Scientists create a global repository for cell engineering

Dr. Jonathan Terechia, a synthetic biologist in Rob, while working on the project.Credits: Professor Natalio Krasnogor / Newcastle University, UK

A cloud-based repository that creates digital fingerprints of artificial microbes has been successfully attempted.

An international team led by Newcastle University is launched CellRepoA database of species and strains that monitor and track organisms manipulated using cell barcodes.Reported in a new study in the journal Nature Communications, The database tracks and organizes the digital data generated during cell engineering. It also molecularly links that data to the relevant live sample.

Globally available and supports this resource International cooperation It also has significant safety benefits, such as limiting the effects of intentionally or accidentally released transgenic microorganisms by allowing faster tracking of biological laboratories of origin and design details.

CellRepo is built on version control, a software engineering concept that records and tracks changes to software code. Scientists believe that version control of cell engineering makes engineering biology more open, reproducible, easier to track and share, and more reliable.

The research team emphasizes the additional benefits of this community resource, such as traceability. It provides accurate documentation of the strain and properly credits the work in the laboratory. The database also focuses on responsibilities by facilitating ownership tracking and assignment.

With access to a global database, researchers can reproduce the results and collaborate more easily. Scientists also claim that repositories improve transparency and reduce costs associated with data and source code loss.

Natario Krasnogor, a professor of computer science and synthetic biology at Newcastle University’s Faculty of Computing, said: CellRepo is its core collaboration platform that allows cell engineers to document their work and share it with others (in their lab or broader). Because CellRepo is a community resource, we will try and contact engineering biologists, synthetic biologists, bioengineers, and life scientists more generally to understand what works and what works. Need to improve! “

Dr. Jonathan Terechia, a synthetic biologist at the project, said:

“I’ve always had misidentification issues during projects. Fortunately, I was able to find and resolve them early on, but this caused a number of good projects that failed or stalled. I can’t imagine. Biologists retroactively build the history of the plasmids and strains I use. You might get the genetic material from someone, but who was the original author? CellRepo Fixes these and other important issues for the experimenter. “

Senior Leanne Hobbs Software Engineer The contents of the project are as follows. “As a software engineer from industry to academia, working on a project where you can use your skills for the public good is a challenge and a pleasure. Version management is a staple of software engineering, and I have these. We are proud to incorporate our tools into engineering biology. “

Dr. Lenka Pelechova, a social scientist working in the Interdisciplinary Computing and Complex Biosystems (ICOS) research group, added: Social scientist, I believe that a responsible research and innovation framework is important in meeting the expectations of society and opening public conversations about new research and technology. In my view, these conversations need to start early, and CellRepo supports this by making the research transparent from the beginning.

Professor Víctor de Lorenzo, research co-author of the Systems and Synthetic Biology Program at Centro Nacional de Biotecnología in Madrid, Spain, said: Efforts to contain recombinant bacteria have had little practical consequences. Instead, CellRepo provides a stable and clear identification of a particular strain that can be closely tracked and associated with digital twins using all available information. “”

Dr. Elena Velázquez, a student in the laboratory of Victor de Lorenzo, added:

“As a synthetic biologist who uses plasmids and strains of various origins all day long, I realized that the plasmids and strains I was using in my experiments were not what I requested. Of course, this was due to scientists. You can’t kindly donate their efforts selfishly, and there’s also an easy way to label and identify if the strain at stake is intended. Because it wasn’t.

“CellRepo is a platform that represents a remarkable advance in this problem, saving researchers around the world a great deal of time and wasted work. In addition, a global repository of strains shared through this platform Invaluable. The open source of samples and the bridge to new collaborations between different laboratories. Thanks to CellRepo, scientists have the potential to speed up research and scientific credibility. “

Co-author Simon Woods, a professor of bioethics at the Center for Policy Ethics and Life Sciences at Newcastle University, said: Achieve transparency and reproducibility. In addition, CellRepo is a new tool of scientific governance that supports responsible and innovative science. ”

The Age of CRAGE: Rapid Engineering Advances in Non-Model Bacteria

For more information:
Version control of biological cells for reliable cell engineering, Nature Communications (2022). DOI: 10.1038 / s41467-022-28350-4

Quote: Scientists of Cell Engineering (February 9, 2022) obtained from https: // on February 9, 2022. Create a global repository

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Scientists create a global repository for cell engineering

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