UCSD - University of California - San Diego
09/30/2025 | Press release | Distributed by Public on 09/30/2025 10:55
Seeing Red: A UC San Diego Invention is Transforming the Way Scientists Track Genes
Published Date
September 30, 2025Article Content
It all started with the idea of finding a better way to monitor genes.
Plant biologists have traditionally employed various techniques to precisely track how information coded in DNA is converted into specific end products, such as proteins, a process known as "gene expression." These include fluorescent proteins that glow when activated to visualize genetic changes unfolding and chemical staining as plants grow and develop. But these gene expression tracking tools, known as "reporters," are typically expensive to implement and require sophisticated instruments and costly chemicals.
Five years ago, UC San Diego biologists unveiled a better way. Their breakthrough innovation has revolutionized how scientists study plants and has snowballed into applications across an expanding list of research fields and into the commercial sector.
In September 2020 Professor Yunde Zhao of the School of Biological Sciences and his colleagues announced their discovery, which they named "RUBY," an inexpensive genetic reporter that provides red tracking signals that are clearly visible to the naked eye. RUBY has ushered in a transformative new era of plant biology, offering insights for a broad assortment of plant species, from key agricultural crops to large fruit trees to ornamental plants (see a visual collection here). RUBY is turning heads in scientific circles as well as public audiences (such as this Wired article).
"It's been a pleasure to see how quickly the scientific community has embraced this technology," said Zhao, a faculty member in the Department of Cell and Developmental Biology. "Researchers have come up to me at conferences to let me know how RUBY positively impacted their research. They are eager to share with me a RUBY plant photo, and sometimes they bring their plants to show me."
Seeing red
Dorothy's ruby red slippers in the "Wizard of Oz" were unforgettable, and the RUBY gene reporter is making an unmistakable impression in laboratories throughout the world. University researchers and commercial businesses now use RUBY as a tool to investigate a wide variety of plants, including rice, corn, soybean, wheat, cabbage, cucumber and avocado.
As word of RUBY spread through the scientific community, researchers found the technology beneficial not only in genetics, but also in a range of other areas. Because plants naturally monitor the conditions of the environment that surrounds them, researchers found that RUBY's clear red signals could be leveraged to provide visual alerts about the presence of pesticides and environmental pollutants. RUBY has also been implemented in studies of plant hormones and stress levels.
"You can use RUBY as a visual marker for environmental changes," said Zhao, "You can monitor things like drought, and the presence of heavy metal pollutants and chemicals."
A Chinese cabbage plant features RUBY's red hues. Credit: Shubin Wang, Institute for Vegetable Research, Shandong Academy of Agricultural Sciences
Department of Cell and Developmental Biology Professor Yunde Zhao. Credit: Erik Jepsen/University Communications
With certain crops, such as peanut plants, farmers tinker with factors such as oil content and composition to find a mix that appeals to their customers. Under traditional methods, such modifications might take several months for plants to mature enough to be properly evaluated.
"With RUBY, you have a visual marker that you can see within a couple of weeks," said Zhao. "If you see red then it means the genomic components are getting into the cells and you can focus on those traits."
Today, the applications of RUBY continue to ripple out. Researchers in laboratories have begun to apply RUBY as a visual tool to study cellular and molecular processes. Scientists at the Australian National University in Canberra, for example, used RUBY to visualize protein-protein interactions in plants, while researchers in Beijing, China, visually monitoredprotein-DNA dynamics. Other researchers have applied the tool to investigate host-parasite interactions. And RUBYs applications keep growing, making RUBY's impact unmistakable, just like Dorothy's slippers.
"RUBY is an elegantly designed and visually striking tool that is proving to be transformative in plant engineering," said Professor Arshad Desai, chair of the Department of Cell and Developmental Biology. "It is an outstanding example of how rigorous basic research, conducted in small and focused lab groups such as the Zhao lab in the School of Biological Sciences, broadly advances fundamental science and drives innovative real-world applications."
The mother of invention
Transgenes are genes that are introduced through genetic engineering methods, such as items labeled "genetically modified organism," or GMO. Once implemented in the genome of a plant, transgenes can be tricky to distinguish from genes that are not genetically engineered. While working on a project seeking to quickly remove transgenes from plant genomes, Zhao looked for a new way to distinguish transgenes from non-transgenes.
A peanut plant genetically infused with the RUBY gene reporter. Credit: Dr. Vijay Sheri, Texas Tech University
The answer came in the form of betalains. These naturally occurring pigments are responsible for the bright colors we see in beets, dragon fruit, Swiss chard and other plants. Zhao and his colleagues saw betalains as a natural marker that could be used to track the activities of specific genes. They created RUBY as a synthetic gene that converts the amino acid tyrosine into red betalain. This "cassette" is then inserted into the plant's genome at the targeted genes of interest. If those genes are expressed, say in the florets of cauliflower or leaves, then the area of focus will bloom with a clear red hue.
When RUBY was first announced to the scientific community, plants were the main focus. But the initial description of the tool in the landmark paper published by Zhao and his colleagues teased the future potential of such a novel technology: "We envision that RUBY can be adapted for applications in some microbes and animals," they noted, "because the substrate tyrosine exists in all cells." In one demonstration in live animals, RUBY was used to generate pink silk from silkworms.
As the research applications of RUBY continue to multiply, another use has emerged. Educators are finding that RUBY can be implemented as a powerful teaching aid. In classrooms and teaching laboratories, educators are now using RUBY's inexpensive and easy-to-use features to teach biological concepts and tools such as genome editing.
RUBY is also spreading into the business sector. In the name of open science, RUBY is complimentary for use in academic labs and classrooms. However, industry users pay a fee to license the technology in commercial business applications. UC San Diego's Office of Innovation and Commercialization reports that 10 commercial licenses have been issued for RUBY in the past two years, spanning from giant multinational Scotts Company (now known as Scotts Miracle-Gro), the producer of consumer lawn and garden products, to tiny spinoffs and startup firms.
Cquesta, a recently launched San Diego-based company spun out of the Salk Institute, is developing new technologies to help plants sequester carbon in soil and make crops more resilient in the face of rising temperatures. RUBY is helping the company visualize genetic changes in crops, including corn, soy, canola and sorghum, focusing on the plant's root systems.
Arabidopsis rose bouquet. Credit: Nick Desnoyer, Grossniklaus Lab, University of Zürich.
"Within Cquesta's business, the RUBY technology is enabling us to accelerate our discovery and development process," said Tim Ulmasov, the CEO of Cquesta. "Our company has used RUBY since the beginning. It's a wonderful visualization tool that tells us what's going on with transgenes from a single cell all the way up to mature plants. It's obvious to me that RUBY is transformative - we couldn't have progressed without it."
A ruby red future
As with innumerable research discoveries, RUBY's development was built on successes and failures that spanned several years and countless lab hours to finally reach fruition. RUBY's development was partially supported by the Tata Institute for Genetics and Society at UC San Diego and other sources. Similar basic, or foundational, research breakthroughs would not be possible without support from funding agencies such as the National Institutes of Health, the National Science Foundation, the U.S. Department of Agriculture and philanthropic organizations that nurture bold ideas through painstaking trial and error over many years, with untold benefits for science and society when they finally reach maturity.
For RUBY, future applications being envisioned by researchers include expanded use in molecular biology in studies of DNA and RNA functions. In plant biology, scientists are considering expanding RUBY's use across agricultural fields, where AI-based drones could one day assist in more efficient resource management by scanning crops for signs of drought or damaging pathogen attacks.
"RUBY is making a difference in so many ways because we have opened it up to all of science," said Zhao. "It's a reminder that fundamental research is so crucial because it often leads to unexpected and important discoveries."
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