By formalizing the relationship between genotype or phenotype and fitness, fitness landscapes harbor information on molecular and evolutionary constraints. The shape of the fitness landscape determines the potential for adaptation and speciation, as well as our ability to predict evolution. Consequently, fitness landscape theory has been invoked across the natural sciences and across multiple levels of biological organization. We review here the existing literature on fitness landscape theory by describing the main types of fitness landscape models, and highlight how these are increasingly integrated into an applicable statistical framework for the study of evolution. Specifically, we demonstrate how the interpretation of experimental studies with respect to fitness landscape models enables a direct link between evolution, molecular biology, and systems biology.
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http://dx.doi.org/10.1016/j.tree.2018.10.009 | DOI Listing |
Plants (Basel)
January 2025
Department Biosciences and Territory, University of Molise, 86090 Pesche, Italy.
In the Mediterranean basin, urban forests are widely recognized as essential landscape components, playing a key role in nature-based solutions by enhancing environmental quality and providing a range of ecosystem services. The selection of woody plant species for afforestation and reforestation should prioritize native species that align with the biogeographical and ecological characteristics of the planting sites. Among these, L.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
Enzyme engineering is limited by the challenge of rapidly generating and using large datasets of sequence-function relationships for predictive design. To address this challenge, we develop a machine learning (ML)-guided platform that integrates cell-free DNA assembly, cell-free gene expression, and functional assays to rapidly map fitness landscapes across protein sequence space and optimize enzymes for multiple, distinct chemical reactions. We apply this platform to engineer amide synthetases by evaluating substrate preference for 1217 enzyme variants in 10,953 unique reactions.
View Article and Find Full Text PDFNat Commun
January 2025
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
Directed evolution (DE) is a powerful tool to optimize protein fitness for a specific application. However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior. Here, we present Active Learning-assisted Directed Evolution (ALDE), an iterative machine learning-assisted DE workflow that leverages uncertainty quantification to explore the search space of proteins more efficiently than current DE methods.
View Article and Find Full Text PDFPNAS Nexus
January 2025
Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01002, USA.
Every protein progresses through a natural lifecycle from birth to maturation to death; this process is coordinated by the protein homeostasis system. Environmental or physiological conditions trigger pathways that maintain the homeostasis of the proteome. An open question is how these pathways are modulated to respond to the many stresses that an organism encounters during its lifetime.
View Article and Find Full Text PDFJ Sports Med Phys Fitness
January 2025
Unit of Cardiovascular Sciences, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy.
Endurance sports have witnessed an increase in female participation, demanding a constant and evolving reassessment of the specific physiological and health implications of female athletes. In the present review, we analyze cardiovascular, hematological adaptations and anthropometry and hormonal fluctuations highlighting sex-specific differences in response to exercise, with estrogen playing a fundamental role in modulating body composition and metabolic processes. Nutritional aspects, in particular energy availability, macronutrient distribution and hydration, are fundamental in supporting training demands and menstrual function.
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