Lab News

How genetic circuits can optimally tune metabolic protein concentrations

Since cells have finite biosynthetic resources for protein synthesis, a rise in one protein concentration is generally at the expense of that of others. A logical consequence is then that phenotypic traits trade-off: cells cannot excel at everything. They cannot grow fast and be very stress tolerant and adaptive to new conditions at the same

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Our take on the practical aspects of genome-scale modeling

Some time ago, we started an initiative in the lab to collect all the best (and worst) practices on how to reconstruct, curate, and simulate genome-scale metabolic models (GEMs). A total of 7 colleagues, including a visiting PhD student Gioele Lazzari from the University of Verona, and a MSc rotation student Steven Wijnen, have put

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Our research featured in Quanta Magazine

Microbiologists are searching for a universal theory of how bacteria form communities based not on their species but on the roles they play. A new article in the popular science magazine Quanta has highlighted our work on metabolic preferences and their genomic markers. How can we identify rules of microbial communities? What are the traits

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Herwig to lead €5M NWO Perspective Grant Consortium for plant-based fermentations

The Netherlands Organisation for Scientific Research (NWO) granted the FERMI Perspective proposal led by Herwig Bachmann from the Systems Biology Lab. The project aims to accelerate the protein transition by improving the taste of plant-based products through fermentation by microbes. With colleagues from the Wageningen University and TU Delft and 10 industrial partners, the project

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We wrote a paper for a special issue celebrating the 50th anniversary of Metabolic Control Analysis

Which metabolic enzymes should a cell change in concentration to give rise to a large change in steady-state metabolic flux? Which enzymes should an experimentalist inhibit to reduce the flux the most? Why are some kinase-phosphatase couples in cellular signal transduction ultra-sensitive to changes in signals, while others are not? What is the function of

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New paper: Genome content predicts the metabolic preferences of bacteria

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

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State of the union of the lab at the Hortus Botanicus

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

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A perspective on physiological trade offs and finite resources for protein-expression

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

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New paper: Lifestyle influences microbiome

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

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Summary of Planetary Health meeting published

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

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