Cellular & Molecular Imaging

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. This is a collection of the samples included in the study, provided by COPO at Earlham Institute.

We used Chlamydomonas reinhardtii motility mutants with disrupted genes homologous to human SPEF2 or DNALI1 to model spermatogenic failure disorders SPGF43 and SPGF83, respectively. We recovered aspects of wild-type motility in these mutants with a small-scale drug screen.

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.

The following data includes raw images, metadata, measurements and processed images as well as classifiers for image segmentations and masks created with the ImageJ/Fiji plugin Labkit to measure the leaf area. This dataset provides all acquired information for my Bachelor's thesis about leaf traits of Bryophyta related moss species.

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Figure 4C) Percentage of Striga hermonthica seeds germinating after 2 days of treatment with Triton X-100 at 15.4 (0.001%) and 1.54 micromoles (0.0001%) concentrations and n-dodecyl-beta- D-maltoside at 15 and 1.5 micromoles concentrations in the presence of GR24 at 1, 0.5, 0.25, and 0.125 nM concentrations, respectively. Figure 7C) Percentage of Striga hermonthica seeds germinating after 2 days of treatment with PAA at 1 and 10 micromoles concentrations in the presence of GR24 at 1, 0.5, 0.25, and 0.125 nM concentrations, respectively.

Motility is a phenotypic readout that indicates an organism’s integration of sensory input from its environment with its ability to move. We developed a microscopy workflow and image analysis pipeline to track motility phenotypes from unicellular algae in high-throughput.

Source data relating to Fig. 7 of the submitted manuscript to Embo Molecular Medicine

to be described

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