Antibiotic resistance in Pseudomonas aeruginosa–Mechanisms, epidemiology and evolution

J Botelho, F Grosso, L Peixe - Drug resistance updates, 2019 - Elsevier
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate
use of these medicines has driven the dissemination of antibiotic resistance (AR) in most …

Epistasis and adaptation on fitness landscapes

C Bank - Annual Review of Ecology, Evolution, and Systematics, 2022 - annualreviews.org
Epistasis occurs when the effect of a mutation depends on its carrier's genetic background.
Despite increasing evidence that epistasis for fitness is common, its role during evolution is …

Drivers and impacts of the most extreme marine heatwave events

A Sen Gupta, M Thomsen, JA Benthuysen… - Scientific reports, 2020 - nature.com
Prolonged high-temperature extreme events in the ocean, marine heatwaves, can have
severe and long-lasting impacts on marine ecosystems, fisheries and associated services …

Low-N protein engineering with data-efficient deep learning

S Biswas, G Khimulya, EC Alley, KM Esvelt… - Nature …, 2021 - nature.com
Protein engineering has enormous academic and industrial potential. However, it is limited
by the lack of experimental assays that are consistent with the design goal and sufficiently …

Empirical fitness landscapes and the predictability of evolution

JAGM De Visser, J Krug - Nature Reviews Genetics, 2014 - nature.com
The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution,
yet it has mostly been used as a superficial metaphor because we know little about its …

Evolutionary mechanisms sha** the maintenance of antibiotic resistance

P Durão, R Balbontín, I Gordo - Trends in microbiology, 2018 - cell.com
Antibiotics target essential cellular functions but bacteria can become resistant by acquiring
either exogenous resistance genes or chromosomal mutations. Resistance mutations …

Epistasis between antibiotic tolerance, persistence, and resistance mutations

I Levin-Reisman, A Brauner, I Ronin… - Proceedings of the …, 2019 - pnas.org
Understanding the evolution of microorganisms under antibiotic treatments is a burning
issue. Typically, several resistance mutations can accumulate under antibiotic treatment …

Experimental design, population dynamics, and diversity in microbial experimental evolution

B Van den Bergh, T Swings, M Fauvart… - … and Molecular Biology …, 2018 - journals.asm.org
In experimental evolution, laboratory-controlled conditions select for the adaptation of
species, which can be monitored in real time. Despite the current popularity of such …

Causes of molecular convergence and parallelism in protein evolution

JF Storz - Nature Reviews Genetics, 2016 - nature.com
To what extent is the convergent evolution of protein function attributable to convergent or
parallel changes at the amino acid level? The mutations that contribute to adaptive protein …

Learning from protein engineering by deconvolution of multi‐mutational variants

F Hollmann, J Sanchis, MT Reetz - … Chemie International Edition, 2024 - Wiley Online Library
This review analyzes a development in biochemistry, enzymology and biotechnology that
originally came as a surprise. Following the establishment of directed evolution of …