Lab News

Bacteria grow in communities of many co-occurring species in , e.g., in your gut, in soil, or in the ocean. A fundamental process in these communities (more specifically, communities of heterotrophic bacteria, i.e., bacteria that utilize organic carbon sources) is that bacteria take up substrates (basically, food) like sugars and amino acids from the environment

A custom of our lab is to start the academic year with a state-of-the-union day at the Hortus Botanicus of Amsterdam. During this day, the PIs give an research overview of the last year, an outlook on the coming year, current duties, and their long-term research vision in the presence of the research (support) staff

Together with Ralf Steuer (Humboldt-University of Berlin, Germany) we recently wrote a review for Bioessays, see https://doi.org/10.1002/bies.202300015. It addresses how we currently view the consequences of finite biosynthetic resources (for protein expression) for cellular tasks such as stress tolerance, growth and adaptation to new conditions. We focus on Escherichia coli and Saccharomyces cerevisiae. We acknowledge

In primate species, a change in lifestyle leads to adjustments in their microbiome. What does this mean?  Over the last years, ARTIS Micropia Professor Remco Kort and his Bioinformatics & Systems Biology student Isabel Houtkamp studied the faeces of the western lowland gorilla. They did this by comparing the composition of the microbiome of the ARTIS gorillas

A new network of over 72 organizations from 12 countries was activated during a convening at ARTIS in Amsterdam on 26–27 September 2022, organized by Remco Kort. Representatives are aligned with the transdisciplinary field and social movement of Planetary Health, which analyzes and addresses the impacts of human disruptions to natural systems on human health

Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex

From June 21-23, Frank is teaching a course at the TU Delft on enzyme kinetics and dynamic models of metabolism. The course information, e.g. the syllabus, can be found here Course information From Enzyme Kinetics to Models of Metabolism.

PhD candidate Maarten Droste is one of the recipients of the famous Red Sock Award for best poster presentation at the SIAM 2023 Conference on Applications of Dynamical Systems in Portland, Oregon. It is a tradition that each prize winner receives a pair of red socks as part of the award. His winning poster, entitled “Determinants of optimal metabolic pathway choice by microorganisms”, is co-authored

After a few years break, finally it was again time for a lab outing. In the lovely setting of Berg en Dal, we enjoyed three days (April 19th-21st) of networking and conviviality. “Mens sana, in corpore sano” they say, so we stretched both our muscles, with plenty of biking, jeu de boules, ping pong and football, and

We combined our expertise in Gene expression regulation, Single-molecule RNA imaging, and Prokaryotic quantitative cell physiology to write a truly multidisciplinary review. It’s the product of a team effort by Alan Gerber (Amsterdam UMC), Sander van Otterdijk (Sysbio),  Frank Bruggeman (Sysbio) and Evelina Tutucci (Sysbio). We discussed state-of-the-art imaging approaches for the measurement and quantitative