diff --git a/content/sbolv-10-years/acs-2012.md b/content/sbolv-10-years/acs-2012.md new file mode 100644 index 00000000..32d29903 --- /dev/null +++ b/content/sbolv-10-years/acs-2012.md @@ -0,0 +1,70 @@ +--- +title: 2012 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 63 +- **Total Figures in All Articles:** 340 +- **Figures Compatible with SBOL Visual:** 87 (25.59%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 36 (41.38%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 18 (20.69%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli|1|0|| +|j5 DNA Assembly Design Automation Software|3|1|| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains|1|0|| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli|4|0|| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications|4|2|| +|Computational Modeling of Synthetic Microbial Biofilms|1|1|:star:| +|Hierarchical Modeling for Synthetic Biology|7|7|:star:| +|Specification and Simulation of Synthetic Multicelled Behaviors|3|3|:star:| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|A Synthetic Biology Approach to Understanding Cellular Information Processing|2|0|| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Stable Maintenance of Multiple Plasmids in E. coli Using a Single Selective Marker|2|0|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Rational Design of Escherichia coli for l-Isoleucine Production|1|1|:star:| +|Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors|1|1|:star:| diff --git a/content/sbolv-10-years/acs-2013.md b/content/sbolv-10-years/acs-2013.md new file mode 100644 index 00000000..4b20d634 --- /dev/null +++ b/content/sbolv-10-years/acs-2013.md @@ -0,0 +1,100 @@ +--- +title: 2013 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 80 +- **Total Figures in All Articles:** 408 +- **Figures Compatible with SBOL Visual:** 99 (24.26%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 61 (61.62%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 36 (36.36%) +# Individual issues + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthesizing Biomolecule-Based Boolean Logic Gates|3|3|:star:| +|Self-Assembly of Synthetic Metabolons through Synthetic Protein Scaffolds: One-Step Purification, Co-immobilization, and Substrate Channeling|2|2|:star:| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Tuning Primary Metabolism for Heterologous Pathway Productivity|1|0|| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Dynamic Modeling of Cellular Populations within iBioSim|1|0|| +|AutoBioCAD: Full Biodesign Automation of Genetic Circuits|2|2|:star:| +|Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells|1|1|:star:| +|SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design|2|2|:star:| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Pigeon: A Design Visualizer for Synthetic Biology|1|1|:star:| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Biology of Antimicrobial Discovery|1|1|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Gene Circuit-Mediated Monitoring of Endogenous Metabolites: Identification of GAL11 as a Novel Multicopy Enhancer of S-Adenosylmethionine Level in Yeast|3|3|:star:| +|Retroactivity Controls the Temporal Dynamics of Gene Transcription|1|0|| +|Analysis and Design of a Genetic Circuit for Dynamic Metabolic Engineering|1|0|| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways|5|5|:star:| +|Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits|2|2|:star:| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Tuning Response Curves for Synthetic Biology|3|0|| +|Engineering the esaR Promoter for Tunable Quorum Sensing-Dependent Gene Expression|1|0|| +|Reliable Prediction of Complex Phenotypes from a Modular Design in Free Energy Space: An Extensive Exploration of the lac Operon|1|0|| +|Expanding the Boolean Logic of the Prokaryotic Transcription Factor XylR by Functionalization of Permissive Sites with a Protease-Target Sequence|6|0|| +|Genetic Sensor for Strong Methylating Compounds|2|2|:star:| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Discovery of Cryptic Polyketide Metabolites from Dermatophytes Using Heterologous Expression in Aspergillus nidulans|2|2|:star:| +|Sequence, Cloning, and Analysis of the Fluvirucin B1 Polyketide Synthase from Actinomadura vulgaris|1|1|:star:| +|Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences|4|3|| +|Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold|2|2|:star:| +|Facile Method for Site-specific Gene Integration in Lysobacter enzymogenes for Yield Improvement of the Anti-MRSA Antibiotics WAP-8294A and the Antifungal Antibiotic HSAF|2|2|:star:| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Artificial Conversion of the Mating-Type of Saccharomyces cerevisiae without Autopolyploidization|4|0|| +|Cell Polarity-Driven Instability Generates Self-Organized, Fractal Patterning of Cell Layers|1|0|| +|Yeast Oligo-Mediated Genome Engineering (YOGE)|1|0|| diff --git a/content/sbolv-10-years/acs-2014.md b/content/sbolv-10-years/acs-2014.md new file mode 100644 index 00000000..12c1c845 --- /dev/null +++ b/content/sbolv-10-years/acs-2014.md @@ -0,0 +1,107 @@ +--- +title: 2014 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 118 +- **Total Figures in All Articles:** 531 +- **Figures Compatible with SBOL Visual:** 113 (21.28%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 53 (46.9%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 27 (23.89%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways|1|1|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Bi-HAC Vector System toward Gene and Cell Therapy|3|0|| +|Engineered DNA Sequence Syntax Inspector|2|2|:star:| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli|1|1|:star:| +|Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli|2|2|:star:| +|Toward a Generalized and High-throughput Enzyme Screening System Based on Artificial Genetic Circuits|2|0|| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering Multicellular Logic in Bacteria with Metabolic Wires|2|2|:star:| +|Evolved Quorum Sensing Regulator, LsrR, for Altered Switching Functions|1|0|| +|Generic Metric to Quantify Quorum Sensing Activation Dynamics|2|1|| +|Reprogramming Microbes to Be Pathogen-Seeking Killers|1|1|:star:| +|Quorum Sensing-Modulated AND-Gate Promoters Control Gene Expression in Response to a Combination of Endogenous and Exogenous Signals|1|0|| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering|1|1|:star:| +|MicroRNA-Based Single-Gene Circuits Buffer Protein Synthesis Rates against Perturbations|2|0|| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Gene Position More Strongly Influences Cell-Free Protein Expression from Operons than T7 Transcriptional Promoter Strength|2|2|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|PR-PR: Cross-Platform Laboratory Automation System|2|2|:star:| +|Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation|2|1|| +|Biological 2-Input Decoder Circuit in Human Cells|1|0|| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|General Applicability of Synthetic Gene-Overexpression for Cell-Type Ratio Control via Reprogramming|1|0|| +|Framework for Engineering Finite State Machines in Gene Regulatory Networks|3|1|| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Development of an Artificial Calcium-Dependent Transcription Factor To Detect Sustained Intracellular Calcium Elevation|1|0|| +|Rule-Based Design of Synthetic Transcription Factors in Eukaryotes|1|0|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Near-infrared Light Responsive Synthetic c-di-GMP Module for Optogenetic Applications|3|3|:star:| +|Refactoring and Optimization of Light-Switchable Escherichia coli Two-Component Systems|2|1|| +|A Golden Gate Modular Cloning Toolbox for Plants|2|1|| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells|3|3|:star:| +|Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation|1|0|| +|Natural LacI from E. coli Yields Faster Response and Higher Level of Expression than the LVA-Tagged LacI|1|1|:star:| +|Standardization of Functional Reporter and Antibiotic Resistance Cassettes to Facilitate the Genetic Engineering of Filamentous Fungi|1|1|:star:| +|Solving a Four-Destination Traveling Salesman Problem Using Escherichia coli Cells As Biocomputers|2|0|| diff --git a/content/sbolv-10-years/acs-2015.md b/content/sbolv-10-years/acs-2015.md new file mode 100644 index 00000000..24730c56 --- /dev/null +++ b/content/sbolv-10-years/acs-2015.md @@ -0,0 +1,122 @@ +--- +title: 2015 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 145 +- **Total Figures in All Articles:** 743 +- **Figures Compatible with SBOL Visual:** 177 (23.82%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 107 (60.45%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 38 (21.47%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Model-Driven Engineering of Gene Expression from RNA Replicons|1|0|| +|Proposed Data Model for the Next Version of the Synthetic Biology Open Language|4|4|:star:| +|Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures|2|0|| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|A Synthetic Anhydrotetracycline-Controllable Gene Expression System in Ralstonia eutropha H16|4|4|:star:| +|Noise Propagation in Synthetic Gene Circuits for Metabolic Control|1|0|| +|Negative Feedback Regulation of Fatty Acid Production Based on a Malonyl-CoA Sensor–Actuator|3|0|| +|Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control|1|1|:star:| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|RADOM, an Efficient In Vivo Method for Assembling Designed DNA Fragments up to 10 kb Long in Saccharomyces cerevisiae|4|0|| +|Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences|1|0|| +|Using Dynamic Noise Propagation to Infer Causal Regulatory Relationships in Biochemical Networks|1|0|| +|Assembly of Highly Standardized Gene Fragments for High-Level Production of Porphyrins in E. coli|2|0|| +|RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering|1|0|| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Rapid Evaluation of Tyrosine Kinase Activity of Membrane-Integrated Human Epidermal Growth Factor Receptor Using the Yeast Gγ Recruitment System|1|0|| +|A Set of Versatile Brick Vectors and Promoters for the Assembly, Expression, and Integration of Synthetic Operons in Methylobacterium extorquens AM1 and Other Alphaproteobacteria|1|0|| +|Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells|1|0|| +|Programming Controlled Adhesion of E. coli to Target Surfaces, Cells, and Tumors with Synthetic Adhesins|1|1|:star:| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems|6|6|:star:| +|Synthetic Tunable Amplifying Buffer Circuit in E. coli|2|0|| +|Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae|5|0|| +|Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002|2|0|| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition|4|0|| +|Expansion of Bisindole Biosynthetic Pathways by Combinatorial Construction|1|0|| +|Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems|1|0|| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology|1|1|:star:| +|Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain|1|0|| +|Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway|1|1|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language|3|3|:star:| +|Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis|1|0|| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector–Coding Sequence Junction|1|0|| +|Regulation of Bacterial Gene Expression by Protease-Alleviated Spatial Sequestration (PASS)|4|0|| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli|1|0|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria|5|4|| +|A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy|1|0|| +|CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae|2|0|| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain|1|0|| +|Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening|1|0|| +|Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum|2|0|| +|Evolutionary Design of Choline-Inducible and -Repressible T7-Based Induction Systems|2|0|| +|Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability|3|3|:star:| diff --git a/content/sbolv-10-years/acs-2016.md b/content/sbolv-10-years/acs-2016.md new file mode 100644 index 00000000..9201822b --- /dev/null +++ b/content/sbolv-10-years/acs-2016.md @@ -0,0 +1,136 @@ +--- +title: 2016 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 169 +- **Total Figures in All Articles:** 886 +- **Figures Compatible with SBOL Visual:** 217 (24.49%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 136 (62.67%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 90 (41.47%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Metabolic Engineering toward Sustainable Production of Nylon-6|1|1|:star:| +|Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9|4|0|| +|CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology|2|2|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Slowing Translation between Protein Domains by Increasing Affinity between mRNAs and the Ribosomal Anti-Shine–Dalgarno Sequence Improves Solubility|1|0|| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Multiple Gene Repression in Cyanobacteria Using CRISPRi|1|1|:star:| +|Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase|1|1|:star:| +|Circumvention of Learning Increases Intoxication Efficacy of Nematicidal Engineered Bacteria|1|1|:star:| +|Measurements of Gene Expression at Steady State Improve the Predictability of Part Assembly|3|3|:star:| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Automatic Control of Gene Expression in Mammalian Cells|1|0|| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs|1|1|:star:| +|Genotype Specification Language|1|1|:star:| +|A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language|4|4|:star:| +|The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs|1|1|:star:| +|Sharing Structure and Function in Biological Design with SBOL 2.0|3|3|:star:| +|Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems|3|3|:star:| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Two Distinct Cyclodipeptide Synthases from a Marine Actinomycete Catalyze Biosynthesis of the Same Diketopiperazine Natural Product|1|1|:star:| +|Optical Control of Peroxisomal Trafficking|1|0|| +|Multiplexed Targeted Genome Engineering Using a Universal Nuclease-Assisted Vector Integration System|3|3|:star:| +|Refactoring the Six-Gene Photosystem II Core in the Chloroplast of the Green Algae Chlamydomonas reinhardtii|1|0|| +|Synthetic Quorum Sensing and Cell–Cell Communication in Gram-Positive Bacillus megaterium|1|0|| +|Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals|3|0|| +|Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model|1|0|| +|A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes|2|2|:star:| +|Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable “Clean” Mutant Selection in Clostridium beijerinckii as an Example|4|4|:star:| +|Repurposing Synechocystis PCC6803 UirS–UirR as a UV-Violet/Green Photoreversible Transcriptional Regulatory Tool in E. coli|1|1|:star:| +|CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum|4|4|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Using RNA as Molecular Code for Programming Cellular Function|2|2|:star:| +|VisBOL: Web-Based Tools for Synthetic Biology Design Visualization|2|2|:star:| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Programming Surface Chemistry with Engineered Cells|1|1|:star:| +|Quorum Sensing Communication Modules for Microbial Consortia|3|2|| +|DATEL: A Scarless and Sequence-Independent DNA Assembly Method Using Thermostable Exonucleases and Ligase|2|2|:star:| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Mammalian Synthetic Biology: Time for Big MACs|2|2|:star:| +|EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology|2|0|| +|Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways|1|0|| +|Library-Aided Probing of Linker Determinants in Hybrid Photoreceptors|1|0|| +|An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology|3|2|| +|SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology|2|0|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Construction and Characterization of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells|4|0|| +|A Cell–Cell Communication-Based Screening System for Novel Microbes with Target Enzyme Activities|1|1|:star:| +|EcoExpress—Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli|1|1|:star:| +|Optimum Rebalancing of the 3-Hydroxypropionic Acid Production Pathway from Glycerol in Escherichia coli|1|0|| +|Metabolic Engineering of Escherichia coli for the Production of 3-Hydroxypropionic Acid and Malonic Acid through β-Alanine Route|1|0|| +|Microbial Synthesis of 5-Aminolevulinic Acid and Its Coproduction with Polyhydroxybutyrate|3|3|:star:| +|Biosensing Vibrio cholerae with Genetically Engineered Escherichia coli|3|3|:star:| +|Development of Colorimetric-Based Whole-Cell Biosensor for Organophosphorus Compounds by Engineering Transcription Regulator DmpR|1|1|:star:| +|Semirational Approach for Ultrahigh Poly(3-hydroxybutyrate) Accumulation in Escherichia coli by Combining One-Step Library Construction and High-Throughput Screening|1|1|:star:| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|The Geobacillus Plasmid Set: A Modular Toolkit for Thermophile Engineering|1|1|:star:| +|Combinatorial Pairwise Assembly Efficiently Generates High Affinity Binders and Enables a “Mix-and-Read” Detection Scheme|1|0|| +|Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors|3|0|| +|Tapping the Unused Potential of Photosynthesis with a Heterologous Electron Sink|1|1|:star:| +|C-Brick: A New Standard for Assembly of Biological Parts Using Cpf1|3|0|| +|Programming Saposin-Mediated Compensatory Metabolic Sinks for Enhanced Ubiquinone Production|1|0|| +|A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design|2|2|:star:| +|Development of Design Rules for Reliable Antisense RNA Behavior in E. coli|5|2|| +|Converting a Natural Protein Compartment into a Nanofactory for the Size-Constrained Synthesis of Antimicrobial Silver Nanoparticles|1|1|:star:| +|OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis|5|5|:star:| +|Multigene Pathway Engineering with Regulatory Linkers (M-PERL)|4|4|:star:| +|Biosynthesis of the High-Value Plant Secondary Product Benzyl Isothiocyanate via Functional Expression of Multiple Heterologous Enzymes in Escherichia coli|2|0|| diff --git a/content/sbolv-10-years/acs-2017.md b/content/sbolv-10-years/acs-2017.md new file mode 100644 index 00000000..870598ca --- /dev/null +++ b/content/sbolv-10-years/acs-2017.md @@ -0,0 +1,163 @@ +--- +title: 2017 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 242 +- **Total Figures in All Articles:** 1266 +- **Figures Compatible with SBOL Visual:** 285 (22.51%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 187 (65.61%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 115 (40.35%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli|1|1|:star:| +|Designing Synthetic Flexible Gene Regulation Networks Using RNA Devices in Cyanobacteria|1|1|:star:| +|Short Synthetic Terminators for Assembly of Transcription Units in Vitro and Stable Chromosomal Integration in Yeast S. cerevisiae|5|2|| +|Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering|3|3|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Discovery of a Phosphonoacetic Acid Derived Natural Product by Pathway Refactoring|1|0|| +|Direct Combinatorial Pathway Optimization|1|0|| +|Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies|5|4|| +|Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic–Organic Interfaces and Electrical Conductivity|1|0|| +|Resource Sharing Controls Gene Expression Bursting|1|0|| +|Characterization of Endogenous and Reduced Promoters for Oxygen-Limited Processes Using Escherichia coli|1|1|:star:| +|Reproducibility of High-Throughput Plate-Reader Experiments in Synthetic Biology|1|0|| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Standardized Markerless Gene Integration for Pathway Engineering in Yarrowia lipolytica|1|0|| +|Introduction of Premature Stop Codons as an Evolutionary Strategy To Rescue Signaling Network Function|2|0|| +|Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species|1|0|| +|Reprogramming the Transcriptional Response to Hypoxia with a Chromosomally Encoded Cyclic Peptide HIF-1 Inhibitor|2|0|| +|A Novel Approach for Gene Expression Optimization through Native Promoter and 5′ UTR Combinations Based on RNA-seq, Ribo-seq, and TSS-seq of Streptomyces coelicolor|1|0|| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design|1|0|| +|Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies|1|0|| +|Controlling Multicycle Replication of Live-Attenuated HIV-1 Using an Unnatural Genetic Switch|2|2|:star:| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters|3|3|:star:| +|Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9|2|1|| +|Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation|2|2|:star:| +|An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli|1|0|| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity|3|0|| +|Recursive DNA Assembly Using Protected Oligonucleotide Duplex Assisted Cloning (PODAC)|2|2|:star:| +|Extracellular Self-Assembly of Functional and Tunable Protein Conjugates from Bacillus subtilis|1|1|:star:| +|Tailoring Escherichia coli for the l-Rhamnose PBAD Promoter-Based Production of Membrane and Secretory Proteins|3|0|| +|Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces|4|4|:star:| +|A Modular Toolkit for Generating Pichia pastoris Secretion Libraries|5|5|:star:| +|Development of a Biosensor Concept to Detect the Production of Cluster-Specific Secondary Metabolites|2|1|| +|A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis|1|1|:star:| +|Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae|1|1|:star:| +|Obtaining a Panel of Cascade Promoter-5′-UTR Complexes in Escherichia coli|1|0|| +|The Impact of DNA Topology and Guide Length on Target Selection by a Cytosine-Specific Cas9|2|2|:star:| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data|5|5|:star:| +|SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design|3|3|:star:| +|A Validator and Converter for the Synthetic Biology Open Language|2|2|:star:| +|Simulation Approach for Timing Analysis of Genetic Logic Circuits|2|2|:star:| +|Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality|1|1|:star:| +|sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology|1|1|:star:| +|Improvement of Squalene Production from CO2 in Synechococcus elongatus PCC 7942 by Metabolic Engineering and Scalable Production in a Photobioreactor|2|0|| +|Measurement of In Vivo Protein Binding Affinities in a Signaling Network with Mass Spectrometry|2|1|| +|Genome Engineering of Virulent Lactococcal Phages Using CRISPR-Cas9|3|0|| +|Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor–Promoter Interplay|4|4|:star:| +|EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors|6|6|:star:| +|Construction and Rescue of a Functional Synthetic Baculovirus|2|2|:star:| +|Repurposing a Two-Component System-Based Biosensor for the Killing of Vibrio cholerae|2|2|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Amplifying Riboswitch Signal Output Using Cellular Wiring|2|2|:star:| +|Rational Design of an Ultrasensitive Quorum-Sensing Switch|1|1|:star:| +|Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis|1|1|:star:| +|A New Improved and Extended Version of the Multicell Bacterial Simulator gro|1|1|:star:| +|Synthetic Protein Scaffolds for Biosynthetic Pathway Colocalization on Lipid Droplet Membranes|2|2|:star:| +|Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid|1|1|:star:| +|Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol|1|1|:star:| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering a Native Inducible Expression System in Shewanella oneidensis to Control Extracellular Electron Transfer|2|2|:star:| +|Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens|2|2|:star:| +|Rapid Generation of Universal Synthetic Promoters for Controlled Gene Expression in Both Gas-Fermenting and Saccharolytic Clostridium Species|2|1|| +|Mini Photobioreactors for in Vivo Real-Time Characterization and Evolutionary Tuning of Bacterial Optogenetic Circuit|1|0|| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin|2|2|:star:| +|Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering|2|2|:star:| +|A Synthetic Circuit for Mercury Bioremediation Using Self-Assembling Functional Amyloids|1|0|| +|Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors|3|0|| +|Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering|1|1|:star:| +|A Versatile Toolbox for the Control of Protein Levels Using Nε-Acetyl-l-lysine Dependent Amber Suppression|4|0|| +|Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise|1|1|:star:| +|Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins|4|4|:star:| +|Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630|1|1|:star:| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|The Timing of Transcriptional Regulation in Synthetic Gene Circuits|3|0|| +|A Tug-of-War Mechanism for Pattern Formation in a Genetic Network|2|0|| +|A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage|1|1|:star:| +|Orthogonal Ribosome Biofirewall|5|0|| +|Genetic Design via Combinatorial Constraint Specification|2|2|:star:| +|Systematic Approaches to Efficiently Produce 2,3-Butanediol in a Marine Cyanobacterium|1|1|:star:| +|Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum|2|2|:star:| +|Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control|2|0|| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Production of Functional Anti-Ebola Antibodies in Pichia pastoris|1|0|| +|Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity|1|0|| +|Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus|1|1|:star:| +|Engineering Isoprene Synthase Expression and Activity in Cyanobacteria |1|1|:star:| +|Genetic Constructor: An Online DNA Design Platform|2|0|| diff --git a/content/sbolv-10-years/acs-2018.md b/content/sbolv-10-years/acs-2018.md new file mode 100644 index 00000000..8a1af3d8 --- /dev/null +++ b/content/sbolv-10-years/acs-2018.md @@ -0,0 +1,180 @@ +--- +title: 2018 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# 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 complaint 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|:star:| +|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|:star:| +|A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria|3|1|| +|A Prototype for Modular Cell Engineering|4|4|:star:| +|Engineering an E. coli Near-Infrared Light Sensor|2|2|:star:| +|Development of a Pigment-Based Whole-Cell Zinc Biosensor for Human Serum|1|1|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia|2|2|:star:| +|Gene-Mediated Chemical Communication in Synthetic Protocell Communities|1|1|:star:| +|Metabolic Feedback Circuits Provide Rapid Control of Metabolite Dynamics|3|2|| +|Native and Engineered Clifednamide Biosynthesis in Multiple Streptomyces spp.|1|1|:star:| +|High-CO2 Requirement as a Mechanism for the Containment of Genetically Modified Cyanobacteria|1|1|:star:| +|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|:star:| +|TARSyn: Tunable Antibiotic Resistance Devices Enabling Bacterial Synthetic Evolution and Protein Production|5|5|:star:| +|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|:star:| +|SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology|1|1|:star:| +|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 complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Labeling RNAs in Live Cells Using Malachite Green Aptamer Scaffolds as Fluorescent Probes|3|3|:star:| +|Directed Evolution of Membrane Transport Using Synthetic Selections|1|1|:star:| +|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|:star:| +|Modular Engineering Intracellular NADH Regeneration Boosts Extracellular Electron Transfer of Shewanella oneidensis MR-1|2|2|:star:| +|Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils|3|2|| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering a Dual Small Molecule Gated ZAP70 Switch in T Cells|1|1|:star:| +|Cell-Free Optogenetic Gene Expression System|2|2|:star:| +|A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria|1|1|:star:| +|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 complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineering the Ultrasensitive Transcription Factors by Fusing a Modular Oligomerization Domain|1|1|:star:| +|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|:star:| +|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|:star:| +|An Automated Design Framework for Multicellular Recombinase Logic|3|2|| +|A Transcription Factor-Based Biosensor for Detection of Itaconic Acid|2|2|:star:| + +## June + +|Article|No. of SBOL Visual complaint 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|:star:| +|Probing Intercell Variability Using Bulk Measurements|1|0|| +|Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation|1|1|:star:| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Rationalizing Context-Dependent Performance of Dynamic RNA Regulatory Devices|2|2|:star:| +|Mutually Orthogonal DNA Replication Systems In Vivo|3|0|| +|Exploring the Nonconserved Sequence Space of Synthetic Expression Modules in Bacillus subtilis|1|1|:star:| + +## August + +|Article|No. of SBOL Visual complaint 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 complaint 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|:star:| +|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 complaint 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|:star:| +|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 complaint 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|:star:| +|Highly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus|1|1|:star:| +|Enhancing the Translational Capacity of E. coli by Resolving the Codon Bias|1|1|:star:| + +## December + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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|:star:| +|Phosphate Lock Residues of Acidothermus cellulolyticus Cas9 Are Critical to Its Substrate Specificity|2|1|| diff --git a/content/sbolv-10-years/acs-2019.md b/content/sbolv-10-years/acs-2019.md new file mode 100644 index 00000000..ecd67762 --- /dev/null +++ b/content/sbolv-10-years/acs-2019.md @@ -0,0 +1,160 @@ +--- +title: 2019 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 287 +- **Total Figures in All Articles:** 1512 +- **Figures Compatible with SBOL Visual:** 432 (28.57%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 219 (50.69%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 126 (29.17%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Designing Spatially Distributed Gene Regulatory Networks To Elicit Contrasting Patterns|1|0|| +|Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli|2|2|:star:| +|Engineering the S-Layer of Caulobacter crescentus as a Foundation for Stable, High-Density, 2D Living Materials|1|0|| +|sboljs: Bringing the Synthetic Biology Open Language to the Web Browser|2|2|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Riboswitch Signal Amplification by Controlling Plasmid Copy Number|2|2|:star:| +|Building Microbial Hosts for Heterologous Production of N-Methylpyrrolinium|2|0|| +|A Regulatory NADH/NAD+ Redox Biosensor for Bacteria|1|1|:star:| +|Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids|7|0|| +|CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Fusarium fujikuroi and Its Application in Strain Engineering for Gibberellic Acid Production|2|2|:star:| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Characterizing Transcriptional Interference between Converging Genes in Bacteria|4|4|:star:| +|Construction of a Nonnatural C60 Carotenoid Biosynthetic Pathway|5|5|:star:| +|Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure|7|7|:star:| +|An Artificial Biosynthetic Pathway for 2-Amino-1,3-Propanediol Production Using Metabolically Engineered Escherichia coli|2|0|| +|Metabolic Engineering of a Homoserine-Derived Non-Natural Pathway for the De NovoProduction of 1,3-Propanediol from Glucose|4|0|| +|Modulating Responses of Toehold Switches by an Inhibitory Hairpin|2|0|| +|Construction of Incoherent Feedforward Loop Circuits in a Cell-Free System and in Cells|2|2|:star:| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Developing Riboswitch-Mediated Gene Regulatory Controls in Thermophilic Bacteria|2|1|| +|Spatiotemporal Gene Repression System in the Heterocyst-Forming Multicellular Cyanobacterium Anabaena sp. PCC 7120|2|2|:star:| +|Building an Inducible T7 RNA Polymerase/T7 Promoter Circuit in Synechocystis sp. PCC6803|4|1|| +|Modeling Genetic Circuit Behavior in Transiently Transfected Mammalian Cells|3|3|:star:| +|An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae|6|0|| +|Direct Aromatic Nitration System for Synthesis of Nitrotryptophans in Escherichia coli|1|1|:star:| +|PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens|1|0|| +|Rapid Assembly of gRNA Arrays via Modular Cloning in Yeast|2|0|| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast|1|0|| +|Endocytosing Escherichia coli as a Whole-Cell Biocatalyst of Fatty Acids|2|0|| +|Genetic Incorporation of Noncanonical Amino Acids Using Two Mutually Orthogonal Quadruplet Codons|1|0|| +|Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications|1|1|:star:| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Design and Evaluation of Synthetic Terminators for Regulating Mammalian Cell Transgene Expression|1|0|| +|Guiding Biomolecular Interactions in Cells Using de Novo Protein–Protein Interfaces|5|0|| +|Expanding the Isoprenoid Building Block Repertoire with an IPP Methyltransferase from Streptomyces monomycini|1|0|| +|Engineering Adenylate Cyclase Activated by Near-Infrared Window Light for Mammalian Optogenetic Applications|2|1|| +|Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning|3|3|:star:| +|Intracellular Noise Level Determines Ratio Control Strategy Confined by Speed–Accuracy Trade-off|1|0|| +|RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium|3|0|| +|Development of a Genetically Encoded Biosensor for Detection of Polyketide Synthase Extender Units in Escherichia coli|2|0|| +|Engineered Reversal of Function in Glycolytic Yeast Promoters|1|0|| +|Characterization of a Panel of Strong Constitutive Promoters from Streptococcus thermophilus for Fine-Tuning Gene Expression|1|0|| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs|3|3|:star:| +|SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information|4|4|:star:| +|pySBOL: A Python Package for Genetic Design Automation and Standardization|1|1|:star:| +|Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)|2|2|:star:| +|A Computational Workflow for the Automated Generation of Models of Genetic Designs|8|8|:star:| +|Design Principles for Compartmentalization and Spatial Organization of Synthetic Genetic Circuits|1|0|| +|An Engineered B. subtilis Inducible Promoter System with over 10 000-Fold Dynamic Range|1|1|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic, Context-Dependent Microbial Consortium of Predator and Prey|2|2|:star:| +|Inducible Gene Switches with Memory in Human T Cells for Cellular Immunotherapy|4|4|:star:| +|Decorating the Outer Surface of Microbially Produced Protein Nanowires with Peptides|2|0|| +|Communicating Structure and Function in Synthetic Biology Diagrams|7|7|:star:| +|Producing Gram-Scale Unnatural Rosavin Analogues from Glucose by Engineered Escherichia coli|2|0|| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Development of a Vanillate Biosensor for the Vanillin Biosynthesis Pathway in E. coli|2|1|| +|A Model for the Spatiotemporal Design of Gene Regulatory Circuits|2|2|:star:| +|Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices|1|0|| +|Genome Engineering of Eubacterium limosum Using Expanded Genetic Tools and the CRISPR-Cas9 System|1|1|:star:| +|Synthetic Biology Tools for the Fast-Growing Marine Bacterium Vibrio natriegens|2|2|:star:| +|Quantification of Interlaboratory Cell-Free Protein Synthesis Variability|1|1|:star:| +|ynthetic Gene Circuits Enable Escherichia coli To Use Endogenous H2S as a Signaling Molecule for Quorum Sensing|5|5|:star:| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Low-Burden Biological Feedback Controllers for Near-Perfect Adaptation|1|1|:star:| +|Amelioration of Diabetes in a Murine Model upon Transplantation of Pancreatic β-Cells with Optogenetic Control of Cyclic Adenosine Monophosphate|1|1|:star:| +|Modular Thermal Control of Protein Dimerization|3|3|:star:| +|SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories|2|2|:star:| +|Development of a Highly Sensitive Whole-Cell Biosensor for Arsenite Detection through Engineered Promoter Modifications|1|1|:star:| +|Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli|1|0|| +|Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization|4|3|| +|An AND-Gated Drug and Photoactivatable Cre-loxP System for Spatiotemporal Control in Cell-Based Therapeutics|4|0|| +|Semisynthesis of the Neuroprotective Metabolite, Serofendic Acid|3|3|:star:| +|Genetic Circuits To Detect Nanomaterial Triggered Toxicity through Engineered Heat Shock Response Mechanism|2|1|| +|Production of Phytochromes by High-Cell-Density E. coli Fermentation|1|0|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Model-Driven Engineering of N-Linked Glycosylation in Chinese Hamster Ovary Cells|2|2|:star:| +|In Vitro Transcriptional Regulation via Nucleic-Acid-Based Transcription Factors|4|2|| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Advancing CRISPR-Based Programmable Platforms beyond Genome Editing in Mammalian Cells|1|0|| +|Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor|1|1|:star:| +|Seeded Chain-Growth Polymerization of Proteins in Living Bacterial Cells|1|0|| +|Pregnenolone Overproduction in Yarrowia lipolytica by Integrative Components Pairing of the Cytochrome P450scc System|2|2|:star:| +|Switching the Ligand Specificity of the Biosensor XylS from meta to para-Toluic Acid through Directed Evolution Exploiting a Dual Selection System|1|1|:star:| +|Engineering New Branches of the Kynurenine Pathway To Produce Oxo-(2-aminophenyl) and Quinoline Scaffolds in Yeast|1|1|:star:| +|Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG)|1|1|:star:| diff --git a/content/sbolv-10-years/acs-2020.md b/content/sbolv-10-years/acs-2020.md new file mode 100644 index 00000000..987d7073 --- /dev/null +++ b/content/sbolv-10-years/acs-2020.md @@ -0,0 +1,192 @@ +--- +title: 2020 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# 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 complaint 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|:star:| +|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|:star:| +|Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices|3|3|:star:| +|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|:star:| +|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 complaint 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|:star:| +|Daisy Chain Topology Based Mammalian Synthetic Circuits for RNA-Only Delivery|9|9|:star:| +|A Validamycin Shunt Pathway for Valienamine Synthesis in Engineered Streptomyces hygroscopicus 5008|1|1|:star:| +|Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing|2|2|:star:| +|Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation|2|2|:star:| +|A Multifunction Lipid-Based CRISPR-Cas13a Genetic Circuit Delivery System for Bladder Cancer Gene Therapy|1|1|:star:| +|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|:star:| + +## March + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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|:star:| +|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|:star:| + +## April + +|Article|No. of SBOL Visual complaint 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|:star:| +|Toolkit Development for Cyanogenic and Gold Biorecovery Chassis Chromobacterium violaceum|3|3|:star:| +|SBOL Visual 2 Ontology|3|3|:star:| + +## May + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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|:star:| +|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 complaint 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|:star:| +|Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences|1|1|:star:| +|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|:star:| +|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 complaint 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|:star:| +|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|:star:| +|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|:star:| +|Highly Efficient Production of l-Histidine from Glucose by Metabolically Engineered Escherichia coli|1|1|:star:| +|MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics|1|1|:star:| +|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|:star:| +|Mapping Protein–Protein Interaction Interface Peptides with Jun-Fos Assisted Phage Display and Deep Sequencing|2|2|:star:| +|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 complaint 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|:star:| +|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|:star:| +|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|:star:| + +## October + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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|:star:| +|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|:star:| + +## November + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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|:star:| +|A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas|1|1|:star:| +|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|:star:| +|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 complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Living Therapeutics: The Next Frontier of Precision Medicine|2|2|:star:| +|A Logic NAND Gate for Controlling Gene Expression in a Circadian Rhythm in Cyanobacteria|3|3|:star:| +|Automating Cloning by Natural Transformation|4|4|:star:| +|Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential|1|1|:star:| +|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|| diff --git a/content/sbolv-10-years/acs-2021.md b/content/sbolv-10-years/acs-2021.md new file mode 100644 index 00000000..8c6a9951 --- /dev/null +++ b/content/sbolv-10-years/acs-2021.md @@ -0,0 +1,239 @@ +--- +title: 2021 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# 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 complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Statistical Design of Experiments for Synthetic Biology|1|1|:star:| +|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|:star:| +|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|:star:| +|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|:star:| +|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|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Promiscuous Installation of d-Amino Acids in Gene-Encoded Peptides|1|1|:star:| +|Biosynthesis of Diverse Type II Polyketide Core Structures in Streptomyces coelicolor M1152|3|3|:star:| +|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|:star:| +|Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons|5|5|:star:| +|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|:star:| +|CRISPRi-Mediated NIMPLY Logic Gate for Fine-Tuning the Whole-Cell Sensing toward Simple Urine Glucose Detection|4|4|:star:| + +## March + +|Article|No. of SBOL Visual complaint 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|:star:| +|A Reporter System for Cytosolic Protein Aggregates in Yeast|2|2|:star:| +|Efficient Production of 1,3-Propanediol from Diverse Carbohydrates via a Non-natural Pathway Using 3-Hydroxypropionic Acid as an Intermediate|2|2|:star:| +|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|:star:| +|Optogenetic Modification of Pseudomonas aeruginosa Enables Controllable Twitching Motility and Host Infection|1|1|:star:| +|Engineering Alternate Ligand Recognition in the PurR Topology: A System of Novel Caffeine Biosensing Transcriptional Antirepressors|3|3|:star:| +|Guanidine Biosensors Enable Comparison of Cellular Turn-on Kinetics of Riboswitch-Based Biosensor and Reporter|1|1|:star:| +|Automated Rational Strain Construction Based on High-Throughput Conjugation|1|1|:star:| + +## April + +|Article|No. of SBOL Visual complaint 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|:star:| +|A Cell Factory of a Fungicolous Fungus Calcarisporium arbuscula for Efficient Production of Natural Products|2|2|:star:| +|Engineering Transcriptional Interference through RNA Polymerase Processivity Control|4|4|:star:| +|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|:star:| +|An Aldolase-Based New Pathway for Bioconversion of Formaldehyde and Ethanol into 1,3-Propanediol in Escherichia coli|1|1|:star:| +|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|:star:| +|Rational Promoter Engineering Enables Robust Terpene Production in Microalgae|5|5|:star:| +|Saccharomyces cerevisiae Synthetic Transcriptional Networks Harnessing dCas12a and Type V-A anti-CRISPR Proteins|4|4|:star:| + +## May + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|Antisense RNA Interference-Enhanced CRISPR/Cas9 Base Editing Method for Improving Base Editing Efficiency in Streptomyces lividans 66|3|3|:star:| +|Improve the Biosynthesis of Baicalein and Scutellarein via Manufacturing Self-Assembly Enzyme Reactor In Vivo|1|1|:star:| +|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|:star:| +|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|:star:| +|Emergent Damped Oscillation Induced by Nutrient-Modulating Growth Feedback|4|0|| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|A Tail Fiber Engineering Platform for Improved Bacterial Transduction-Based Diagnostic Reagents|2|2|:star:| +|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|:star:| +|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|:star:| +|Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803|2|2|:star:| +|Data-Driven and in Silico-Assisted Design of Broad Host-Range Minimal Intrinsic Terminators Adapted for Bacteria|2|2|:star:| +|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|:star:| +|Combining Metabolic and Monoterpene Synthase Engineering for de Novo Production of Monoterpene Alcohols in Escherichia coli|1|1|:star:| +|High-Yielding Terpene-Based Biofuel Production in Rhodobacter capsulatus|1|1|:star:| +|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 complaint 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|:star:| +|The pIT5 Plasmid Series, an Improved Toolkit for Repeated Genome Integration in E. coli|3|3|:star:| +|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|:star:| +|Engineering a Bifunctional ComQXPA-PsrfA Quorum-Sensing Circuit for Dynamic Control of Gene Expression in Corynebacterium glutamicum|6|6|:star:| +|SBOLCanvas: A Visual Editor for Genetic Designs|2|2|:star:| + +## August + +|Article|No. of SBOL Visual complaint 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|:star:| +|High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters|1|1|:star:| +|A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution|1|1|:star:| +|The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications in Vibrio natriegens|6|6|:star:| +|Development of a N-Acetylneuraminic Acid-Based Sensing and Responding Switch for Orthogonal Gene Regulation in Cyanobacterial Synechococcus Strains|4|4|:star:| +|Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation|3|3|:star:| +|Metabolic Engineering of Escherichia coli for High-Yield Production of (R)-1,3-Butanediol|1|1|:star:| +|Synthetic Cellobiose-Inducible Regulatory Systems Allow Tight and Dynamic Controls of Gene Expression in Streptomyces|4|4|:star:| +|Reprogramming Escherichia coli Metabolism for Bioplastics Synthesis from Waste Cooking Oil|3|3|:star:| +|A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia coli|1|1|:star:| +|Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy|1|1|:star:| +|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|:star:| + +## September + +|Article|No. of SBOL Visual complaint 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|:star:| +|Expression of Alternative Nitrogenases in Rhodopseudomonas palustris Is Enhanced Using an Optimized Genetic Toolset for Rapid, Markerless Modifications|1|1|:star:| +|Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20|1|1|:star:| +|Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis|4|4|:star:| +|Adaptive Optimization Boosted the Production of Moenomycin A in the Microbial Chassis Streptomyces albus J1074|3|3|:star:| +|A DNA Inversion System in Eukaryotes Established via Laboratory Evolution|5|5|:star:| +|Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection|2|2|:star:| +|Synthetic Biology Knowledge System|2|2|:star:| +|Construction and Characterization of a Gradient Strength Promoter Library for Fine-Tuned Gene Expression in Bacillus licheniformis|1|1|:star:| +|Modular and Single-Cell Sensors of Bacterial Ser/Thr Kinase Activity|1|1|:star:| +|Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria|4|4|:star:| +|An Integrative Toolbox for Synthetic Biology in Rhodococcus|3|3|:star:| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules|1|1|:star:| +|Efficient Production of 2′-Fucosyllactose from l-Fucose via Self-Assembling Multienzyme Complexes in Engineered Escherichia coli|1|1|:star:| +|Development of Genetically Encoded Biosensors for Reporting the Methyltransferase-Dependent Biosynthesis of Semisynthetic Macrolide Antibiotics|1|1|:star:| +|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|:star:| +|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|:star:| +|Curation Principles Derived from the Analysis of the SBOL iGEM Data Set|3|3|:star:| +|Visualized Multigene Editing System for Aspergillus niger|4|4|:star:| +|Construction of a Fusellovirus with a Minimal Set of Genes|2|2|:star:| +|Metabolic Engineering of Gas-Fermenting Clostridium ljungdahlii for Efficient Co-production of Isopropanol, 3-Hydroxybutyrate, and Ethanol|2|2|:star:| +|BioParts—A Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform|3|3|:star:| +|Engineering a CRISPRi Circuit for Autonomous Control of Metabolic Flux in Escherichia coli|4|4|:star:| +|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|:star:| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization|1|1|:star:| +|Engineering Wired Life: Synthetic Biology for Electroactive Bacteria|3|3|:star:| +|Modular Synthetic Biology Toolkit for Filamentous Fungi|2|2|:star:| +|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|:star:| +|Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application|1|1|:star:| +|A Novel and Efficient Genome Editing Tool Assisted by CRISPR-Cas12a/Cpf1 for Pichia pastoris|2|2|:star:| +|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|:star:| +|Strategy for Producing the High-Quality Glycopeptide Antibiotic A82846B in Amycolatopsis orientalis Based on the CRISPR-Cas12a System|1|1|:star:| +|Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis|2|2|:star:| +|Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems|3|3|:star:| +|Development of a Transcription Factor-Based Diamine Biosensor in Corynebacterium glutamicum|4|4|:star:| +|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|:star:| +|Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription|2|0|| +|Synthetic Biology Curation Tools (SYNBICT)|1|1|:star:| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast|2|2|:star:| +|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|:star:| +|Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits|4|4|:star:| +|Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity|4|4|:star:| +|Biosynthesis of Poly(3HB-co-3HP) with Variable Monomer Composition in Recombinant Cupriavidus necator H16|2|2|:star:| +|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|:star:| +|Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering|1|0|| diff --git a/content/sbolv-10-years/acs-2022.md b/content/sbolv-10-years/acs-2022.md new file mode 100644 index 00000000..7b92c4dd --- /dev/null +++ b/content/sbolv-10-years/acs-2022.md @@ -0,0 +1,276 @@ +--- +title: 2022 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# Summary + +- **Total Articles Analyzed:** 393 +- **Total Figures in All Articles:** 2068 +- **Figures Compatible with SBOL Visual:** 595 (28.77%) +- **Figures Compatible with SBOL Visual & Fully Compliant:** 487 (81.85%) +- **Figures Compatible with SBOL Visual & Following Best Practices:** 245 (41.18%) +# Individual issues + +## January + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Biology in Chimeric Antigen Receptor T (CAR T) Cell Engineering|3|3|:star:| +|Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory|1|0|| +|Repurposing the Homing Endonuclease I-SceI for Positive Selection and Development of Gene-Editing Technologies|1|1|:star:| +|Development and Application of a New Arabinose-Inducible Vector in High-Attachment Strain Stenotrophomonas AGS-1 from Aerobic Granular Sludge|2|0|| +|CRISPR-Cas9-mediated Large Cluster Deletion and Multiplex Genome Editing in Paenibacillus polymyxa|2|2|:star:| +|Reprogramming the Biosynthesis of Precursor Peptide to Create a Selenazole-Containing Nosiheptide Analogue|3|3|:star:| +|TALE.Sense: A Versatile DNA Sensor Platform for Live Mammalian Cells|4|0|| +|Engineering a Controllable Targeted Protein Degradation System and a Derived OR-GATE-Type Inducible Gene Expression System in Synechococcus elongatus PCC 7942|4|4|:star:| +|Synergistic Metabolism of Glucose and Formate Increases the Yield of Short-Chain Organic Acids in Escherichia coli|1|0|| +|Multiloci Manipulation of Baculovirus Genome Reveals the Pivotal Role of Homologous Regions in Viral DNA Replication, Progeny Production, and Enhancing Transcription|1|0|| +|Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation|1|1|:star:| +|Artificial Consortium of Three E. coli BL21 Strains with Synergistic Functional Modules for Complete Phenanthrene Degradation|2|0|| +|Interaction of Bare dSpCas9, Scaffold gRNA, and Type II Anti-CRISPR Proteins Highly Favors the Control of Gene Expression in the Yeast S. cerevisiae|1|0|| +|Episome-Based Gene Expression Modulation Platform in the Model Diatom Phaeodactylum tricornutum|4|1|| +|Cell-Free Gene Expression Dynamics in Synthetic Cell Populations|2|2|:star:| +|Mapping of Nonhomologous End Joining-Mediated Integration Facilitates Genome-Scale Trackable Mutagenesis in Yarrowia lipolytica|3|3|:star:| +|Antibiotic-Efficient Genetic Cassette for the TEM-1 β-Lactamase That Improves Plasmid Performance|2|2|:star:| +|Evolving a Generalist Biosensor for Bicyclic Monoterpenes|3|3|:star:| +|Engineering a Dynamic Controllable Infectivity Switch in Bacteriophage T7|1|0|| +|Design and Characterization of an Optogenetic System in Pichia pastoris|1|0|| +|CRISPR-Based Construction of a BL21 (DE3)-Derived Variant Strain Library to Rapidly Improve Recombinant Protein Production|4|4|:star:| +|A Self-Sustained System Spanning the Primary and Secondary Metabolism Stages to Boost the Productivity of Streptomyces|8|7|| +|Bio-SCAN: A CRISPR/dCas9-Based Lateral Flow Assay for Rapid, Specific, and Sensitive Detection of SARS-CoV-2|1|0|| +|Cheating the Cheater: Suppressing False-Positive Enrichment during Biosensor-Guided Biocatalyst Engineering|3|3|:star:| +|CS-Cells: A CRISPR-Cas12 DNA Device to Generate Chromosome-Shredded Cells for Efficient and Safe Molecular Biomanufacturing|3|1|| +|Engineering a Synthetic Pathway for Tyrosol Synthesis in Escherichia coli|2|0|| +|CRISPR/Cas-Based Genome Editing for Human Gut Commensal Bacteroides Species|2|2|:star:| +|Engineering of the Ligand Specificity of Transcriptional Regulator XylS by Deep Mutational Scanning|1|1|:star:| +|Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei|3|0|| +|A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii|2|2|:star:| + +## February + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Combating Infectious Diseases with Synthetic Biology|2|0|| +|Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion|2|0|| +|Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers|4|0|| +|Regulatory Part Engineering for High-Yield Protein Synthesis in an All-Streptomyces-Based Cell-Free Expression System|4|4|:star:| +|EMMA-CAD: Design Automation for Synthetic Mammalian Constructs|4|4|:star:| +|Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering|1|1|:star:| +|Synthetic Biology Toolkit for Marker-Less Integration of Multigene Pathways into Pichia pastoris via CRISPR/Cas9|2|2|:star:| +|One-Step In Vivo Assembly of Multiple DNA Fragments and Genomic Integration in Komagataella phaffii|3|0|| +|Conversion of the OmpF Porin into a Device to Gather Amyloids on the E. coli Outer Membrane|1|0|| +|Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion|1|0|| +|Engineering a Xylose-Utilizing Synechococcus elongatus UTEX 2973 Chassis for 3-Hydroxypropionic Acid Biosynthesis under Photomixotrophic Conditions|2|2|:star:| +|Codon-Restrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters|3|3|:star:| +|Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts|5|5|:star:| +|A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis|2|0|| +|Enhancement of l-Pipecolic Acid Production by Dynamic Control of Substrates and Multiple Copies of the pipA Gene in the Escherichia coli Genome|1|1|:star:| +|Secretory Production of Tocotrienols in Saccharomyces cerevisiae|1|0|| +|Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine|1|0|| +|Engineered Mutants of a Marine Photosynthetic Purple Nonsulfur Bacterium with Increased Volumetric Productivity of Polyhydroxyalkanoate Bioplastics|1|0|| +|Highly Reversible Tunable Thermal-Repressible Split-T7 RNA Polymerases (Thermal-T7RNAPs) for Dynamic Gene Regulation|3|0|| +|Establishment of Green- and Red-Fluorescent Reporter Proteins Based on the Fluorescence-Activating and Absorption-Shifting Tag for Use in Acetogenic and Solventogenic Anaerobes|1|0|| +|Encoding Genetic Circuits with DNA Barcodes Paves the Way for Machine Learning-Assisted Metabolite Biosensor Response Curve Profiling in Yeast|1|1|:star:| +|Uncovering the Distinct Properties of a Bacterial Type I-E CRISPR Activation System|2|2|:star:| +|GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems|1|0|| + +## March + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Genetic Reversible Feynman Gate in a Single E. coli Cell and Its Application in Bacterial to Mammalian Cell Information Transfer|2|1|| +|Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis|1|1|:star:| +|Genome Engineering in Mycoplasma gallisepticum Using Exogenous Recombination Systems|5|0|| +|Conjugation-Based Genome Engineering in Deinococcus radiodurans|3|0|| +|Versatile Design of Intracellular Protein-Responsive Translational Regulation System for Synthetic mRNA|4|0|| +|A Dual-Purpose Real-Time Indicator and Transcriptional Integrator for Calcium Detection in Living Cells|1|0|| +|Design of Synthetic Mammalian Promoters Using Highly Palindromic Subsequences|1|0|| +|Engineering Transcription Factor XylS for Sensing Phthalic Acid and Terephthalic Acid: An Application for Enzyme Evolution|1|1|:star:| +|Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast|1|0|| +|Precise Thermal Regulation of Engineered Bacteria Secretion for Breast Cancer Treatment In Vivo|2|0|| +|Heterologous Synthesis and Secretion of Ricinoleic Acid in Starmerella bombicola with Sophorolipid as an Intermediate|1|1|:star:| +|Cre/lox-Mediated Chromosomal Integration of Biosynthetic Gene Clusters for Heterologous Expression in Aspergillus nidulans|2|2|:star:| +|Metabolic Division in an Escherichia coli Coculture System for Efficient Production of Kaempferide|5|5|:star:| +|Programmable Synthetic Upstream Activating Sequence Library for Fine-Tuning Gene Expression Levels in Saccharomyces cerevisiae|2|2|:star:| +|RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks|4|0|| +|PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies|3|3|:star:| +|Polymer Encapsulation of Bacterial Biosensors Enables Coculture with Mammalian Cells|1|1|:star:| +|Transcriptome Analysis of Bacillus licheniformis for Improving Bacitracin Production|1|1|:star:| +|RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry|6|6|:star:| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Designing Biological Circuits: From Principles to Applications|1|1|:star:| +|Bioorthogonal Chemical Epigenetic Modifiers Enable Dose-Dependent CRISPR Targeted Gene Activation in Mammalian Cells|2|1|| +|Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell–Cell Adhesion|5|1|| +|Phage Enzyme-Assisted Direct In Vivo DNA Assembly in Multiple Microorganisms|1|1|:star:| +|A CRISPR–Cas9 System-Mediated Genetic Disruption and Multi-fragment Assembly in Starmerella bombicola|5|5|:star:| +|DNA Input Classification by a Riboregulator-Based Cell-Free Perceptron|4|0|| +|[NiFe] Hydrogenase Accessory Proteins HypB–HypC Accelerate Proton Conversion to Enhance the Acid Resistance and d-Lactic Acid Production of Escherichia coli|1|0|| +|Construction and Application of a High-Throughput In Vivo Screening Platform for the Evolution of Nitrile Metabolism-Related Enzymes Based on a Desensitized Repressive Biosensor|5|0|| +|Genomic Iterative Replacements of Large Synthetic DNA Fragments in Corynebacterium glutamicum|3|0|| +|De Novo Production of Plant 4′-Deoxyflavones Baicalein and Oroxylin A from Ethanol in Crabtree-Negative Yeast|1|1|:star:| +|A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers|2|2|:star:| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds|4|4|:star:| +|DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control|1|1|:star:| +|Transcriptional Interference in Toehold Switch-Based RNA Circuits|4|4|:star:| +|Simulation-Based Engineering of Time-Delayed Safety Switches for Safer Gene Therapies|2|2|:star:| +|Increased Production of Riboflavin by Coordinated Expression of Multiple Genes in Operons in Bacillus subtilis|3|0|| +|Exploration of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Activity in Yeast|1|0|| +|Tuning Geraniol Biosynthesis via a Novel Decane-Responsive Promoter in Candida glycerinogenes|1|0|| +|Engineering Antisense Oligonucleotides as Antibacterial Agents That Target FMN Riboswitches and Inhibit the Growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli|1|0|| +|Combining CRISPR–Cpf1 and Recombineering Facilitates Fast and Efficient Genome Editing in Escherichia coli|3|3|:star:| +|Rerouting Fluxes of the Central Carbon Metabolism and Relieving Mechanism-Based Inactivation of l-Aspartate-α-decarboxylase for Fermentative Production of β-Alanine in Escherichia coli|1|0|| +|LOICA: Integrating Models with Data for Genetic Network Design Automation|2|2|:star:| + +## June + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Transcription-Associated Fluorescence-Activated Droplet Sorting for Di-rhamnolipid Hyperproducers|1|1|:star:| +|Temporal Expression of Transcription Factor ID2 Improves Natural Killer Cell Differentiation from Human Pluripotent Stem Cells|1|0|| +|Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli|1|0|| +|Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2|1|1|:star:| +|Efficient Synthesis of Phycocyanobilin by Combinatorial Metabolic Engineering in Escherichia coli|1|0|| +|High-Throughput Regulatory Part Prototyping and Analysis by Cell-Free Protein Synthesis and Droplet Microfluidics|3|1|| +|Efficient Single-Nucleotide Microbial Genome Editing Achieved Using CRISPR/Cpf1 with Maximally 3′-End-Truncated crRNAs|1|1|:star:| +|Dynamic Control Strategy to Produce Riboflavin with Lignocellulose Hydrolysate in the Thermophile Geobacillus thermoglucosidasius|2|2|:star:| + +## July + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors|5|4|| +|Optimal LentiCRISPR-Based System for Sequential CRISPR/Cas9 Screens|1|0|| +|Engineering a Synthetic Dopamine-Responsive Riboswitch for In Vitro Biosensing|1|0|| +|High-Throughput Aminoacyl-tRNA Synthetase Engineering for Genetic Code Expansion in Yeast|1|0|| +|Control-Based Continuation: A New Approach to Prototype Synthetic Gene Networks|1|1|:star:| +|Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site|1|1|:star:| +|Light-Induced Patterning of Electroactive Bacterial Biofilms|1|1|:star:| +|Mitigating Host Burden of Genetic Circuits by Engineering Autonegatively Regulated Parts and Improving Functional Prediction|5|5|:star:| +|Tunable Temperature-Sensitive Transcriptional Activation Based on Lambda Repressor|2|2|:star:| +|pySBOL3: SBOL3 for Python Programmers|1|1|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species|6|5|| +|PeroxiHUB: A Modular Cell-Free Biosensing Platform Using H2O2 as Signal Integrator|2|0|| +|A Modified Yeast Two-Hybrid Platform Enables Dynamic Control of Expression Intensities to Unmask Properties of Protein–Protein Interactions|1|0|| +|Second-Generation Escherichia coli SuptoxR Strains for High-Level Recombinant Membrane Protein Production|1|0|| +|Decoupling Growth and Production by Removing the Origin of Replication from a Bacterial Chromosome|1|0|| +|Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase|5|0|| +|Engineering Agrobacterium tumefaciens Adhesion to Target Cells|1|0|| +|Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae|1|0|| +|Whole-Cell Biosensor and Producer Co-cultivation-Based Microfludic Platform for Screening Saccharopolyspora erythraea with Hyper Erythromycin Production|1|0|| +|Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors|3|0|| +|Deciphering the Rules of Ribosome Binding Site Differentiation in Context Dependence|2|0|| +|Building the Plant SynBio Toolbox through Combinatorial Analysis of DNA Regulatory Elements|2|0|| +|Proteolytically Activated CRAC Effectors through Designed Intramolecular Inhibition|3|0|| +|Synergistic Improvement of 5-Aminolevulinic Acid Production with Synthetic Scaffolds and System Pathway Engineering|1|0|| +|Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System|2|0|| +|Integrating CRISPR-Cas12a with a crRNA-Mediated Catalytic Network for the Development of a Modular and Sensitive Aptasensor|2|2|:star:| +|Stress-Tolerant, Recyclable, and Renewable Biocatalyst Platform Enabled by Engineered Bacterial Spores|4|4|:star:| +|Engineering Metabolic Pathways for Cofactor Self-Sufficiency and Serotonin Production in Escherichia coli|4|4|:star:| +|BMSS2: A Unified Database-Driven Modeling Tool for Systematic Biomodel Selection|1|0|| + +## September + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Overcoming Leak Sensitivity in CRISPRi Circuits Using Antisense RNA Sequestration and Regulatory Feedback|4|4|:star:| +|Malarial Antibody Detection with an Engineered Yeast Agglutination Assay|1|1|:star:| +|Genome Editing by CRISPR/Cas12 Recognizing AT-Rich PAMs in Shewanella oneidensis MR-1|4|4|:star:| +|Mobile Translation Systems Generate Genomically Engineered Escherichia coli Cells with Improved Growth Phenotypes|1|0|| +|An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria|2|0|| +|Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases|5|2|| +|Evolution-Guided Biosynthesis of Terpenoid Inhibitors|2|0|| +|Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis|1|0|| +|GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants|4|0|| +|CRISPR/Cpf1-Mediated Multiplex and Large-Fragment Gene Editing in Staphylococcus aureus|5|2|| +|A Network Approach to Genetic Circuit Designs|3|2|| +|Modular Use of the Uniquely Small Ring A of Mersacidin Generates the Smallest Ribosomally Produced Lanthipeptide|1|0|| +|Enzymatic Supercoiling of Bacterial Chromosomes Facilitates Genome Manipulation|1|0|| +|Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803|7|1|| +|A Universal Method for Developing Autoinduction Expression Systems Using AHL-Mediated Quorum-Sensing Circuits|2|2|:star:| + +## October + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment|4|1|| +|Interaction between the Anchoring Domain of A-Kinase Anchoring Proteins and the Dimerization and Docking Domain of Protein Kinase A: A Potent Tool for Synthetic Biology|1|0|| +|Synonymous Codons and Hydrophobicity Optimization of Post-translational Signal Peptide PelB Increase Phage Display Efficiency of DARPins|1|0|| +|A p-Coumaroyl-CoA Biosensor for Dynamic Regulation of Naringenin Biosynthesis in Saccharomyces cerevisiae|2|0|| +|A Versatile in Vivo DNA Assembly Toolbox for Fungal Strain Engineering|1|1|:star:| +|Steady-State Operation of a Cell-Free Genetic Band-Detection Circuit|2|2|:star:| +|Construction of an rAAV Producer Cell Line through Synthetic Biology|1|0|| +|Novel Split Intein-Mediated Enzymatic Channeling Accelerates the Multimeric Bioconversion Pathway of Ginsenoside|2|2|:star:| +|Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1|3|0|| +|SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies|2|1|| +|Optogenetic Control of Bacterial Expression by Red Light|1|0|| +|Induced CD45 Proximity Potentiates Natural Killer Cell Receptor Antagonism|2|0|| +|Efficient Bacterial Genome Engineering throughout the Central Dogma Using the Dual-Selection Marker tetAOPT|5|1|| +|Reprogramming T7RNA Polymerase in Escherichia coli Nissle 1917 under Specific Lac Operon for Efficient p-Coumaric Acid Production|3|0|| +|Light-Dependent Control of Bacterial Expression at the mRNA Level|3|2|| +|Discovery and Heterologous Expression of Microginins from Microcystis aeruginosa LEGE 91341|3|3|:star:| +|Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo|2|1|| +|Building an Artificial Plant Cell Wall on a Lipid Bilayer by Assembling Polysaccharides and Engineered Proteins|1|0|| +|Analysis of Slow-Cycling Variants of the Light-Inducible Nuclear Protein Export System LEXY in Mammalian Cells|1|0|| +|GroovDB: A Database of Ligand-Inducible Transcription Factors|2|0|| +|The VEGAS Platform Is Unsuitable for Mammalian Directed Evolution|2|1|| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage|2|0|| +|Harnessing Escherichia coli’s Native Machinery for Detection of Vitamin C (Ascorbate) Deficiency|2|0|| +|Unusual Class I Lanthipeptides from the Marine Bacteria Thalassomonas viridans|3|2|| +|Synthetic Biology Toolbox, Including a Single-Plasmid CRISPR-Cas9 System to Biologically Engineer the Electrogenic, Metal-Resistant Bacterium Cupriavidus metallidurans CH34|2|1|| +|Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast|2|0|| +|AgeMTPT, a Catalyst for Peptide N-Terminal Modification|1|1|:star:| +|Genetic Code Expansion in Pseudomonas putida KT2440|2|2|:star:| +|Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes|4|4|:star:| +|MGCEP 1.0: A Genetic-Engineered Marine-Derived Chassis Cell for a Scaled Heterologous Expression Platform of Microbial Bioactive Metabolites|3|1|| +|Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape|3|1|| +|Engineering a Rhodopsin-Based Photo-Electrosynthetic System in Bacteria for CO2 Fixation|1|0|| +|Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis|1|0|| +|EasyGuide Plasmids Support in Vivo Assembly of gRNAs for CRISPR/Cas9 Applications in Saccharomyces cerevisiae|1|0|| + +## December + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Ribosome Stalling of N-Linked Glycoproteins in Cell-Free Extracts|1|1|:star:| +|Robotic Construction and Screening of Lanthipeptide Variant Libraries in Escherichia coli|2|2|:star:| +|Targeting Transcriptional and Translational Hindrances in a Modular T7RNAP Expression System in Engineered Pseudomonas putida|8|0|| +|Two-Layered Microfluidic Devices for High-Throughput Dynamic Analysis of Synthetic Gene Circuits in E. coli|3|3|:star:| +|High Titer of (S)-Equol Synthesis from Daidzein in Escherichia coli|3|0|| +|Tuning of Gene Expression in Clostridium phytofermentans Using Synthetic Promoters and CRISPRi|4|0|| +|Hybrid Nucleic Acid-Quantum Dot Assemblies as Multiplexed Reporter Platforms for Cell-Free Transcription Translation-Based Biosensors|1|1|:star:| +|Rapid and Accurate Assembly of Large DNA Assisted by In Vitro Packaging of Bacteriophage|6|3|| +|Computer-Based Design of a Cell Factory for High-Yield Cytidine Production|1|1|:star:| +|Enzymatic Synthesis of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase|1|1|:star:| +|Modulating DHA-Producing Schizochytrium sp. toward Astaxanthin Biosynthesis via a Seamless Genome Editing System|4|3|| +|Characterization of Eight Bacterial Biosensors for Microbial Diagnostic and Therapeutic Applications |1|0|| +|Autoinduction Expression Modules for Regulating Gene Expression in Bacillus subtilis|2|2|:star:| diff --git a/content/sbolv-10-years/acs-2023.md b/content/sbolv-10-years/acs-2023.md new file mode 100644 index 00000000..f46736ac --- /dev/null +++ b/content/sbolv-10-years/acs-2023.md @@ -0,0 +1,209 @@ +--- +title: 2023 ACS Synthetic Biology Issues + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- +# 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 complaint 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|:star:| +|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|:star:| +|Engineering Pheromone-Mediated Quorum Sensing with Enhanced Response Output Increases Fucosyllactose Production in Saccharomyces cerevisiae|3|3|:star:| +|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 complaint 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|:star:| +|Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis|5|5|:star:| +|A Ubiquitous Chromatin Opening Element and DNA Demethylation Facilitate Doxycycline-Controlled Expression during Differentiation and in Transgenic Mice|3|3|:star:| +|Engineering the Substrate Specificity of Toluene Degrading Enzyme XylM Using Biosensor XylS and Machine Learning|1|1|:star:| +|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|:star:| +|A Suite of New Strain Construction Vectors for Gene Expression Knockdown in Budding Yeast|3|0|| + +## March + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference|2|2|:star:| +|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|:star:| +|Autoinduction AND Gate Inhibits Cell Lysis to Enhance Protein Production in Bacillus subtilis Controlled by Population Density and Cell Physiological State|4|4|:star:| +|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|:star:| + +## April + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases|1|1|:star:| +|Marine Biofilm Engineered to Produce Current in Response to Small Molecules|3|3|:star:| +|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|:star:| +|Reconstruction of the Native Biosynthetic System of Carotenoids in E. coli─Biosynthesis of a Series of Carotenoids Specific to Paprika Fruit|1|1|:star:| +|Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis|2|2|:star:| +|Modular Pathway Compartmentalization for Agroclavine Overproduction in Saccharomyces cerevisiae|1|0|| +|Clonal Amplification-Enhanced Gene Expression in Synthetic Vesicles|6|6|:star:| +|CRISPR/Cas12a-Mediated Genome Editing in Thioalkalivibrio versutus|2|2|:star:| +|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|:star:| +|Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories|1|1|:star:| + +## May + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Sourcing Phage-Encoded Terminators Using ONT-cappable-seq for SynBio Applications in Pseudomonas|1|1|:star:| +|TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors|1|1|:star:| +|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|:star:| +|Immortalized Bovine Satellite Cells for Cultured Meat Applications|1|1|:star:| + +## June + +|Article|No. of SBOL Visual complaint 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|:star:| +|In Vivo Sampling of Intracellular Heterogeneity of Pseudomonas putida Enables Multiobjective Optimization of Genetic Devices|3|3|:star:| +|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|:star:| + +## July + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria|2|1|| +|Bayesian Optimization for Design of Multiscale Biological Circuits|1|1|:star:| +|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|:star:| + +## August + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Noise Minimization in Cell-Free Gene Expression|3|3|:star:| +|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|:star:| +|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|:star:| +|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|:star:| +|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|:star:| + +## September + +|Article|No. of SBOL Visual complaint 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|:star:| +|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|:star:| +|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 complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Signal Amplification for Cell-Free Biosensors, an Analog-to-Digital Converter|3|3|:star:| +|Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling|1|1|:star:| +|Plasmid Crosstalk in Cell-Free Expression Systems|4|3|| +|Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise|2|2|:star:| +|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|:star:| +|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|:star:| + +## November + +|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices|| +| :---: | :---: | :---: | :---: | +|Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis|2|2|:star:| +|Investigating and Modeling the Factors That Affect Genetic Circuit Performance|1|1|:star:| +|Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast|1|1|:star:| +|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|:star:| +|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 complaint 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|:star:| +|Standardization of Fluorescent Reporter Assays in Synthetic Biology across the Visible Light Spectrum|1|1|:star:| +|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|:star:| +|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|:star:| +|GENETTA: a Network-Based Tool for the Analysis of Complex Genetic Designs|1|1|:star:| +|Changes in Coding and Efficiency through Modular Modifications to a One Pot PURE System for In Vitro Transcription and Translation|2|2|:star:| diff --git a/content/sbolv-10-years/guidelines.md b/content/sbolv-10-years/guidelines.md new file mode 100644 index 00000000..fb7b9afa --- /dev/null +++ b/content/sbolv-10-years/guidelines.md @@ -0,0 +1,100 @@ +# SBOL Visual Guidelines + +## Compliance Guidelines + +- **Features on Different Backbones** + Features MUST NOT be on the same backbone if they are not located on the same sequence. + +- **Single-Stranded Backbone Representation** + Single-stranded regions of nucleic acid constructs MUST use a single line to indicate the backbone. + +- **Feature Glyph Alignment** + The bounding box of a feature glyph MUST be in contact with the backbone. + +- **Feature Glyph Role** + The glyph used for a feature MUST contain the role of the feature. + +- **Molecular Species Glyph Type** + The glyph used for a molecular species MUST contain the type of the molecular species. + +- **Molecular Species Glyph Position** + The bounding box of a molecular species MUST NOT contact a nucleic acid construct unless it interacts with it. + +- **Interaction Crossover Pattern** + Interactions that intersect MUST use a crossover pattern that “diverts” to indicate the distinction between edges. + +- **Interaction Glyph Type** + The glyph used for an interaction MUST contain the type of the interaction. + +- **Multi-Head Edge Consistency** + An edge with multiple heads MUST use the same glyph for each head. + +- **Interaction Node Glyph Type** + The glyph used for an interaction node MUST contain the type of the interaction. + +- **Edge Connection Rule** + An edge MUST NOT connect to the head or tail of another edge. + +- **Subsystem Boundary Respect** + Glyphs for sequence features and molecular species MUST NOT intersect the boundary of a subsystem. + +- **Interface Rectangle Rule** + If an interface rectangle is used to indicate that a feature is part of the interface of a subsystem, then any interaction crossing the boundary and connecting with that feature MUST pass through the interface rectangle. + +--- + +## Best Practices Guidelines + +- **Double-Stranded Backbone Representation** + In a diagram with both single- and double-stranded nucleic acid constructs, double-stranded constructs SHOULD use double-lined backbones. + +- **Horizontal Backbone Orientation** + Nucleic acid backbones SHOULD be horizontal unless using non-horizontal structure to indicate physical attributes (e.g., closed loop for cyclic plasmid or complex shapes showing secondary structure). + +- **Plasmid and Locus Glyph Shapes** + Backbones SHOULD use the shape of plasmid and locus glyphs to indicate those features, and the omitted detail glyph to indicate context not shown. + +- **Feature Presence on Backbones** + A nucleic acid backbone SHOULD have at least one feature glyph unless it is an assembly diagram. + +- **Backbone Alignment** + Glyphs SHOULD follow the recommendation for backbone alignment in the glyph specification. + +- **Reverse Complement Orientation** + Reverse complement SHOULD be consistently indicated by 180-degree rotation, not horizontal-only inversion. + +- **Inline Orientation** + Inline 5’ to 3’ SHOULD be drawn left to right, and reverse complement right to left. + +- **Feature Overlap Guidelines** + Nucleic acid features SHOULD NOT overlap unless their locations overlap (flexible on bounding box overlap if the glyph itself does not overlap). + +- **Intended Feature Overlap** + Nucleic acid features SHOULD overlap if their locations overlap. + +- **Specific Glyph Usage for Nucleic Acids** + A nucleic acid SHOULD use the RECOMMENDED version of the most specific applicable glyph. Novel, more-specific glyphs are acceptable. + +- **Specific Glyph Usage for Molecular Species** + A molecular species SHOULD use the RECOMMENDED version of the most specific applicable glyph. Novel, more-specific glyphs are acceptable. + +- **Overlap Representation for Molecular Species** + If a molecular species overlaps a nucleic acid construct, the location of the overlap SHOULD correspond with the location of the interaction; the molecular species glyph SHOULD be distinct from a sequence feature glyph, and the location SHOULD be represented with a feature glyph appropriate to the interaction. + +- **Avoid Crossing Interaction Edges** + Two interaction edges SHOULD NOT cross one another. + +- **Interaction Glyph Specificity** + An interaction SHOULD use the RECOMMENDED version of the most specific applicable glyph. Novel, more-specific glyphs are acceptable. + +- **Interaction Node Glyph Specificity** + An interaction node SHOULD use the RECOMMENDED version of the most specific applicable glyph. Novel, more-specific glyphs are acceptable. + +- **Multi-Head/Tail Edge Connection Rule** + An edge SHOULD NOT connect to only one head of a multi-head arrow or only one tail of a multi-tail arrow. + +- **Subsystem Boundary Design** + The boundary of a subsystem SHOULD be a rectangle or rounded rectangle with sides oriented vertically and horizontally, and SHOULD be larger and have a different line style than other glyphs. + +- **Object Name Association** + If an object’s name is displayed, it SHOULD be clearly visually connected to the object’s associated glyph. diff --git a/content/sbolv-10-years/index.md b/content/sbolv-10-years/index.md new file mode 100644 index 00000000..19159eda --- /dev/null +++ b/content/sbolv-10-years/index.md @@ -0,0 +1,61 @@ +--- +title: "A Decade of SBOL Visual" +subtitle: 10 Years of Standardized Genetic Design Diagrams +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +--- + +## Welcome to the SBOL Community’s retrospective on SBOL Visual! + +Since its introduction in 2013, the SBOL Visual standard has played a key role in ensuring that diagrams of genetic designs are clear, consistent, and easily understood. + +Our community conducted a retrospective analysis of every ACS Synthetic Biology manuscript published between 2012 and 2023 to assess how well SBOL Visual has been adopted. + +### Our Approach +For each manuscript, we: +- **Reviewed the Main Manuscript:** Focused on the published figures. +- **Counted the Figures:** Recorded the total number of images per paper. +- **Assessed SBOL Visual Compatibility:** Identified which figures could be considered as SBOL Visual images. +- **Checked Compliance:** Determined whether SBOL Visual complaint figures followed the SBOL Visual standard +- **Checked Best Practices:** Determined whether SBOL Visual complaint figures followed recommended SBOL Visual best practices. + +### Explore the Data by Year +We have created dedicated pages that summarize our findings for each year. These pages include: + +- The total number of images (per paper) +- The number of images compatible with SBOL Visual +- The number of images following SBOL Visual standard guidelines +- The number of images following SBOL Visual best practices + +Please explore the individual summaries below: + +- [2012 Analysis](acs-2012) +- [2013 Analysis](acs-2013) +- [2014 Analysis](acs-2014) +- [2015 Analysis](acs-2015) +- [2016 Analysis](acs-2016) +- [2017 Analysis](acs-2017) +- [2018 Analysis](acs-2018) +- [2019 Analysis](acs-2019) +- [2020 Analysis](acs-2020) +- [2021 Analysis](acs-2021) +- [2022 Analysis](acs-2022) +- [2023 Analysis](acs-2023) + + +### About Our Work +This effort accompanies our upcoming manuscript, "A Decade of SBOL Visual: The Adoption of a Diagram Standard," and reflects the collective work of the SBOL Community. By tracking how genetic design diagrams have evolved over time, we aim to both celebrate progress and highlight areas where further improvements can support clear scientific communication. + +### Get Involved +We welcome your feedback and ideas on how to further improve the clarity and usability of SBOL Visual. Feel free to reach out to us or join the discussion in our community forums. + +*Thank you for being part of our journey to make synthetic biology diagrams more accessible and standardized!* \ No newline at end of file