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Microscopy dataset underlying the results presented in the article "E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients".

Imaging Methods: fluorescence microscopy phase contrast microscopy

Organisms: Escherichia coli

Lunaphore COMET (cyclic immunofluorescent) data of the liver, together with IMC from adjacent tissue slices.

Imaging Methods: fluorescence microscopy

Organisms: Homo sapiens

Raw two-channel TIRF microscopy images (488 nm and 640 nm) generated for particle detection and ROI-based colocalization analysis. The dataset includes experimental and control image sets acquired under identical imaging conditions. Images were analyzed using custom ImageJ (Fiji) macros to identify particles in each channel and quantify spatial co-occurrence based on ROI overlap.

Imaging Methods: fluorescence microscopy

Organisms: Mus musculus

Raw data corresponding to the publication, "Cell surface localisation of GPI-anchored receptors in Trypanosoma brucei", published in eLife (https://doi.org/10.7554/eLife.107191.1)

Organisms: Trypanosoma brucei brucei

Parkinson’s disease is considered biologically a neuronal alpha-synuclein disease, largely ignoring the more widespread alpha-synuclein deposition that occurs in astrocytes. Recent single cell transcriptomics have identified early astrocytic differences in both Parkinson’s disease and mouse models with an increase in reactive astrocytes associated with proteostasis. To identify whether astrocytes accumulate alpha-synuclein before or after neurons, the present study histologically assessed astrocytes and alpha-synuclein accumulation in the M83 A53T transgenic mouse model of Parkinson’s disease prior to significant neuronal alpha-synuclein accumulation. The brains of M83 A53T transgenic (n=5) and wild-type (n=4) mice were perfusion fixed and serial sections of the midbrain and striatum processed for multiplex labelling. Digital images were captured from standardised sampling regions and astrocyte quantitation performed using QuPath software. Multivariate linear region models with Turkey posthoc tests were used to evaluate the effects of genotype on regional astrocyte morphology and numbers. The density of astrocytes within the substantia nigra pars compacta was approximately 30% greater compared with other sampled regions (P<0.005). Small aggregates of alpha-synuclein were observed in astrocytic processes, including in wild-type mice where a quarter of all astrocytes had an obvious alpha-synuclein aggregate. Compared to wild-type, A53T transgenic astrocytes had significantly enlarged somas (P<0.001) with more processes (P<0.001) consistent with a reactive phenotype. The expression of vascular endothelial growth factor A was present in analysed astrocytes, but not the synthesising enzyme for vitamin D CYP27B1. The A53T transgenic mice had more than double the numbers of astrocytes (P<0.001) and 2.5 times more astrocytes with alpha-synuclein aggregates compared to wild-type mice (P<0.001). These data suggest that -synuclein is normally cleared by astrocytes and that the substantia nigra pars compacta requires more astrocytic support than other midbrain dopaminergic regions or the striatum. This adds another vulnerability factor to those already known for the substantia nigra. In the A53T transgenic mouse model, astrocytes have an early upregulation of their clearance of alpha-synuclein aggregates. While speculative, a loss of this ability to take up alpha-synuclein in these regions may precipitate the selective neuronal degeneration and pathologies observed in Parkinson’s disease. As we move to a biological definition for this disease, understanding this early role of astrocytes needs to be considered further.

Imaging Methods: confocal microscopy

Organisms: Mus musculus

Understanding the molecular anatomy and neural connectivity of the brain requires imaging technologies that can map the 3D nanoscale distribution of specific proteins in the context of brain ultrastructure. Light and electron microscopy (EM) visualize either specific labels or anatomical ultrastructure but combining molecular specificity with anatomical context is challenging. Here, we present pan-Expansion Microscopy of tissue (pan-ExM-t), an all-optical imaging method that combines ~16-24-fold linear expansion with fluorescent pan-stainings of proteins and lipids (providing EM-like ultrastructural context), and immunolabeling (for molecular imaging). We demonstrate the versatility of this approach by imaging synaptic and cell-specific antibodies in the ultrastructural 3D context of pre and postsynaptic densities, neuropil nanoarchitecture, and cellular organelles in dissociated neuron cultures and mouse brain tissue sections. Furthermore, we demonstrate tracing of neuronal circuitry from pan-ExM-t image volumes, suggesting that any laboratory with access to a confocal microscope can now localize specific molecules within nanoscale cellular and circuit contexts.

Imaging Methods: spinning disk confocal microscopy

Organisms: Mus musculus

The transition to parenthood brings significant changes in behavior toward offspring. For instance, in anticipation of their offspring, male mice shift from infanticidal to caregiving behaviors. While the release of oxytocin from the paraventricular hypothalamus (PVH) plays a critical role in paternal caregiving, it does not fully account for the entire behavioral shift. The specific downstream neurons and signaling mechanisms involved in this process remain obscure. Here, we demonstrate that PVH vasopressin neurons also essentially contribute to a paternal behavioral shift. This vasopressin signal is partially transmitted through oxytocin receptors (OTRs) expressed in the anterior commissure and medial nuclei of the preoptic area. These OTR-expressing neurons receive inputs from both PVH oxytocin and vasopressin neurons and are responsible for expressing paternal caregiving behaviors. Collectively, this non-canonical vasopressin-to-OTR crosstalk within specific limbic circuits acts as a pivotal regulator of paternal behavioral changes in mice.

Imaging Methods: CSV files pulsed illumination recorded image

Organisms: Mus musculus

Glioblastomas function as intricate cellular networks that extend into the surrounding brain tissue facilitating long distance communication. This malignant connectivity spans from the tumor core to remote infiltration zones, supporting the concept of glioblastoma as a whole-brain disease. With growing ethical concerns in biomedical research and the inherent limitations of animal models in recapitulating human glioblastoma biology, there is an increasing demand for human ex vivo platforms capable of capturing the full infiltration spectrum from the tumor core to single-cell dispersion. Here, we present a three-dimensional (3D), fully human ex vivo glioblastoma model (”Core2Edge”) that replicates this extensive infiltration range while preserving the intratumoral heterogeneity of the original tumor. This model involves implanting fluorescently labeled human glioblastoma organoids (GBOs) into organotypic human brain slices, maintaining the genetic integrity and cytoarchitecture of both brain and tumor. By combining tissue expansion with light-sheet fluorescence microscopy, we achieve super-resolution, 3D imaging of the entire GBO-brain slice model. This approach allows for the study of initial infiltration steps, in-depth analysis of the invasive front, exploration of cell-cell interactions between tumor cells and the tumor microenvironment, and offers a platform for drug screening and testing, reducing the need for animal models. Once GBOs are prepared, the protocol takes approximately 7-12 days. Key steps include brain slice preparation (~4-6 h, depending on quantity), one day for initial culture before GBO staining and transplantation, a variable culture period (up to 10 days), and fixation (~8 h). Additional time is required for downstream analyses, including imaging, sequencing, and proteomics.

Organisms: Homo sapiens

MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis: In multicellular organisms, germ cells’ transformation into haploid gametes requires that they transition from mitosis to meiosis, whereby they stop mitotic cycling and enter the meiotic cell cycle. In mammals, transcriptional activator STRA8-MEIOSIN mediates the decision to enter the meiotic cell cycle by triggering the G1-to-meiotic S phase transition. However, the molecular basis by which mammalian germ cells prevent continued mitotic cycling before entering the meiotic cell cycle remains unclear. Here, we investigate MEIOC’s role in the mitosis-to-meiosis transition during mouse oogenesis by analyzing proliferation, cell cycle transcriptomics, and cell cycle-associated protein expression. MEIOC was previously shown to destabilize mRNA and repress the mitotic program after meiotic entry. Here, we demonstrate that MEIOC prevents continued mitotic cycling prior to meiotic entry in oogenic cells. We find that the mitosis-to-meiosis transition involves the repression of G1/S cyclin CCNA2 at the transcript and protein levels, and that MEIOC downregulates CCNA2 protein expression. In addition, MEIOC promotes entry into meiotic S phase by increasing Meiosin transcript abundance and consequently activating the STRA8-MEIOSIN transcription factor. Given that STRA8-MEIOSIN upregulates Meioc expression, MEIOC and STRA8-MEIOSIN form a positive feedback loop to reinforce timely meiotic initiation. We also demonstrate that BMP signaling halts mitotic cycling and promotes meiotic entry by upregulating MEIOC. We conclude that, in mouse oogenic cells, the transition from mitosis to meiosis occurs as two molecularly regulated steps– (i) halt of mitotic cycling and (ii) entry into the meiotic cell cycle – and that MEIOC modifies the cell cycle program to facilitate both steps in this transition. This study was published in: Ushuhuda EG*, Nguyen JT*, Pfaltzgraff NG, Wenner SM, Kofron M, Mikedis MM. MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis. Development. 2025 Nov 25:dev205037. PMID: 41287933. * equal contribution

Imaging Methods: spinning disk confocal microscopy

Organisms: Mus musculus

Radiation damage remains a fundamental limitation in cryo-electron microscopy (cryo-EM), constraining the total electron dose that can be used and thus hindering high-resolution imaging of biological specimens. Recent studies have proposed that temporally structured or pulsed electron beams could reduce radiation damage by allowing time for energy dissipation between individual electron interactions. To evaluate this hypothesis, we conducted a systematic investigation using a radio-frequency (RF) driven 300 kV Titan Krios microscope equipped with cold field emission gun (c-FEG) to generate highly regular pulsed electron beams for specimens under cryogenic conditions. We compared radiation damage in three representative samples: paraffin 2D crystals, bacteriorhodopsin (purple membrane) 2D crystals, and plunge-frozen tobacco mosaic virus (TMV) in vitreous ice, under both pulsed and conventional random illumination, while keeping all other imaging conditions constant. Radiation damage was quantified by tracking the decay of computed diffraction intensities to determine the critical dose (Ne). We observed no statistically significant difference in critical dose between pulsed and random illumination across all 3 samples. Our findings provide a critical reference point for future development and evaluation of temporally modulated electron sources in cryo-EM instrumentation.

Imaging Methods: electron microscopy

Although it is well known that the morphology of Gram-negative rods changes on exposure to antibiotics, the morphology of antibiotic-resistant bacteria in the absence of antibiotics has not been widely investigated. Here, we studied the morphologies of 10 antibiotic-resistant strains of Escherichia coli and used bioinformatics tools to classify the resistant cells under light microscopy in the absence of antibiotics. The antibiotic-resistant strains showed differences in morphology from the sensitive parental strain, and the differences were most prominent in the quinolone-and β-lactam-resistant bacteria. A cluster analysis revealed increased proportions of fatter or shorter cells in the antibiotic-resistant strains. A correlation analysis of morphological features and gene expression suggested that genes related to energy metabolism and antibiotic resistance were highly correlated with the morphological characteristics of the resistant strains. Our newly proposed deep learning method for single-cell classification achieved a high level of performance in classifying quinolone-and β-lactam-resistant strains.

Imaging Methods: recorded image

Organisms: Escherichia coli

Collective migration of epithelial cells is a fundamental process in multicellular pattern formation. As they expand their territory, cells are exposed to various physical forces generated by cell–cell interactions and the surrounding microenvironment. While the physical stress applied by neighbouring cells has been well studied, little is known about how the niches that surround cells are spatio-temporally remodelled to regulate collective cell migration and pattern formation. Here, the authors analysed how the spatio-temporally remodelled extracellular matrix (ECM) alters the resistance force exerted on cells so that the cells can expand their territory. Multiple microfabrication techniques, optical tweezers, as well as mathematical models were employed to prove the simultaneous construction and breakage of ECM during cellular movement, and to show that this modification of the surrounding environment can guide cellular movement. Furthermore, by artificially remodelling the microenvironment, they showed that the directionality of collective cell migration, as well as the three-dimensional branch pattern formation of lung epithelial cells, can be controlled. Their results thus confirm that active remodelling of cellular microenvironment modulates the physical forces exerted on cells by the ECM, which contributes to the directionality of collective cell migration and consequently, pattern formation.

Imaging Methods: recorded image phase contrast microscopy time lapse microscopy fluorescence microscopy confocal microscopy

Organisms: Homo sapiens Canis lupus familiaris