Publications related to Metabolic theory of ecology

Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms

Christof Holliger, Julien Maillard, Romain Hamelin, Mathilde Stéphanie Willemin, Florence Armand

IntroductionDesulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy meta ...

Frontiers Media SA2023

Seeing the forest for the trees through metabolic scaling

Andrea Rinaldo, Amos Maritan

We demonstrate that when power scaling occurs for an individual tree and in a forest, there is great resulting simplicity notwithstanding the underlying complexity characterizing the system over many size scales. Our scaling framework unifies seemingly dis ...

2022

Constraint-based metabolic control analysis for rational strain engineering

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

Theory-based scaling laws of near and far scrape-off layer widths in single-null L-mode discharges

Paolo Ricci, Holger Reimerdes, Jan Horacek, Cedric Kar-Wai Tsui, Maurizio Giacomin, Adriano Stagni

Theory-based scaling laws of the near and far scrape-off layer (SOL) widths are analytically derived for L-mode diverted tokamak discharges by using a two-fluid model. The near SOL pressure and density decay lengths are obtained by leveraging a balance amo ...

IOP Publishing Ltd2021

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Vassily Hatzimanikatis, Sofia Tsouka

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

EPFL2020

Modeling biochemical reaction networks in complex intracellular environments

Daniel Robert Weilandt

Whether one aims to design treatments for diseases such as cancer or diabetes, engineer cells to produce valuable biochemicals sustainably, or to grasp the behavior of living organisms, it is essential to understand how cells react to genetic, environmenta ...

EPFL2020

Allometric Scaling of physiologically-relevant organoids

Andrea Rinaldo

The functional and structural resemblance of organoids to mammalian organs suggests that they might follow the same allometric scaling rules. However, despite their remarkable likeness to downscaled organs, non-luminal organoids are often reported to posse ...

Nature Research2019

Scaling as a key conceptual tool for the interpretation of empirical and experimental patterns in ecology and biology

Silvia Zaoli

This thesis is concerned with regular patterns found in ecology and biology, their linkages and the statistical description of their fluctuations around average trends. Among such patterns, often conforming to power laws, well-known examples include the Sp ...

EPFL2018

Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral

Anders Meibom, Louise Helene Soegaard Jensen, Emma Mary Gibbin

Under homoeostatic conditions, the relationship between the coralPocillopora damicornisandVibrio coralliilyticusiscommensal. An increase in temperature, or in the abundance ofV. coralliilyticus, can turn this association pathogenic,causing tissue lysis, ex ...

2019

Nutritional Ketosis Increases NAD+/NADH Ratio in Healthy Human Brain: An in Vivo Study by 31P-MRS

Rolf Gruetter, Lijing Xin, Özlem Ipek, Mojgan Masoodi, Nicolas Christinat, Maya Shevlyakova

Ketones represent an important alternative fuel for the brain under glucose hypo-metabolic conditions induced by neurological diseases or aging, however their metabolic consequences in healthy brains remain unclear. Here we report that ketones can increase ...

2018

Covariations in ecological scaling laws fostered by community dynamics

Andrea Rinaldo, Andrea Giometto, Silvia Zaoli, Amos Maritan

Scaling laws in ecology, intended both as functional relationships among ecologically relevant quantities and the probability distributions that characterize their occurrence, have long attracted the interest of empiricists and theoreticians. Empirical evi ...

2017

Ecological strategies and metabolic trade-offs of complex environmental biofilms

Tom Ian Battin, Hannes Markus Peter

Microorganisms aggregated into matrix-enclosed biofilms dominate microbial life in most natural, engineered, and medical systems. Despite this, the ecological adaptations and metabolic trade-offs of the formation of complex biofilms are currently poorly un ...

Nature Publishing Group2017

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Vassily Hatzimanikatis

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how ...

Elsevier2017

Refined Analysis of Brain Energy Metabolism Using In Vivo Dynamic Enrichment of 13C Multiplets

Rolf Gruetter, Bernard Lanz, Nicolas Kunz, João Miguel das Neves Duarte, Masoumeh Dehghani Moghadam

Carbon-13 nuclear magnetic resonance spectroscopy in combination with the infusion of (13)C-labeled precursors is a unique approach to study in vivo brain energy metabolism. Incorporating the maximum information available from in vivo localized (13)C spect ...

Sage Publications Ltd2016

Association of PCK1 with Body Mass Index and Other Metabolic Features in Patients With Psychotropic Treatments

Pierre Magistretti, Aurélie Delacrétaz

Weight gain is a major health problem among psychiatric populations. It implicates several receptors and hormones involved in energy balance and metabolism. Phosphoenolpyruvate carboxykinase 1 is a rate-controlling enzyme involved in gluconeogenesis, glyce ...

Lippincott, Williams & Wilkins2015

Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS

Anders Meibom, Stéphane Laurent Escrig, Martin Ackermann

Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is u ...

Frontiers Media SA2015

Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum

Stepan Tymoshenko

Understanding of metabolism in disease-causing microorganisms promotes drug design through the identification of the enzymes whose activity is indispensable for important cellular functions of the pathogens. Nowadays such understanding arises from experime ...

EPFL2015

Capacity Scaling of Cognitive Networks: Beyond Interference-Limited Communication

Michael Christoph Gastpar

The capacity scaling laws of two overlaid networks are investigated, which are located in the same area sharing the same wireless resources with different priorities. The primary network can be regarded as an existing communication system operated in a lic ...

Institute of Electrical and Electronics Engineers2014

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti

Mathematical modeling is an essential tool for a comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possib ...

2013

Metabolic principles of river basin organization

Andrea Rinaldo

The metabolism of a river basin is defined as the set of processes through which the basin maintains its structure and responds to its environment. Green (or biotic) metabolism is measured via transpiration and blue (or abiotic) metabolism through runoff. ...

2011