Illumina supports enhanced genomics-based discovery and training programs at UC San Diego


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

The Illumina Lab at Scholander Hall is one of two new Automation Hubbs on the Scripps Oceanography campus. Photos by Erik Jepsen/University Communications.

The Scripps Institution of Oceanography at the University of California, San Diego today announced that Illuminateda world leader in the development and application of genomics technology to improve human and environmental health, has provided researchers from the Scripps Center for Marine Biotechnology and Biomedicine new scientific equipment to create discovery and training programs based on genomics and laboratory automation. Additionally, the Illumina Corporate Foundation donated $973,000 for additional materials to commission the equipment and set up two labs on the Scripps Oceanography campus.

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

“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 transfer of equipment, we hope to enable the acceleration of discoveries in marine biology that could improve human and planetary health. We’re also excited to put this automated technology in the hands of future scientists who will drive the next era of discovery on a scale we can barely imagine today.

PhD student Kayla Wilson operates a new bulk reagent dispenser in the Illumina lab.

In the Illumina lab at Scholander Hall, PhD student Kayla Wilson operates a new bulk reagent dispenser, which can quickly fill well plates with two different liquids. Postdoctoral researcher 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 manipulation, and more. The equipment will allow researchers to screen thousands of cells per day, observe protein evolution, analyze DNA isolation for microbiome studies, characterize gene expression patterns at early development, determine the effects of toxic substances on developing embryos, etc. High-capacity computing equipment and a new liquid chromatography mass spectrometry system for rapid analysis were 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 the CMBB whose lab focuses on the discovery of drug leads and toxins from marine organisms and the development of biosynthetic cell factories to make sustainable products. Hamdoun is a marine biologist working to generate new, genetically activated 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 the first 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 help both Scripps Laboratories understand the chemical interactions between microorganisms and their chemical signals, enabling researchers to better understand human health and develop sustainable bio-based solutions.

A pipetting robot dilutes samples into a plate for imaging in the Illumina lab.

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

Much of this research requires the individual analysis of hundreds of samples, a process that “was quite laborious and slow,” Hamdoun said. This new equipment will allow researchers in his laboratory to image and process thousands of samples per week, whereas they were previously limited to a few hundred. The potential gains from this are substantial, and Hamdoun points out that these tools will “invigorate 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, enabling them to better understand how genes are structured during embryonic development and how they change throughout. throughout this development.

Moore predicts that this equipment will lead to the discovery of even more new molecules that could save lives.

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

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

“We are excited to create opportunities that connect scientists from local universities with industry,” said Sharon Vidal, Senior Director of Corporate Social Responsibility at Illumina. “Preparing our future workforce with access to the latest innovations in life sciences is a win-win situation for everyone.”

Moore Lab National Institutes of Health (NIH) postdoctoral fellow Timothy Fallon agrees.

Hamdoun Lab graduate students Yoon Lee, Nathan Chang, and Evan Tjeerdema work in the new Illumina Lab.

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

“Students today need to be familiar with solving biological problems at these enormous scales, and that simply cannot be done without the use of laboratory automation and experimental design and big data computing,” said Fallon, who helped lead the automation hub’s development effort. “That’s why the support is so exciting. It allows us to build the facilities and courses needed to both teach these cutting-edge topics and apply them in our research.”

Hamdoun says a significant portion of Scripps students end up pursuing careers in biotechnology, and these new systems will allow them to be exposed to equipment that is common in industry much earlier in their studies.

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

For Moore Lab NIH postdoctoral fellow April Lukowski, liquid-manipulating robots increase her efficiency in X-ray crystallography, where she works to crystallize proteins to understand their structures. This process tells scientists how proteins work so they can modify them into something that could be useful in drug development or manufacturing. She went from spending two hours manually pipetting 96 crystallization conditions to preparing the same amount of samples in just two minutes, dramatically speeding up the discovery process.

A new bulk reagent dispenser in the Illumina lab.

A new bulk reagent dispenser in the Illumina lab at Scholander Hall can quickly fill well plates with two different liquids. By increasing efficiency, it can speed up the discovery process.

While this equipment lives at UC San Diego, the Scripps Automation Center will benefit the wider research community, with access available to faculty and students at nearby institutions such as State University. from San Diego.

With these significant contributions to Scripps, CMBB envisioned 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-based discovery.

Illumina’s support was part of the Campaign for UC San Diegoa comprehensive university-wide fundraising effort that ended June 30, 2022 and raised a total of $3.05 billion to continue the university’s non-traditional path to breakthrough ideas , unexpected answers, vital discoveries and impact on the planet.

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