68 papers
The AlphaFold Protein Structure Database has been expanded to include 1.8 million high-confidence protein complexes across nearly 4,800 proteomes, providing a foundational resource for understanding molecular interactions and facilitating functional discovery across biology.
This paper presents an expedient, biology-laboratory-compatible method for synthesizing functional perfluoropolyether fluorosurfactants via direct carbodiimide coupling, enabling in-house production of customizable surfactants that support diverse droplet microfluidic applications such as genomic screening, thermocycling, and protein crystallization.
This paper presents an improved "tRNA array method version 2" that overcomes previous translational limitations by identifying and modifying specific tRNA groups and adding a leader sequence, thereby enabling the simultaneous in vitro synthesis of 21 tRNAs with activity comparable to individually prepared tRNAs for robust gene expression systems.
This study demonstrates that light-guided actin polymerization within giant unilamellar vesicles can drive directed motility and membrane protrusions, establishing a minimal synthetic platform for understanding cell migration and developing autonomous bioengineered systems.
Transient attenuation of actomyosin contractility reprograms confluent epithelial cells into a protrusion-driven, leader-like state by coordinating cytoskeletal, adhesive, and ERK signaling changes, thereby triggering a transition from solid-like to fluid-like tissue behavior.
This study demonstrates that engineering *E. coli* Nissle 1917 to produce curli fibers fused with a TLR2 antagonist (SSL3) effectively transforms these naturally inflammatory amyloids into programmable immune modulators that robustly suppress innate immune activation in human cells, establishing a design principle for tuning host-microbe interactions at mucosal surfaces.
This study combines automated liquid handling with an active learning framework to efficiently optimize the composition of the PURE protein synthesis system, achieving up to a 3-fold yield improvement while revealing that optimal formulations are DNA concentration-dependent and gene-specific.
By employing a two-stage dynamic control strategy that combines competitive pathway valves and NADPH flux regulators, researchers engineered an *E. coli* strain capable of producing 140 g/L of ethylene glycol from xylose at 92% of the theoretical yield in fed-batch bioreactors.
This study introduces a novel conditional guide RNA (intcgRNA) that utilizes endogenous intronic sequences as triggers to restrict Cas9-mediated gene editing to specific cell types expressing the target gene, thereby significantly reducing off-target effects in vivo.
This paper introduces CombinGym, a benchmark platform featuring 14 curated datasets and a comprehensive evaluation of machine learning algorithms to address the gap in combinatorial protein design, demonstrating that leveraging lower-order mutation data significantly improves the prediction and experimental engineering of higher-order protein variants.
This study presents a systematic engineering approach in *Escherichia coli* that successfully creates robust two-input AND logic switches by optimizing transcription factor sensors and establishing critical design rules to suppress leakiness and manage sequence-context dependencies in combinatorial promoters.
This study demonstrates that while *Lacticaseibacillus rhamnosus* GG is the most effective host for expressing therapeutic phenylalanine ammonia-lyase, its activity is primarily limited by substrate transport, which can be significantly enhanced (3–4-fold) through the expression of heterologous transporters rather than chemical surfactant treatment.
The Cepeda Framework is a modular, safety-first preclinical architecture that integrates five regulatory principles and five companion protocols to coordinate partial rejuvenation across all twelve official hallmarks of aging, utilizing a 3:2:1 OCT4:SOX2:KLF4 stoichiometric ratio and a nine-safeguard defense-in-depth system validated through 21,000 computational simulation cycles to ensure efficacy while preventing uncontrolled pluripotency.
This study systematically characterizes seven chemically inducible promoters in *Zymomonas mobilis*, including four novel systems, demonstrating their compatibility with the Golden Gate cloning framework and identifying VanRAM-PvanCC and CinRAM-Pcin as particularly promising tools for future metabolic engineering applications.
This paper demonstrates that engineered *E. coli* can implement a genetically encoded local learning rule using plasmid copy-number ratios as persistent memory, enabling physical learning and supervised adaptation in single and multicellular bacterial populations for applications ranging from logic gates to autonomous biological hardware.
This multi-lab study establishes bacterial microcompartment shells as a versatile, modular platform for covalently encapsulating diverse enzymes via the SpyCatcher-SpyTag system, demonstrating successful self-assembly, retention of activity, enhanced stability, and cooperative multi-enzyme function for robust metabolic engineering applications.
This study establishes a comprehensive genetic and process engineering platform in *Cupriavidus necator* that enables the customizable biomanufacturing of functionalized PHA nanoparticles with tunable material properties, enhanced production yields via co-culturing, and surface bioconjugation capabilities for diverse applications in biomedicine and sustainability.
By analyzing novel endogenous editing data across diverse species, this study reveals that CRISPR-Cas9 efficiency is governed by highly context-dependent factors, such as site competition and local geometry, arguing against the existence of a universal predictive model while demonstrating that repair outcome trends remain conserved.
This manuscript has been withdrawn because the authors could not confirm the bioactivity of the isolated peptides, which were likely contaminated with antibiotics during the co-purification process.
This paper presents a standardized and experimentally validated plasmid toolkit, featuring improved vectors for assembly, delivery, and counterselection, designed to streamline and enhance the efficiency of large-scale genome writing in mammalian cells using the mSwAP-In method.