Article
Chemistry, Physical
Edurne Avellanal-Zaballa, Alejandro Prieto-Castaneda, Carolina Diaz-Norambuena, Jorge Banuelos, Antonia R. Agarrabeitia, Inmaculada Garcia-Moreno, Santiago de la Moya, Maria J. Ortiz
Summary: This paper presents a protocol for designing dyads and triads based on BODIPY dyes as singlet oxygen photosensitizers or energy transfer molecular cassettes without halogens. Photonic characterization shows the crucial role of the BODIPY-BODIPY linkage in finely modulating the balance between the triplet state population and fluorescence decay.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Editorial Material
Ecology
Veronika Bernhauerova
Summary: The simultaneous evolution of vaccine-induced immune escape and virulence leads to different outcomes.
NATURE ECOLOGY & EVOLUTION
(2022)
Review
Biochemical Research Methods
Luciano A. Abriata, Matteo Dal Peraro
Summary: Coupling residue coevolution estimations with machine learning methods is transforming protein structure prediction, particularly for proteins without clear homologous templates like in the recent CASP competition. However, making these advances accessible to non-experts and ensuring correct interpretation of predicted models still requires further development of web resources and tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Joshua M. Borin, Sarit Avrani, Jeffrey E. Barrick, Katherine L. Petrie, Justin R. Meyer
Summary: Training bacteriophages on target hosts before therapy can prolong suppression of antibiotic-resistant bacteria by delaying the evolution of resistance. Evolution of resistance to trained phages is more costly and requires multiple mutations, making them more effective in combating resistance. Transfer of genetic information from host genomes through recombination can enhance phage fitness and improve treatment outcomes, highlighting the potential of training in phage therapy development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Benjamin R. Harrison, Jessica M. Hoffman, Ariana Samuelson, Daniel Raftery, Daniel E. L. Promislow
Summary: Comparative phylogenetic studies have shed light on the evolution of metabolites across 50 million years in the genus Drosophila, revealing the conserved effects of sex and age on the metabolome. Modules in the metabolome show evidence of coevolution, enriched for specific biochemical pathways, and potentially influenced by functional relationships. These coevolutionary patterns differ between sexes and are affected by age, with some modules associated with lifespan variation, particularly in older flies, suggesting a role of metabolic associations in lifespan evolution over millions of years.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Alberto M. Rivera, Damien B. Wilburn, Willie J. Swanson
Summary: The rapid evolution of fertilization proteins has led to diversity in molecular structure and function. The study focuses on the ZP-N domains in vertebrate egg coat glycoproteins, which have diversified in structure and function. The modular ZP-N domains are associated with another domain type and have a stabilizing network absent in free domains.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Patrick Rynkiewicz, Miranda L. Lynch, Feng Cui, Andre O. Hudson, Gregory A. Babbitt
Summary: Utilizing machine learning and molecular dynamics simulations, this study reveals evolutionarily conserved binding dynamics between different Betacoronavirus strains from bat CoV-HKU4 to human endemic/emergent strains. Conserved dynamics regions of ACE2 involve N-terminal helix and a region encompassing residues K353, Q325.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemical Research Methods
Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo, Yanjie Wei
Summary: Sequence-based residue contact prediction is crucial for protein structure reconstruction. Different methods have different application scenarios, with multi-input DL methods showing the best overall performance. However, there is still room for improvement in current methods.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Zoology
Jing-Song Zhang, Hai-Quan Wang, Jie Xia, Kun Sha, Shu-Tao He, Hao Dai, Xiao-Hu Hao, Yi-Wei Zhou, Qiu Wang, Ke-Ke Ding, Zhang-Lei Ju, Wen Wang, Luo-Nan Chen
Summary: The divergence and evolution of plants and animals have contributed to ecological diversity. An extensive analysis of multi-omics sequences in animal and plant species revealed different evolutionary trends in promoter and transcription factor features. Promoters and TFs exhibited antagonistic coevolution in the animal kingdom but mutualistic coevolution in the plant kingdom. These distinct coevolutionary patterns potentially drive the divergence, divergent evolution, and ecological diversity of plants and animals.
ZOOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Shilpi Chaurasia, Julien Y. Dutheil
Summary: Compensatory substitutions occur when advantageous mutations restore fitness lost due to previous deleterious mutations. This study presents an atlas of intra-protein compensatory substitutions built using a phylogenetic approach and a dataset of 1,630 bacterial protein families. Through the analysis of evolutionary and structural properties, it is shown that compensatory mutations are rare but widespread in proteins. Coevolving residues are typically evolving slowly and located in the protein core, and they are more often in contact than expected by chance. The findings provide insights into the relationship between protein structure and fitness landscape.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Eduardo Dessupoio Moreira Dias, Marley Maria Bernardes Rebuzzi Vellasco, Andre Vargas Abs da Cruz
Summary: This study proposes a new neuroevolution model, QNCo, for agent coordination problems. QNCo utilizes paradigms from quantum physics and biological coevolution to autonomously obtain the best neural network topology for each agent, showing promising results in solving prey-predator, multi-rover tasks, and mobile telephony coverage.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Katrine K. Lund-Hansen, Colin Olito, Edward H. Morrow, Jessica K. Abbott
Summary: Antagonistic interactions between the sexes are important drivers of evolutionary divergence. When loci under interlocus sexual conflict are located on the sex chromosomes, it can lead to cycles of antagonistic coevolution between them and therefore between the sexes. Experimental crosses using Drosophila melanogaster showed that disrupting putatively coevolved sex chromosome pairs resulted in increased male reproductive success but also in lower offspring viability, with these sexually antagonistic fitness effects appearing to be resolved after 25 generations of experimental evolution. Population genetic models of antagonistic coevolution based on empirical results support the conclusion that antagonistic coevolution between the sex chromosomes is plausible and may drive genetic and phenotypic divergence between populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Runxi Shen, Miwa Wenzel, Philipp W. Messer, Charles F. Aquadro
Summary: Selective pressures on DNA sequences can be captured by the McDonald-Kreitman (MK) test. The nature of these selective forces often remains unknown. Amino acid fixations driven by natural selection in genes are associated with genetic arms races or changes in biological purposes. Simulations reveal that the proportion of adaptive amino acid fixations and the power of the MK test are lower in a buffering model compared to an arms race/change-in-function model.
Article
Multidisciplinary Sciences
Michael Lynch
Summary: Most aspects of the molecular biology of cells involve specific recognition at the nucleotide and/or amino acid levels, which leads to debates on the rates of sequence evolution. This study introduces a general model to evaluate the influence of population sizes, mutation rates, selection strength, and recombination on the rate of evolution at functionally interacting sites. The theory is particularly relevant to interactions between organelle-and nuclear-encoded proteins, offering predictions on coevolutionary rates based on drift, selection, and mutation intensities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Kejue Jia, Mesih Kilinc, Robert L. Jernigan
Summary: The sequence correlations in protein multiple sequence alignments can be used to predict protein dynamics. Elastic network protein dynamics models rely on contacts within the alignment and obtain normal modes of motion from the inverse of the contact map. Coarse-graining at the level of one point per amino acid allows for the direct connection between sequence and dynamics, making it possible to obtain protein dynamics using only the sequence information.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
