AI Article Synopsis
Article Abstract
Motivation: Understanding the population genetics of complex polygenic traits during adaptation is challenging.
Results: Here, we implement a forward-in-time population-genetic simulator (STUN) based on Wright-Fisher dynamics. STUN is a flexible and user-friendly software package for simulating the polygenic adaptation of recombining haploid populations using either new mutations or standing genetic variation. STUN assumes that populations adapt to sudden environmental changes by undergoing selection on a new fitness landscape. With pre-implemented fitness landscape models like Rough Mount Fuji, NK, Block, additive, and House-of-Cards, users can explore the effect of different levels of epistasis (ruggedness of the fitness landscape). Custom fitness landscapes and recombination maps can also be defined. STUN empowers both experimentalists and advanced programmers to study the evolution of complex polygenic traits and to dissect the adaptation process.
Availability And Implementation: STUN is implemented in Rust. Its source code is available at https://github.com/banklab/STUN and archived on Zenodo under doi: 10.5281/zenodo.10246377. The repository includes a link to the software's manual and binary files for Linux, macOS and Windows.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10703519 | PMC |
| http://dx.doi.org/10.1093/bioadv/vbad164 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Active learning-assisted directed evolution.
Nat 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 PDFDiscovering genetic modulators of the protein homeostasis system through multilevel analysis.
PNAS 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 PDFFemale athletes: a state-of-the-art review of multiorgan influence of exercise training.
J 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.
View Article and Find Full Text PDFShould CAR-T cell therapy be considered a standard of care for patients with refractory diffuse large B-cell lymphoma in second line treatment?
Expert Opin Biol Ther
January 2025
Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA.
Introduction: CAR-T therapy has transformed the treatment landscape for relapsed/refractory diffuse large B-cell lymphomas (DLBCL).
Areas Covered: This article reviews the existing evidence for using CAR-T therapy as a second-line treatment. Two major phase 3 trials, ZUMA-7 and TRANSFORM, have shown that axi-cel and liso-cel, respectively, offer superior outcomes compared to historical standard chemoimmunotherapy and consolidation with autologous hematopoietic stem cell transplantation (auto-HCT).
Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation.
Mol Biol Evol
January 2025
Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, Paris 75005, France.
Modifiers of recombination rates have been described but the selective pressures acting on them and their effect on adaptation to novel environments remain unclear. We performed experimental evolution in the nematode Caenorhabditis elegans using alternative rec-1 alleles modifying the position of meiotic crossovers along chromosomes without detectable direct fitness effects. We show that adaptation to a novel environment is impaired by the allele that decreases recombination rates in the genomic regions containing fitness variation.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!