Illumina Supports Enhanced Genomics-Enabled Discovery and Training Programs at UC San Diego

New laboratory automation technology will advance marine biomedical research, preparing students for biotech workforce

The Illumina Laboratory in Scholander Hall is one of two new automation Hubbs on the Scripps Oceanography campus. Photos by Erik Jepsen/University Communications.

Scripps Institution of Oceanography at the University of California San Diego announced today that Illumina, a global leader in development and application of genomic technology to improve human and environmental health, has provided researchers at the Center for Marine Biotechnology and Biomedicine at Scripps new scientific equipment to build genomics and laboratory automation-enabled discovery and training programs. Additionally, the Illumina Corporate Foundation donated $973,000 for additional materials to bring the equipment into operation and set up two laboratories on the Scripps Oceanography campus.

The Center for Marine Biotechnology and Biomedicine (CMBB) at Scripps focuses on research at the intersection of ocean sciences and human health. This support from Illumina will be used in the development of an automation hub to enable advanced synthetic biology, marine drug compound library curation, microbiome science, marine model organism cell biology and more. It will also become a training tool for students as they prepare to enter the biotechnology and genomics workforce.

“Illumina is dedicated to creating opportunities to invite innovation and work collaboratively to unlock the potential of genomics,” said Ashley Van Zeeland, vice president and head of Open Innovation at Illumina. “With this equipment transfer, we hope to enable the acceleration of discoveries in marine biology that could improve both human and planetary health. We are also thrilled to get this automated technology into the hands of future scientists who will drive the next era of discovery at a scale we can hardly imagine today.”

In the Illumina Lab in Scholander Hall, PhD student Kayla Wilson operates a new bulk reagent dispenser, which can rapidly fill well plates with two different liquids. Postdoctoral scholar Timothy Fallon programs a liquid handling robot.

This technology provided to Scripps Oceanography includes high-throughput screening equipment such as robotic liquid handlers, imaging processing stations, robotic arms for microplate handling, and more. The equipment will allow researchers to screen thousands of cells a day, observe protein evolutions, analyze DNA isolation for microbiome studies, characterize gene expression patterns during early development, determine the effects of toxicants on developing embryos, and more. High-capacity computing equipment and a new liquid-chromatography mass spectrometry system that enables rapid analysis was also included.

The two new laboratories will be operated by professors Bradley Moore and Amro Hamdoun. Moore is a marine chemical biologist and director of CMBB whose lab is focused on the discovery of drug leads and toxins from marine organisms and the development of biosynthetic cellular factories to make sustainable products. Hamdoun is a marine biologist working to generate new, genetically-enabled marine cell biological model organisms useful for ongoing biomedical research. Hamdoun Lab graduate students Yoon Lee, Evan Tjeerdema, and Nathan Chang are also examining how different environmental stressors and harmful chemicals—such as persistent organic pollutants like flame retardants and legacy pesticides—interact during early life stages of embryo development in sea urchins. These interactions have implications for understanding the health impacts of in utero chemical exposures for humans.

The use of genomics can aid the two Scripps labs in understanding chemical interactions between microorganisms and their chemical signals, thus enabling researchers to better understand human health and develop bio-based sustainable solutions.

A pipetting robot dilutes samples into a plate for imaging in the Illumina Laboratory in Hubbs Hall.

Much of this research requires individually analyzing hundreds of samples, a process that “was pretty labor intensive and slow,” said Hamdoun. This new equipment will allow researchers in his lab to image and process thousands of samples a week when they were previously limited to a couple hundred. The potential gains from this are substantial, and Hamdoun emphasizes that these tools will “supercharge our work” over the next few years. In particular, the new image processing station will allow the team to examine subcellular structures and expression patterns, allowing them to better understand how genes are patterned during embryonic development and how they change throughout this development.

Moore predicts that this equipment will allow for the discovery of even more new molecules with life-saving potential.

“This support allows us to dream big,” added Moore. “It allows us to do experiments that we thought were going to be too difficult, too hard, or too expensive to do by allowing us to miniaturize the way we look at things, and be able to access so many more samples than we can do right now.”

The equipment will also provide immense training opportunities for students, giving them experience in genomics and laboratory automation that is critical in today’s life science and biotechnology workforce. The life science industry in San Diego is significant, supporting 175,000 jobs and generating about $41 billion in economic activity, according to Biocom, the California life sciences trade group.

“We are thrilled to create opportunities that connect local university scientists to industry,” said Sharon Vidal, senior director of corporate social responsibility at Illumina. “Preparing our future workforce with access to the latest innovation in life science is a win win for all.”

Moore Lab National Institutes of Health (NIH) Postdoctoral Fellow Timothy Fallon agrees.

From left to right, Hamdoun Lab graduate students Yoon Lee, Nathan Chang, and Evan Tjeerdema work in the new Illumina Laboratory in Hubbs Hall.

“Today’s students need to be familiar with solving biological problems at these huge scales, and that simply can’t be done without the use of laboratory automation and big data experimental design and informatics,” said Fallon, who helped spearhead the effort to develop the automation hub. “This is why the support is so exciting. It allows us to build the facilities and coursework to both teach these cutting-edge topics, and to apply them in our research.”

Hamdoun says that a significant portion of Scripps students end up pursuing careers in biotech, and these new systems will enable them to gain exposure to equipment that is commonplace in the industry much earlier in their education.

“This allows students to come out of Scripps and UC San Diego better equipped to work and compete in the modern life sciences industry,” says Hamdoun. “This has always been very central to us—to best prepare our students for positions in industry and increase the diversity of people working outside of academia.”

For Moore Lab NIH Postdoctoral Fellow April Lukowski, the robotic liquid handlers are increasing her efficiency in X-ray crystallography, where she works to crystallize proteins to understand their structures. This process informs scientists how the proteins work so they can modify them into something that might be useful in drug development or manufacturing. She has gone from spending two hours manually pipetting 96 crystallization conditions to preparing the same amount of samples in only two minutes, dramatically speeding up the discovery process.

A new bulk reagent dispenser in the Illumina Lab in Scholander Hall can rapidly fill well plates with two different liquids. By increasing efficiency, this can speed up the discovery process.

While this equipment lives at UC San Diego, the automation hub at Scripps will benefit the broader research community, with access available for faculty and students from neighboring institutions such as San Diego State University.

With these significant contributions to Scripps, CMBB envisions the creation of a new facility that would become the Biomedical Automation Facility. This facility could become a state-of-the-art hub for high-throughput screening equipment and genomics-enabled discovery.

Illumina’s support was a part of the Campaign for UC San Diego, a university-wide comprehensive fundraising effort that concluded June 30, 2022 and raised a total of $3.05 billion to continue the university’s nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact.