2020 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 302
- Total Figures in All Articles: 1455
- Figures Compatible with SBOL Visual: 339 (23.3%)
- Figures Compatible with SBOL Visual & Fully Compliant: 275 (81.12%)
- Figures Compatible with SBOL Visual & Following Best Practices: 128 (37.76%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor | 3 | 0 | |
| Design of Mammalian ON-Riboswitches Based on Tandemly Fused Aptamer and Ribozyme | 1 | 1 | ⭐ |
| Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida | 3 | 0 | |
| Artificial Cells Capable of Long-Lived Protein Synthesis by Using Aptamer Grafted Polymer Hydrogel | 1 | 0 | |
| Design of a Transcriptional Biosensor for the Portable, On-Demand Detection of Cyanuric Acid | 3 | 3 | ⭐ |
| Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices | 3 | 3 | ⭐ |
| Tunable Repression of Key Photosynthetic Processes Using Cas12a CRISPR Interference in the Fast-Growing Cyanobacterium Synechococcus sp. UTEX 2973 | 3 | 2 | |
| Cell-Free Protein Synthesis as a Prototyping Platform for Mammalian Synthetic Biology | 5 | 5 | ⭐ |
| Orthogonal Protein-Responsive mRNA Switches for Mammalian Synthetic Biology | 1 | 0 | |
| mpCRISTAR: Multiple Plasmid Approach for CRISPR/Cas9 and TAR-Mediated Multiplexed Refactoring of Natural Product Biosynthetic Gene Clusters | 2 | 0 |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast | 3 | 1 | |
| Light-Inducible Recombinases for Bacterial Optogenetics | 2 | 0 | |
| Engineering a DNAzyme-Based Operon System for the Production of DNA Nanoscaffolds in Living Bacteria | 3 | 2 | |
| Heterologous Production of Lasso Peptide Capistruin in a Burkholderia Host | 1 | 1 | ⭐ |
| Daisy Chain Topology Based Mammalian Synthetic Circuits for RNA-Only Delivery | 9 | 9 | ⭐ |
| A Validamycin Shunt Pathway for Valienamine Synthesis in Engineered Streptomyces hygroscopicus 5008 | 1 | 1 | ⭐ |
| Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing | 2 | 2 | ⭐ |
| Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation | 2 | 2 | ⭐ |
| A Multifunction Lipid-Based CRISPR-Cas13a Genetic Circuit Delivery System for Bladder Cancer Gene Therapy | 1 | 1 | ⭐ |
| Genetic Encoding of Targeted Magnetic Resonance Imaging Contrast Agents for Tumor Imaging | 1 | 0 | |
| Active Analyte Import Improves the Dynamic Range and Sensitivity of a Vitamin B12 Biosensor | 3 | 2 | |
| Engineered Recombinant Escherichia coli Probiotic Strains Integrated with F4 and F18 Fimbriae Cluster Genes in the Chromosome and Their Assessment of Immunogenic Efficacy in Vivo | 2 | 1 | |
| De Novo Designed Protein-Interaction Modules for In-Cell Applications | 3 | 3 | ⭐ |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers | 1 | 1 | ⭐ |
| Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol | 1 | 0 | |
| Genetic Code Expansion, Protein Expression, and Protein Functionalization in Bacillus subtilis | 4 | 0 | |
| SPLIT: Stable Protein Coacervation Using a Light Induced Transition | 1 | 0 | |
| Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering | 1 | 0 | |
| Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection | 3 | 3 | ⭐ |
| Development of High-Performance Whole Cell Biosensors Aided by Statistical Modeling | 5 | 0 | |
| Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System | 1 | 1 | ⭐ |
| New Insight into Plasmid-Driven T7 RNA Polymerase in Escherichia coli and Use as a Genetic Amplifier for a Biosensor | 3 | 1 | |
| Expanding the CRISPR Toolbox in Culicine Mosquitoes: In Vitro Validation of Pol III Promoters | 1 | 1 | ⭐ |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| A New Biosensor for Stilbenes and a Cannabinoid Enabled by Genome Mining of a Transcriptional Regulator | 3 | 1 | |
| Balancing Cell Populations Endowed with a Synthetic Toggle Switch via Adaptive Pulsatile Feedback Control | 1 | 0 | |
| Comparative Dose–Response Analysis of Inducible Promoters in Cyanobacteria | 5 | 0 | |
| Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha | 5 | 4 | |
| Designing an Artificial Pathway for the Biosynthesis of a Novel Phenazine N-Oxide in Pseudomonas chlororaphis HT66 | 2 | 2 | ⭐ |
| Toolkit Development for Cyanogenic and Gold Biorecovery Chassis Chromobacterium violaceum | 3 | 3 | ⭐ |
| SBOL Visual 2 Ontology | 3 | 3 | ⭐ |
May
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Multiplex Generation, Tracking, and Functional Screening of Substitution Mutants Using a CRISPR/Retron System | 3 | 3 | ⭐ |
| A Synthetic Genetic Circuit Enables Precise Quantification of Direct Repeat Deletion in Bacteria | 2 | 0 | |
| A Synthetic Malonyl-CoA Metabolic Oscillator in Komagataella phaffii | 4 | 4 | ⭐ |
| Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli | 2 | 1 | |
| A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks | 2 | 0 | |
| Engineering Stable Pseudomonas putida S12 by CRISPR for 2,5-Furandicarboxylic Acid (FDCA) Production | 4 | 1 | |
| A Novel Biosynthetic Pathway for the Production of Acrylic Acid through β-Alanine Route in Escherichia coli | 3 | 3 | ⭐ |
| Introduction of the Menaquinone Biosynthetic Pathway into Rhodobacter sphaeroides and de Novo Synthesis of Menaquinone for Incorporation into Heterologously Expressed Integral Membrane Proteins | 2 | 1 |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Microbial Synthesis of Human-Hormone Melatonin at Gram Scales | 1 | 0 | |
| Comprehensive Analysis of Genomic Safe Harbors as Target Sites for Stable Expression of the Heterologous Gene in HEK293 Cells | 2 | 0 | |
| Dynamic Cell Programming with Quorum Sensing-Controlled CRISPRi Circuit | 3 | 0 | |
| A Small-Molecule-Responsive Riboswitch Enables Conditional Induction of Viral Vector-Mediated Gene Expression in Mice | 5 | 0 | |
| Two-Component Biosensors: Unveiling the Mechanisms of Predictable Tunability | 1 | 1 | ⭐ |
| Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences | 1 | 1 | ⭐ |
| sRNA-Based Screening Chromosomal Gene Targets and Modular Designing Escherichia coli for High-Titer Production of Aglycosylated Immunoglobulin G | 3 | 0 | |
| Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid Based on Stereochemistry Regulation in Bacillus amyloliquefaciens | 1 | 0 | |
| Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas | 4 | 4 | ⭐ |
| Construction of Inducible Genetic Switch for the Global Regulator WblA To Sustain Both Overproduction of Tiancimycins and On-Demand Sporulation in Streptomyces sp. CB03234 | 3 | 0 | |
| Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli | 1 | 0 |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop | 2 | 0 | |
| Purification of an Intact Human Protein Overexpressed from Its Endogenous Locus via Direct Genome Engineering | 1 | 0 | |
| Artificial Protein-Responsive Riboswitches Upregulate Non-AUG Translation Initiation in Yeast | 6 | 0 | |
| Controlled Functional Zonation of Hepatocytes In Vitro by Engineering of Wnt Signaling | 1 | 0 | |
| Universal Actuator for Efficient Silencing of Escherichia coli Genes Based on Convergent Transcription Resistant to Rho-Dependent Termination | 3 | 3 | ⭐ |
| Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection | 1 | 0 | |
| Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories | 2 | 0 | |
| A Library of Tunable, Portable, and Inducer-Free Promoters Derived from Cyanobacteria | 1 | 1 | ⭐ |
| Identification of a Strong Quorum Sensing- and Thermo-Regulated Promoter for the Biosynthesis of a New Metabolite Pesticide Phenazine-1-carboxamide in Pseudomonas strain PA1201 | 1 | 1 | ⭐ |
| Highly Efficient Production of l-Histidine from Glucose by Metabolically Engineered Escherichia coli | 1 | 1 | ⭐ |
| MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics | 1 | 1 | ⭐ |
| CRISPR-Mediated Activation of Biosynthetic Gene Clusters for Bioactive Molecule Discovery in Filamentous Fungi | 3 | 1 | |
| Development of a Proline-Based Selection System for Reliable Genetic Engineering in Chinese Hamster Ovary Cells | 5 | 5 | ⭐ |
| Mapping Protein–Protein Interaction Interface Peptides with Jun-Fos Assisted Phage Display and Deep Sequencing | 2 | 2 | ⭐ |
| De Novo Engineering of Corynebacterium glutamicum for l-Proline Production | 3 | 0 | |
| Site-Directed Mutagenesis of Large Biosynthetic Gene Clusters via Oligonucleotide Recombineering and CRISPR/Cas9 Targeting | 2 | 0 |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Applications of CRISPR in a Microbial Cell Factory: From Genome Reconstruction to Metabolic Network Reprogramming | 3 | 0 | |
| FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data | 1 | 1 | ⭐ |
| Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes | 1 | 0 | |
| Optogenetic Control of Heterologous Metabolism in E. coli | 1 | 0 | |
| Tuning Extracellular Electron Transfer by Shewanella oneidensis Using Transcriptional Logic Gates | 4 | 4 | ⭐ |
| Conditional Recruitment to a DNA-Bound CRISPR–Cas Complex Using a Colocalization-Dependent Protein Switch | 4 | 0 | |
| Genetic Circuit Dynamics: Hazard and Glitch Analysis | 2 | 2 | ⭐ |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| In Vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli Using Microfluidics | 1 | 1 | ⭐ |
| Construction of Fully Segregated Genomic Libraries in Polyploid Organisms Such as Synechocystis sp. PCC 6803 | 2 | 0 | |
| Securing the Exchange of Synthetic Genetic Constructs Using Digital Signatures | 2 | 0 | |
| Homologous Quorum Sensing Regulatory Circuit: A Dual-Input Genetic Controller for Modulating Quorum Sensing-Mediated Protein Expression in E. coli | 2 | 2 | ⭐ |
| Design, Evolution, and Characterization of a Xylose Biosensor in Escherichia coli Using the XylR/xylO System with an Expanded Operating Range | 1 | 0 | |
| A RAGE Based Strategy for the Genome Engineering of the Human Respiratory Pathogen Mycoplasma pneumoniae | 2 | 2 | ⭐ |
| Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida | 1 | 0 | |
| Exploiting Single Domain Antibodies as Regulatory Parts to Modulate Monoterpenoid Production in E. coli | 1 | 0 | |
| Protecting Linear DNA Templates in Cell-Free Expression Systems from Diverse Bacteria | 1 | 1 | ⭐ |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits | 3 | 0 | |
| Integrative Biosynthetic Gene Cluster Mining to Optimize a Metabolic Pathway to Efficiently Produce l-Homophenylalanine in Escherichia coli | 3 | 0 | |
| Biosynthesis of the Calorie-Free Sweetener Precursor ent-Kaurenoic Acid from CO2 Using Engineered Cyanobacteria | 1 | 1 | ⭐ |
| Aptamer-Mediated Control of Polyadenylation for Gene Expression Regulation in Mammalian Cells | 5 | 0 | |
| De Novo Biosynthesis of Multiple Pinocembrin Derivatives in Saccharomyces cerevisiae | 1 | 1 | ⭐ |
| Decoupling Protein Production from Cell Growth Enhances the Site-Specific Incorporation of Noncanonical Amino Acids in E. coli | 1 | 0 | |
| Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction | 2 | 2 | ⭐ |
| A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas | 1 | 1 | ⭐ |
| Optimally Designed Model Selection for Synthetic Biology | 1 | 0 | |
| An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models | 1 | 1 | ⭐ |
| A Lambda Red and FLP/FRT-Mediated Site-Specific Recombination System in Komagataeibacter xylinus and Its Application to Enhance the Productivity of Bacterial Cellulose | 1 | 0 |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Living Therapeutics: The Next Frontier of Precision Medicine | 2 | 2 | ⭐ |
| A Logic NAND Gate for Controlling Gene Expression in a Circadian Rhythm in Cyanobacteria | 3 | 3 | ⭐ |
| Automating Cloning by Natural Transformation | 4 | 4 | ⭐ |
| Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential | 1 | 1 | ⭐ |
| Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering | 2 | 0 | |
| Analysis of Complex DNA Rearrangements during Early Stages of HAC Formation | 5 | 0 | |
| Synthetic Virus-like Particles for Glutathione Biosynthesis | 1 | 0 | |
| Random Chromosomal Integration and Screening Yields E. coli K-12 Derivatives Capable of Efficient Sucrose Utilization | 3 | 0 | |
| Creating Red Light-Switchable Protein Dimerization Systems as Genetically Encoded Actuators with High Specificity | 2 | 0 | |
| Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage | 1 | 0 | |
| Single Cell Characterization of a Synthetic Bacterial Clock with a Hybrid Feedback Loop Containing dCas9-sgRNA | 2 | 1 | |
| In Vivo Biogenesis of a De Novo Designed Iron–Sulfur Protein | 1 | 0 |
