Reconstructing organisms in silico: genome-scale models and their emerging applications

X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Oxidative stress and antioxidants in age-related macular degeneration

N Kushwah, K Bora, M Maurya, MC Pavlovich, J Chen - Antioxidants, 2023 - mdpi.com
Oxidative stress plays a crucial role in aging-related eye diseases, including age-related
macular degeneration (AMD), cataracts, and glaucoma. With age, antioxidant reparative …

Genome-scale metabolic modeling enables in-depth understanding of big data

A Passi, JD Tibocha-Bonilla, M Kumar, D Tec-Campos… - Metabolites, 2021 - mdpi.com
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …

Effects of electrolysed water combined with ultrasound on inactivation kinetics and metabolite profiles of Escherichia coli biofilms on food contact surface

L Zhao, CN Poh, J Wu, X Zhao, Y He, H Yang - Innovative food science & …, 2022 - Elsevier
This study aimed to better understand the overall metabolic responses of Escherichia coli
biofilms to the combined stresses of ultrasound and low concentration acidic electrolysed …

Crossroads in the evolution of plant specialized metabolism

TP Rieseberg, A Dadras, JMR Fürst-Jansen… - Seminars in Cell & …, 2023 - Elsevier
The monophyletic group of embryophytes (land plants) stands out among photosynthetic
eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety …

Neurotoxicity of MDMA: main effects and mechanisms

G Costa, K Gołembiowska - Experimental neurology, 2022 - Elsevier
Preclinical and clinical studies indicate that 3, 4-methylenedioxymethamphetamine
(MDMA;'ecstasy'), in addition to having abuse potential, may elicit acute and persistent …

Microbiome re-assembly boosts anaerobic digestion under volatile fatty acid inhibition: focusing on reactive oxygen species metabolism

M Yan, Z Hu, Z Duan, Y Sun, T Dong, X Sun, F Zhen… - Water Research, 2023 - Elsevier
The accumulation of volatile fatty acids (VFAs) in anaerobic digestion (AD) systems resulting
from food waste overload poses a risk of system collapse. However, limited understanding …

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

K Rychel, K Decker, AV Sastry, PV Phaneuf… - Nucleic acids …, 2021 - academic.oup.com
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a
powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons) …

Effects of BPA, BPS, and BPF on oxidative stress and antioxidant enzyme expression in bovine oocytes and spermatozoa

M Nguyen, R Sabry, OS Davis, LA Favetta - Genes, 2022 - mdpi.com
Bisphenol A (BPA) and its analogs, bisphenol S (BPS) and bisphenol F (BPF), might impact
fertility by altering oxidative stress pathways. Here, we hypothesize that bisphenols-induced …

[HTML][HTML] Strategies to increase tolerance and robustness of industrial microorganisms

MT Mohedano, O Konzock, Y Chen - Synthetic and Systems Biotechnology, 2022 - Elsevier
The development of a cost-competitive bioprocess requires that the cell factory converts the
feedstock into the product of interest at high rates and yields. However, microbial cell …