2023 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 344
- Total Figures in All Articles: 1766
- Figures Compatible with SBOL Visual: 378 (21.4%)
- Figures Compatible with SBOL Visual & Fully Compliant: 279 (73.81%)
- Figures Compatible with SBOL Visual & Following Best Practices: 138 (36.51%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering the Biosynthesis of Late-Stage Vinblastine Precursors Precondylocarpine Acetate, Catharanthine, Tabersonine in Nicotiana benthamiana | 3 | 0 | |
| Continuous Directed Evolution of a Feedback-Resistant Arabidopsis Arogenate Dehydratase in Plantized Escherichia coli | 1 | 0 | |
| A Logically Reversible Double Feynman Gate with Molecular Engineered Bacteria Arranged in an Artificial Neural Network-Type Architecture | 1 | 0 | |
| CaExTun: Mitigating Cas9-Related Toxicity in Streptomyces through Species-Specific Expression Tuning with Randomized Constitutive Promoters | 2 | 2 | ⭐ |
| Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast | 2 | 0 | |
| Genetically Encoded Detection of Biosynthetic Protease Inhibitors | 2 | 0 | |
| Reconstitution of Multi-Protein Complexes through Ribozyme-Assisted Polycistronic Co-Expression | 1 | 0 | |
| Tuning the Transcriptional Activity of the CaMV 35S Promoter in Plants by Single-Nucleotide Changes in the TATA Box | 1 | 1 | ⭐ |
| Engineering Pheromone-Mediated Quorum Sensing with Enhanced Response Output Increases Fucosyllactose Production in Saccharomyces cerevisiae | 3 | 3 | ⭐ |
| Developing Cyanobacterial Quorum Sensing Toolkits: Toward Interspecies Coordination in Mixed Autotroph/Heterotroph Communities | 1 | 0 | |
| Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM–OGAB Method | 3 | 0 | |
| A Universal Strategy to Promote Secretion of G+/G– Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses | 1 | 0 |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Circular Guide RNA for Improved Stability and CRISPR-Cas9 Editing Efficiency in Vitro and in Bacteria | 1 | 0 | |
| A Dueling-Competent Signal-Sensing Module Guides Precise Delivery of Cargo Proteins into Target Cells by Engineered Pseudomonas aeruginosa | 1 | 0 | |
| Signal Peptide Efficiency: From High-Throughput Data to Prediction and Explanation | 1 | 0 | |
| Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods | 3 | 0 | |
| Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator | 1 | 1 | ⭐ |
| Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis | 5 | 5 | ⭐ |
| A Ubiquitous Chromatin Opening Element and DNA Demethylation Facilitate Doxycycline-Controlled Expression during Differentiation and in Transgenic Mice | 3 | 3 | ⭐ |
| Engineering the Substrate Specificity of Toluene Degrading Enzyme XylM Using Biosensor XylS and Machine Learning | 1 | 1 | ⭐ |
| Simplified Construction of Engineered Bacillus subtilis Host for Improved Expression of Proteins Harboring Noncanonical Amino Acids | 1 | 0 | |
| Tail-Engineered Phage P2 Enables Delivery of Antimicrobials into Multiple Gut Pathogens | 3 | 3 | ⭐ |
| A Suite of New Strain Construction Vectors for Gene Expression Knockdown in Budding Yeast | 3 | 0 |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| A Biological OR(XNOR) Logic Gate Couples Carbon Source and Transgene Expression Switching in a Komagataella phaffii (Pichia pastoris) Strain Co-producing Process-Enhancing Lipase and a Virus-like Particle (VLP) Vaccine | 1 | 1 | ⭐ |
| Optical Control of Cell Signaling with Red/Far-Red Light-Responsive Optogenetic Tools in Caenorhabditis elegans | 1 | 0 | |
| P1 Bacteriophage-Enabled Delivery of CRISPR-Cas9 Antimicrobial Activity Against Shigella flexneri | 3 | 1 | |
| Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis | 4 | 0 | |
| Construction of Osmotic Pressure Responsive Vacuole-like Bacterial Organelles with Capsular Polysaccharides as Building Blocks | 1 | 1 | ⭐ |
| New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference | 2 | 2 | ⭐ |
| Simulations Reveal High Efficiency and Confinement of a Population Suppression CRISPR Toxin-Antidote Gene Drive | 1 | 0 | |
| Metabolic Engineering for Efficient Ketocarotenoid Accumulation in the Green Microalga Chlamydomonas reinhardtii | 3 | 3 | ⭐ |
| Autoinduction AND Gate Inhibits Cell Lysis to Enhance Protein Production in Bacillus subtilis Controlled by Population Density and Cell Physiological State | 4 | 4 | ⭐ |
| In Silico Prediction and Mining of Exporters for Secretory Bioproduction of Terpenoids in Saccharomyces cerevisiae | 1 | 0 | |
| Engineering Modular and Highly Sensitive Cell-Based Biosensors for Aromatic Contaminant Monitoring and High-Throughput Enzyme Screening | 2 | 0 | |
| SynBioSuite: A Tool for Improving the Workflow for Genetic Design and Modeling | 1 | 1 | ⭐ |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases | 1 | 1 | ⭐ |
| Marine Biofilm Engineered to Produce Current in Response to Small Molecules | 3 | 3 | ⭐ |
| Inducible Synthetic Growth Regulation Using the ClpXP Proteasome Enhances cis,cis-Muconic Acid and Glycolic Acid Yields in Saccharomyces cerevisiae | 1 | 0 | |
| Standard Intein Gene Expression Ramps (SIGER) for Protein-Independent Expression Control | 2 | 2 | ⭐ |
| Reconstruction of the Native Biosynthetic System of Carotenoids in E. coli─Biosynthesis of a Series of Carotenoids Specific to Paprika Fruit | 1 | 1 | ⭐ |
| Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis | 2 | 2 | ⭐ |
| Modular Pathway Compartmentalization for Agroclavine Overproduction in Saccharomyces cerevisiae | 1 | 0 | |
| Clonal Amplification-Enhanced Gene Expression in Synthetic Vesicles | 6 | 6 | ⭐ |
| CRISPR/Cas12a-Mediated Genome Editing in Thioalkalivibrio versutus | 2 | 2 | ⭐ |
| Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement | 1 | 0 | |
| In Vitro Transcription/Translation-Coupled DNA Replication through Partial Regeneration of 20 Aminoacyl-tRNA Synthetases | 4 | 4 | ⭐ |
| Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories | 1 | 1 | ⭐ |
May
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Sourcing Phage-Encoded Terminators Using ONT-cappable-seq for SynBio Applications in Pseudomonas | 1 | 1 | ⭐ |
| TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors | 1 | 1 | ⭐ |
| A Suite of Constitutive Promoters for Tuning Gene Expression in Plants | 5 | 4 | |
| Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits | 1 | 1 | ⭐ |
| Immortalized Bovine Satellite Cells for Cultured Meat Applications | 1 | 1 | ⭐ |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering Outer Membrane Vesicles to Increase Extracellular Electron Transfer of Shewanella oneidensis | 3 | 0 | |
| Cell-Free Biosensing Genetic Circuit Coupled with Ribozyme Cleavage Reaction for Rapid and Sensitive Detection of Small Molecules | 2 | 2 | ⭐ |
| In Vivo Sampling of Intracellular Heterogeneity of Pseudomonas putida Enables Multiobjective Optimization of Genetic Devices | 3 | 3 | ⭐ |
| Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801 | 1 | 0 | |
| Modulating Sensitivity of an Erythromycin Biosensor for Precise High-Throughput Screening of Strains with Different Characteristics | 2 | 1 | |
| Constructing Marine Bacterial Metabolic Chassis for Potential Biorefinery of Red Algal Biomass and Agaropectin Wastes | 2 | 1 | |
| Engineering an Efficient Expression Using Heterologous GAL Promoters and Transcriptional Activators in Saccharomyces cerevisiae | 1 | 0 | |
| Characterizing a Propionate Sensor in E. coli Nissle 1917 | 1 | 1 | ⭐ |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries | 3 | 0 | |
| Application of CRISPR in Filamentous Fungi and Macrofungi: From Component Function to Development Potentiality | 2 | 0 | |
| Understanding Autologous Spliceostatin Transcriptional Regulation to Derive Parts for Heterologous Expression in a Burkholderia Bacterial Host | 2 | 2 | ⭐ |
| Remotely Controllable Engineered Bacteria for Targeted Therapy of Pseudomonas aeruginosa Infection | 2 | 0 | |
| Assembly of Microbial Communities Engaging in Metabolic Division of Labor in a Diffusion-Limited Environment Is Governed by Metabolic Flux | 1 | 0 | |
| CRISPR-Associated Transposase for Targeted Mutagenesis in Diverse Proteobacteria | 1 | 1 | ⭐ |
| Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria | 2 | 1 | |
| Bayesian Optimization for Design of Multiscale Biological Circuits | 1 | 1 | ⭐ |
| Programmable Acetylation Modification of Bacterial Proteins by a Cas12a-Guided Acetyltransferase | 1 | 0 | |
| Modular and Flexible Molecular Device for Simultaneous Cytosine and Adenine Base Editing at Random Genomic Loci in Filamentous Fungi | 1 | 0 | |
| Leaderless Bicistronic Design for Precise and Reliable Control of Gene Expression in Corynebacterium Glutamicum | 2 | 0 | |
| Developing a Base Editing System for Marine Roseobacter Clade Bacteria | 3 | 2 | |
| RNA-Guided DNA Transposition in Corynebacterium glutamicum and Bacillus subtilis | 2 | 2 | ⭐ |
August
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Noise Minimization in Cell-Free Gene Expression | 3 | 3 | ⭐ |
| Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis | 2 | 0 | |
| Identifying Antisense Oligonucleotides to Disrupt Small RNA Regulated Antibiotic Resistance via a Cell-Free Transcription–Translation Platform | 1 | 1 | ⭐ |
| Engineered Artificial Human Neutrophils Exhibit Mature Functional Performance | 1 | 0 | |
| Targeted In Vivo Mutagenesis in Yeast Using CRISPR/Cas9 and Hyperactive Cytidine and Adenine Deaminases | 2 | 2 | ⭐ |
| Multiplicity of the Agrobacterium Infection of Nicotiana benthamiana for Transient DNA Delivery | 1 | 0 | |
| Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes | 1 | 1 | ⭐ |
| Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes | 1 | 0 | |
| Cell Free Bacteriophage Synthesis from Engineered Strains Improves Yield | 1 | 0 | |
| A Cell-Free Biosensor for Assessment of Hyperhomocysteinemia | 1 | 1 | ⭐ |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Dual Input-Controlled Synthetic mRNA Circuit for Bidirectional Protein Expression Regulation | 3 | 0 | |
| Tailored Synthetic sRNAs Dynamically Tune Multilayer Genetic Circuits | 3 | 0 | |
| Tuning Methylation-Dependent Silencing Dynamics by Synthetic Modulation of CpG Density | 1 | 0 | |
| CRAPS: Chromosomal-Repair-Assisted Pathway Shuffling in Yeast | 3 | 1 | |
| Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium | 3 | 3 | ⭐ |
| Design–Build–Test of Synthetic Promoters for Inducible Gene Regulation in Alphaproteobacteria | 5 | 0 | |
| Systematic Engineering of Saccharomyces cerevisiae Chassis for Efficient Flavonoid-7-O-Disaccharide Biosynthesis | 2 | 0 | |
| Engineering a Streptococcus Cas9 Ortholog with an RxQ PAM-Binding Motif for PAM-Free Gene Control in Bacteria | 1 | 1 | ⭐ |
| Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs | 1 | 0 | |
| A Layered Genetic Design Enables the Yeast Galactose Regulon to Respond to Cyanamide | 1 | 0 |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Signal Amplification for Cell-Free Biosensors, an Analog-to-Digital Converter | 3 | 3 | ⭐ |
| Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling | 1 | 1 | ⭐ |
| Plasmid Crosstalk in Cell-Free Expression Systems | 4 | 3 | |
| Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise | 2 | 2 | ⭐ |
| At-Home, Cell-Free Synthetic Biology Education Modules for Transcriptional Regulation and Environmental Water Quality Monitoring | 2 | 0 | |
| Development of CRISPR/Cas9-Based Genome Editing Tools for Polyploid Yeast Cyberlindnera jadinii and Its Application in Engineering Heterologous Steroid-Producing Strains | 2 | 0 | |
| Metabolic Engineering of Pichia pastoris for High-Level Production of Lycopene | 1 | 0 | |
| Conditional Control of Universal CAR T Cells by Cleavable OFF-Switch Adaptors | 1 | 0 | |
| Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant–Microbe Interactions | 2 | 0 | |
| Synthetic Gene Circuits Combining CRISPR Interference and CRISPR Activation in E. coli: Importance of Equal Guide RNA Binding Affinities to Avoid Context-Dependent Effects | 4 | 4 | ⭐ |
| Development of an Efficient Recombinant Protein Expression System in Clostridium saccharoperbutylacetonicum Based on the Bacteriophage T7 System | 2 | 0 | |
| Development of a CRISPR/Cas9D10A Nickase (nCas9)-Mediated Genome Editing Tool in Streptomyces | 1 | 1 | ⭐ |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis | 2 | 2 | ⭐ |
| Investigating and Modeling the Factors That Affect Genetic Circuit Performance | 1 | 1 | ⭐ |
| Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast | 1 | 1 | ⭐ |
| Toward Minimal Transcription–Translation Machinery | 3 | 1 | |
| Efficient Protein Expression and Biosynthetic Gene Cluster Regulation in Bacillus subtilis Driven by a T7-BOOST System | 2 | 1 | |
| Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies | 3 | 0 | |
| Cold Exposure and Oral Delivery of GLP-1R Agonists by an Engineered Probiotic Yeast Strain Have Antiobesity Effects in Mice | 1 | 1 | ⭐ |
| Heterologous Single-Strand DNA-Annealing and Binding Protein Enhance CRISPR-Based Genome Editing Efficiency in Komagataella phaffii | 3 | 0 | |
| Nonsterilized Fermentation of Crude Glycerol for Polyhydroxybutyrate Production by Metabolically Engineered Vibrio natriegens | 3 | 2 | |
| Developing the Limosilactobacillus reuteri Chassis through an Endogenous Programmable Endonuclease-Based Genome Editing Tool | 5 | 0 |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Automated Platform for the Plasmid Construction Process | 1 | 0 | |
| Tunable Dynamics in a Multistrain Transcriptional Pulse Generator | 1 | 1 | ⭐ |
| Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum | 1 | 1 | ⭐ |
| Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes | 2 | 1 | |
| Yeast Metabolic Engineering for Biosynthesis of Caffeic Acid-Derived Phenethyl Ester and Phenethyl Amide | 1 | 0 | |
| Standardized Representation of Parts and Assembly for Build Planning | 6 | 6 | ⭐ |
| MS2 Virus-like Particles as a Versatile Peptide Presentation Platform: Insights into the Deterministic Abilities for Accommodating Heterologous Peptide Lengths | 1 | 0 | |
| Establishing Tunable Genetic Logic Gates with Versatile Dynamic Performance by Varying Regulatory Parameters | 6 | 0 | |
| Using Methyl Bromide for Interspecies Cell–Cell Signaling and As a Reporter in a Model Soil Consortium | 2 | 2 | ⭐ |
| GENETTA: a Network-Based Tool for the Analysis of Complex Genetic Designs | 1 | 1 | ⭐ |
| Changes in Coding and Efficiency through Modular Modifications to a One Pot PURE System for In Vitro Transcription and Translation | 2 | 2 | ⭐ |
