Lab News

An integrative view on how metabolic fluxes sustain growth of liver cancer cells

Jurgen Haanstra and Bas Teusink collaborated with several research groups on interdisciplinary research combining wetlab experiments with computational models. Haanstra and Teusink collaborated with research groups in Gothenburg (Sweden), Groningen and Heidelberg (Germany). Their work on a quantitative analysis of amino acid metabolism in liver cancer, with Jurgen as co-first author, was just published in

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Standardising the quality of genome scale models

Moritz Bieber, Christian Lieven (Biosustain, DTU), Brett Olivier and Bas Teusink (AIMMS, VU Amsterdam) and a worldwide community of scientists developed quality control tools for systems biology models in Nature Biotechnology Mathematical models are key tool to understand complex biological systems. In particular, constraint-based, genome scale, models (GSM’s) can relate the physiological property of a

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Herwig and Chrats gave a science talk in a bar

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Photo competition 2019

The winning photograph and his creator.

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Fifteen different models of overflow metabolism convey a single message: overflow metabolism is caused by two growth-limiting constraints.

We recently published an article in which we reviewed the different approaches that describe a puzzling metabolic phenomenon called overflow metabolism: (https://doi.org/10.1007/s00018-019-03380-2). Many different organisms secrete ‘overflow products’ in conditions where they grow and reproduce fast. For example, many yeasts produce ethanol, Escherichia coli produces acetate, and cancer cells produce lactate. This behaviour seems counter-intuitive

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Change of the section Name

The System Bioinformatics section has a new name and from now on will be known as: Systems Biology Lab

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In press: Sebastián’s meticulous comparison of genome-scale metabolic reconstruction tools is published!

A genome-scale metabolic reconstruction is a network of all biochemical reactions that can occur in a cell. These reconstructions have proven to be very useful because they can be used to make phenotypic predictions. Many computational tools to create these reconstructions have been created (or updated) recently, making these genome-scale reconstructions available for everyone. However,

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Daan and NWA-Ideeëngenerator

Systeembioinformaticus Daan de Groot met Self-organising adaptation: a universal mechanism for microbial protein expression regulation Cellen kunnen zich aanpassen aan, en groeien in, een verbluffende hoeveelheid omgevingen. Dit lijkt, gezien de eenvoud van individuele cellen, een onmogelijke prestatie. Maar hoe zit dit als een populatie cellen gaat samenwerken? De onderzoekers stellen een universeel mechanisme voor

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Chrats published 2 papers

Two papers were recently published by Chrats about microbial communities. In the first paper, the authors show how microbial communities change during wine fermentations, what are the differences in microbial composition between vineyards and which ones are the species that are present during problematic fermentations. In the second paper, which is a first-authorship for Chrats,

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Paul published a review

JBAH-Vol.9 No.10 2019.pdf Journal of Biology, Agriculture and Healthcare www.iiste.org Vol.9, No.10, 2019 From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation Abstract Molecular ecology researches are rapidly advancing the knowledge of microorganisms associated with petroleum hydrocarbon degradation, one of the major large-scale pollutants in terrestrial ecosystems. The design and monitoring of bioremediation

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