Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern…

Background Cultivated spinach (Spinacia oleracea) is a highly nutritional crop species of great economical value that belongs to a genus of dioecious plant species with both homomorphic and heteromorphic sex chromosomes. The wild spinach species Spinacia turkestanica and Spinacia tetrandra are important genetic sources for improving cultivated spinach and excellent material for studying sex…

The creation-selection-mutation model makes predictions regarding the fitness of asexual and sexual populations in an environment that incorporates both positive and negative selection. The model predicts the optimal spontaneous mutation rate for a sexual population as one in which the fitness losses associated with positive and negative selection are equal. The model depends upon three mutation…

How perennial organisms adapt to environments is a key question in biology. To address this question, we investigated ten natural black poplar (Populus nigra) populations from Western Europe, a keystone forest tree of riparian ecosystems. We assessed the role of (epi)genetic regulation in driving tree species evolution and adaptation over several millions of years (macro-evolution) up to a few…

The transformer-based models, such as GPT-31 and DALL-E2, have achieved unprecedented breakthroughs in the field of natural language processing and computer vision. The inherent similarities between natural language and biological sequences have prompted a new wave of inferring the grammatical rules underneath the biological sequences. In genomic study, it is worth noting that DNA sequences alone…

Protein misfolding diseases, such as prion diseases, Alzheimer’s, and Parkinson’s, share a common molecular mechanism involving the misfolding and aggregation of specific proteins. There is an urgent need for point-of-care (POC) diagnostic technologies that can accurately detect these misfolded proteins, facilitating early diagnosis and intervention. Here, we introduce the Microfluidic Quaking…

Itaconic acid is an emerging platform chemical with extensive applications. It is currently produced by Aspergillus terreus through biological fermentation. However, A. terreus is a fungal pathogen and needs additional morphology controls, and therefore the production remains problematic. Here, we reprogrammed the GRAS yeast Yarrowia lipolytica metabolism for competitive itaconic acid production….

Encapsulins, self-assembling protein nanocages derived from prokaryotes, are promising nanoparticle-based drug delivery systems (NDDS). However, the in vivo behavior and fate of encapsulins are poorly understood. In this pre-clinical study, we probe the interactions between the model encapsulin from Thermotoga maritima (TmEnc) and key biological barriers encountered by NDDS. Here, a purified…

Deep neural networks display impressive performance but suffer from limited interpretability. Biology-inspired deep learning, where the architecture of the computational graph is based on biological knowledge, enables unique interpretability where real-world concepts are encoded in hidden nodes, which can be ranked by importance and thereby interpreted. In such models trained on single-cell…

The stoichiometry of molecular components within supramolecular biological complexes is often an important property to understand their biological functioning, particularly within their native environment. While there are well established methods to determine stoichiometry in vitro, it is presently challenging to precisely quantify this property in vivo, especially with single molecule resolution…