Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

Bioreactor Design and Operational System

Bioreactor Design and Operational System

Bioreactors are engineered vessels designed to cultivate microorganisms under controlled conditions for industrial bioprocessing. They maintain sterility and allow precise regulation of pH, temperature, oxygen, and nutrient levels to optimize microbial growth and metabolite production. Bioreactors range from small laboratory units of 1 liter to industrial systems holding up to 500,000 liters, though only about 75% of their volume is actively used for fermentation. The remaining headspace...

Bioreactor Controls-III

Bioreactor Controls-III

Strain improvement is a foundational strategy in industrial microbiology aimed at maximizing microbial productivity, particularly because natural isolates typically yield commercially valuable products in very low concentrations. Although optimizing the culture medium and environmental conditions can improve yields, these adjustments are inherently limited by the organism’s genetic potential. As a result, the focus shifts toward genetic modifications to enhance biosynthetic capacity. The...

Designing Growth Media for Bioreactors

Designing Growth Media for Bioreactors

Growth media provide essential nutrients that support cell growth and metabolism, thereby enhancing the yield of valuable products such as enzymes, antibiotics, and biomass. Designing an effective growth medium involves balancing all components to prevent nutrient limitations or toxic excesses, both of which can impair growth and reduce product yields.Composition of a Typical Growth MediumA typical growth medium contains carbon and nitrogen sources, salts, vitamins, trace elements, and...

Combinatorial Gene Control

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...

Methods of Medium Optimization

Methods of Medium Optimization

Optimizing growth media enhances microbial proliferation and maximizes product yield. Statistical experimental design methodologies provide structured and reproducible approaches, offering progressively higher levels of robustness and efficiency.The One-Factor-at-a-Time (OFAT) MethodThe One-Factor-at-a-Time (OFAT) method involves adjusting a single variable while keeping all others constant. However, it cannot detect interactions between variables, often leading to suboptimal outcomes when...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Discovery of potent low-toxicity antimicrobial peptides through diffusion modeling.

Nature communications·2026

Same author

Artificial intelligence for food innovation.

Nature food·2026

Same author

Community-Acquired Pneumonia Manifested by Acute Abdominal Pain: A Case Report.

Case reports in infectious diseases·2026

Same author

Perceptions surrounding intranasal naloxone use and access among a population experiencing homelessness.

Exploratory research in clinical and social pharmacy·2026

Same author

Artificial intelligence for plant-based meat alternatives: Pathways to a sustainable future.

Food research international (Ottawa, Ont.)·2026

Same author

Translating dietary standards into healthy meals with few-ingredient substitutions.

PLOS digital health·2026

Search research articles

Related Experiment Video

Updated: May 11, 2026

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

SBROME: a scalable optimization and module matching framework for automated biosystems design.

Linh Huynh¹, Athanasios Tsoukalas, Matthias Köppe

¹Department of Computer Science and UC Davis Genome Center, University of California-Davis, CA 95616, United States.

ACS Synthetic Biology

|May 10, 2013

Summary

This summary is machine-generated.

We developed a Synthetic Biology Reusable Optimization Methodology (SBROME) to automate biodesign. This approach enables scalable circuit construction by reusing characterized modules, facilitating complex synthetic biology designs.

More Related Videos

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

Published on: December 15, 2017

Related Experiment Videos

Last Updated: May 11, 2026

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

Published on: December 15, 2017

Area of Science:

Synthetic Biology
Biodesign Automation
Computational Biology

Background:

Scaling synthetic biology designs is challenging due to increasing part availability and circuit complexity.
Existing methods lack efficient frameworks for reusing previously characterized biological modules.
Automation is crucial for managing the complexity of large-scale synthetic circuit development.

Purpose of the Study:

To propose a scalable framework for biodesign automation using a divide-and-conquer approach.
To enable the reuse of previously constructed and characterized circuits or modules.
To facilitate the implementation of synthetic biology designs scalable to hundreds of nodes.

Main Methods:

The Synthetic Biology Reusable Optimization Methodology (SBROME) transforms user-defined circuits and matches them against a module database.
Circuits are decomposed into subcircuits, populated with optimal parts, and then characterized.
Characterized subcircuits are added back to the module database for future reuse.

Main Results:

SBROME was successfully applied to design a modular 3-input multiplexer.
The methodology demonstrated the effective utilization of pre-existing logic gates and characterized biological parts.
The framework supports the integration of previously validated components into new designs.

Conclusions:

SBROME provides a scalable and reusable framework for automating biodesign.
This methodology addresses the challenge of increasing complexity in synthetic biology.
The approach promotes efficient development and reuse of biological parts and circuits.