Cellular & Molecular Imaging

Filtered tomograms

Experimental Slimfield imaging data and tracking analysis of Rubisco and linker mixtures in vitro, including stoichiometry and colocalisation of pyrenoid proteins. As used in the manuscript for fitting titration curves to extract molecular properties of the liquid pyrenoid matrix.

Vaginal cytology images from adult Sprague Dawley rats for estrous tracking using Track-by-Day method. Cells are stained with H&E and full smear was imaged at 4x (tiles stitched) on a Keyence BZX700 microscope. Two sets are included in this archive: single-field smear images for four rats (Figure 6a), and full-smear images corresponding to cohort of n=12 (Figure 6b, c). These images correspond to sample dataset in Figure 6b, c in "The Track-by-day method for monitoring the rodent estrous cycle" (Raimondi et al., Current Protocols).

In multicellular organisms, tissue architecture reflects not only dedicated patterning genes but the integrated state of core cellular physiology. Whether the same holds for the communities that bacteria build has been difficult to test at scale. To this end, we developed µPULLI, a high-throughput platform that pairs low-magnification, label-free brightfield timelapse microscopy with computer vision. Using µPULLI, we screened a genome-wide Vibrio cholerae transposon library. Our screen revealed that community architecture is governed as much by core physiology as by dedicated biofilm genes: perturbations to central metabolism, cofactor biosynthesis, and cell-envelope architecture each leave distinctive, pathway-specific fingerprints on how a community develops. These fingerprints arise through both transcriptional and non-transcriptional mechanisms, including cell-surface changes invisible to RNA sequencing. Small molecules drive communities predictably through this phenotype space, and the principle holds across taxonomically diverse pathogens. Emergent community architecture thus encodes the integrated physiological state of its constituent cells, revealing a rich, largely untapped layer of biological information that can be read from simple, low-magnification brightfield videos of growing cultures.

Fluorescence imaging across the near-infrared (NIR, 700–1000 nm) and shortwave infrared (SWIR, 1000–2000 nm) regions offers significant advantages for biomedical applications, yet photophysical enhancements achieved with NIR and SWIR chromophores observed in solution often fail to translate to complex biological environments. Fluorous-soluble fluorophores, fluorofluorophores, face additional challenges, exhibiting poor brightness and photostability when dissolved in perfluorocarbons (PFCs) due to unfavorable interactions with the fluorous phase. Here, we report counterion exchange as a strategy to enhance the photophysical properties of two heptamethine cyanine fluorofluorophore for NIR and SWIR imaging. Exchanging the small chloride counterion with a large, fluorinated aryl borate counterions significantly improved the brightness (10-fold) and photostability (57-fold) in PFCs. These enhancements were successfully translated across multiple biological systems from macrophage cells to NIR imaging zebrafish retinal tissue and finally to SWIR imaging in mice. These results demonstrate that strategic counterion modification provides a straightforward approach to optimize fluorofluorophores, with solution-phase improvements that translate to in vivo NIR and SWIR imaging.

A library of 1024 pesticides was screened at sublethal doses for effects on the behaviour of Drosophila third instar larvae.

This dataset includes microscopy and sequence data related to the study and used in the figures. It includes light and electron microscopy images. The sample preparation, image acquisition and analysis protocols are described in the methods.

Live cell imaging movies and IHC data from Drosophila Neurons together with computer simulation results.

Background Microsporidia sp. MB, a microsporidian symbiont found naturally in Anopheles mosquitoes, has potential as a novel malaria control tool since it can inhibit Plasmodium development and transmission. The most feasible MB-based Plasmodium control strategy would involve dissemination through live mosquito releases, or release of spores infective to mosquito larvae. To implement either strategy, establishment of stable mosquito colonies carrying MB at a high frequency is likely to be essential. The progeny of field caught An. gambiae s.l from Burkina Faso were isolated for individual egg laying and tested for MB. The progeny of the MB positive females were pooled and this process was repeated for multiple generations. The relative density of MB in different life stages and tissues of the An. coluzzii host was examined using a novel duplex qPCR assay. We also examined the impact of MB on fecundity through individualization for egg laying and counting of eggs. Finally, we examined laid eggs for presence of MB spores. Results Three An. coluzzii colonies and one An. gambiae s.l hybrid colony were established with high prevalence and density of MB and were maintained for more than two years with minimal intervention. MB prevalence and density was highest in eggs and adult females and lowest in L4 larvae; in adults density was highest in the gonads. Additionally, MB density increased in ovary samples following blood feeding which was likely due to the activation of sporogony. The production of spores is the reason why MB-carrying females lay more white non-hatching eggs and show a small reduction in fecundity. Conclusions Establishment of several stable MB carrying An. gambiae s.l colonies and understanding the impact of spores on fecundity are significant steps forward in developing MB as a malaria control tool.

Live cell imaging movies and IHC data from Drosophila Neurons together with computer simulation results.