IMSB News

The group was one of 19 labs across ETH Zurich to be certified in the LEAF pilot project.

Jonas started his PhD in the group in December, working on protein phosphorylation and post-translational modifications in E. coli. Welcome back Jonas, and viel Erfolg!

The SCS Simon-Widmer Award honors distinguished scientists for their contribution to fundamental and applied analytical science and the education of analytical scientists.

Vilhelmiina starts in January to work on microbial interactions in seawater communities. Good luck Vilhelmiina!

 Daniela won the best poster award at the "EMBO:Multiomics to Mechanisms symposium." Congratulations Daniela!

Evgeniya successfully denfended her PhD thesis on phosphoregulation in coordinating E. coli metabolism. Congratulations Evgeniya!

Karin successfully defended her PhD thesis on "Microbial metabolism along the digestive tract and identification of regulatory mechanisms". Congratulations Karin!

Congrats Evgeniya for winning the best talk award at the 4th International conference on post-translational modifications in Bacteria (https://www.sysbio.se/ptmbact2020/).

Daniela won the best poster award at the EMBO:Multiomics to Mechanisms symposium (https://blogs.embl.org/events/2021/10/14/multiomics-to-mechanisms-best-poster-awards/). Congratulations Daniela! 

Chris Gruber won the best poster prize at the first in person conference (Quantitative Modeling of Cell Metabolism in Kopenhagen) this year. Congrats Chris!

Julian recently joined the Sauer group and will be developing experimental approaches for systematic determination of metabolite inputs into transcriptional regulatory networks and characterize the regulatory programs dictating metabolic shifts.  

Philipp succesfully defended his PhD thesis titled: "Towards connecting membrane organisation and cellular homeostasis in prokaryotes by lipidomics". Congratulations to Philipp and wishes of success in future challenges.  

A joint paper from the Basan, Hwa, Paulsson, and Sauer labs reports how rapid microbial growth in one condition compromises the ability to quickly switch to new conditions. This remarkably conserved tradeoff emerges directly from the biochemistry of central metabolism and can mathematically predict broadly disparate growth rates on different substrates. 

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The IMSB labs of Paola Picotti, Uwe Sauer and Mattia Zampieri are part of the just granted National Center of Competence in Research to fight antibiotic-resistant bacteria (NCCR AntiResist). It is a collaboration with colleagues at the Biozentrum and University Hospital Basel and the ETH Department of Biosystems in Basel. The aim is to find new antibiotics and develop alternative strategies to combat antibiotic-resistant bacteria by linking basic research directly with clinical research.

Microbes need to coordinate utilization of nutrients but the triggering signals remain unclear. A recent "Nat Comm" paper by the Zampieri & Sauer groups (IMSB) developed a computational approach to identify the intracellular signals that prioritize amino acid over glucose degradation from dynamic exo-metabolome data.

In a joint collaboration, researchers from Denmark and Sauer Group at IMSB have shown that bacteria produce a specific stress molecule, divide more slowly, and thus save energy when they are exposed to antibiotics. The new knowledge is expected to form the basis for development of a new type of antibiotics.

Whether dormant bacteria begin to reproduce is no accident. Rather, they are simply waiting for a clear signal from a single protein in the cell interior. The Sauer lab have now deciphered the molecular mechanisms behind this.

We are honored and proud to announce that George Rosenberger (Aebersold lab), Daniel Sévin (Sauer lab), and Andreas Kühne (Zamboni lab) won the prestigious ETH Silver Medal for Oustanding Doctoral Theses. Congratulations!  

Duncan Holbrook-Smith won a prestigious HFSP scholarship for his postdoc project at the Sauer lab, on exploiting non-targeted metabolomics for parallelized discovery of chemical probes for receptor-like proteins, and using those chemical probes to better understand the specific roles of receptor-like proteins in that system. Now he has the problem of deciding which fellowship to accept………

Michael Zimmermann and Paul Murima won the Swiss TB 2017 Award for their Nature Communications paper "A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria." CONGRATULATIONS!

How do gene (knock-outs) affect metabolite levels? We tested this systematically for > 3'800 genes in E. coli and found several suprises.

About 15'000 high-throughput, non-targeted metabolomics analyses were acquired to study >1'200 functionally uncharacterized proteins. The study was just published by Daniel Sévin and co. in Nature Methods.

Congratulations!

The subject of his massive work was "Development and application of graph-based computational methods to elucidate the functional role of metabolism in human skin". Congratulations!

We congratulate Daniel for his work on "Nontargeted metabolomics appraoches for enzyme discovery and high-resolution metabolome profiling"

In collaboration with the Sauer lab, Mercedes Gomez de Agüero and Stephanie C. Ganal-Vonarburg from the Maurice Müller Laboratories (DKF), University of Bern, describe in detail how in gestating mice, the mother’s community of microbes shapes the immune system of the offspring.

The Sauer Lab developed an experimental-computational approach to identify regulatory needles in metabolic haystacks. By using steady-state ¹³C flux, metabolites and transcript data, the approach revealed the sparse and transition-dependent regulators that drive transitions between carbon sources in Escherichia coli. Thus, pseudo-transition analysis is a novel approach to efficiently explore the vast regulatory landscape of dynamic adaptations using relatively few stationary observations.

In a collaborative effort of the Sauer and Zamboni labs at IMSB and the Berry Lab at NIH, Michael and his co-workers integrated dynamic changes in the secretion and uptake of metabolites with genome-scale metabolic network reconstructions and identified active metabolic routes necessary for mycobacteria survival under hypoxic conditions.

The Zamboni and Sauer Lab developed a platform for real-time metabolome profiling by directly injecting living bacteria, yeast or higher cell suspensions into a high-resolution time-of-flight mass spectrometer. We congratulate Hannes and all the coauthors.

In a review published in "Current opinion in Microbiology“, we discuss the division-of-labor between the different regulatory layers in making microbial metabolic decisions, and highlight the current challenges we are facing when elucidating the role of posttranslational regulation.

In collaboration with the Sauer lab, Hai Li & Julien P. Limenitakis from the Maurice Müller Laboratories (DKF), University of Bern, describe in detail the compositional differences between lumen and outer mucus layer of the intestine in mice and its consequence for the present microbiota.

In collaboration with the Sauer lab, Pablo Ivan Nikel from the Centro Nacional de Biotecnologia (CNB-CSIC, Spain), describes a cyclic operation of the pentose phosphate, Entner-Doudoroff and glycolytic pathways in Pseudomonas putida.

In two related dynamic omics studies, researchers from the Aebersold and Sauer lab identified causal metabolic signals and functionality of protein phosphorylation in TOR signaling.

Tobias Fuhrer and Uwe Sauer lab contributed to the study lead by Manuel Cánovas (Uni. de Murcia, Spain). 

Large-scale study published by the Sauer Lab in collaboration with Christian von Meering (Uni Zurich)  

We congratulate and thank Daniel and Andreas for assembling this criticial review.

An interview to Prof. Uwe Sauer published in the SystemsX.ch newsletter

Congratulations!

We congratulate the Hall lab (Biozentrum Basel) and the Lavigne/Briers group (KU Leuven)

Welcome!

Daniel Sévins wins 1 (out of 5) awards at the D-BIOL 2014 symposium in Davos.

In collaboration with the Sauer lab, researcher from Dundee and Singapore University investigated mammalian cell size related differences in cytoskeletal and mitochondrial gene expression as well as in lipid and mitochondrial metabolism.

The Sauer Lab characterized metabolism under starvation conditions in two model bacteria, with one eye on ecology and one eye on biotechnology.

Alpha-Keto acids (e.g. glyoxylate, oxaloacetate, pyruvate, ...) are highly reactive and thus unstable compounds. We established a new method for in situ stabilization and quantification by mass spectrometry. The technique also allows determination of labeling patterns.

The Sauer Lab reviewed and delineated general principles of metabolic regulation by comparing the microbial model organisms E. coli, B. subtilis and S. cerevisiae.

People from the Sauer group wrote a review about computational models of metabolism. The focus was on models that include reaction kinetics in order to simulate dynamics of metabolic networks. The finding is that such models experience a paradigm shift away from fitting parameters towards identifying key regulatory interactions.

Using a novel metabolomics method, the Sauer group discovered a previously unknown mechanism bacteria use to cope with osmotic stress.

The Zamboni lab demonstrated and applied a method for selective and yet non-targeted profiling of Coenzyme A derivatives in cellular extracts

Daniel received a Nature Reviews Microbiology Poster Award at the EMBO Symposium: New Approaches and Concepts in Microbiology in Heidelberg

Congratulations!!

at the Conference from Genomes to Systems in Heidelberg

Daniel Sévin won a Prize for Best Master Thesis by the University of Mannheim for his work done in the Sauer Lab. Congratulations!

An ETH Silver medal was awarded to Jörg Büscher for his PhD Thesis under the supervision of Prof. U. Sauer

at the FEBS Advanced Course in Systems Biology in Innsbruck