Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes

Autor: Daniel R. Garza, F. A. Bastiaan von Meijenfeldt, Bram van Dijk, Annemarie Boleij, Martijn A. Huynen, Bas E. Dutilh

Publikováno v: BMC Ecology and Evolution, Vol 22, Iss 1, Pp 1-16 (2022)

Abstract Background Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires ex

Externí odkaz: https://doaj.org/article/8e4bf5a7f4c44470800c816b7fe51f4c

Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements

Autor: Bram van Dijk, Paulien Hogeweg, Hilje M Doekes, Nobuto Takeuchi

Publikováno v: eLife, Vol 9 (2020)

Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study

Externí odkaz: https://doaj.org/article/2cdae1dac1f24c3dae3d0cf3daa4574c

Towards evolutionary predictions: Current promises and challenges

Autor: Meike T. Wortel, Deepa Agashe, Susan F. Bailey, Claudia Bank, Karen Bisschop, Thomas Blankers, Johannes Cairns, Enrico Sandro Colizzi, Davide Cusseddu, Michael M. Desai, Bram van Dijk, Martijn Egas, Jacintha Ellers, Astrid T. Groot, David G. Heckel, Marcelle L. Johnson, Ken Kraaijeveld, Joachim Krug, Liedewij Laan, Michael Lässig, Peter A. Lind, Jeroen Meijer, Luke M. Noble, Samir Okasha, Paul B. Rainey, Daniel E. Rozen, Shraddha Shitut, Sander J. Tans, Olivier Tenaillon, Henrique Teotónio, J. Arjan G. M. de Visser, Marcel E. Visser, Renske M. A. Vroomans, Gijsbert D. A. Werner, Bregje Wertheim, Pleuni S. Pennings

Publikováno v: Evolutionary Applications
Evolutionary Applications 16 (2023) 1
Evolutionary Applications, 16(1), 3-21. Wiley
Evolutionary Applications, 16(1), 3-21
Wortel, M T, Agashe, D, Bailey, S F, Bank, C, Bisschop, K, Blankers, T, Cairns, J, Colizzi, E S, Cusseddu, D, Desai, M M, van Dijk, B, Egas, M, Ellers, J, Groot, A T, Heckel, D G, Johnson, M L, Kraaijeveld, K, Krug, J, Laan, L, Lässig, M, Lind, P A, Meijer, J, Noble, L M, Okasha, S, Rainey, P B, Rozen, D E, Shitut, S, Tans, S J, Tenaillon, O, Teotónio, H, de Visser, J A G M, Visser, M E, Vroomans, R M A, Werner, G D A, Wertheim, B & Pennings, P S 2023, ' Towards evolutionary predictions : Current promises and challenges ', Evolutionary Applications, vol. 16, no. 1, pp. 3-21 . https://doi.org/10.1111/eva.13513
Wortel, Meike T; Agashe, Deepa; Bailey, Susan F; Bank, Claudia; Bisschop, Karen; Blankers, Thomas; Cairns, Johannes; Colizzi, Enrico Sandro; Cusseddu, Davide; Desai, Michael M; van Dijk, Bram; Egas, Martijn; Ellers, Jacintha; Groot, Astrid T; Heckel, David G; Johnson, Marcelle L; Kraaijeveld, Ken; Krug, Joachim; Laan, Liedewij; Lässig, Michael; ... (2023). Towards evolutionary predictions: Current promises and challenges. Evolutionary applications, 16(1), pp. 3-21. Wiley 10.1111/eva.13513

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, agricultu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71e4f50b149bf5f0028da42a53dcebc0
https://hdl.handle.net/21.11116/0000-000B-51E0-C21.11116/0000-000C-6FB0-121.11116/0000-000C-22DC-6

Looking from the Inside: How Children Render Character’s Perspectives in Freely Told Fantasy Stories

Autor: Max van Duijn, Bram van Dijk, Marco Spruit

Publikováno v: Proceedings of the 4th Workshop of Narrative Understanding (WNU2022).

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6a09f41f99c3414ab6be02752e08f445
https://doi.org/10.18653/v1/2022.wnu-1.8

Transposable elements promote the evolution of genome streamlining

Autor: Frederic Bertels, Lianne Stolk, Paul B. Rainey, Nobuto Takeuchi, Bram van Dijk

Publikováno v: Philosophical Transactions of the Royal Society B: Biological Sciences
Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::42f02aeaa8b7c0d390179fa589ee00da
https://pubmed.ncbi.nlm.nih.gov/34839699