Hydrogels are emerging as sustainable alternatives to petroleum-based foams and pots in horticulture due to their high porosity, enhancing water and nutrient retention. This study develops κ-carrageenan (Carr)-based hydrogels incorporating hydrolyzed (HSW) and nonhydrolyzed red seaweed (WSW) (0–50 wt %) to introduce biostimulant properties for soilless cultivation. Hydrogels were analyzed for swelling in different media, solubility, microstructure (SEM), physicochemical interactions (FTIR, XRD), and mechanical properties, revealing high porosity, superabsorbent behavior (swelling up to 6000%), and reduced compression modulus with increasing seaweed content. Their biostimulant effect was assessed on Arabidopsis thaliana, with 20 wt % HSW hydrogels promoting enhanced root and shoot growth. Additionally, the hydrogels inhibited Fusarium solani, demonstrating antifungal properties. These results highlight the potential of Carr-seaweed hydrogels as multifunctional substrates for sustainable plant cultivation.

Lacto-N-neotetraose (LNnT) is a key human milk oligosaccharide (HMO) with important prebiotic functions, supporting the growth of beneficial gut microbiota and contributing to infant health. Constructing plasmid-free strains via metabolic engineering for LNnT biosynthesis represents a feasible strategy for efficient industrial-scale production. This study integrates various strategies to construct plasmid-free strains capable of efficiently producing LNnT. Building on the previously developed Escherichia coli MG1655 strain for lacto-N-triose II (LNTri II) production, Hplex2B (encoding β1,4-galactosyltransferase) was incorporated, and its copy number was optimized to construct a complete and efficient biosynthetic pathway. By integrating an extra copy of the multidrug efflux pump gene mdfA, the strain tolerance was improved, resulting in a higher yield of LNnT. The integration of expression cassettes for key genes in the glycosyl donor synthesis pathway (including glmS, glmM, glmU, galU, and galE) with varying promoter strengths optimized the supply and balance. The subsequent removal of a key feedback inhibition circuit directed the reaction toward the synthesis of LNnT. The final strain, after successive optimization, produced LNnT at 7.76 g/L in shake flask culture and 34.24 g/L in a 5 L bioreactor, with precursor LNTri II concentrations of 0.58 g/L and 1.61 g/L, respectively.

Allosteric interactions in proteins are key to biological regulation and the efficacy of many drugs. The extent to which allostery is conserved in evolutionarily-related proteins is unknown, with implications for predicting, engineering and therapeutically targeting allostery. Here we directly address this question by constructing seven comprehensive allosteric maps for five homologous human proteins. The comparative maps reveal a modular allosteric architecture with conserved distant-dependent allosteric decay across the protein core connecting to protein-specific allosteric extensions to surfaces. These allosteric augmentations use both structurally-conserved residues and homolog-specific domain extensions. Our data provide the first comparative multidimensional protein energy landscapes and suggest that allostery evolves via the gain-and-loss of peripheral extensions to a conserved allosteric core.

Subinhibitory antibiotic exposures are common in clinical and environmental contexts, yet their effects on bacterial growth dynamics remain incompletely understood. We studied the temporal response of Escherichia coli to a panel of bactericidal ("cidal") and bacteriostatic ("static") antibiotics at sub-minimum inhibitory concentrations (sub-MIC). We uncover a sharp dynamical distinction between the two classes. Bacteriostatic antibiotics reduce the initial growth rate in a dose-dependent manner, similar to nutrient limitation physiological responses. In contrast, bactericidal antibiotics do not alter initial growth rates - cells continue to grow as fast as untreated cells - until an abrupt slowdown in growth rate. The onset of slowdown occurs earlier with increasing dose, suggesting a damage accumulation mechanism leading to a lethal threshold. Cidals also show a steeper dose-response curve. We propose that bacteria respond to cidal antibiotics with a "grow-fast-then-crash" strategy that is adaptive for transient lethal threats, whereas static antibiotics trigger stress adaptation and slower growth. While clinical outcomes of statics and cidals may be similar at full inhibitory doses, these sub-MIC dynamical signatures could influence resistance evolution and treatment outcomes in biofilms or partially resistant strains. Our findings offer a dynamic framework for antibiotic classification and raise new questions about how bacteria respond to sublethal antibiotic stress.

We have developed a simple and highly efficient in vivo method to iteratively relocate functional chromosomal loci onto an episome in Escherichia coli by utilizing synthetic DNA fragments. In this in vivo cut’n’paste procedure, “cutting” is executed by the RNA-guided DNA endonuclease Cas9 and a set of guides, while “pasting” is facilitated by the phage λ Red recombinase, which are all synthesized on easily curable plasmids. To demonstrate the utility of this approach, we commercially obtained synthetic DNA fragments containing locus-specific homology regions, antibiotic marker cassettes, and standardized Cas9 target sequences. By using these locus-specific synthetic DNA fragments, we relocated 7 functional chromosomal loci. Scarless relocation mutants of the trg, aer, tsr, malHM, malQT, macB-nadA, and folA chromosomal loci were obtained as antibiotic-resistant isolates by combining Cas9 counterselection with the restoration of an antibiotic marker cassette. The additional antibiotic marker cassettes and standardized Cas9 target sequences present in the synthetic DNA fragments are inherently eliminated upon completion of the procedure, enabling iterative processing of loci. This procedure should be widely useful, especially in genome (re-)engineering of E. coli and other bacteria because the procedure can be done on wild-type cells.

Transposons impact eukaryotic genome size and evolution. Horizontal transfer of transposons (HTT) is important for their long-term persistence, but has only been systematically studied in animals, and thus the abundance, impact, and factors that shape HTTs in lineages outside animals is unknown. Fungi are at least as ancient and diverse as animals and are characterized by extensive genome size variation caused by transposons. Here, we screened 1,348 genomes across fungal biodiversity, genome sizes, and lifestyles to detect extensive HTTs, that generated on average 7% but up to 70% of the transposon content in some taxa. We in total identified at least 5,518 independent HTTs, mostly involving Tc1/Mariner DNA transposons. While the majority of HTTs occur between closely related taxa, irrespective of their lifestyles, HTTs were particularly common in Mucoromycotina, Sordariomycetes, Dothideomycetes, and Leotiomycetes. Importantly, species lacking fungal-specific defense mechanisms against transposons and those with gene-sparse and repeat-rich genomic compartments are involved in significantly higher number of HTTs, unveiling ecological and genomic factors shaping HTTs. Our findings thus illuminate the dynamic landscape of HTTs in fungi, providing the framework to further study the impact of HTTs on genome evolution and the processes that mediate transposon transfers within and between eukaryotic lineages.

Gas vesicles (GVs) are genetically encodable, air-filled protein nanostructures that have rapidly emerged as a versatile platform for biomedical imaging, cell tracking, and therapeutic delivery. However, their heterologous expression in non-native hosts such as Escherichia coli can be challenging due to the complex assembly process, which often involves around ten different proteins and can lead to proteotoxic stress and impair cell growth. Here, we report the observation of a drop in cell density occurring 8 to 16 hours after GV induction in E. coli. To address these, we developed a dual-inducer transcriptional regulation system that enables orthogonal control of GV assembly factor proteins and the shell protein over a range of stoichiometries. Sequential induction in time, in which assembly factor expression is initiated before shell protein expression, restored normal bacterial growth and prevented lysis without compromising GV production. Further analysis revealed that varying the interval between the two induction steps affected both GV yields and cellular stress. By preserving cell integrity with GV expression, our approach enhances the utility of GV-expressing bacteria in applications that demand population-wide cellular stability and facilitates their broader application in biomedical engineering and synthetic biology.