AIMC Topic: Evolution, Molecular

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Heterogeneity of genetic sequence within quasi-species of influenza virus revealed by single-molecule sequencing.

eLife
Influenza viruses exhibit high mutation rates and extensive genetic diversity, which hinder effective vaccine development and facilitate immune evasion (Taubenberger and Morens, 2006; Barr et al., 2010). These mutations arise from the error-prone vir...

Genome-wide association study reveals genetic architecture and evolution of human retinal pigmentation.

Science advances
Pigmentation varies widely across humans and is shaped by melanin quantity, type, and spatial distribution. Retinal pigmentation protects against light-induced damage, yet its genetic and evolutionary bases remain unclear. We developed a deep learnin...

Coevolutionary signals in multiple sequence alignments improve virulence factor prediction with an MSA Transformer.

Scientific reports
Identification of virulence factors (VFs) is critical for expanding our knowledge on bacterial pathogenesis and also for developing targeted strategies for the prevention and treatment of related infectious diseases. Understanding virulence factors r...

Rubisco is slow across the tree of life.

Proceedings of the National Academy of Sciences of the United States of America
Rubisco is the main gateway through which inorganic carbon enters the biosphere, catalyzing the vast majority of carbon fixation on Earth. This pivotal enzyme has long been observed to be kinetically constrained. Yet, this impression is based on kine...

Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.

Journal of virology
The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of art...

A deep learning framework for lysine 2-hydroxyisobutyrylation site prediction using evolutionary feature representation.

Scientific reports
Lysine 2-hydroxyisobutyrylation (Khib) has emerged as a crucial Post-Translational Modification (PTM) with significant roles in diverse biological processes ranging from gene expression to metabolic regulation. Despite its importance, computational a...

Temperature adaptation in structure and function in lactate dehydrogenase-A reflects convergent evolution in a few key protein regions.

Proceedings of the National Academy of Sciences of the United States of America
Adaptive differences in the thermal stabilities of enzyme structure and function play critical roles in establishing the thermal optima and limits of all organisms. Thus, understanding the mechanisms underlying these adaptations can yield insights in...

Integrative genomics and genetics from evolutionary insights to precision breeding in peanuts (Arachis Hypogaea L.).

Functional & integrative genomics
Peanut (Arachis hypogaea L.), a globally important oilseed crop, increasingly challenged by rising edible oil demands as well as biotic and abiotic stresses. This review synthesizes recent advances in peanut genomics, evolutionary biology, and breedi...

Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution.

eLife
Phytopathogens secrete effector molecules to manipulate host immunity and metabolism. Recent advances in structural genomics have identified fungal effector families whose members adopt similar folds despite sequence divergence, highlighting their im...

AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.

Science advances
Evolutionary instability is a persistent challenge in synthetic biology, often leading to the loss of heterologous gene expression over time. Here, we present STABLES, a gene fusion strategy that links a gene of interest (GOI) to an essential endogen...