2021 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 327
- Total Figures in All Articles: 1759
- Figures Compatible with SBOL Visual: 457 (25.98%)
- Figures Compatible with SBOL Visual & Fully Compliant: 382 (83.59%)
- Figures Compatible with SBOL Visual & Following Best Practices: 262 (57.33%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Statistical Design of Experiments for Synthetic Biology | 1 | 1 | ⭐ |
| Fine-Tuning Multi-Gene Clusters via Well-Characterized Gene Expression Regulatory Elements: Case Study of the Arginine Synthesis Pathway in C. glutamicum | 3 | 1 | |
| YESS 2.0, a Tunable Platform for Enzyme Evolution, Yields Highly Active TEV Protease Variants | 2 | 2 | ⭐ |
| Repurposing the Endogenous Type I-E CRISPR/Cas System for Gene Repression in Gluconobacter oxydans WSH-003 | 3 | 2 | |
| Plasmid Vectors for in Vivo Selection-Free Use with the Probiotic E. coli Nissle 1917 | 4 | 0 | |
| Engineering Bacteria to Produce Pure Phage-like Particles for Gene Delivery | 1 | 1 | ⭐ |
| A Golden-Gate Based Cloning Toolkit to Build Violacein Pathway Libraries in Yarrowia lipolytica | 2 | 0 | |
| Engineering an Optogenetic CRISPRi Platform for Improved Chemical Production | 2 | 1 | |
| Optimization of a p-Coumaric Acid Biosensor System for Versatile Dynamic Performance | 3 | 0 | |
| Rational Design of Single Copy Expression Cassettes in Defined Chromosomal Sites Overcomes Intraclonal Cell-to-Cell Expression Heterogeneity and Ensures Robust Antibody Production | 1 | 0 | |
| An Aspergillus nidulans Platform for the Complete Cluster Refactoring and Total Biosynthesis of Fungal Natural Products | 5 | 0 | |
| Metabolic Engineering of Escherichia coli for De Novo Production of 1,5-Pentanediol from Glucose | 6 | 6 | ⭐ |
| Engineered Bacterial Production of Volatile Methyl Salicylate | 1 | 0 | |
| A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria | 1 | 1 | ⭐ |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Promiscuous Installation of d-Amino Acids in Gene-Encoded Peptides | 1 | 1 | ⭐ |
| Biosynthesis of Diverse Type II Polyketide Core Structures in Streptomyces coelicolor M1152 | 3 | 3 | ⭐ |
| Macrolide Biosensor Optimization through Cellular Substrate Sequestration | 1 | 0 | |
| Rational Design of the N-Terminal Coding Sequence for Regulating Enzyme Expression in Bacillus subtilis | 4 | 4 | ⭐ |
| Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons | 5 | 5 | ⭐ |
| A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens | 1 | 0 | |
| A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology | 3 | 3 | ⭐ |
| CRISPRi-Mediated NIMPLY Logic Gate for Fine-Tuning the Whole-Cell Sensing toward Simple Urine Glucose Detection | 4 | 4 | ⭐ |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration | 1 | 0 | |
| Small Antisense DNA-Based Gene Silencing Enables Cell-Free Bacteriophage Manipulation and Genome Replication | 2 | 2 | ⭐ |
| A Reporter System for Cytosolic Protein Aggregates in Yeast | 2 | 2 | ⭐ |
| Efficient Production of 1,3-Propanediol from Diverse Carbohydrates via a Non-natural Pathway Using 3-Hydroxypropionic Acid as an Intermediate | 2 | 2 | ⭐ |
| Genetically Engineered Methanotroph as a Platform for Bioaugmentation of Chemical Pesticide Contaminated Soil | 3 | 2 | |
| Metabolic Engineering of Saccharomyces cerevisiae for Ethyl Acetate Biosynthesis | 2 | 2 | ⭐ |
| Optogenetic Modification of Pseudomonas aeruginosa Enables Controllable Twitching Motility and Host Infection | 1 | 1 | ⭐ |
| Engineering Alternate Ligand Recognition in the PurR Topology: A System of Novel Caffeine Biosensing Transcriptional Antirepressors | 3 | 3 | ⭐ |
| Guanidine Biosensors Enable Comparison of Cellular Turn-on Kinetics of Riboswitch-Based Biosensor and Reporter | 1 | 1 | ⭐ |
| Automated Rational Strain Construction Based on High-Throughput Conjugation | 1 | 1 | ⭐ |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology | 1 | 0 | |
| Engineered Regulon to Enable Autonomous Azide Ion Biosensing, Recombinant Protein Production, and in Vivo Glycoengineering | 4 | 0 | |
| Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains | 1 | 1 | ⭐ |
| A Cell Factory of a Fungicolous Fungus Calcarisporium arbuscula for Efficient Production of Natural Products | 2 | 2 | ⭐ |
| Engineering Transcriptional Interference through RNA Polymerase Processivity Control | 4 | 4 | ⭐ |
| An Automated Tabletop Continuous Culturing System with Multicolor Fluorescence Monitoring for Microbial Gene Expression and Long-Term Population Dynamics | 2 | 0 | |
| Genetically Intact Bioengineered Spores of Bacillus subtilis | 1 | 0 | |
| An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus | 2 | 2 | ⭐ |
| An Aldolase-Based New Pathway for Bioconversion of Formaldehyde and Ethanol into 1,3-Propanediol in Escherichia coli | 1 | 1 | ⭐ |
| Recombinant Protein Stability in Cyanobacteria | 5 | 0 | |
| Engineering a Central Carbon Metabolism Pathway to Increase the Intracellular Acetyl-CoA Pool in Synechocystis sp. PCC 6803 Grown under Photomixotrophic Conditions | 3 | 3 | ⭐ |
| Rational Promoter Engineering Enables Robust Terpene Production in Microalgae | 5 | 5 | ⭐ |
| Saccharomyces cerevisiae Synthetic Transcriptional Networks Harnessing dCas12a and Type V-A anti-CRISPR Proteins | 4 | 4 | ⭐ |
May
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology | 4 | 0 | |
| Engineered Microbial Routes for Human Milk Oligosaccharides Synthesis | 1 | 0 | |
| Cheetah: A Computational Toolkit for Cybergenetic Control | 1 | 1 | ⭐ |
| The Tryptophan-Induced tnaC Ribosome Stalling Sequence Exposes High Amino Acid Cross-Talk That Can Be Mitigated by Removal of NusB for Higher Orthogonality | 1 | 1 | ⭐ |
| Antisense RNA Interference-Enhanced CRISPR/Cas9 Base Editing Method for Improving Base Editing Efficiency in Streptomyces lividans 66 | 3 | 3 | ⭐ |
| Improve the Biosynthesis of Baicalein and Scutellarein via Manufacturing Self-Assembly Enzyme Reactor In Vivo | 1 | 1 | ⭐ |
| Creating RNA Specific C-to-U Editase from APOBEC3A by Separation of Its Activities on DNA and RNA Substrates | 1 | 0 | |
| Impact of Porous Matrices and Concentration by Lyophilization on Cell-Free Expression | 1 | 1 | ⭐ |
| A Whole-Cell Bacterial Biosensor for Blood Markers Detection in Urine | 3 | 0 | |
| Optogenetic Amplification Circuits for Light-Induced Metabolic Control | 2 | 0 | |
| Systematically Engineered Fatty Acid Catabolite Pathway for the Production of (2S)-Naringenin in Saccharomyces cerevisiae | 1 | 0 | |
| Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters | 9 | 0 | |
| Spatiotemporal Manipulation of the Mismatch Repair System of Pseudomonas putida Accelerates Phenotype Emergence | 3 | 3 | ⭐ |
| Emergent Damped Oscillation Induced by Nutrient-Modulating Growth Feedback | 4 | 0 |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| A Tail Fiber Engineering Platform for Improved Bacterial Transduction-Based Diagnostic Reagents | 2 | 2 | ⭐ |
| Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers | 1 | 0 | |
| GTR 2.0: gRNA-tRNA Array and Cas9-NG Based Genome Disruption and Single-Nucleotide Conversion in Saccharomyces cerevisiae | 1 | 0 | |
| Genetically Programmable Microbial Assembly | 1 | 1 | ⭐ |
| Establishment of a Biosensor-based High-Throughput Screening Platform for Tryptophan Overproduction | 1 | 0 | |
| A Computational Framework for Identifying Promoter Sequences in Nonmodel Organisms Using RNA-seq Data Sets | 2 | 0 | |
| Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits | 5 | 5 | ⭐ |
| Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803 | 2 | 2 | ⭐ |
| Data-Driven and in Silico-Assisted Design of Broad Host-Range Minimal Intrinsic Terminators Adapted for Bacteria | 2 | 2 | ⭐ |
| Microbially Guided Discovery and Biosynthesis of Biologically Active Natural Products | 3 | 0 | |
| Engineering Gac/Rsm Signaling Cascade for Optogenetic Induction of the Pathogenicity Switch in Pseudomonas aeruginosa | 1 | 1 | ⭐ |
| Combining Metabolic and Monoterpene Synthase Engineering for de Novo Production of Monoterpene Alcohols in Escherichia coli | 1 | 1 | ⭐ |
| High-Yielding Terpene-Based Biofuel Production in Rhodobacter capsulatus | 1 | 1 | ⭐ |
| Ecofriendly Synthesis of l-Carnosine in Metabolically Engineered Corynebacterium glutamicum by Reinforcing Precursor Accumulation | 1 | 0 | |
| Dual Regulation of Cytoplasm and Peroxisomes for Improved Α-Farnesene Production in Recombinant Pichia pastoris | 1 | 0 |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways | 3 | 2 | |
| A Biosensor for Detection of Indole Metabolites | 1 | 1 | ⭐ |
| The pIT5 Plasmid Series, an Improved Toolkit for Repeated Genome Integration in E. coli | 3 | 3 | ⭐ |
| Yeast Synthetic Minimal Biosensors for Evaluating Protein Production | 1 | 0 | |
| Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts | 3 | 2 | |
| Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria | 3 | 3 | ⭐ |
| Engineering a Bifunctional ComQXPA-PsrfA Quorum-Sensing Circuit for Dynamic Control of Gene Expression in Corynebacterium glutamicum | 6 | 6 | ⭐ |
| SBOLCanvas: A Visual Editor for Genetic Designs | 2 | 2 | ⭐ |
August
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Genetically Encoding Ultrastable Virus-like Particles Encapsulating Functional DNA Nanostructures in Living Bacteria | 2 | 0 | |
| Localized Proteolysis for the Construction of Intracellular Asymmetry in Escherichia coli | 3 | 3 | ⭐ |
| High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters | 1 | 1 | ⭐ |
| A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution | 1 | 1 | ⭐ |
| The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications in Vibrio natriegens | 6 | 6 | ⭐ |
| Development of a N-Acetylneuraminic Acid-Based Sensing and Responding Switch for Orthogonal Gene Regulation in Cyanobacterial Synechococcus Strains | 4 | 4 | ⭐ |
| Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation | 3 | 3 | ⭐ |
| Metabolic Engineering of Escherichia coli for High-Yield Production of (R)-1,3-Butanediol | 1 | 1 | ⭐ |
| Synthetic Cellobiose-Inducible Regulatory Systems Allow Tight and Dynamic Controls of Gene Expression in Streptomyces | 4 | 4 | ⭐ |
| Reprogramming Escherichia coli Metabolism for Bioplastics Synthesis from Waste Cooking Oil | 3 | 3 | ⭐ |
| A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia coli | 1 | 1 | ⭐ |
| Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy | 1 | 1 | ⭐ |
| Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies | 1 | 0 | |
| Exploring the Tunability and Dynamic Properties of MarR-PmarO Sensor System in Escherichia coli | 2 | 0 | |
| A System for the Evolution of Protein–Protein Interaction Inducers | 2 | 0 | |
| VisBOL2—Improving Web-Based Visualization for Synthetic Biology Designs | 3 | 3 | ⭐ |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering | 7 | 0 | |
| High-Titer Production of Olivetolic Acid and Analogs in Engineered Fungal Host Using a Nonplant Biosynthetic Pathway | 1 | 1 | ⭐ |
| Expression of Alternative Nitrogenases in Rhodopseudomonas palustris Is Enhanced Using an Optimized Genetic Toolset for Rapid, Markerless Modifications | 1 | 1 | ⭐ |
| Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20 | 1 | 1 | ⭐ |
| Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis | 4 | 4 | ⭐ |
| Adaptive Optimization Boosted the Production of Moenomycin A in the Microbial Chassis Streptomyces albus J1074 | 3 | 3 | ⭐ |
| A DNA Inversion System in Eukaryotes Established via Laboratory Evolution | 5 | 5 | ⭐ |
| Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection | 2 | 2 | ⭐ |
| Synthetic Biology Knowledge System | 2 | 2 | ⭐ |
| Construction and Characterization of a Gradient Strength Promoter Library for Fine-Tuned Gene Expression in Bacillus licheniformis | 1 | 1 | ⭐ |
| Modular and Single-Cell Sensors of Bacterial Ser/Thr Kinase Activity | 1 | 1 | ⭐ |
| Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria | 4 | 4 | ⭐ |
| An Integrative Toolbox for Synthetic Biology in Rhodococcus | 3 | 3 | ⭐ |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules | 1 | 1 | ⭐ |
| Efficient Production of 2′-Fucosyllactose from l-Fucose via Self-Assembling Multienzyme Complexes in Engineered Escherichia coli | 1 | 1 | ⭐ |
| Development of Genetically Encoded Biosensors for Reporting the Methyltransferase-Dependent Biosynthesis of Semisynthetic Macrolide Antibiotics | 1 | 1 | ⭐ |
| Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection | 6 | 3 | |
| Rational Design and Characterization of Nitric Oxide Biosensors in E. coli Nissle 1917 and Mini SimCells | 3 | 3 | ⭐ |
| Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies | 1 | 1 | ⭐ |
| Curation Principles Derived from the Analysis of the SBOL iGEM Data Set | 3 | 3 | ⭐ |
| Visualized Multigene Editing System for Aspergillus niger | 4 | 4 | ⭐ |
| Construction of a Fusellovirus with a Minimal Set of Genes | 2 | 2 | ⭐ |
| Metabolic Engineering of Gas-Fermenting Clostridium ljungdahlii for Efficient Co-production of Isopropanol, 3-Hydroxybutyrate, and Ethanol | 2 | 2 | ⭐ |
| BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform | 3 | 3 | ⭐ |
| Engineering a CRISPRi Circuit for Autonomous Control of Metabolic Flux in Escherichia coli | 4 | 4 | ⭐ |
| ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida | 4 | 0 | |
| Tailoring Genetic Elements of the Plasmid-Driven T7 System for Stable and Robust One-Step Cloning and Protein Expression in Broad Escherichia coli | 5 | 5 | ⭐ |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization | 1 | 1 | ⭐ |
| Engineering Wired Life: Synthetic Biology for Electroactive Bacteria | 3 | 3 | ⭐ |
| Modular Synthetic Biology Toolkit for Filamentous Fungi | 2 | 2 | ⭐ |
| Point-of-Care Analyte Quantification and Digital Readout via Lysate-Based Cell-Free Biosensors Interfaced with Personal Glucose Monitors | 2 | 0 | |
| CRISPR-Cas-Mediated Tethering Recruits the Yeast HMR Mating-Type Locus to the Nuclear Periphery but Fails to Silence Gene Expression | 1 | 0 | |
| Characterization of Constitutive Promoters for the Elicitation of Secondary Metabolites in Myxobacteria | 2 | 2 | ⭐ |
| Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application | 1 | 1 | ⭐ |
| A Novel and Efficient Genome Editing Tool Assisted by CRISPR-Cas12a/Cpf1 for Pichia pastoris | 2 | 2 | ⭐ |
| Yeast Surface Display for In Vitro Biosynthetic Pathway Reconstruction | 1 | 0 | |
| Engineering a Supersecreting Strain of Escherichia coli by Directed Coevolution of the Multiprotein Tat Translocation Machinery | 2 | 0 | |
| Improved Stability of Engineered Ammonia Production in the Plant-Symbiont Azospirillum brasilense | 3 | 3 | ⭐ |
| Strategy for Producing the High-Quality Glycopeptide Antibiotic A82846B in Amycolatopsis orientalis Based on the CRISPR-Cas12a System | 1 | 1 | ⭐ |
| Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis | 2 | 2 | ⭐ |
| Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems | 3 | 3 | ⭐ |
| Development of a Transcription Factor-Based Diamine Biosensor in Corynebacterium glutamicum | 4 | 4 | ⭐ |
| Broadening the Toolkit for Quantitatively Evaluating Noncanonical Amino Acid Incorporation in Yeast | 1 | 0 | |
| Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development | 1 | 1 | ⭐ |
| Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription | 2 | 0 | |
| Synthetic Biology Curation Tools (SYNBICT) | 1 | 1 | ⭐ |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast | 2 | 2 | ⭐ |
| The ProUSER2.0 Toolbox: Genetic Parts and Highly Customizable Plasmids for Synthetic Biology in Bacillus subtilis | 1 | 0 | |
| RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates | 1 | 1 | ⭐ |
| Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits | 4 | 4 | ⭐ |
| Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity | 4 | 4 | ⭐ |
| Biosynthesis of Poly(3HB-co-3HP) with Variable Monomer Composition in Recombinant Cupriavidus necator H16 | 2 | 2 | ⭐ |
| Exploiting Noise, Non-Linearity, and Feedback for Differential Control of Multiple Synthetic Cells with a Single Optogenetic Input | 1 | 0 | |
| An Optogenetic Toolbox for Synergistic Regulation of Protein Abundance | 3 | 0 | |
| Expansion of the Yeast Modular Cloning Toolkit for CRISPR-Based Applications, Genomic Integrations and Combinatorial Libraries | 5 | 0 | |
| Channeling Anabolic Side Products toward the Production of Nonessential Metabolites: Stable Malate Production in Synechocystis sp. PCC6803 | 1 | 0 | |
| Engineered l-Lactate Responding Promoter System Operating in Glucose-Rich and Anoxic Environments | 2 | 2 | ⭐ |
| Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering | 1 | 0 |
