Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Joshua Hawley, Cerys Manning, Veronica Biga, Paul Glendinning, Nancy Papalopulu
Summary: This study presents a computational model to explain the expression dynamics of the HES5 gene in neural tissue development. The model suggests that extending Notch signaling to non-neighboring progenitor cells generates the observed spatial periodicity. Additionally, introducing periodic perturbations of Notch signaling by differentiating cells induces temporal switching in the spatial pattern.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biology
Juan Carlos Cerpa, Alessandro Piccin, Margot Dehove, Marina Lavigne, Eric J. Kremer, Mathieu Wolff, Shauna L. Parkes, Etienne Coutureau
Summary: Organisms need to track the relationship between actions and consequences in order to make decisions, which relies on circuits in the brain. There is functional heterogeneity within certain areas of the brain in rodents. Neuromodulatory agents play a crucial role in prefrontal functions and behavioral flexibility.
Review
Engineering, Mechanical
Gui-Quan Sun, Hong-Tao Zhang, Jin-Shan Wang, Jing Li, Yi Wang, Li Li, Yong-Ping Wu, Guo-Lin Feng, Zhen Jin
Summary: This research delves into the key issue of population distribution in ecological systems and how it characterizes the relationship between populations, space-time structure, and evolution laws. It systematically summarizes the related results in pattern formation of ecological systems, showcasing the mechanisms of different patterns. This work offers valuable insights into understanding the complexity of ecosystems and can be applied in various related fields such as epidemiology, medical science, and atmospheric science.
NONLINEAR DYNAMICS
(2021)
Article
Neurosciences
Albert Park, Alexander D. Jacob, Hwa-Lin (Liz) Hsiang, Paul W. Frankland, John G. Howland, Sheena A. Josselyn
Summary: This study investigates the role of engram neurons in the lateral amygdala in rewarding cue-cocaine memory, showing that these neurons are important for behavior consistent with recall of the memory and for reinstatement of memory-guided behavior after extinction. The reactivation of the original engram is found to be necessary for memory-guided behavior to occur. The findings indicate the critical role of the lateral amygdala in the larger brain-wide engram system.
NEUROPSYCHOPHARMACOLOGY
(2023)
Article
Developmental Biology
Joana Santos Teixeira, Thea van den Berg, Kirsten ten Tusscher
Summary: Priming is a process that prepatterns future sites for lateral root formation through elevations in auxin concentration and signalling. Prebranch site formation involves a two-step process of initial signal mediated by auxin concentration and memorization mediated by auxin signalling capacity. The crucial aspect is the activation in response to time-integrated auxin signalling.
Article
Physics, Multidisciplinary
Akiko M. Nakamasu
Summary: Research finds that pigment patterns on the body trunk of growing fish follow a Turing pattern, and laser ablation experiments reveal interactions among pigment cells. However, the molecular mechanisms responsible for Turing pattern formation in this system remain unknown. The study uses partial differential equation models for numerical and mathematical analysis.
FRONTIERS IN PHYSICS
(2022)
Article
Mathematics, Applied
Joshua W. Moore, Trevor C. Dale, Thomas E. Woolley
Summary: This study investigates the formation of fine-grain patterns produced by juxtacrine signalling in cellular domains. A theoretical framework combining concepts from graph and control theory is used to analyze cellular connectivity and behaviour. The results show that the symmetry of multicellular bilayer structures can drive the formation of laminar patterns, independent of the specific dynamical details. The study also highlights the importance of intense cell signalling polarity and proposes a biological process for bilayer stratification in mammary organoids.
IMA JOURNAL OF APPLIED MATHEMATICS
(2022)
Article
Biology
Simon Schardt, Sabine C. Fischer
Summary: This study presents a mathematical model based on signaling that can reliably generate spatially heterogeneous cell type patterns with specified proportions. By controlling a single model parameter, the proportions of different cell types can be controlled.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Environmental Sciences
David A. Olson, John H. Offenberg, Michael Lewandowski, Tadeusz E. Kleindienst, Kenneth S. Docherty, Mohammed Jaoui, Jonathan Krug, Theran P. Riedel
Summary: This research utilized data mining methods to analyze laboratory data and identified key factors influencing the formation of secondary organic aerosol (SOA).
ATMOSPHERIC ENVIRONMENT
(2021)
Article
Plant Sciences
Yinwei Zeng, Inge Verstraeten, Hoang Khai Trinh, Robin Lardon, Sebastien Schotte, Damilola Olatunji, Thomas Heugebaert, Christian Stevens, Mussa Quareshy, Richard Napier, Sara Paola Nastasi, Alex Costa, Bert De Rybel, Catherine Bellini, Tom Beeckman, Steffen Vanneste, Danny Geelen
Summary: This study reveals the molecular processes involved in the initiation of adventitious root (AR) formation along the hypocotyl of Arabidopsis seedlings exposed to light. The results show that AR induction by HYSPARIN involves nuclear TIR1/AFB and plasma membrane TMK auxin signaling, as well as multiple downstream LR development genes. Additionally, SAUR19, OFP4, and AGC2 are identified as novel regulators of AR formation.
Article
Environmental Studies
Woo Jin Lee, Sung Il Kwag, Young Dae Ko
Summary: This paper proposes an eco-friendly platoon formation strategy for a heterogeneous fleet of electric vehicles for a single route, and finds that the type of adjacent vehicles influences the energy savings of each vehicle, with a bell-shaped platoon configuration generally effective for energy saving.
TRANSPORTATION RESEARCH PART D-TRANSPORT AND ENVIRONMENT
(2021)
Article
Biology
Tatsuya Hayashi, Fumitaka Yura, Jun Mada, Hiroki Kurihara, Tetsuji Tokihiro
Summary: A two-dimensional mathematical model for dynamics of endothelial cells in angiogenesis is studied, showing that the oblateness of ellipses and the magnitude of contact rotation significantly influence the shape of vascular patterns and elongation of branches.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Agronomy
Wang Rui, Zhang Dandan, Li Shengnan, Gao Jinlan, Han Liebao, Qiu Jinlong
Summary: Lateral root growth inhibition is a simple and reliable measurement for studying PTI in rice plants, and it can be applied to various rice cultivars and wild species.
Article
Biology
Jesus A. Tapia, Argelia Reid, John Reid, Saul M. Dominguez-Nicolas, Elias Manjarrez
Summary: This study uses a mathematical model to demonstrate the potential transition of post-scratching locomotion in cats through shared neuronal circuits. The model replicates the experimental observations, revealing the mechanism of transition between two rhythmic movements and the flexible connectivity in the spinal cord circuitry.
Article
Biology
Hernan Morales-Navarrete, Hidenori Nonaka, Andre Scholich, Fabian Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L. Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, Frank Juelicher, Benjamin M. Friedrich, Marino Zerial
Article
Cell Biology
Hanh Thi-Kim Vu, Sarah Mansour, Michael Kuecken, Corinna Blasse, Cyril Basquin, Juliette Azimzadeh, Eugene Wimberly Myers, Lutz Brusch, Jochen Christian Rink
DEVELOPMENTAL CELL
(2019)
Article
Biochemistry & Molecular Biology
Kirstin Meyer, Hernan Morales-Navarrete, Sarah Seifert, Michaela Wilsch-Braeuninger, Uta Dahmen, Elly M. Tanaka, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial
MOLECULAR SYSTEMS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Fabian Segovia-Miranda, Hernan Morales-Navarrete, Michael Kuecken, Vincent Moser, Sarah Seifert, Urska Repnik, Fabian Rost, Mario Brosch, Alexander Hendricks, Sebastian Hinz, Christoph Roecken, Dieter Luetjohann, Yannis Kalaidzidis, Clemens Schafmayer, Lutz Brusch, Jochen Hampe, Marino Zerial
Article
Cell Biology
Erik Kolbe, Susanne Aleithe, Christiane Rennert, Luise Spormann, Fritzi Ott, David Meierhofer, Robert Gajowski, Claus Stoepel, Stefan Hoehme, Michael Kuecken, Lutz Brusch, Michael Seifert, Witigo von Schoenfels, Clemens Schafmayer, Mario Brosch, Ute Hofmann, Georg Damm, Daniel Seehofer, Jochen Hampe, Rolf Gebhardt, Madlen Matz-Soja
Article
Biochemical Research Methods
Andre Scholich, Simon Syga, Hernan Morales-Navarrete, Fabian Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Juelicher, Benjamin M. Friedrich
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemical Research Methods
T. J. Sego, Josua O. Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Cell Biology
Arthur Boutillon, Sophie Escot, Amelie Elouin, Diego Jahn, Sebastian Gonzalez-Tirado, Joern Starruss, Lutz Brusch, Nicolas B. David
Summary: During zebrafish gastrulation, the migration of polster cells guides the extension of the embryonic axis, and each cell is oriented by its followers through mechanotransduction.
DEVELOPMENTAL CELL
(2022)
Article
Biochemistry & Molecular Biology
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Frohlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry Jakubowski, Ryann Jordan, Matus Kalas, Matthias Koenig, Wolfram Liebermeister, Rahuman S. Malik Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Mueller, Chris J. Myers, Aurelien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loic Pauleve, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Joern Starruss, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
Summary: Computational models have great potential in accelerating bioscience, bioengineering, and medicine. However, reproducing and reusing simulations is still challenging due to the different formats and methods used by different software tools. To address this issue, we developed BioSimulators, a central registry that provides consistent interfaces and recommendations for simulation tools, using standards and validation tools to ensure consistency. We anticipate that BioSimulators will facilitate the exchange, reproduction, and combination of simulations by modelers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Sebastian S. Roeder, Petra Burkardt, Fabian Rost, Julian Rode, Lutz Brusch, Roland Coras, Elisabet Englund, Karl Hakansson, Goran Possnert, Mehran Salehpour, Daniel Primetzhofer, Laszlo Csiba, Sarolta Molnar, Gabor Mehes, Anton B. Tonchev, Stefan Schwab, Olaf Bergmann, Hagen B. Huttner
Summary: Using a combination of methods, evidence for postnatal neurogenesis in the human amygdala was found. This discovery provides new insight into neuronal exchange and cell renewal.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Paula Heinke, Fabian Rost, Julian Rode, Palina Trus, Irina Simonova, Eniko Lazar, Joshua Feddema, Thilo Welsch, Kanar Alkass, Mehran Salehpour, Andrea Zimmermann, Daniel Seehofer, Goran Possnert, Georg Damm, Henrik Druid, Lutz Brusch, Olaf Bergmann
Summary: This study used retrospective radiocarbon birth dating to investigate the turnover of human liver cells. The results showed that human hepatocytes undergo continuous and lifelong renewal, which keeps the liver young. Diploid hepatocytes have a higher birth rate than polyploid hepatocytes, and the transition between diploid and polyploid cells is limited under homeostatic conditions.
Article
Biochemistry & Molecular Biology
Carlotta Mayer, Sophie Nehring, Michael Kuecken, Urska Repnik, Sarah Seifert, Aleksandra Sljukic, Julien Delpierre, Hernan Morales-Navarrete, Sebastian Hinz, Mario Brosch, Brian Chung, Tom Karlsen, Meritxell Huch, Yannis Kalaidzidis, Lutz Brusch, Jochen Hampe, Clemens Schafmayer, Marino Zerial
Summary: Hepatocytes dynamically respond to bile acids and bile flow, but little is known about their response to intraluminal pressure. This study reveals that hepatocytes form apical bulkheads in response to obstructed bile flow, which protect bile canaliculi against elevated pressure. The loss of apical bulkheads leads to abnormally dilated canaliculi, highlighting the importance of canalicular pressure in liver diseases.
Article
Mathematics, Interdisciplinary Applications
Robert Mueller, Arthur Boutillon, Diego Jahn, Joern Starruss, Nicolas B. David, Lutz Brusch
Summary: Collective cell migration is a crucial process in biological development and tissue repair, but it can become malignant during tumor invasion. Mathematical and computational models are essential for understanding the self-organization mechanisms that drive collective migration from individual cell interactions. This study explores how guidance stimuli are integrated when multiple cells interact simultaneously, using an individual-based model. The results show that collective cell migration remains robust and qualitatively the same regardless of the variant of stimulus integration considered. This study highlights the importance of individual-based modeling for understanding collective phenomena arising from cell-cell interactions.
FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS
(2023)
Article
Multidisciplinary Sciences
Oleksandr Ostrenko, Jochen Hampe, Lutz Brusch
SCIENTIFIC REPORTS
(2019)
