Zoom Celebration

Zoom Celebration at SysBioLab. 

Zoom screen shot

Rinke has a tenure track position in Delft, Bas got a new project granted, and Frank published a massive paper in Current Biology together with Johan, all on the same (Mon)day.

With such good news it is time to celebrate! Lets open the bottle (that will be delivered to you today) together.

Enjoy and stay healthy! Rinke, Bas and Frank

On behalf of all of us, Congratulations and thank you for the surprise.

A special thanks goes to the delivery boy! Thanks for bringing it to us.

Paper by Niclas, Johan and Frank

Biphasic Cell-Size and Growth-Rate

Homeostasis by Single Bacillus subtilis Cells

Abstract

The growth rate of single bacterial cells is continuously disturbed by random fluctuations in biosynthesis rates and by deterministic cell-cycle events, such as division, genome duplication, and septum formation. It is not understood whether, and how, bacteria reject these growth-rate disturbances. Here, we quantified growth and constitutive protein expression dynamics of single Bacillus subtilis cells as a function of cell-cycle progression. We found that, even though growth at the population level is exponential, close inspection of the cell cycle of thousands of single Bacillus subtilis cells reveals systematic deviations from exponential growth. Newborn cells display varying growth rates that depend on their size. When they divide, growth-rate variation has decreased, and growth rates have become birth size independent. Thus, cells indeed compensate for growth-rate disturbances and achieve growth-rate homeostasis. Protein synthesis and growth of single cells displayed correlated, biphasic dynamics from cell birth to division. During a first phase of variable duration, the absolute rates were approximately constant and cells behaved as sizers. In the second phase, rates increased, and growth behavior exhibited characteristics of a timer strategy. These findings demonstrate that, just like size homeostasis, growth-rate homeostasis is an inherent property of single cells that is achieved by cell-cycle-dependent rate adjustments of biosynthesis and growth.

Read the whole paper

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 PNAS.

Metabolic changes are a well-known hallmark of cancer, but an integrative view on how metabolic fluxes sustain (high) growth rates is often lacking. In this study the authors used a combination of experimental measurements and computational modelling to understand metabolism of HepG2 liver cancer cells during in vitro growth at different glucose levels.  The measured fluxes of glucose, pyruvate, lactate and amino acids during growth were integrated with a genome-scale reconstruction of liver cancer metabolism to estimate the intracellular metabolic fluxes that should be operational to sustain this growth.

The analysis published in PNAS shows that many amino acids are consumed at rates exceeding the need for biomass formation. The intracellular fluxes indicate that a large part of the glutamine that is consumed is metabolised in the cytosol to support biosynthetic processes. A large part of the glutamate that results from these processes is excreted. This led to the hypothesis that inhibition of glutamate export would decrease growth and this was validated in an experiment where glutamate export was inhibited.

The work shows that genome-scale metabolic models constrained with measured fluxes can be used to estimate the effects of inhibitors of metabolic reactions.

Herwig and Chrats gave a science talk in a bar

On the 11th of February Herwig and Chrats embraced the challenge of talking to a non-scientific audience in an event hosted by Pint of Science. In their enthusiastic talks they explained how microbial communities and particular species contribute to the process of cheese and wine making, and how do scientists achieve distinct final products by using different combinations of microbes. The atmosphere was casual and Herwig and Chrats were impressed by the originality of the questions they got! Besides their talks, there was a cheese and wine tasting activity very much appreciated by the audience that now knows better how to select their perfect cheese/wine. The event was a great success!

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 dat een populatie cellen in staat stelt te overleven, maar waar individuele cellen zouden falen.

Vijf VU-projecten ontvangen uit het NWA-programma (Nationale Wetenschapsagenda) Ideeëngenerator ieder een financiering van 50.000 euro voor de looptijd van één jaar om hun idee verder te onderzoeken.

https://vunet.login.vu.nl/actual/pages/News/newsdetail.aspx?cid=tcm:164-917436-16&showTranslationError=1

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 techniques for hydrocarbons rely on a thorough understanding of the diversity of enzymes involved in the processes of hydrocarbon degradation and the microbes that harbor their allocated genes. This review describes the impact of hydrocarbon pollution on soil microbial communities, the state of the art of detecting functional genes, and functional groups. We will focus on i) the structure, function and succession behavior of microbial communities exposed to hydrocarbons, ii) key genes and pathways, iii) future prospect into bioremediation of petroleum hydrocarbons in aerobic environments. The aim is to get a fundamental insight in these issues to ultimately improve petroleum hydrocarbons bioremediation.

Julia wins photo competition at the End-of-Summer drinks.

Although the weather still gives the idea that summer didn’t end yet, we had end-of-summer drinks last week. It was a nice get-together and many people joined for a drink and a chat.. The drinks were accompanied by a photo competition with 21 entries. During the drinks the photos were hanging on the wall for the participants to judge which photo stood out most and should win a prize. Ten pictures got at least one vote, but there was a clear winner: Julia’s picture of a duck in Leiden got 7 votes and made her the winner of our competition. She won a 500-piece puzzle of an image of of O|2. Congratulations!

After the voting, lively discussions arose on who had sent in which picture. As the pictures were a clear added value to the first-floor balcony, they were still there by the end of the week – and remained a talking point.