Alumna Profile: Jen Dionne (PhD '09)

Jennifer (Jen) Dionne (PhD '09) channels the principles of nanophotonics to engineer new solutions for global health and sustainability. Growing up in Rhode Island, her inspiration to pursue science came from watching the X-Files, where she saw how interdisciplinary teamwork could tackle unsolved mysteries. Currently an Associate Professor of Materials Science and Radiology at Stanford, Dionne's research is focused on creating impactful and innovative solutions for growing existential threats, like antimicrobial resistance. Outside of her research group, Dionne also served as the Senior Associate Vice Provost for research platforms/shared facilities at Stanford, a role informed by her involvement with Caltech's Kavli Nanoscience Institute (KNI), and is currently co-founder of Pumpkinseed and Deputy Director of a DOE National Quantum Science Center, Q-NEXT.

ENGenuity caught up with Dionne, who was originally profiled in 2018, to learn about her recent work and how her Caltech experience influenced her approach to interdisciplinary collaboration.

ENGenuity: How would you describe your professional contributions and what you're currently doing?

Jennifer Dionne: My work devises new methods to control light on the nanoscale, to detect molecules and to direct their chemical transformations. Light has a certain size associated with it — its wavelength. Shrinking light down to deeply subwavelength dimensions (and doing so efficiently) requires new tricks of electromagnetism and quantum physics. For the past 14 years, I've pursued this research through my role as a faculty member in the materials science and engineering department at Stanford. I also have an appointment in the radiology department in the school of medicine, and am Deputy Director of a DOE National Quantum Center, Q-NEXT. My lab members are an interdisciplinary team of physicists, chemists, biologists, and engineers, all passionate about improving global health and sustainability. I think some of the best ideas come from a convergence of disciplines, and I try to train my students to speak multiple scientific "languages." Our research contributions include new optical sensors that enable sensitive and rapid detection of molecules and other biomarkers ranging from nucleic acids and proteins in marine samples to bacteria in sputum, blood, and wastewater. We also devise light-driven methods to catalyze high-yield and selective chemical reactions to sustainably transform molecules into useful products.

For the past several years, I have also served as the Senior Associate Vice Provost of Shared Facilities/Research Platforms at Stanford. In this role, working closely with the Vice Provost and Dean of Research, I led the upgrading of and fundraising for a new generation of Shared Research Facilities, including instrumentation, staffing, education, and translation. Many of my contributions in this role were inspired by my time as a student at Caltech, where I saw the power of shared facilities: central labs or resources that contain instruments or computing resources that are not possible for any one individual PI to acquire. These shared facilities help bring students from different disciplines together—they serve as "watering holes" for researchers to meet, share their work, and brainstorm new, "out-of-the-box" ideas. The Kavli Nanoscience Institute at Caltech (KNI) is a great example of such a shared facility and was instrumental in my time as a PhD student. At Stanford, I've loved working across the Schools of Engineering, Medicine, Sustainability, and Humanities and Sciences to strengthen the community of shared research facilities, and devise programs that improve how we train the next generation of STEM scholars in these facilities.

I'm currently focused on getting a new company, Pumpkinseed, off the ground. Pumpkinseed is focused on high-resolution protein sequencing, especially in the immunology domain. There are about 20,000 protein-coding genes, but nearly a million proteoforms. The diversity of proteoforms comes from "post-translational modifications" — molecules that bind to amino acids and change the protein structure and fold. Protein sequence and structure has a huge impact on protein function. We strive to help improve development of therapeutics and vaccines with better understanding of the type and quantity of proteoforms. It's been rewarding to translate some of my lab's scientific innovations from the past decade into solutions that can benefit end-users.

ENGenuity: Is there a particular class or professor at Caltech that made the biggest impact on you?

Dionne: Caltech is such a small place that it is easy to get to know everyone. I have to give a shoutout to my PhD advisor, Harry Atwater [Otis Booth Leadership Chair, Division of Engineering and Applied Science; Howard Hughes Professor of Applied Physics and Materials Science; Director, Liquid Sunlight Alliance]. He is a renaissance man. He was able to juggle so much, from teaching to soccer coaching to advising 30+ students, while still coming up with state-of-the-art, frontier, out-of-the-box science ideas. He was not only an incredible scientist, but also an amazing mentor. I'll also give a shoutout to John Preskill [Richard P. Feynman Professor of Theoretical Physics; Allen V. C. Davis and Lenabelle Davis Leadership Chair, Institute for Quantum Science and Technology], an inspiring professor in my first-year quantum physics class. Beyond his mind-blowing research that linked quantum information and astrophysics, he knew how to write some great poems to introduce colloquia speakers.

ENGenuity: What gives you the most satisfaction in your work?

Dionne: We're living at a remarkable time in history. Humans have devised many incredible inventions and systems that allow us to live longer, healthier, and more fulfilling lives. Yet, some of these systems are severely outdated in the way they use energy, with potentially catastrophic consequences on ecosystem health. My lab, and many researchers in the community, are working to create modern solutions to sustainability. These include new methods to monitor human and environmental health, and new methods for energy-efficient chemical manufacturing. It's been fulfilling to train students in sustainability research, and also to have our lab alum leave Stanford to further advance this research. Many of my students/postdocs are now professors at top universities like MIT, Berkeley, and Northwestern, and many have gone onto exciting roles advancing sustainability in industry, at start-ups, in policy, and in science communications. I find fulfillment in mentoring lab members and helping them succeed in their careers. What also gives me fulfillment is translating these laboratory-rooted ideas into products that can help make for a more sustainable future.

ENGenuity: Can you share an example of a translational solution that has come out of your lab?

Dionne: One recent example is my lab's work on bacterial identification and antibiotic susceptibility testing, especially on tuberculosis (TB). TB is a bacterial infection of the lungs, and approximately 10 million individuals contract the infection each year. To determine which antibiotic a TB-positive individual should be given, the bacteria generally need to be cultured. But it can take weeks for TB to grow.

According to the CDC, nearly half of all patients are treated with the wrong antibiotic type or dose or unnecessarily treated with antibiotics. Consequently, we're seeing a rise in antimicrobial resistance, where patients aren't responding to treatment because the bacteria are resistant to antibiotics. The World Health Organization (WHO) predicts that antimicrobial resistance will be the leading cause of death by 2050.

My lab devised a combination of techniques that allows for rapid identification of TB and its drug susceptibility/resistance. We look at the bacteria's optical scattering signature in a process called Raman spectroscopy. Raman spectroscopy reports on all the molecular vibrations of a sample, providing an information-rich "fingerprint" of the cell. We collected Raman spectra from thousands of TB cells with different antibiotic resistance profiles, then built machine learning (ML) models to interpret the scattering signature. Within a few-seconds, an optical scan can determine if the TB is resistant to a particular antibiotic.

My lab's work on bacteria has been fulfilling, showing that a combination of techniques from physics and engineering (like Raman, nanophotonics, and ML) can be potentially used to displace gold-standard culturing approaches. We now have a miniaturized, low-cost platform, suitable for deployment in TB-endemic regions, to determine which antibiotic a patient should be treated with more quickly.

We are now collecting more patient sputum samples and expanding our catalog of bacterial Raman signatures. Working with my colleague, Professor Manu Prackash and his lab, we hope to deploy this tool in TB endemic regions to find the TB in sputum and then within minutes determine the appropriate antibiotic to prescribe. We want to combat the problem of antimicrobial resistance by eliminating some of the bottlenecks in determining drug susceptibility, giving individuals the right antibiotics at the right time. I think there is hope for a healthier, more equitable future, and working to realize that future is what fulfills me.

ENGenuity: What is your favorite story?

Dionne: I recently read One Day in the Life of Ivan Denisovich by Aleksandr Solzhenitsyn. The leading character, Ivan "Shukhov" was wrongly accused of being a spy and put in a Soviet Union prison camp. The story portrays each detail of his day, from him waking up, going to work in the gulag, and overcoming countless obstacles. Shukhov has such a hopeful perspective of the whole ordeal. He comes to accept his fate and make the most of it while he is there. It is a story about overcoming obstacles, hoping for the best, and not letting the tragedy of the situation get in the way of moving forward. It is one of the most compelling stories that I have read in a while.

My husband, Nhat, is an immigrant from Vietnam, and this story has many parallels with his family's multi-year journey to get to the U.S. Nhat's story is probably one of my favorites — showing how the bonds of love and friendship can inspire us to overcome any obstacle if we stay strong and positive.

ENGenuity: What is your favorite destination?

Dionne: Zanzibar. It is a beautiful island off the coast of Tanzania, and not the Africa that you might expect. They have the most beautiful beaches on the Indian Ocean that at high tide are perfect for swimming and at low tide reveal miles of seaweed farms. On the other side of the island is Stone Town — birth town of one of my favorite artists, Freddy Mercury. Stone Town is a UNESCO world heritage site with beautiful architecture and the most ornate wooden doors: every entrance is an artistic experience. Zanzibar is an inspiring, incredible confluence of old and new, rock and pop, what has been and what could be.

ENGenuity: What keeps you up at night?

I have two sons who are almost seven and nine. Getting them to bed is like an Olympic ceremony, but tons of fun. So that keeps me up at night. More seriously, what keeps me up is thinking about what the future could hold. I am hopeful that we can create a future where everyone has equitable access to healthcare, clean water, clean energy, better education, and the opportunity to pursue their passions without having to worry about providing for their families. Technology can enable a more just, verdant future for everyone, as long as scientists, engineers, policymakers, and the public can come together to help realize that future.

ENGenuity: What gets you up in the morning?

Running. I love going on long distance runs, especially on trails to spend more time in nature. I usually compete in four or so half marathons every year. I find that running is a good endorphin boost: it gets me energized for the day, helps me process my thoughts and priorities, and gives me a bit less guilt indulging in my favorite snack, chocolate-covered almonds!