bioRxiv Synthetic Biology
@bioRxiv_synbio
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Joined April 2021
Harnessing Plasmid Crosstalk in Transcription Factor Mediated Cell-Free Biosensors https://t.co/ub6sPwEvLr
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Plasmid crosstalk--unexpected changes to protein expression levels due to interactions between genetic cassettes in cell-free systems--complicates the creation of multi-plasmid cell-free tools. While...
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Discovery and Functional Characterization of Salinity-Responsive Promoters in Pseudomonas putida KT2440 https://t.co/SsKY8rnAR5
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Microbial bioprocesses are associated with environmental advantages, but their freshwater demand remains a challenge. Seawater is abundant and a sustainable alternative; however, high salinity often...
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An Ehrlich-inspired retrobiosynthesis of pharmaceutical scaffolds https://t.co/UtS7NUMiiB
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Brewer's yeast (Saccharomyces cerevisiae) acquires nitrogen from branched-chain and aromatic amino acids via the Ehrlich pathway, generating flavor (fusel) byproducts. Recently, diverting 4-hydroxy...
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Optimizing cytochrome P450 activity for quillaic acid biosynthesis in Saccharomyces cerevisiae https://t.co/VkuxtJSNs3
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QS-21, a saponin extract from the Chilean tree Quillaja saponaria, is gaining popularity as a potent vaccine adjuvant, but its production is constrained due to its low natural abundance and complex...
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Billion-Scale Deciphering of Human Gene Regulatory Grammar https://t.co/k5Xka55b1C
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biorxiv.org
Predicting how DNA sequence specifies gene expression remains a core challenge across regulatory genomics. Most predictive assays and models depend on native genomic DNA, constraining the full...
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Designing Convergent Overlapping Genes with Transformer Encoder Models and Lightweight Structural Proxies https://t.co/Yg65jE3dBa
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biorxiv.org
Overlapping genes allow multiple proteins to be encoded from a single DNA sequence, including convergent (antisense; tail-to-tail) orientations across three reading frames (phases 0, 1, and 2), with...
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Engineering butyrate-producing Lachnospiraceae to treat metabolic disease https://t.co/HDMKYtoBVu
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Engineering native gut bacteria offers a route to persistent, programmable therapeutics, yet many dominant taxa remain genetically intractable. Lachnospiraceae are a prevalent and abundant family in...
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Two-Year Field Trial of Genetically Engineered American Chestnut Reveals Greater Fungal Blight Tolerance Compared to Wild-Type ... https://t.co/n7m8P2TYyk
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The American chestnut (Castanea dentata) was a foundational forest canopy species in eastern North America until an imported fungal blight (caused by Cryphonectria parasitica) rendered it functiona...
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Genomic Perception Fusion: A Lightweight, Interpretable Kernel for Protein Functional Tuning https://t.co/lDD3dIne51
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Protein design has been transformed by deep generative models ,but at the cost of interpretability, accessibility, and integration with sparse experimental feedback. Here, we introduce Genomic...
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Rewiring protein function through genetically encoded oxidative chemistry https://t.co/HNrZ4iERZ9
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Cargo-directed assembly of nonviral nucleocapsid with controlled size https://t.co/AapFIoyPTU
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Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits https://t.co/8Xp4hu2mNB
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biorxiv.org
Implementing logic functions in living cells is a fundamental area of interest among synthetic biologists. The goal of designing biochemical circuits in synthetic biology is to make modular and...
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Genetic incorporation of diverse non-canonical amino acids for histidine substitution https://t.co/VRIp1ppo9I
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biorxiv.org
Using genetic code expansion, canonical amino acid residues can be site-specifically substituted by non-canonical amino acids (ncAAs) with modified chemical properties. This technique has enabled...
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Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis https://t.co/Vwrt4vp2XL
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biorxiv.org
3-Hydroxy fatty acids (3-HFAs) are versatile intermediates for bio-based polymers, fuels, and surfactants, and are advancing circular economy manufacturing. We built an acyl– CoA ligase-deficient...
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Rhodo-Box: a Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides https://t.co/VG1XDBOw75
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Rhodobacter sphaeroides is a purple non-sulphur alphaproteobacterium with a highly versatile metabolism. This microorganism holds promise as a chassis for sustainable biomanufacturing of numerous...
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PHYCUT: Scalable multiplex CRISPR/Cas9 editing forgenome engineering in the diatom Phaeodactylumtricornutum https://t.co/d6VP1t1xAV
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Diatoms are globally significant microalgae that contribute ∼ 20% of oxygen production and exhibit remarkable metabolic diversity. The marine diatom Phaeodactylum tricornutum has emerged as a...
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Engineered orthogonal translation systems from metagenomic libraries expand the genetic code https://t.co/mgojp3E2cb
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biorxiv.org
Genetic code expansion with non-canonical amino acids (ncAAs) opens new opportunities for the function and design of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporat...
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A comprehensive genetic toolkit for Zymomonas mobilis; allowing rapid, high-resolution, combinatorial engineering of metabolic pathways. https://t.co/pUygjedGnJ
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The lack of robust genetic tools has hindered the precise engineering of Zymomonas mobilis , a key organism for the bioproduction of many commodity chemicals. Here, we developed a library of synthe...
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Optimized quantitative bacterial two-hybrid (qB2H) for protein-protein interaction assessment https://t.co/b6enU7Yxhd
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Characterizing mutation effects on protein-protein interactions (PPIs) is crucial for elucidating protein structure and function. Massively parallel PPI variant analyses such as deep mutational...
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Adaptive evolution of engineered Saccharomyces cerevisiae in favored and unusual chemical environments https://t.co/s54nPL4WCG
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biorxiv.org
Engineered microbial cells can produce a wide range of industrially relevant chemicals such as pharmaceuticals, fuels, and material precursors. The use of microbial cells for chemical production from...
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