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Zheng, Xuan (author), Betjes, M.A. (author), Ender, Pascal (author), Goos, Yvonne J. (author), Huelsz-Prince, Guizela (author), Clevers, Hans (author), van Zon, Jeroen S. (author), Tans, S.J. (author)Organoids are a major new tool to study tissue renewal. However, characterizing the underlying differentiation dynamics remains challenging. Here, we developed TypeTracker, which identifies cell fates by AI-enabled cell tracking and propagating end point fates back along the branched lineage trees. Cells that ultimately migrate to the villus...journal article 2023
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Wehrens, Martijn (author), Krah, Laurens H.J. (author), Towbin, Benjamin D. (author), Hermsen, Rutger (author), Tans, S.J. (author)The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying...journal article 2023
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Naqvi, Mohsin M. (author), Avellaneda, Mario J. (author), Roth, Andrew (author), Koers, Eline J. (author), Roland, A.P.J. (author), Sunderlikova, Vanda (author), Kramer, Günter (author), Rye, Hays S. (author), Tans, S.J. (author)The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding...journal article 2022
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Büke, F. (author), Grilli, Jacopo (author), Cosentino Lagomarsino, Marco (author), Bokinsky, G.E. (author), Tans, S.J. (author)Growth and division are central to cell size. Bacteria achieve size homeostasis by dividing when growth has added a constant size since birth, termed the adder principle, by unknown mechanisms.<sup>1</sup><sup>,</sup><sup>2</sup> Growth is well known to be regulated by guanosine tetraphosphate (ppGpp), which controls diverse processes from...journal article 2022
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Mashaghi, Alireza (author), Moayed, Fatemeh (author), Koers, Eline J. (author), Zheng, Yang (author), Till, K. (author), Kramer, Günter (author), Mayer, Matthias P. (author), Tans, S.J. (author)The chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using...journal article 2022
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Wortel, Meike T. (author), Agashe, Deepa (author), Bailey, Susan F. (author), Bank, Claudia (author), Bisschop, Karen (author), Blankers, Thomas (author), Laan, L. (author), Meijer, Jeroen (author), Tans, S.J. (author)Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for...review 2022
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Berenger-Currias, N.M.L.P. (author), Mircea, Maria (author), Adegeest, Esmée (author), van den Berg, Patrick R. (author), Feliksik, Marleen (author), Hochane, Mazène (author), Idema, T. (author), Tans, S.J. (author), Semrau, Stefan (author)Stem-cell derived in vitro systems, such as organoids or embryoids, hold great potential for modeling in vivo development. Full control over their initial composition, scalability, and easily measurable dynamics make those systems useful for studying specific developmental processes in isolation. Here we report the formation of gastruloids...journal article 2022
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Mulla, Yuval (author), Avellaneda, Mario J. (author), Roland, A.P.J. (author), Baldauf, L. (author), Jung, Wonyeong (author), Kim, Taeyoon (author), Tans, S.J. (author), Koenderink, G.H. (author)Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion<sup>1</sup> and cellular mechanosensing<sup>2</sup>. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides ‘strength on demand<sup>3</sup>’, thus enabling cells to increase...journal article 2022
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McKenzie, R. (author), Keizer, Emma M. (author), Vink, J.N.A. (author), van Lopik, Jasper (author), Büke, F. (author), Kalkman, Vera (author), Fleck, Christian (author), Tans, S.J. (author), Brouns, S.J.J. (author)While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR...journal article 2022
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- Tans, S.J. (author) journal article 2022
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Betjes, M.A. (author), Zheng, X.Z. (author), Kok, R.N.U. (author), van Zon, Jeroen S. (author), Tans, S.J. (author)Organoids have emerged as powerful model systems to study organ development and regeneration at the cellular level. Recently developed microscopy techniques that track individual cells through space and time hold great promise to elucidate the organizational principles of organs and organoids. Applied extensively in the past decade to embryo...review 2021
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Wruck, F.R. (author), Tian, Pengfei (author), Kudva, Renuka (author), Best, Robert B. (author), von Heijne, Gunnar (author), Tans, S.J. (author), Katranidis, Alexandros (author)Proteins commonly fold co-translationally at the ribosome, while the nascent chain emerges from the ribosomal exit tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is not well understood. Here, we combine optical...journal article 2021
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Bertolini, Matilde (author), Fenzl, Kai (author), Kats, Ilia (author), Wruck, F.R. (author), Tippmann, Frank (author), Schmitt, Jaro (author), Auburger, Josef Johannes (author), Tans, S.J. (author), Bukau, Bernd (author), Kramer, Günter (author)Accurate assembly of newly synthesized proteins into functional oligomers is crucial for cell activity. In this study, we investigated whether direct interaction of two nascent proteins, emerging from nearby ribosomes (co-co assembly), constitutes a general mechanism for oligomer formation. We used proteome-wide screening to detect nascent...journal article 2021
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Kok, R.N. (author), Hebert, Laetitia (author), Huelsz-Prince, Guizela (author), Goos, Yvonne J. (author), Zheng, X.Z. (author), Bozek, Katarzyna (author), Stephens, Greg J. (author), Tans, S.J. (author), Van Zon, Jeroen S. (author)Time-lapse microscopy is routinely used to follow cells within organoids, allowing direct study of division and differentiation patterns. There is an increasing interest in cell tracking in organoids, which makes it possible to study their growth and homeostasis at the singlecell level. As tracking these cells by hand is prohibitively time...journal article 2020
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Avellaneda, Mario J. (author), Koers, Eline J. (author), Minde, David P. (author), Sunderlikova, Vanda (author), Tans, S.J. (author)Many proteins form dynamic complexes with DNA, RNA, and other proteins, which often involves protein conformational changes that are key to function. Yet, methods to probe these critical dynamics are scarce. Here we combine optical tweezers with fluorescence imaging to simultaneously monitor the conformation of individual proteins and their...journal article 2020
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Nghe, Philippe (author), Kogenaru, Manjunatha (author), Tans, S.J. (author)Sign epistasis is a central evolutionary constraint, but its causal factors remain difficult to predict. Here we use the notion of parameterised optima to explain epistasis within a signalling cascade, and test these predictions in Escherichia coli. We show that sign epistasis arises from the benefit of tuning phenotypic parameters of cascade...journal article 2018
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- Tans, R.L.M. (author) master thesis 2017
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De Martino, M. (author), Ershov, D. (author), van den Berg, P.J. (author), Tans, S.J. (author), Meyer, A.S. (author)Microorganisms have developed an elaborate spectrum of mechanisms to respond and adapt to environmental stress conditions. Among these is the expression of dps, coding for the DNA-binding protein from starved cells. Dps becomes the dominant nucleoid- organizing protein in stationary-phase Escherichia coli cells and is required for robust...journal article 2016
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Moayed, F. (author), Mashaghi, A. (author), Tans, S.J. (author)Many applications in biosensing, biomaterial engineering and single molecule biophysics require multiple non-covalent linkages between DNA, protein molecules, and surfaces that are specific yet strong. Here, we present a novel method to join proteins and dsDNA molecule at their ends, in an efficient, rapid and specific manner, based on the...journal article 2013
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- Tans, S.J. (author) doctoral thesis 1998
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