bacteria are a model system for understanding pattern formation and collective cell behaviors. When starving, cells aggregate into fruiting bodies to form metabolically inert spores. During predation, cells self-organize into traveling cell-density waves termed ripples. Both phase-contrast and fluorescence microscopy are used to observe these patterns but each has its limitations. Phase-contrast images have higher contrast, but the resulting image intensities lose their correlation with cell density. The intensities of fluorescence microscopy images, on the other hand, are well-correlated with cell density, enabling better segmentation of aggregates and better visualization of streaming patterns in between aggregates; however, fluorescence microscopy requires the engineering of cells to express fluorescent proteins and can be phototoxic to cells. To combine the advantages of both imaging methodologies, we develop a generative adversarial network that converts phase-contrast into synthesized fluorescent images. By including an additional histogram-equalized output to the state-of-the-art pix2pixHD algorithm, our model generates accurate images of aggregates and streams, enabling the estimation of aggregate positions and sizes, but with small shifts of their boundaries. Further training on ripple patterns enables accurate estimation of the rippling wavelength. Our methods are thus applicable for many other phenotypic behaviors and pattern formation studies.
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http://dx.doi.org/10.3390/microorganisms9091954 | DOI Listing |
EMBO J
January 2025
Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
Chromosome segregation relies on kinetochores that assemble on specialized centromeric chromatin containing a histone H3 variant. In budding yeast, a single centromeric nucleosome containing Cse4 assembles at a sequence-defined 125 bp centromere. Yeast centromeric sequences are poor templates for nucleosome formation in vitro, suggesting the existence of mechanisms that specifically stabilize Cse4 nucleosomes in vivo.
View Article and Find Full Text PDFACS Infect Dis
January 2025
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States.
Half the world's population is at risk of developing a malaria infection, which is caused by parasites of the genus . Currently, resistance has been identified to all clinically available antimalarials, highlighting an urgent need to develop novel compounds and better understand common mechanisms of resistance. We previously identified a novel tetrahydro-β-carboline compound, PRC1590, which potently kills the malaria parasite.
View Article and Find Full Text PDFHeliyon
January 2025
Transmission Electronic Microscopy Laboratory, Electronic Microscopy Unit, Department of Biology, University of Cauca, Popayán, 190002, Colombia.
A green methodology for the synthesis of carbon quantum dots (CQDs) from coffee husk without the use of any toxic solvents is proposed in this work. Sonochemical exfoliation of biochar, obtained from the thermal carbonization of coffee husk (from a certified coffee seeds) at low temperature in an air-restricted atmosphere, is described as an alternative procedure for the sustainable production of CQDs. The synthesized CQDs exhibited blue fluorescence with a strong maximum emission band at 410 nm when excited at a maximum absorption wavelength of 330 nm.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Institute of Neurophysiology and NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany.
The bimolecular fluorescence complementation (BiFC) technique is a powerful tool for visualizing protein-protein interactions in vivo. It involves genetically fused nonfluorescent fragments of green fluorescent protein (GFP) or its variants to the target proteins of interest. When these proteins interact, the GFP fragments come together, resulting in the reconstitution of a functional fluorescent protein complex that can be observed using fluorescence microscopy.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Institute of Physical Chemistry, University of Göttingen, Göttingen, Germany.
We present two innovative approaches to investigate the dynamics of membrane fusion and the strength of protein-membrane interactions. The first approach employs pore-spanning membranes (PSMs), which allow for the observation of protein-assisted fusion processes. The second approach utilizes colloidal probe microscopy with membrane-coated probes with reconstituted proteins.
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