New cloud-based repository creates digital fingerprint of modified microorganisms

A cloud-based repository that creates a digital fingerprint of modified microorganisms has been successfully tested.

An international team led by Newcastle University has launched CellRepo, a species and strain database that uses cellular barcodes to monitor and track modified organisms. Reported in a new study in the journal Nature Communication, the database tracks and organizes the digital data produced during cell engineering. It also molecularly links this data to associated living samples.

Available worldwide, this resource supports international collaboration and has significant safety benefits, such as limiting the impact of deliberately or accidentally released genetically modified microorganisms by enabling faster tracing of organisms. laboratory origin and design details.

CellRepo is based on version control, a concept from software engineering that records and tracks changes to software code. Scientists believe that version control for cell engineering will make engineering biology more open, reproducible, easier to trace and share, and more reliable.

The research team highlights additional benefits of this community resource, such as traceability – providing exact documentation of a strain and proper crediting of lab work. The database also emphasizes accountability by making it easier to track and assign ownership.

With access to a global database, researchers will be able to replicate results and collaborate more easily. The scientists also say the repository will improve transparency and reduce costs associated with data and source code loss.

Lead author Natalio Krasnogor, professor of computer science and synthetic biology at Newcastle University’s School of Computing, said: “Engineering biology is not rocket science. It is much, much more difficult. And because of that, it’s imperative that we do it more openly. and more collaborative. CellRepo, at its core, is a collaboration platform where cellular engineers can document their work and share it with others (within their own lab or more widely). By enabling greater collaboration and transparent sharing of modified strains, we hope to speed up and improve synthetic biology processes and reporting for everyone. CellRepo is a community resource and as such we invite engineering biologists, synthetic biologists, biotechnologists and life scientists more generally to try it out and contact us so we know what works and what should be. improved!”

I have always had problems with misidentification during my projects. Luckily I was able to find them early on and fix them, but I can’t imagine how many good projects have failed or stalled because of this. Another part of my time as a biologist is spent retroactively building up the history of the plasmids and strains I use. I may be getting the genetic material from someone, but who was the original author? Sometimes I get lucky and it’s just a paper, sometimes it’s down a rabbit hole that can end up in the 80s. CellRepo solves these and other important problems for experimenters. “

Dr. Jonathan Tellechea, synthetic biologist in the project

Leanne Hobbs, the project’s senior software engineer, explains: “As a software engineer coming from industry to university, it has been both a challenge and a pleasure to work on a project where I can use my skills for the public good. Version control is a staple of software engineering and I am proud that we are now bringing these tools to engineering biology.”

Dr Lenka Pelechova, a social scientist working in the Interdisciplinary Computing and Complex Biosystems (ICOS) research group, added: “As a social scientist, I believe that the framework for research and d “Responsible innovation is crucial to meeting societal expectations and opening up public conversations about new research and technologies. In my view, these conversations should start early and CellRepo supports this by making research transparent from the start.”

Study co-author Professor Víctor de Lorenzo, from the Systems and Synthesis Biology program at the Centro Nacional de Biotecnología in Madrid, Spain, said: “Given the innate tendency of artificial constructs to mutate and to overcome any kind of genetic firewall, decades of recombinant bacteria containment efforts have yielded little practical results.Instead, CellRepo offers stable and unequivocal identification of given strains that can be rigorously tracked and matched to digital twins with all available information; if necessary for countermeasures, ownership or liability purposes.”

Elena Velázquez, PhD student in Víctor de Lorenzo’s lab, added:

“As a synthetic biologist who works all day with plasmids and strains of different origins, I usually find that the plasmid or strain I used in my experiments was not what I I had asked. This, of course, cannot be blamed on the scientists who kindly donate their hard work selflessly and, moreover, because there was no easy way to label and identify whether the strain in play was the one wanted.

“CellRepo is a platform that represents an incredible breakthrough in this field and can save a ton of time and unnecessary work for researchers around the world. form can be an invaluable open-source of samples and a bridge for new collaborations between different laboratories. Thanks to CellRepo, scientists have the possibility of accelerating their investigations and the reliability of their science.”

Co-author Simon Woods, Professor of Bioethics at Newcastle University’s Policy Ethics and Life Sciences Research Centre, added: “Wide adoption of the CellRepo platform will make a major beneficial contribution to science culture by providing a mechanism that ensures traceability. and transparency and replicability. Moreover, CellRepo is a new scientific governance instrument that supports responsible yet innovative science.