{"entity": "researcher", "timestamp": "2026-09-25T23:04:32.382Z", "family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "affiliations": ["Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Husarg. 3, SE-75124, Uppsala, Sweden. elias.amselem@icm.uu.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fc32cd4a9df4689ae7666976507ff64.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fc32cd4a9df4689ae7666976507ff64"}}, "publications": [{"entity": "publication", "iuid": "ea6aa744d35e4a9db1d154ec972126dc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea6aa744d35e4a9db1d154ec972126dc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea6aa744d35e4a9db1d154ec972126dc"}}, "title": "Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle.", "authors": [{"family": "Karempudi", "given": "Praneeth", "initials": "P", "orcid": "0000-0002-5925-8669", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eb5f566aed1c4a30b83908dcde2fa49c.json"}}, {"family": "Gras", "given": "Konrad", "initials": "K"}, {"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fc32cd4a9df4689ae7666976507ff64.json"}}, {"family": "Zikrin", "given": "Spartak", "initials": "S"}, {"family": "Schirman", "given": "Dvir", "initials": "D", "orcid": "0000-0001-5175-0176", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04de2dcb666d4e89ace7b70fbd086390.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7001138c10bf4a6d84075057ba30c8b9.json"}}], "type": "journal article", "published": "2024-11-05", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1443", "issn-l": "2399-3642"}, "abstract": "The intracellular position of genes may impact their expression, but it has not been possible to accurately measure the 3D position of chromosomal loci. In 2D, loci can be tracked using arrays of DNA-binding sites for transcription factors (TFs) fused with fluorescent proteins. However, the same 2D data can result from different 3D trajectories. Here, we have developed a deep learning method for super-resolved astigmatism-based 3D localization of chromosomal loci in live E. coli cells which enables a precision better than 61 nm at a signal-to-background ratio of ~4 on a heterogeneous cell background. Determining the spatial localization of chromosomal loci, we find that some loci are at the periphery of the nucleoid for large parts of the cell cycle. Analyses of individual trajectories reveal that these loci are subdiffusive both longitudinally (x) and radially (r), but that individual loci explore the full radial width on a minute time scale.", "doi": "10.1038/s42003-024-07155-9", "pmid": "39501081", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11538341"}, {"db": "pii", "key": "10.1038/s42003-024-07155-9"}, {"db": "figshare", "key": "10.17044/scilifelab.25998934"}], "notes": [], "created": "2026-09-23T11:36:13.274Z", "modified": "2026-09-23T11:36:13.331Z"}, {"entity": "publication", "iuid": "a97586a0eae1452f9a5989ee5abbc8b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a97586a0eae1452f9a5989ee5abbc8b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a97586a0eae1452f9a5989ee5abbc8b7"}}, "title": "Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization.", "authors": [{"family": "Amselem", "given": "Elias", "initials": "E", "orcid": "0000-0003-2846-9225", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fc32cd4a9df4689ae7666976507ff64.json"}}, {"family": "Broadwater", "given": "Bo", "initials": "B", "orcid": "0000-0002-5870-2457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92ebccc4bf8548e5bb39f504e66af319.json"}}, {"family": "H\u00e4vermark", "given": "Tora", "initials": "T", "orcid": "0000-0002-3794-3243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/254d5e78504d4afa9280816edc600763.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8811-2629", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5832644dbf7c44bd9bbc788e966b977e.json"}}, {"family": "Elf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5522-1810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7001138c10bf4a6d84075057ba30c8b9.json"}}], "type": "journal article", "published": "2023-03-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1336", "issn-l": "2041-1723"}, "abstract": "Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.", "doi": "10.1038/s41467-023-36879-1", "pmid": "36906676", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10008558"}, {"db": "pii", "key": "10.1038/s41467-023-36879-1"}], "notes": [], "created": "2026-09-23T11:13:53.389Z", "modified": "2026-09-23T11:13:53.599Z"}]}