Toward a systematic design of smart probiotics

R Choudhary, R Mahadevan - Current Opinion in Biotechnology, 2020 - Elsevier
Synthetic biology has been instrumental in turning microbes into cell-factories capable of
diverse processes. A recent application has been to convert them into living therapeutics …

Noise propagation in synthetic gene circuits for metabolic control

DA Oyarzun, JB Lugagne, GBV Stan - ACS synthetic biology, 2015 - ACS Publications
Dynamic control of enzyme expression can be an effective strategy to engineer robust
metabolic pathways. It allows a synthetic pathway to self-regulate in response to changes in …

[HTML][HTML] Mathematical modeling of atopic dermatitis reveals “double-switch” mechanisms underlying 4 common disease phenotypes

E Domínguez-Hüttinger, P Christodoulides… - Journal of Allergy and …, 2017 - Elsevier
Background The skin barrier acts as the first line of defense against constant exposure to
biological, microbial, physical, and chemical environmental stressors. Dynamic interplay …

Synthetic gene circuits for metabolic control: design trade-offs and constraints

DA Oyarzún, GBV Stan - Journal of the Royal Society …, 2013 - royalsocietypublishing.org
A grand challenge in synthetic biology is to push the design of biomolecular circuits from
purely genetic constructs towards systems that interface different levels of the cellular …

A theoretical study of lipid accumulation in the liver—Implications for nonalcoholic fatty liver disease

J Schleicher, R Guthke, U Dahmen, O Dirsch… - … et Biophysica Acta (BBA …, 2014 - Elsevier
A hallmark of the nonalcoholic fatty liver disease is the accumulation of lipids. We developed
a mathematical model of the hepatic lipid dynamics to simulate the fate of fatty acids in …

Mathematical Modeling of Streptococcus pneumoniae Colonization, Invasive Infection and Treatment

E Domínguez-Hüttinger, NJ Boon, TB Clarke… - Frontiers in …, 2017 - frontiersin.org
Streptococcus pneumoniae (Sp) is a commensal bacterium that normally resides on the
upper airway epithelium without causing infection. However, factors such as co-infection …

Hybrid models of genetic networks: Mathematical challenges and biological relevance

L Glass, R Edwards - Journal of theoretical biology, 2018 - Elsevier
We review results concerning dynamics in a class of hybrid ordinary differential equations
which incorporates logical control to yield piecewise linear equations. These equations …

Dynamics of complex feedback architectures in metabolic pathways

M Chaves, DA Oyarzún - Automatica, 2019 - Elsevier
Cellular metabolism contains intricate arrays of feedback control loops. These are a key
mechanism by which cells adapt and survive environmental disturbances. Gene regulation …

Maintaining maximal metabolic flux by gene expression control

R Planqué, J Hulshof, B Teusink… - PLOS Computational …, 2018 - journals.plos.org
One of the marvels of biology is the phenotypic plasticity of microorganisms. It allows them to
maintain high growth rates across conditions. Studies suggest that cells can express …

Design of a bistable switch to control cellular uptake

DA Oyarzún, M Chaves - Journal of The Royal Society …, 2015 - royalsocietypublishing.org
Bistable switches are widely used in synthetic biology to trigger cellular functions in
response to environmental signals. All bistable switches developed so far, however, control …