Publications related to Saccharomyces

Modeling, analysis, and design of complex biological networks

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

The N-Terminal Region of Yeast Protein Phosphatase Ppz1 Is a Determinant for Its Toxicity

Maria Lopez Malo

The Ppz enzymes are Ser/Thr protein phosphatases present only in fungi that are characterized by a highly conserved C-terminal catalytic region, related to PP1c phosphatases, and a more divergent N-terminal extension. In Saccharomyces cerevisiae, Ppz phosp ...

MDPI2020

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Vassily Hatzimanikatis, Sofia Tsouka

Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...

2020

Adaptive damage retention mechanism enables healthier yeast population

Riccardo Dainese

During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replica ...

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD2019

Labor division in engineered cross-kingdom consortia: Consolidated bioprocessing of lignocellulosic biomass to carboxylic acids

Robert Lawrence Shahab

Lignocellulose is a renewable source of fixed carbon and a promising substrate for the production of chemicals and fuels in second generation biorefineries. In this thesis, we engineered artificial microbial consortia for consolidated bioprocessing (CBP) o ...

EPFL2019

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh

Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic ...

2017

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Vassily Hatzimanikatis, Paolo Angelino, Howard Riezman, Georgios Savoglidis

We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the met ...

Academic Press Inc Elsevier Science2016

Castles fall from inside: Evidence for dominant internal photo-catalytic mechanisms during treatment of Saccharomyces cerevisiae by photo-Fenton at near-neutral pH

César Pulgarin, Sami Rtimi, Stefanos Giannakis, Cristina del Socorro Lonfat

In this work, the antimicrobial effects of the photo-Fenton process on yeast cells were tested (Saccharomyces cerevisiae), an essential eukaryotic unicellular model of living cells. Near-neutral pH was used in all studies, while iron sulfate and iron citra ...

Elsevier2016

Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species

Benjamin Marcel Daniel Rothé

Box C/D small nucleolar ribonucleoparticles (snoRNPs) support 2'-O-methylation of several target RNAs. They share a common set of four core proteins (SNU13, NOP58, NOP56, and FBL) that are assembled on different guide small nucleolar RNAs. Assembly of thes ...

Cell Press2016

Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis

Fabrice David, Howard Riezman, Manuele Piccolis

The regulatory pathways required to maintain eukaryotic lipid homeostasis are largely unknown. We developed a systematic approach to uncover new players in the regulation of lipid homeostasis. Through an unbiased mass spectrometry-based lipidomic screening ...

Amer Soc Cell Biology2014

Replication of Telomeres and the Regulation of Telomerase

Joachim Lingner, Verena Pfeiffer

Telomeres are the physical ends of eukaryotic chromosomes. They protect chromosome ends from DNA degradation, recombination, and DNA end fusions, and they are important for nuclear architecture. Telomeres provide a mechanism for their replication by semico ...

Cold Spring Harbor Lab Press, Publications Dept2013

Telomeric Repeat Containing RNAs and the Response to Telomere Deprotection in Saccharomyces Cerevisiae

Andrea Bernardo Panza

Telomeres are the DNA/RNA/protein structures at the end of linear eukaryotic chromosomes, which protect them against the DNA damage repair machinery, preventing chromosome end-to-end fusions and aberrant recombination. Moreover, telomeres compensate for th ...

EPFL2012

GTPase Activity Plays a Key Role in the Pathobiology of LRRK2

Darren Moore

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are associated with late-onset, autosomal-dominant, familial Parkinson's disease (PD) and also contribute to sporadic disease. The LRRK2 gene encodes a large protein with multiple domains, includin ...

Public Library of Science2010

Data Reconciliation of Concentration Estimates from Mid-Infrared and Dielectric Spectral Measurements for Improved On-Line Monitoring of Bioprocesses

Dominique Bonvin, Urs von Stockar, Ian William Marison, Michael Amrhein, Michal Dabros

Real-time data reconciliation of concentration estimates of process analytes and biomass in microbial fermentations is investigated. A Fourier-transform mid-infrared spectrometer predicting the concentrations of process metabolites is used in parallel with ...

2009

Related mechanisms for end processing at telomeres and DNA double-strand breaks

Joachim Lingner, Nahid Iglesias

In a recent issue of Molecular Cell, Bonetti et al. (2009) identify in the yeast Saccharomyces cerevisiae that the molecular activities that generate 3' overhangs at telomeric DNA ends are the same as those that resect DNA at double-strand breaks. ...

2009

Functional differentiation of tbf1 orthologues in fission and budding yeasts

Viesturs Simanis, Elena Cano

In Saccharomyces cerevisiae, TBF1, an essential gene, influences telomere function but also has other roles in the global regulation of transcription. We have identified a new member of the tbf1 gene family in the mammalian pathogen Pneumocystis carinii. W ...

2009

Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense mediated mRNA decay

Joachim Lingner

The Smg proteins Smg5, Smg6 and Smg7 are involved in nonsense-mediated RNA decay (NMD) in metazoans, but no orthologs have been found in the budding yeast Saccharomyces cerevisiae. Sequence alignments reveal that yeast Ebs1p is similar in structure to the ...

2007

Functional characterization of Pneumocystis carinii brl1 by transspecies complementation analysis

Viesturs Simanis

Pneumocystis jirovecii is a fungus which causes severe opportunistic infections in immunocompromised humans. The brl1 gene of P. carinii infecting rats was identified and characterized by using bioinformatics in conjunction with functional complementation ...

2007

On-Line Recalibration of Spectral Measurements Using Metabolite Injections and Dynamic Orthogonal Projection

Urs von Stockar, Michael Amrhein, Michal Dabros, Pamandeep Singh Gujral

Spectrometers are enjoying increasing popularity in bioprocess monitoring due to their non-invasiveness and in-situ sterilizability. Their on-line applicability and high measurement frequency create an interesting opportunity for process control and optimi ...

2007

Development of a new reporter system for the detection of protein-protein interactions in living cells

Petra Tafelmeyer

Split-protein sensors have become an important tool for the analysis of protein-protein interactions in living cells. In general, two interacting proteins are expressed as fusion proteins with a pair of inactive fragments of a reporter enzyme. Interaction- ...

EPFL2004