Publications related to Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

The impact of different methods of increasing the intensity of compassion in engineering ethics cases

Roland John Tormey, Nihat Kotluk

Despite the growing interest in emotions in engineering education, empirical research on incorporating them into engineering ethics education is limited. Therefore, we designed this experimental study to assess how different methods for integrating compass ...

2024

“But of course i’m going to look happy” or “He needed to know I was angry”? Comparing use of emotional labour in teamwork in engineering and hospitality students

Roland John Tormey, Nihat Kotluk

Being able to work effectively in a team is a vital professional skill but how do students in different disciplines, engineering and hospitality, display their emotions when working together? We investigated their self-reported use of emotional labour stra ...

EAPRIL - European Association for Practitioner Research on Improving Learning2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

First-principles thermodynamics of precipitation in aluminum-containing refractory alloys

Anirudh Raju Natarajan

Materials for high -temperature environments are actively being investigated for deployment in aerospace and nuclear applications. This study uses computational approaches to unravel the crystallography and thermodynamics of a promising class of refractory ...

Pergamon-Elsevier Science Ltd2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

The magnet feeders for the European DEMO fusion reactor: Conceptual design and recent advances

Rainer Wesche, Frédéric Michel, Roberto Guarino

The magnet feeders are part of the critical systems of a fusion reactor since they represent the interface between the in-cryostat components at 4.5 K and the room-temperature cryogenic plant and power supply. The European DEMO tokamak foresees 16 toroidal ...

2024

Mean-field transport equations and energy theorem for plasma edge turbulent transport

Reinart Andreas J. Coosemans

This paper establishes a mean-field equation set and an energy theorem to provide a theoretical basis in view of the development of self-consistent, physics-based turbulent transport models for mean-field transport codes. A rigorous averaging procedure ide ...

Cambridge University Press2024

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

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

Educating Engineering Students to Address Bias and Discrimination Within Their Project Teams

Siara Ruth Isaac, Roland John Tormey, Nihat Kotluk

What training should engineering students receive to enable them to contribute to reducing bias, discrimination and the persistent lack of diversity in engineering? Collaboration is central to professional engineering work and, consequently, teamwork and g ...

2023

Engineering Materials for Neurotechnology

Diego Ghezzi

Neurotechnology applies methods and devices to mitigate the burden of neurological and mental disorders. In particular, neural interfaces establish a long-term, seamless, symbiotic integration between implants and neural tissue. Materials play a pivotal ro ...

WILEY-V C H VERLAG GMBH2023

Compassion and Engineering Students’ Moral Reasoning: The Emotional Experience of Engineering Ethics Cases

Roland John Tormey, Nihat Kotluk

Background: There has been an increase in interest in emotion in engineering and science ethics education. There is also evidence that emotional content in case studies may improve students’ learning and enhance awareness, understanding, and motivation con ...

American Society for Engineering Education2023

Emotional labor experienced in team-projects: A comparison of engineering and hospitality students

Roland John Tormey, Nihat Kotluk

Team projects are an integral part of the student learning experience. However, emotions can significantly affect student performance during team projects. Students use different emotion regulation strategies, such as surface-acting (emotive dissonance) an ...

2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Christel Sybille Hassler

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at l ...

SPRINGERNATURE2023