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November 16, 2021
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Date: November 16, 2021
Speaker: Patrick J. Westfall, PhD, Senior Director of Cell Biology, Inscripta Inc
Abstract: Discovery in biological research was historically driven by empirical methods. The advent of biological engineering, propelled by technological developments and new tools, has made rational hypothesis-driven design and engineering of biological systems more feasible and common. Although they are often seen as opposing approaches, the empirical and rational methods can work together to accelerate fundamental research and product development. Whereas forward engineering is guided by informed design of known biological pathways and processes, the exploratory empirical methods allow to expand the design space beyond the scope of current knowledge. This webinar discusses the advantages of each method and how they could be implemented in tandem to advance biological engineering.
REGISTER
October 14, 2021
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Date: October 14, 2021
Speaker: Tyson Shepherd, PhD, Microbial Engineering Applications Manager, Inscripta
Abstract: Heterologous protein expression in model organisms has many applications, including protein engineering, production of industrial enzymes and therapeutics, and structure-function discovery. Heterologous proteins are commonly expressed from plasmids to facilitate cloning and genetic manipulation. However, plasmid-based expression has many drawbacks, such as reduced stability and limited control over gene copy number. With CRISPR editing, chromosomal gene integration and subsequent editing has become more accessible, enabling thorough examination of protein expression and function. In this webinar, we demonstrate how we generated an E. coli saturation mutagenesis library for a chromosomally expressed green fluorescent protein (GFP) using the OnyxTM platform. We identify several engineered variants with increased fluorescence or altered spectral characteristics, including literature validated and novel variants. We also generate a library of all predicted E. coli promoters and ribosome binding sites (RBS) and quantify their strength using the engineered high-expression GFP reporter system. These high-throughput experiments yield insights into native regulatory sequences and demonstrate the advantages of heterologous protein engineering directly in the host genome.
VIEW MORE
September 13, 2021
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Date: September 13, 2021
Speaker: Katherine Krouse, Sr. Research Associate, Applications Development, Inscripta
Abstract: Biological responses to environmental stress can arise from multiple genetic solutions encoding tolerance mechanisms. In order to investigate the response to osmotic pressure in E. coli, we used an automated CRISPR editing workflow to generate a diverse cell population that included gene knockouts and different strength promoter substitution libraries targeting almost every gene in the genome. The resulting 25,000-variant pooled library was studied under a titrated salt challenge and the population dynamics were tracked using plasmid barcodes. By mapping 300,000 data points, we identified clear enrichment and depletion patterns and connected those back to functional genome annotations. We were able to rapidly validate our experiment with the performance of known salt stress tolerance loci, such as rpoE and osmE, and discover new gene targets.
VIEW MORE
August 25, 2021
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Date: August 25, 2021
Speaker: Eric Abbate
Abstract: Heterologous protein production is an indispensable tool in biotechnology and biopharma for manufacturing enzymes, protein therapeutics, and more. Generating robust production strains involves strategies that target the protein itself as well as the host genome. Despite advances in strain engineering, optimization of protein production is still limited by the ability to access the broad sequence space, constrained by traditional, low-throughput, and laborious methods like promoter substitutions or random mutagenesis. Here we use a genome-wide, multiplexed, targeted editing approach that can generate diverse edit types in both the heterologous gene and across the host genome to optimize production of cellobiohydrolase I enzyme (CHB1) in S. cerevisiae. The edits conferring improved CBH1 expression span cellular processes important for protein production, including transcription, translation, secretion, and protein degradation pathways.
VIEW MORE
July 28, 2021
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Date: July 28, 2021
Speaker: Bram Van den Bergh — Postdoctoral Researcher, KU Leuven | FWO | VIB Centre for Microbiology
Abstract: Bacterial persistence is a potential cause of antibiotic therapy failure. Recent studies have shown that persistence is a highly evolvable trait, reaching varying frequencies within populations, depending on the selective conditions that are applied (e.g. the treatment frequency). Theory predicts that population bottlenecks, frequently encountered during host-to-host transmission and antibiotic treatment, have far-reaching effects on the evolutionary dynamics of persistence. Here, we used a combination of experimental evolution and barcoded knockout libraries to examine this hypothesis. Small bottlenecks were found to restrict the adaptive potential of populations and result in more heterogeneous evolutionary outcomes, suggest that the fitness landscape of persistence has a rugged topography. Furthermore, sequencing data revealed genes that are potentially involved in persistence, including previously known as well as novel targets.
VIEW MORE
June 15, 2021
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
Date: June 15, 2021
Speaker: Tyson Shepherd
Abstract: During this webinar, discover how Inscripta experts generated an Escherichia coli saturation mutagenesis library against an integrated green fluorescent protein (GFP) using CRISPR-based technology, in a few short weeks.
Watch Video
May 26, 2021
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Date: May 26, 2021
Speaker: Sri Kosaraju — President & CEO, Inscripta; Grant Murphy — Director of Protein Engineering, Merck & Co; Chris Savile — Chief Operations Officer, Willow Biosciences; Barry Canton — Chief Technical Officer, Gingko Bioworks
Abstract: The panel of industry leaders discuss technologies and microbial applications of synthetic biology in biopharma bioproduction.
Watch Video
May 25, 2021
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Date: May 25, 2021
Speaker: Bryan Leland
Abstract: In this webinar, we will discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
Watch Video
April 27, 2021
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Date: April 27, 2021
Speaker: Eric Abbate
Abstract: Lysine, predominately used as an animal feed supplement, is a multi-billion-dollar industry however supply is limited due to the cost of current production methods. This webinar will share case studies how Inscripta leveraged its new CRISPR-based technology to design, generate, and screen libraries totaling > 200,000 single edits to improve lysine production in E. coli. Dozens of beneficial edits across the entire genome were discovered to accelerate the Design-Generate-Test-Learn cycle and increase the lysine production by 14,000-fold — ushering in the next era of genome editing.
View More
March 30, 2021
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
Date: March 30, 2021
Speaker: Tyson Shepherd
Abstract: Since its introduction, CRISPR has become a core genome editing tool that has transformed biological research. First-generation CRISPR technologies were limited in scalability, accessibility, edit variety, and ease of use, restricting their potential. Inscripta’s Onyx™ platform addresses these limitations by combining easy-to-use, intuitive software with a push-button automated benchtop device, enabling high-efficiency, massively-parallel, precision-engineered edits to Saccharomyces cerevisiae and Escherichia coli genomes. In this webinar , Tyson Shepherd will present applications in E. coli that leverage this platform. He will show how a library totaling more than 25,000 different designs and a separate library of 900 designs yielded new biochemical insights underpinning tolerance to a panel of growth-inhibitory compounds. These applications demonstrate the power of the Onyx platform to usher in a new era of genome editing.
Watch Video
January 26, 2021
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
Date: January 26, 2021
Speaker: Liselot Dewachter and Laura Klitten
Abstract: In this study, we used the high-throughput CRISPR-based Onyx platform to perform saturation mutagenesis on four different essential genes involved in cell envelope synthesis in E. coli. 22,790 edits were designed. We used these saturation mutagenesis libraries to probe the essentiality of all different residues. Edits that could not be introduced suggests those residues are essential for protein function. We identified known essential amino acids (i.e. catalytic residues and residues involved in substrate binding), thereby validating our experimental approach. Several residues that were previously not known to be essential were identified. We expect our results to offer vastly improved insights into protein function, help fight against antibiotic resistance and aid structure-based drug design targeted against these essential proteins.
Watch Video
October 20, 2020
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Date: October 20, 2020
Speaker: Bryan Leland
Abstract: In this webinar, we discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise, genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
Watch Video
September 30, 2020
Massively parallel microbial genome engineering using the Onyx Platform
Massively parallel microbial genome engineering using the Onyx Platform
Date: September 30, 2020
Speaker: Nandini Krishnamurthy
Abstract: While transformative, first-generation CRISPR technologies remain limited across multiple important dimensions including scalability, editing efficiency, types of modifications available, and ease of use. Inscripta’s Onyx platform addresses these limitations by offering push-button, high efficiency, massively parallel, and precise delivery of diverse edit types across the genomes of S. cerevisiae and E. coli. The platform simplifies previously complex CRISPR strain engineering workflows by offering an end-to-end solution from design through engineered strain library and analytics, including software, reagents and a benchtop instrument. Join us to learn more about this platform and see examples of engineering genomes at unprecedented scale end efficiency.
Watch Video
September 1, 2020
Rapid Forward Engineering of Biological Systems: Part 2 Combinatorial Optimization
Rapid Forward Engineering of Biological Systems: Part 2 Combinatorial Optimization
Date: September 1, 2020
Speaker: Richard Fox
Abstract: Many of the governing rules of biology are still not known nor well understood. Thus, forward engineering of biological systems will continue to rely on empirical methods. A central challenge in forward engineering is to find genetic interventions that lead to improved function. Combinatorial optimization (fueled by large-scale diversity generation) takes ideas that show promise and recombines them in novel configurations to leverage the principles of evolutionary optimization. This optimization process is further accelerated through strategies that incorporate machine learning. Such models are interrogated to efficiently guide new library designs. Strategies and tools to effectively apply the principles of diversity generation (and combinatorial optimization) have been developed over the last two decades and are now routinely used to rapidly engineer biological systems.
Watch Video
August 25, 2020
Rapid Forward Engineering of Biological Systems: Part 1 Diversity Generation
Rapid Forward Engineering of Biological Systems: Part 1 Diversity Generation
Date: August 25, 2020
Speaker: Richard Fox
Abstract: Significant potential exists to harness the power of biology to better humanity and the environment, however, substantial challenges remain. Forward engineering of biological systems will continue to rely on empirical methods. Diversity generation is one of two key principles needed to reach desired outcomes in a rapid, efficient and cost-effective manner. Sequence space is vast. A central challenge in forward engineering is to find genetic interventions that lead to improved function. A large-scale diversity generation approach, where many thousands of ideas are rapidly tested, has proved to be crucial to addressing this challenge. Strategies and tools to effectively apply the principles of diversity generation (and combinatorial optimization) have been developed over the last two decades and are now routinely used to rapidly engineer biological systems.
Watch Video
July 28, 2020
Rebuilding evolutionary success Using Inscripta’s Onyx Digital Genome Engineering Platform to ease and enhance ALE experiments
Rebuilding evolutionary success Using Inscripta’s Onyx Digital Genome Engineering Platform to ease and enhance ALE experiments
Date: July 28, 2020
Speaker: Tyson Shepherd, PhD
Abstract:
Watch Video
May 14, 2020
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Date: May 14, 2020
Speaker: Stephen Federowicz
Abstract: Massively parallel genome engineering enables rapid and simultaneous evaluation of genotype-phenotype relationships at a genomic scale. With the Inscripta Onyx Platform, we replaced every promoter in the E. coli genome with one of five synthetic constitutive promoters across an expression ladder. Additionally, we generated two versions of a genome scale knockout library by inserting three premature stop codons in every gene at two different positions near the 5’ end. We then pooled these libraries for a total of 23,576 genomic edits, and under strong selective pressure quantified shifts in the edited populations to determine relative strain performance. We readily identify thousands of genotype-phenotype interactions that confirm known mechanisms and reveal large sets of novel interactions – demonstrating the power of high-efficiency automated genome engineering.
Watch Video
July 28, 2021
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Date: July 28, 2021
Speaker: Bram Van den Bergh — Postdoctoral Researcher, KU Leuven | FWO | VIB Centre for Microbiology
Abstract: Bacterial persistence is a potential cause of antibiotic therapy failure. Recent studies have shown that persistence is a highly evolvable trait, reaching varying frequencies within populations, depending on the selective conditions that are applied (e.g. the treatment frequency). Theory predicts that population bottlenecks, frequently encountered during host-to-host transmission and antibiotic treatment, have far-reaching effects on the evolutionary dynamics of persistence. Here, we used a combination of experimental evolution and barcoded knockout libraries to examine this hypothesis. Small bottlenecks were found to restrict the adaptive potential of populations and result in more heterogeneous evolutionary outcomes, suggest that the fitness landscape of persistence has a rugged topography. Furthermore, sequencing data revealed genes that are potentially involved in persistence, including previously known as well as novel targets.
VIEW MORE
May 26, 2021
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Date: May 26, 2021
Speaker: Sri Kosaraju — President & CEO, Inscripta; Grant Murphy — Director of Protein Engineering, Merck & Co; Chris Savile — Chief Operations Officer, Willow Biosciences; Barry Canton — Chief Technical Officer, Gingko Bioworks
Abstract: The panel of industry leaders discuss technologies and microbial applications of synthetic biology in biopharma bioproduction.
Watch Video
January 26, 2021
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
Date: January 26, 2021
Speaker: Liselot Dewachter and Laura Klitten
Abstract: In this study, we used the high-throughput CRISPR-based Onyx platform to perform saturation mutagenesis on four different essential genes involved in cell envelope synthesis in E. coli. 22,790 edits were designed. We used these saturation mutagenesis libraries to probe the essentiality of all different residues. Edits that could not be introduced suggests those residues are essential for protein function. We identified known essential amino acids (i.e. catalytic residues and residues involved in substrate binding), thereby validating our experimental approach. Several residues that were previously not known to be essential were identified. We expect our results to offer vastly improved insights into protein function, help fight against antibiotic resistance and aid structure-based drug design targeted against these essential proteins.
Watch Video
July 28, 2020
Rebuilding evolutionary success Using Inscripta’s Onyx Digital Genome Engineering Platform to ease and enhance ALE experiments
Rebuilding evolutionary success Using Inscripta’s Onyx Digital Genome Engineering Platform to ease and enhance ALE experiments
Date: July 28, 2020
Speaker: Tyson Shepherd, PhD
Abstract:
Watch Video
November 16, 2021
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Date: November 16, 2021
Speaker: Patrick J. Westfall, PhD, Senior Director of Cell Biology, Inscripta Inc
Abstract: Discovery in biological research was historically driven by empirical methods. The advent of biological engineering, propelled by technological developments and new tools, has made rational hypothesis-driven design and engineering of biological systems more feasible and common. Although they are often seen as opposing approaches, the empirical and rational methods can work together to accelerate fundamental research and product development. Whereas forward engineering is guided by informed design of known biological pathways and processes, the exploratory empirical methods allow to expand the design space beyond the scope of current knowledge. This webinar discusses the advantages of each method and how they could be implemented in tandem to advance biological engineering.
REGISTER
October 14, 2021
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Date: October 14, 2021
Speaker: Tyson Shepherd, PhD, Microbial Engineering Applications Manager, Inscripta
Abstract: Heterologous protein expression in model organisms has many applications, including protein engineering, production of industrial enzymes and therapeutics, and structure-function discovery. Heterologous proteins are commonly expressed from plasmids to facilitate cloning and genetic manipulation. However, plasmid-based expression has many drawbacks, such as reduced stability and limited control over gene copy number. With CRISPR editing, chromosomal gene integration and subsequent editing has become more accessible, enabling thorough examination of protein expression and function. In this webinar, we demonstrate how we generated an E. coli saturation mutagenesis library for a chromosomally expressed green fluorescent protein (GFP) using the OnyxTM platform. We identify several engineered variants with increased fluorescence or altered spectral characteristics, including literature validated and novel variants. We also generate a library of all predicted E. coli promoters and ribosome binding sites (RBS) and quantify their strength using the engineered high-expression GFP reporter system. These high-throughput experiments yield insights into native regulatory sequences and demonstrate the advantages of heterologous protein engineering directly in the host genome.
VIEW MORE
September 13, 2021
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Date: September 13, 2021
Speaker: Katherine Krouse, Sr. Research Associate, Applications Development, Inscripta
Abstract: Biological responses to environmental stress can arise from multiple genetic solutions encoding tolerance mechanisms. In order to investigate the response to osmotic pressure in E. coli, we used an automated CRISPR editing workflow to generate a diverse cell population that included gene knockouts and different strength promoter substitution libraries targeting almost every gene in the genome. The resulting 25,000-variant pooled library was studied under a titrated salt challenge and the population dynamics were tracked using plasmid barcodes. By mapping 300,000 data points, we identified clear enrichment and depletion patterns and connected those back to functional genome annotations. We were able to rapidly validate our experiment with the performance of known salt stress tolerance loci, such as rpoE and osmE, and discover new gene targets.
VIEW MORE
August 25, 2021
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Date: August 25, 2021
Speaker: Eric Abbate
Abstract: Heterologous protein production is an indispensable tool in biotechnology and biopharma for manufacturing enzymes, protein therapeutics, and more. Generating robust production strains involves strategies that target the protein itself as well as the host genome. Despite advances in strain engineering, optimization of protein production is still limited by the ability to access the broad sequence space, constrained by traditional, low-throughput, and laborious methods like promoter substitutions or random mutagenesis. Here we use a genome-wide, multiplexed, targeted editing approach that can generate diverse edit types in both the heterologous gene and across the host genome to optimize production of cellobiohydrolase I enzyme (CHB1) in S. cerevisiae. The edits conferring improved CBH1 expression span cellular processes important for protein production, including transcription, translation, secretion, and protein degradation pathways.
VIEW MORE
July 28, 2021
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
Date: July 28, 2021
Speaker: Bram Van den Bergh — Postdoctoral Researcher, KU Leuven | FWO | VIB Centre for Microbiology
Abstract: Bacterial persistence is a potential cause of antibiotic therapy failure. Recent studies have shown that persistence is a highly evolvable trait, reaching varying frequencies within populations, depending on the selective conditions that are applied (e.g. the treatment frequency). Theory predicts that population bottlenecks, frequently encountered during host-to-host transmission and antibiotic treatment, have far-reaching effects on the evolutionary dynamics of persistence. Here, we used a combination of experimental evolution and barcoded knockout libraries to examine this hypothesis. Small bottlenecks were found to restrict the adaptive potential of populations and result in more heterogeneous evolutionary outcomes, suggest that the fitness landscape of persistence has a rugged topography. Furthermore, sequencing data revealed genes that are potentially involved in persistence, including previously known as well as novel targets.
VIEW MORE
June 15, 2021
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
Date: June 15, 2021
Speaker: Tyson Shepherd
Abstract: During this webinar, discover how Inscripta experts generated an Escherichia coli saturation mutagenesis library against an integrated green fluorescent protein (GFP) using CRISPR-based technology, in a few short weeks.
Watch Video
May 26, 2021
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Delivering on the Promise: Synthetic Biology in Biopharma Bioproduction
Date: May 26, 2021
Speaker: Sri Kosaraju — President & CEO, Inscripta; Grant Murphy — Director of Protein Engineering, Merck & Co; Chris Savile — Chief Operations Officer, Willow Biosciences; Barry Canton — Chief Technical Officer, Gingko Bioworks
Abstract: The panel of industry leaders discuss technologies and microbial applications of synthetic biology in biopharma bioproduction.
Watch Video
May 25, 2021
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Date: May 25, 2021
Speaker: Bryan Leland
Abstract: In this webinar, we will discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
Watch Video
April 27, 2021
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Date: April 27, 2021
Speaker: Eric Abbate
Abstract: Lysine, predominately used as an animal feed supplement, is a multi-billion-dollar industry however supply is limited due to the cost of current production methods. This webinar will share case studies how Inscripta leveraged its new CRISPR-based technology to design, generate, and screen libraries totaling > 200,000 single edits to improve lysine production in E. coli. Dozens of beneficial edits across the entire genome were discovered to accelerate the Design-Generate-Test-Learn cycle and increase the lysine production by 14,000-fold — ushering in the next era of genome editing.
View More
March 30, 2021
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
Date: March 30, 2021
Speaker: Tyson Shepherd
Abstract: Since its introduction, CRISPR has become a core genome editing tool that has transformed biological research. First-generation CRISPR technologies were limited in scalability, accessibility, edit variety, and ease of use, restricting their potential. Inscripta’s Onyx™ platform addresses these limitations by combining easy-to-use, intuitive software with a push-button automated benchtop device, enabling high-efficiency, massively-parallel, precision-engineered edits to Saccharomyces cerevisiae and Escherichia coli genomes. In this webinar , Tyson Shepherd will present applications in E. coli that leverage this platform. He will show how a library totaling more than 25,000 different designs and a separate library of 900 designs yielded new biochemical insights underpinning tolerance to a panel of growth-inhibitory compounds. These applications demonstrate the power of the Onyx platform to usher in a new era of genome editing.
Watch Video
October 20, 2020
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Date: October 20, 2020
Speaker: Bryan Leland
Abstract: In this webinar, we discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise, genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
Watch Video
September 30, 2020
Massively parallel microbial genome engineering using the Onyx Platform
Massively parallel microbial genome engineering using the Onyx Platform
Date: September 30, 2020
Speaker: Nandini Krishnamurthy
Abstract: While transformative, first-generation CRISPR technologies remain limited across multiple important dimensions including scalability, editing efficiency, types of modifications available, and ease of use. Inscripta’s Onyx platform addresses these limitations by offering push-button, high efficiency, massively parallel, and precise delivery of diverse edit types across the genomes of S. cerevisiae and E. coli. The platform simplifies previously complex CRISPR strain engineering workflows by offering an end-to-end solution from design through engineered strain library and analytics, including software, reagents and a benchtop instrument. Join us to learn more about this platform and see examples of engineering genomes at unprecedented scale end efficiency.
Watch Video
September 1, 2020
Rapid Forward Engineering of Biological Systems: Part 2 Combinatorial Optimization
Rapid Forward Engineering of Biological Systems: Part 2 Combinatorial Optimization
Date: September 1, 2020
Speaker: Richard Fox
Abstract: Many of the governing rules of biology are still not known nor well understood. Thus, forward engineering of biological systems will continue to rely on empirical methods. A central challenge in forward engineering is to find genetic interventions that lead to improved function. Combinatorial optimization (fueled by large-scale diversity generation) takes ideas that show promise and recombines them in novel configurations to leverage the principles of evolutionary optimization. This optimization process is further accelerated through strategies that incorporate machine learning. Such models are interrogated to efficiently guide new library designs. Strategies and tools to effectively apply the principles of diversity generation (and combinatorial optimization) have been developed over the last two decades and are now routinely used to rapidly engineer biological systems.
Watch Video
August 25, 2020
Rapid Forward Engineering of Biological Systems: Part 1 Diversity Generation
Rapid Forward Engineering of Biological Systems: Part 1 Diversity Generation
Date: August 25, 2020
Speaker: Richard Fox
Abstract: Significant potential exists to harness the power of biology to better humanity and the environment, however, substantial challenges remain. Forward engineering of biological systems will continue to rely on empirical methods. Diversity generation is one of two key principles needed to reach desired outcomes in a rapid, efficient and cost-effective manner. Sequence space is vast. A central challenge in forward engineering is to find genetic interventions that lead to improved function. A large-scale diversity generation approach, where many thousands of ideas are rapidly tested, has proved to be crucial to addressing this challenge. Strategies and tools to effectively apply the principles of diversity generation (and combinatorial optimization) have been developed over the last two decades and are now routinely used to rapidly engineer biological systems.
Watch Video
May 14, 2020
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Date: May 14, 2020
Speaker: Stephen Federowicz
Abstract: Massively parallel genome engineering enables rapid and simultaneous evaluation of genotype-phenotype relationships at a genomic scale. With the Inscripta Onyx Platform, we replaced every promoter in the E. coli genome with one of five synthetic constitutive promoters across an expression ladder. Additionally, we generated two versions of a genome scale knockout library by inserting three premature stop codons in every gene at two different positions near the 5’ end. We then pooled these libraries for a total of 23,576 genomic edits, and under strong selective pressure quantified shifts in the edited populations to determine relative strain performance. We readily identify thousands of genotype-phenotype interactions that confirm known mechanisms and reveal large sets of novel interactions – demonstrating the power of high-efficiency automated genome engineering.
Watch Video
November 16, 2021
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Date: November 16, 2021
Speaker: Patrick J. Westfall, PhD, Senior Director of Cell Biology, Inscripta Inc
Abstract: Discovery in biological research was historically driven by empirical methods. The advent of biological engineering, propelled by technological developments and new tools, has made rational hypothesis-driven design and engineering of biological systems more feasible and common. Although they are often seen as opposing approaches, the empirical and rational methods can work together to accelerate fundamental research and product development. Whereas forward engineering is guided by informed design of known biological pathways and processes, the exploratory empirical methods allow to expand the design space beyond the scope of current knowledge. This webinar discusses the advantages of each method and how they could be implemented in tandem to advance biological engineering.
REGISTER
October 14, 2021
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Heterologous Protein Engineering and characterization of native regulatory elements in E. coli using Massively Parallel CRISPR Editing
Date: October 14, 2021
Speaker: Tyson Shepherd, PhD, Microbial Engineering Applications Manager, Inscripta
Abstract: Heterologous protein expression in model organisms has many applications, including protein engineering, production of industrial enzymes and therapeutics, and structure-function discovery. Heterologous proteins are commonly expressed from plasmids to facilitate cloning and genetic manipulation. However, plasmid-based expression has many drawbacks, such as reduced stability and limited control over gene copy number. With CRISPR editing, chromosomal gene integration and subsequent editing has become more accessible, enabling thorough examination of protein expression and function. In this webinar, we demonstrate how we generated an E. coli saturation mutagenesis library for a chromosomally expressed green fluorescent protein (GFP) using the OnyxTM platform. We identify several engineered variants with increased fluorescence or altered spectral characteristics, including literature validated and novel variants. We also generate a library of all predicted E. coli promoters and ribosome binding sites (RBS) and quantify their strength using the engineered high-expression GFP reporter system. These high-throughput experiments yield insights into native regulatory sequences and demonstrate the advantages of heterologous protein engineering directly in the host genome.
VIEW MORE
September 13, 2021
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Identifying genome-wide targets of osmotic stress tolerance in E. coli using CRISPR-mediated forward engineering
Date: September 13, 2021
Speaker: Katherine Krouse, Sr. Research Associate, Applications Development, Inscripta
Abstract: Biological responses to environmental stress can arise from multiple genetic solutions encoding tolerance mechanisms. In order to investigate the response to osmotic pressure in E. coli, we used an automated CRISPR editing workflow to generate a diverse cell population that included gene knockouts and different strength promoter substitution libraries targeting almost every gene in the genome. The resulting 25,000-variant pooled library was studied under a titrated salt challenge and the population dynamics were tracked using plasmid barcodes. By mapping 300,000 data points, we identified clear enrichment and depletion patterns and connected those back to functional genome annotations. We were able to rapidly validate our experiment with the performance of known salt stress tolerance loci, such as rpoE and osmE, and discover new gene targets.
VIEW MORE
June 15, 2021
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
CRISPR-based multiplexed genome editing for improved heterologous protein engineering and expression in E. coli
Date: June 15, 2021
Speaker: Tyson Shepherd
Abstract: During this webinar, discover how Inscripta experts generated an Escherichia coli saturation mutagenesis library against an integrated green fluorescent protein (GFP) using CRISPR-based technology, in a few short weeks.
Watch Video
April 27, 2021
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Proteins, Pathways and Genomes: Innovations in Forward Engineering
Date: April 27, 2021
Speaker: Eric Abbate
Abstract: Lysine, predominately used as an animal feed supplement, is a multi-billion-dollar industry however supply is limited due to the cost of current production methods. This webinar will share case studies how Inscripta leveraged its new CRISPR-based technology to design, generate, and screen libraries totaling > 200,000 single edits to improve lysine production in E. coli. Dozens of beneficial edits across the entire genome were discovered to accelerate the Design-Generate-Test-Learn cycle and increase the lysine production by 14,000-fold — ushering in the next era of genome editing.
View More
March 30, 2021
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
A New Era in Forward Engineering of Proteins, Pathways and Genomes using the Onyx™ Platform
Date: March 30, 2021
Speaker: Tyson Shepherd
Abstract: Since its introduction, CRISPR has become a core genome editing tool that has transformed biological research. First-generation CRISPR technologies were limited in scalability, accessibility, edit variety, and ease of use, restricting their potential. Inscripta’s Onyx™ platform addresses these limitations by combining easy-to-use, intuitive software with a push-button automated benchtop device, enabling high-efficiency, massively-parallel, precision-engineered edits to Saccharomyces cerevisiae and Escherichia coli genomes. In this webinar , Tyson Shepherd will present applications in E. coli that leverage this platform. He will show how a library totaling more than 25,000 different designs and a separate library of 900 designs yielded new biochemical insights underpinning tolerance to a panel of growth-inhibitory compounds. These applications demonstrate the power of the Onyx platform to usher in a new era of genome editing.
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January 26, 2021
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
High-throughput CRISPR editing using the Onyx platform identifies essential residues in proteins
Date: January 26, 2021
Speaker: Liselot Dewachter and Laura Klitten
Abstract: In this study, we used the high-throughput CRISPR-based Onyx platform to perform saturation mutagenesis on four different essential genes involved in cell envelope synthesis in E. coli. 22,790 edits were designed. We used these saturation mutagenesis libraries to probe the essentiality of all different residues. Edits that could not be introduced suggests those residues are essential for protein function. We identified known essential amino acids (i.e. catalytic residues and residues involved in substrate binding), thereby validating our experimental approach. Several residues that were previously not known to be essential were identified. We expect our results to offer vastly improved insights into protein function, help fight against antibiotic resistance and aid structure-based drug design targeted against these essential proteins.
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September 30, 2020
Massively parallel microbial genome engineering using the Onyx Platform
Massively parallel microbial genome engineering using the Onyx Platform
Date: September 30, 2020
Speaker: Nandini Krishnamurthy
Abstract: While transformative, first-generation CRISPR technologies remain limited across multiple important dimensions including scalability, editing efficiency, types of modifications available, and ease of use. Inscripta’s Onyx platform addresses these limitations by offering push-button, high efficiency, massively parallel, and precise delivery of diverse edit types across the genomes of S. cerevisiae and E. coli. The platform simplifies previously complex CRISPR strain engineering workflows by offering an end-to-end solution from design through engineered strain library and analytics, including software, reagents and a benchtop instrument. Join us to learn more about this platform and see examples of engineering genomes at unprecedented scale end efficiency.
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May 14, 2020
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Massively parallel genome engineering followed by pooled growth selections for rapid target discovery in microbes
Date: May 14, 2020
Speaker: Stephen Federowicz
Abstract: Massively parallel genome engineering enables rapid and simultaneous evaluation of genotype-phenotype relationships at a genomic scale. With the Inscripta Onyx Platform, we replaced every promoter in the E. coli genome with one of five synthetic constitutive promoters across an expression ladder. Additionally, we generated two versions of a genome scale knockout library by inserting three premature stop codons in every gene at two different positions near the 5’ end. We then pooled these libraries for a total of 23,576 genomic edits, and under strong selective pressure quantified shifts in the edited populations to determine relative strain performance. We readily identify thousands of genotype-phenotype interactions that confirm known mechanisms and reveal large sets of novel interactions – demonstrating the power of high-efficiency automated genome engineering.
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November 16, 2021
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Newton’s Cradle: Exploring rational and empirical design space with Engineering Biology
Date: November 16, 2021
Speaker: Patrick J. Westfall, PhD, Senior Director of Cell Biology, Inscripta Inc
Abstract: Discovery in biological research was historically driven by empirical methods. The advent of biological engineering, propelled by technological developments and new tools, has made rational hypothesis-driven design and engineering of biological systems more feasible and common. Although they are often seen as opposing approaches, the empirical and rational methods can work together to accelerate fundamental research and product development. Whereas forward engineering is guided by informed design of known biological pathways and processes, the exploratory empirical methods allow to expand the design space beyond the scope of current knowledge. This webinar discusses the advantages of each method and how they could be implemented in tandem to advance biological engineering.
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August 25, 2021
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Improving heterologous protein production in yeast with massively parallel CRISPR genome editing
Date: August 25, 2021
Speaker: Eric Abbate
Abstract: Heterologous protein production is an indispensable tool in biotechnology and biopharma for manufacturing enzymes, protein therapeutics, and more. Generating robust production strains involves strategies that target the protein itself as well as the host genome. Despite advances in strain engineering, optimization of protein production is still limited by the ability to access the broad sequence space, constrained by traditional, low-throughput, and laborious methods like promoter substitutions or random mutagenesis. Here we use a genome-wide, multiplexed, targeted editing approach that can generate diverse edit types in both the heterologous gene and across the host genome to optimize production of cellobiohydrolase I enzyme (CHB1) in S. cerevisiae. The edits conferring improved CBH1 expression span cellular processes important for protein production, including transcription, translation, secretion, and protein degradation pathways.
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May 25, 2021
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Massively Parallel CRISPR Genome Editing in S. cerevisiae
Date: May 25, 2021
Speaker: Bryan Leland
Abstract: In this webinar, we will discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
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October 20, 2020
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Massively parallel CRISPR genome editing in S. cerevisiae using the Onyx Platform
Date: October 20, 2020
Speaker: Bryan Leland
Abstract: In this webinar, we discuss our work using the Onyx platform to perform genome-wide engineering of S. cerevisiae for various applications including target discovery to increase glycerol utilization, strain optimization, and forward engineering. These applications are enabled by Onyx’s ability to deliver diverse edit types that regulate gene function and expression beyond simple gene knock-outs. In total, dozens of libraries of engineered cells, containing over 100,000 precise, genomic edits have been created and tested to accelerate forward engineering and genomic discovery.
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September 30, 2020
Massively parallel microbial genome engineering using the Onyx Platform
Massively parallel microbial genome engineering using the Onyx Platform
Date: September 30, 2020
Speaker: Nandini Krishnamurthy
Abstract: While transformative, first-generation CRISPR technologies remain limited across multiple important dimensions including scalability, editing efficiency, types of modifications available, and ease of use. Inscripta’s Onyx platform addresses these limitations by offering push-button, high efficiency, massively parallel, and precise delivery of diverse edit types across the genomes of S. cerevisiae and E. coli. The platform simplifies previously complex CRISPR strain engineering workflows by offering an end-to-end solution from design through engineered strain library and analytics, including software, reagents and a benchtop instrument. Join us to learn more about this platform and see examples of engineering genomes at unprecedented scale end efficiency.
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Service & Support
Inscripta™ provides dedicated support through every step of your genome engineering experiments. Our Field Applications, Field Service, and Technical Support teams assist you with in-depth project consultation, customized applications design, comprehensive instrument installation, training and maintenance, and detailed data analysis and interpretation. When you are ready to begin, you can log in to the Inscripta Engineering Portal to upload genomes, design experiments, place orders, monitor instrument runs, and analyze results.
For help with our software, consumables, assays, and the Onyx™ Instrument, contact us at support@inscripta.com.