across thousands of neurons. However, fluorescence intensity-based measurements generally cannot report baseline or absolute calcium levels and may confound neuromodulatory regulation of calcium handling with changes in action potential firing. Fluorescence lifetime sensors are insensitive to many artifacts that plague intensity-based measures and report absolute substrate levels, including those at rest. However, relatively few lifetime sensors for neuronal signals exist, and developing new sensors is typically difficult and low-yield. Here, we introduce a new rapid lifetime sensor development (RALISED) platform, which we use to build a new GCaMP8m-based high-speed lifetime calcium sensor, termed LifeCamp. We show that LifeCamp enables comparison of baseline calcium signals in cell culture, brain slices, and mice. In addition, we show that LifeCamp enables the detection of fast action potential-evoked calcium transients in single neurons from brain slices and in behaving mice. Using LifeCamp, we discovered calcium baseline changes associated with neuronal activity in brain slices and behaving mice, as well as slow average calcium changes in neuronal populations of freely moving mice. Altogether, this study highlights the utility of the RALISED method to rapidly develop new lifetime sensors and the application of the LifeCamp calcium lifetime sensor to study fast and slow calcium signaling. Significance statementWe developed a new high-speed, sensitive calcium lifetime sensor (LifeCamp) using a novel rapid lifetime sensor development (RALISED) platform. LifeCamp has high sensitivity and a large substrate-dependent lifetime change (<1ns), allowing for the capture of baseline calcium levels, transient calcium changes, and neuronal firing in vitro and behaving animals. LifeCamp lifetime measurement is insensitive to artifacts that plague conventional intensity imaging and enables absolute comparison of baseline and transient calcium changes across cells, brain regions, and experimental conditions. Hence, LifeCamp is a powerful tool that enables a more accurate and in-depth understanding of neuronal activity and calcium signaling.

neuroscience↗

bioRxiv2023

blik: an extensible napari plugin for cryo-ET data visualisation, annotation and analysis

Powerful, workflow-agnostic and interactive visualisation is essential for the ad-hoc, human-in-the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and annotation of cryo-ET data, they are often integrated as part of monolithic processing pipelines, or focused on a specific task and offering limited reusability and extensibility. With each software suite presenting its own pros and cons and often tools tailored to address specific challenges, seamless integration between available pipelines is often a difficult task. As part of the effort to enable such flexibility and move the software ecosystem towards a more collaborative and modular approach, we developed blik, an open-source napari plugin for visualisation and annotation of cryo-ET data (source code: https://github.com/brisvag/blik). blik offers fast, interactive, and user-friendly 3D visualisation thanks to napari, and is built with extensibility and modularity at the core. Data is handled and exposed through well-established scientific Python libraries such as numpy arrays and pandas dataframes. Reusable components (such as data structures, file read/write, and annotation tools) are developed as independent Python libraries to encourage reuse and community contribution. By easily integrating with established image analysis tools - even outside of the cryo-ET world - blik provides a versatile platform for interacting with cryo-ET data. On top of core visualisation features - interactive and simultaneous visualisation of tomograms, particle picks and segmentations - blik provides an interface for interactive tools such as manual particle picking, surface-based and filament-based particle picking and image segmentation, as well as simple filtering tools. Additional self-contained napari plugins developed as part of this work also implement interactive plotting and selection based on particle features, and label interpolation for easier segmentation. Finally, we highlight the differences with existing software and showcase bliks applicability in biological research.

bioinformatics↗

bioRxiv2021

Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans. In particular, four Deinococcus-specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans. One of these, DdrC, is expressed shortly after exposure to {gamma}-radiation and is rapidly recruited to the nucleoid. In vitro, DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.2 [A] and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.

microbiology↗

bioRxiv2019

Cell morphology and nucleoid dynamics in dividing D. radiodurans

Our knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here, we reveal that Deinococcus radiodurans, a relatively large, spherical bacterium, possessing a multipartite genome, and well-known for its radioresistance, constitutes a valuable system for the study of nucleoids in cocci. Using advanced microscopy, we show that as D. radiodurans progresses through its cell cycle, it undergoes coordinated morphological changes at both the cellular and nucleoid level. D. radiodurans nucleoids were found to be highly condensed, but also surprisingly dynamic, adopting multiple distinct configurations and presenting a novel chromosomal arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the centre of cells. Single-molecule and ensemble studies of the abundant histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings clearly demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression.

microbiology↗