Kia ora, hello! I’m Jian, a Research Associate and the Image Analysis Specialist at the BioFrontiers Advanced Light Microscopy Core (ALMC). In my current position, I collaborate with biologists, computer scientists, and engineers, to develop innovative imaging methods and analysis software to enable breakthroughs in cellular biology.
Originally from New Zealand, I received my undergraduate and graduate degrees in Physics from the University of Otago. I then moved to the United States to complete my postdoctoral training at the Washington University in St Louis and the University of Colorado Boulder. During my academic training, I invented new methods to image through thick, optically scattering media, using photoacoustics and wavefront shaping and quantum optics resources.
I have been in my current position at the ALMC for four years, initially in a part-time capacity (25% FTE) before being promoted to full-time status in 2019. During my time here, I have established and grown the image analysis capabilities of the ALMC by developing automated analysis pipelines, allowing large sets of images to be analyzed with a single command. Additionally, I have developed customized solutions to process images containing more complex objects, such as actin fibers or organelles, which were previously unable to be analyzed or would have required manual annotation. Most of the code I have developed is available online (see the projects page for more details).
My work has enabled multidisciplinary collaborations with over 15 different research groups from four different departments throughout the university and the local community. These collaborations have resulted in ground-breaking discoveries, including the first observation of degradation of a bacterial microcompartment, as well as shedding light on the role of zinc on the mammalian cell cycle.
Apart from research, I also train students, postdoctoral researchers, and faculty in cutting-edge image analysis methods. I teach a cross-listed course ( MCDB/BCHM 4312/5312 Quantitative Optical Imaging) during the fall semesters, as well as organizing workshops during the rest of the academic year. I am also building a new website to provide programming and image analysis training for biologists.
PhD in Physics, 2011
University of Otago, Dunedin, New Zealand
BSc in Physics, 2006
University of Otago, Dunedin, New Zealand
Carboxysomes, prototypical bacterial microcompartments (BMCs) found in cyanobacteria, are large (~1 GDa) and essential protein complexes that enhance CO2 fixation. While carboxysome biogenesis has been elucidated, the activity dynamics, lifetime, and degradation of these structures have not been investigated, owing to the inability of tracking individual BMCs over time in vivo. We have developed a fluorescence-imaging platform to simultaneously measure carboxysome number, position, and activity over time in a growing cyanobacterial population, allowing individual carboxysomes to be clustered on the basis of activity and spatial dynamics. We have demonstrated both BMC degradation, characterized by abrupt activity loss followed by polar recruitment of the deactivated complex, and a subclass of ultraproductive carboxysomes. Together, our results reveal the BMC life cycle after biogenesis and describe the first method for measuring activity of single BMCs in vivo. Single cell and organelle measurements reveal activity dynamics and degradation of the carbon-fixing cyanobacterial carboxysome. Single cell and organelle measurements reveal activity dynamics and degradation of the carbon-fixing cyanobacterial carboxysome.
Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source–sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.
Non-invasively focusing light into strongly scattering media, such as biological tissue, is highly desirable but challenging. Recently, ultrasonically guided wavefront-shaping technologies have been developed to address this limitation. So far, the focusing resolution of most implementations has been limited by acoustic diffraction. Here, we introduce nonlinear photoacoustically guided wavefront shaping (PAWS), which achieves optical diffraction-limited focusing in scattering media. We develop an efficient dual-pulse excitation approach to generate strong nonlinear photoacoustic signals based on the Grueneisen relaxation effect. These nonlinear photoacoustic signals are used as feedback to guide iterative wavefront optimization. As a result, light is effectively focused to a single optical speckle grain on the scale of 5-7 μm, which is ~10 times smaller than the acoustic focus, with an enhancement factor of ~6,000 in peak fluence. This technology has the potential to benefit many applications that require a highly confined strong optical focus in tissue.
jian.tay [at] colorado.edu
3415 Colorado Avenue, UCB 596
Boulder, CO 80309