Biology subjects

Dobbs, J. M.

Publications and source records attributed to Dobbs, J. M..

5 recordsLinked to original sources

bioRxiv2026

Cryo-FIB lamellae enable ultra-high excitation laser intensities for cryogenic super-resolution fluorescence imaging

Super-resolution cryogenic correlative light and electron microscopy (SR-cryo-CLEM) integrates molecular specificity and structure on the single-molecule level, but contemporary approaches require low laser powers to preserve specimen vitrification. Here, we perform SR-cryo-CLEM via single molecule localization microscopy (SMLM) on thin biological lamellae and demonstrate that their geometry and minimally-absorbent composition permit excitation laser powers three orders of magnitude higher than standard cryo-EM grids, allowing improved localization precision and imaging speeds.

molecular biology↗

bioRxiv2026

A stable cryogenic fluorescence microscope for correlative super-resolution light and electron microscopy

Cryogenic correlative light and electron microscopy (cryo-CLEM) enables visualization of biological specimens with molecular specificity while preserving near-native macromolecular structure. However, the severely limited resolution of conventional cryo-fluorescence microscopes restricts the accuracy of correlation with cryo-electron microscopy. Super-resolution cryogenic CLEM (SR-cryo-CLEM) offers a potential solution, but presents substantial technical challenges, including mechanical instability and ice contamination. Here, we introduce a modular cryogenic light microscope optimized for single-molecule localization microscopy (cryo-SMLM) that mitigates such limitations. The system is constructed primarily from off-the-shelf components, enabling straightforward and cost-effective assembly, and is operated using fully open-source Python software for flexible and customizable control. The mechanically and thermally stabilized architecture, combined with an axial focus-lock system, maintains sample positioning within a standard deviation of 40 nm. Ice contamination is minimized by imaging inside a purged enclosure, enabling prolonged acquisitions. Together, the platform provides robust localization precision, reproducible imaging performance, and an accessible solution for SR-cryo-CLEM.

molecular biology↗

bioRxiv2026

Optimizing data quality and completeness in visual proteomics experiments

Cryo-electron tomography (cryo-ET) is fast developing from a tool primarily used to investigate structures of individual macromolecular complexes in situ into a high-resolution probe for molecular processes within diverse functional contexts in intact cells. It is thus increasingly necessary that the data are analyzed and quantified as completely as possible. But annotating and structurally characterizing macromolecular complexes with a high degree of completeness is a significant challenge, especially for smaller molecular targets. In particular, it is difficult to avoid incomplete localizations of complexes, false identifications, or losses during computational classification. To address these issues, we assessed parameters in data processing, including the role of voxel size in template matching, the effects of Volta phase plate imaging on localization, classification, and map refinement, and the extent to which multi-particle-based refinement of tiltseries improves these data processing steps. Our analyses provide practical guidelines that help maximize completeness in cellular cryo-ET data; accurate description of the sample is crucial for visual proteomics experiments, and these optimizations help ensure that data annotation and analysis are comprehensive.

molecular biology↗

bioRxiv2025

Single-cell visual proteomics of a minimal bacterium reveals structural coordination in gene expression

Translation is a central process in gene expression. Regulation of this process is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk to processes like transcription or translocation. Here, we used cryo-electron tomography of native and antibiotic-perturbed Mycoplasma pneumoniae cells to resolve 140 maps that recapitulate bacterial translation during the initiation, elongation, termination, and recycling phases. We visualized multiple transcription-translation complexes, allowing us to propose a threading-based translation reinitiation mechanism, and to provide structural evidence for a long-hypothesized supercomplex that coordinates transcription, translation, and membrane attachment. We further resolved abundant membrane-associated large ribosomal subunits, and suggest that dissociation from membranes depends on the conditional initiation of new translation, consistent with a conserved mechanism in mammalian cells. This work visualizes the multilayered control of bacterial translation and demonstrates the power of in-cell structural biology to investigate regulatory circuits in gene expression.

molecular biology↗

bioRxiv2025

Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy

Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at 640 nm exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.

molecular biology↗