2018 ACS Synthetic Biology Issues
Summary
- Total Articles Analyzed: 305
- Total Figures in All Articles: 1615
- Figures Compatible with SBOL Visual: 429 (26.56%)
- Figures Compatible with SBOL Visual & Fully Compliant: 242 (56.41%)
- Figures Compatible with SBOL Visual & Following Best Practices: 98 (22.84%)
Individual issues
January
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Multiplexed CRISPR/Cas9 Genome Editing and Gene Regulation Using Csy4 in Saccharomyces cerevisiae | 3 | 0 | |
| Design and Selection of a Synthetic Feedback Loop for Optimizing Biofuel Tolerance | 2 | 0 | |
| Dynamic Control of Aptamer–Ligand Activity Using Strand Displacement Reactions | 2 | 2 | ⭐ |
| Reconfigurable Analog Signal Processing by Living Cells | 1 | 0 | |
| Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology | 1 | 1 | ⭐ |
| A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria | 3 | 1 | |
| A Prototype for Modular Cell Engineering | 4 | 4 | ⭐ |
| Engineering an E. coli Near-Infrared Light Sensor | 2 | 2 | ⭐ |
| Development of a Pigment-Based Whole-Cell Zinc Biosensor for Human Serum | 1 | 1 | ⭐ |
February
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia | 2 | 2 | ⭐ |
| Gene-Mediated Chemical Communication in Synthetic Protocell Communities | 1 | 1 | ⭐ |
| Metabolic Feedback Circuits Provide Rapid Control of Metabolite Dynamics | 3 | 2 | |
| Native and Engineered Clifednamide Biosynthesis in Multiple Streptomyces spp. | 1 | 1 | ⭐ |
| High-CO2 Requirement as a Mechanism for the Containment of Genetically Modified Cyanobacteria | 1 | 1 | ⭐ |
| Functional Characterization of Insulation Effect for Synthetic Gene Circuits in Mammalian Cells | 3 | 0 | |
| Perfect Adaptation and Optimal Equilibrium Productivity in a Simple Microbial Biofuel Metabolic Pathway Using Dynamic Integral Control | 1 | 1 | ⭐ |
| TARSyn: Tunable Antibiotic Resistance Devices Enabling Bacterial Synthetic Evolution and Protein Production | 5 | 5 | ⭐ |
| Sporobeads: The Utilization of the Bacillus subtilis Endospore Crust as a Protein Display Platform | 2 | 1 | |
| A Workflow for In Vivo Evaluation of Candidate Inputs and Outputs for Cell Classifier Gene Circuits | 3 | 1 | |
| An Autoregulated Fine-Tuning Strategy for Titer Improvement of Secondary Metabolites Using Native Promoters in Streptomyces | 2 | 0 | |
| Quantitatively Predictable Control of Cellular Protein Levels through Proteasomal Degradation | 2 | 0 | |
| Orthogonality and Burdens of Heterologous AND Gate Gene Circuits in E. coli | 2 | 0 | |
| New Intracellular Shikimic Acid Biosensor for Monitoring Shikimate Synthesis in Corynebacterium glutamicum | 2 | 1 | |
| Toward Predictable 5′UTRs in Saccharomyces cerevisiae: Development of a yUTR Calculator | 4 | 1 | |
| Reprogramming One-Carbon Metabolic Pathways To Decouple l-Serine Catabolism from Cell Growth in Corynebacterium glutamicum | 2 | 1 | |
| Photosynthetic Production of Sunscreen Shinorine Using an Engineered Cyanobacterium | 1 | 1 | ⭐ |
| SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology | 1 | 1 | ⭐ |
| Biosynthesis of Orthogonal Molecules Using Ferredoxin and Ferredoxin-NADP+ Reductase Systems Enables Genetically Encoded PhyB Optogenetics | 5 | 0 | |
| Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630 | 1 | 0 |
March
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Labeling RNAs in Live Cells Using Malachite Green Aptamer Scaffolds as Fluorescent Probes | 3 | 3 | ⭐ |
| Directed Evolution of Membrane Transport Using Synthetic Selections | 1 | 1 | ⭐ |
| Rewiring Calcium Signaling for Precise Transcriptional Reprogramming | 3 | 1 | |
| Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data | 1 | 0 | |
| Tandem Histone-Binding Domains Enhance the Activity of a Synthetic Chromatin Effector | 2 | 0 | |
| Multilevel Regulation of Bacterial Gene Expression with the Combined STAR and Antisense RNA System | 3 | 1 | |
| Expanding One-Pot Cell-Free Protein Synthesis and Immobilization for On-Demand Manufacturing of Biomaterials | 1 | 1 | ⭐ |
| Modular Engineering Intracellular NADH Regeneration Boosts Extracellular Electron Transfer of Shewanella oneidensis MR-1 | 2 | 2 | ⭐ |
| Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils | 3 | 2 |
April
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering a Dual Small Molecule Gated ZAP70 Switch in T Cells | 1 | 1 | ⭐ |
| Cell-Free Optogenetic Gene Expression System | 2 | 2 | ⭐ |
| A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria | 1 | 1 | ⭐ |
| T7 Polymerase Expression of Guide RNAs in vivo Allows Exportable CRISPR-Cas9 Editing in Multiple Yeast Hosts | 1 | 0 | |
| Engineered Production of Short-Chain Acyl-Coenzyme A Esters in Saccharomyces cerevisiae | 1 | 0 | |
| Generation of a Synthetic Human Chromosome with Two Centromeric Domains for Advanced Epigenetic Engineering Studies | 4 | 0 | |
| Development of a Plasmid-Free Biosynthetic Pathway for Enhanced Muconic Acid Production in Pseudomonas chlororaphis HT66 | 3 | 1 |
May
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering the Ultrasensitive Transcription Factors by Fusing a Modular Oligomerization Domain | 1 | 1 | ⭐ |
| Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression | 1 | 0 | |
| Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection | 2 | 0 | |
| Exploring the Promiscuity of Phenol Hydroxylase from Pseudomonas stutzeri OX1 for the Biosynthesis of Phenolic Compounds | 1 | 1 | ⭐ |
| Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State | 1 | 0 | |
| Modularization and Response Curve Engineering of a Naringenin-Responsive Transcriptional Biosensor | 5 | 1 | |
| Overproduction of Fatty Acid Ethyl Esters by the Oleaginous Yeast Yarrowia lipolytica through Metabolic Engineering and Process Optimization | 1 | 1 | ⭐ |
| An Automated Design Framework for Multicellular Recombinase Logic | 3 | 2 | |
| A Transcription Factor-Based Biosensor for Detection of Itaconic Acid | 2 | 2 | ⭐ |
June
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design | 2 | 0 | |
| An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth | 1 | 1 | ⭐ |
| Probing Intercell Variability Using Bulk Measurements | 1 | 0 | |
| Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation | 1 | 1 | ⭐ |
July
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Rationalizing Context-Dependent Performance of Dynamic RNA Regulatory Devices | 2 | 2 | ⭐ |
| Mutually Orthogonal DNA Replication Systems In Vivo | 3 | 0 | |
| Exploring the Nonconserved Sequence Space of Synthetic Expression Modules in Bacillus subtilis | 1 | 1 | ⭐ |
August
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Predicting Transcriptional Output of Synthetic Multi-input Promoters | 3 | 0 | |
| Promoter Engineering for Enhanced P(3HB-co-4HB) Production by Halomonas bluephagenesis | 2 | 0 | |
| An Engineered Constitutive Promoter Set with Broad Activity Range for Cupriavidus necator H16 | 4 | 2 | |
| Fluorescent Guide RNAs Facilitate Development of Layered Pol II-Driven CRISPR Circuits | 3 | 0 |
September
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Human Artificial Chromosome with Regulated Centromere: A Tool for Genome and Cancer Studies | 6 | 1 | |
| A Biosensor Strategy for E. coli Based on Ligand-Dependent Stabilization | 1 | 0 | |
| Engineering Riboswitches in Vivo Using Dual Genetic Selection and Fluorescence-Activated Cell Sorting | 1 | 0 | |
| A Synthetic Microbial Operational Amplifier | 4 | 0 | |
| A Single-Component Optogenetic System Allows Stringent Switch of Gene Expression in Yeast Cells | 2 | 0 | |
| Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii | 6 | 2 | |
| Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational–Experimental Platform | 1 | 0 | |
| A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit | 4 | 0 | |
| A Robust and Quantitative Reporter System To Evaluate Noncanonical Amino Acid Incorporation in Yeast | 2 | 0 | |
| Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut | 1 | 1 | ⭐ |
| Metabolic Engineering of Escherichia coli for Efficient Production of 2-Pyrone-4,6-dicarboxylic Acid from Glucose | 2 | 0 | |
| Large Scale Synthetic Site Saturation GPCR Libraries Reveal Novel Mutations That Alter Glucose Signaling | 2 | 0 |
October
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| A Genetically Encoded Protein Polymer for Uranyl Binding and Extraction Based on the SpyTag–SpyCatcher Chemistry | 1 | 1 | ⭐ |
| A Genetically Encoded Biosensor for Monitoring Isoprene Production in Engineered Escherichia coli | 3 | 1 | |
| Artificial Repeat-Structured siRNA Precursors as Tunable Regulators for Saccharomyces cerevisiae | 4 | 0 | |
| Enhancing Light-Driven 1,3-Propanediol Production by Using Natural Compartmentalization of Differentiated Cells | 3 | 2 |
November
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Rational Control of Calcium Carbonate Precipitation by Engineered Escherichia coli | 1 | 0 | |
| Transcription Driven by Reversible Photocontrol of Hyperstable G-Quadruplexes | 1 | 0 | |
| Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control | 2 | 0 | |
| Systematic Analysis of Bottlenecks in a Multibranched and Multilevel Regulated Pathway: The Molecular Fundamentals of l-Methionine Biosynthesis in Escherichia coli | 1 | 0 | |
| Retroelement-Based Genome Editing and Evolution | 4 | 0 | |
| Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System | 3 | 1 | |
| A Yeast-Based Biosensor for Screening of Short- and Medium-Chain Fatty Acid Production | 1 | 1 | ⭐ |
| Highly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus | 1 | 1 | ⭐ |
| Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias | 1 | 1 | ⭐ |
December
| Article | No. of SBOL Visual compliant images | No. of SBOL Visual images following Best practices | |
|---|---|---|---|
| Selective Enrichment of Slow-Growing Bacteria in a Metabolism-Wide CRISPRi Library with a TIMER Protein | 1 | 1 | ⭐ |
| Cell-Based Biosensor with Dual Signal Outputs for Simultaneous Quantification of Phenylacetic Acid and Phenylethylamine | 1 | 0 | |
| A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference | 2 | 2 | ⭐ |
| Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to the Antimalarial Drug Fosmidomycin in E. coli | 1 | 0 | |
| An Optimized Bistable Metabolic Switch To Decouple Phenotypic States during Anaerobic Fermentation | 4 | 1 | |
| Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators | 3 | 3 | ⭐ |
| Phosphate Lock Residues of Acidothermus cellulolyticus Cas9 Are Critical to Its Substrate Specificity | 2 | 1 |
