Lingyan Shi, Ph.D.
University of California, San Diego
Seminar Information

Understanding how metabolism functions in multicellular organisms is essential for revealing the fundamental mechanisms of numerous biological processes. Our research has developed multimodal microscopy which integrate deuterium-probed stimulated Raman scattering (DO-SRS), multiphoton fluorescence (MPF), and second harmonic generation (SHG) into a unified nanoscopy. We have converted the metabolic imaging platform into a super resolution multiplex nanoscopy by developing A-PoD and PRM algorithms, for delivering 59 nm resolution volumetric imaging capabilities. By using various deuterated molecules—including glucose, amino acids, fatty acids, and water molecules—as bioorthogonal metabolic probes. The process of enzymatic incorporation of deuterium generates carbon-deuterium (C-D) bonds in newly formed molecules, detectable by DO-SRS within the spectral cell-silence region of the Raman spectrum, which identifies them apart from older molecules. This nanoscopy provides new biological insights into the metabolic heterogeneity of various cells and organ tissues under physiological and pathological conditions. One of the significant findings is that the over-expressed tau proteins significantly altered the lipid metabolism in aged or Alzheimer's brains, and an excessive amount of newly formed lipid droplets were accumulated in glia cells, and this phenomenon can be rescued by the activation of AMPK. This nanoscopy imaging platform can be used for disease detection, diagnosis, drug discovery, and assessing drug efficacy or resistance, as well as for mechanistic understanding of scientific fundamentals in aging processes and disease development.
Lingyan Shi is currently a tenured Associate Professor in the Shu Chien Gene Lay Department of Bioengineering at UCSD. She joined UCSD in 2019, following her postdoctoral training in the Department of Chemistry at Columbia University. Her lab at UCSD focuses on developing high-resolution metabolic nanoscopy to study aging processes and related diseases. Notably, she discovered the "Golden Window" for deep tissue imaging and pioneered the "DO-SRS" metabolic imaging platform, which visualizes metabolic dynamics in cellular organelles, and tissues. At UC San Diego, her group further advanced stimulated Raman scattering (SRS) microscopy into super-resolution multiplex nanoscopy by developing A-PoD and PRM algorithms, revealing various lipid metabolic changes in organ tissues during aging and disease. She discovered that the over-expressed tau proteins significantly altered the lipid metabolism in aged or Alzheimer's brains, and an excessive amount of newly formed lipid droplets were accumulated in glia cells.Dr. Shi holds 10 awarded patents and 8 pending. She won Blavatnik Regional Award for Young Scientists (2018), Nature Light Science&Applications’ Rising Star Award (2021), the Advancing Bioimaging Scialog Fellow Award 2023, the David L. Williams Lecture Scholarship Award (2023), the Sloan Research Fellowship in Chemistry (2023), the BMES-Cellular Molecular Bioengineering Rising Star Faculty Award (2024), the Davos Summit iCANx Young Scientist Award (2024), Featured in the 2025 Optics notebook, women in optics, ICBME Rising Star Award 2025, and IUPS Young Faculty Award 2025.