The early stages of the virus-cell interaction have long evaded observation by existing microscopy methods due to the rapid diffusion of virions in the extracellular space and the large three-dimensional cellular structures involved. A huge challenge in tracking processes over 3D volumes is that the temporal resolution becomes limited by the volumetric imaging rate. This is a huge barrier for fast-moving objects that cover large distances between images. The key to breaking this speed limit is to apply a multimodal method, where the tracking element is unburdened by the temporal overhead of trying to image an entire volume. Enter 3D Tracking and Imaging (3D-TrIm) microscopy. The key is to use an active-feedback tracking method to “lock on” to the virus (3D-SMART, https://nature.com/articles/s41467-020-17444-6). With the rapidly moving virion locked in the focal volume of the microscope, the temporal resolution becomes limited only by the photon collection rate. To provide cellular context, we used a sparse-sampling volumetric imaging approach (3D-FASTR, https://doi.org/10.1364/OE.27.036241). Together, high-speed 3D single-virus tracking in volumetric context can be achieved. #teamTrIm (former grad student Dr. Courtney Johnson, postdoc Dr. Jack Exell, grad student Yuxin Lin, and undergrad alum Jonathan Aguilar) put in years of effort to make this scope a reality. Using 3D-TrIm, the team captured the early contacts of viruses with the cell surface in unprecedented detail, including in epithelial cultures, the front line of defense for viral infection.

Read more in the full paper recently published at Nature Methods.

To learn more about why 3D-TrIm is such a big advance to single-virus tracking, see the wonderful “News & Views” from Dr. Sergi Padilla-Parra – “Next-generation single virus tracking”

Details can also be found at Duke Today! Sound up when watching the video 🎧

To date, active-feedback tracking has relied on the assumption of zero background, which makes the calculation of the particle location at high-speeds feasible. However, the assumption of zero or even constant background does not reflect real environments, where large changes in background can lead to tracking failure. To address this hurdle, grad student Stacey Niver has developed an algorithm to actively estimate both the particle brightness and local background in real time. Combined online Bayesian and windowed estimation of background and signal (COBWEBS) surpasses existing active-feedback localization methods in terms of tracking robustness in the presence of dramatic changes in local background signals. This algorithm will dramatically improve our ability to track rapidly moving particles in high background environments. Read about Stacey’s work in the Journal of Chemical Physics, online now!

Want to join our team of rock star microscopists? Apply to Duke Chemistry! You can learn more about the program and meet some members of our team at the upcoming Duke Chemistry Virtual Open House on Wednesday, November 2nd, 7-9 PM ET. Registration closes October 26th.

Register here: https://chem.duke.edu/openhouse

Shawn Yu’s collaborative work with Antonio Garcia and Prof. Suzanne Blum (https://blumgroupuci.squarespace.com/) has been selected as a supplemental cover in the current issue of JACS! The paper demonstrates the first (!) measurements of solution-phase single-particle chemical kinetics and can be found here: https://pubs.acs.org/doi/10.1021/jacs.2c04990. Congratulations to Shawn and our friends in the Blum Lab!!

Welcome to the new cohort of Duke Chemistry graduate students!

Are you interested in capturing biology and chemistry at speeds and scales previously impossible? Want to learn more about the initial contacts of viruses with host tissue or analyze the behavior of single molecules in complex environments? Like to build things or work with your hands? Like to code or want to learn how to code? If any of these fit you, come do a rotation with us! If you want more information, just contact Kevin directly. For more information on current projects, head over to the Research Overview page.

We have two “subgroup” meetings that prospective students are welcome to join. All meetings held in FFSC 2219:

Tuesdays 10:30 AM: Single-molecule tracking methodology

Wednesdays 1:00 PM: Virus tracking

Rising 3rd-year graduate student Yuxin Lin has been awarded the prestigious John T. Chambers Scholar award from the Fitzpatrick Institute of Photonics. The highly-selective Chambers scholar award will fund the next two years of Yuxin’s graduate work. Way to go, Yuxin!!

More info about the John T. Chambers Scholars award: http://fitzpatrick.duke.edu/education/fellowships

Dr. Courtney Johnson’s 3D Tracking and Imaging (3D-TrIm, preprint) microscope was highlighted by Mad City Labs in an article on Photonics Online. Mad City stages are central to our particle tracking scopes, so it was a delight to work with them on the piece. Read more below:

Despite the fact that most chemistry occurs in the solution phase, single-molecule approaches to chemistry have been limited to surface tethered studies. In collaborative work with the Blum Laboratory at the University of California, Irvine, lead author Donggeng (Shawn) Yu has demonstrated that active-feedback 3D single-particle tracking can untether single-particle chemical kinetics by “locking on” to freely diffusing and growing polymer particles. Using 3D-SMART, Shawn was able to measure the changing size of polymer particles formed by the ring-opening metathesis polymerization (ROMP) of norbornene. These data revealed the growth rates of individual particles, with the surprising observation that polymer particle growth rate was correlated with depth within the sample, demonstrating emergent heterogeneity while particles are still freely diffusing in solution. See more in the recent publication in JACS ASAP!

https://pubs.acs.org/doi/10.1021/jacs.2c04990

In just one short week, Kevin has the honor of giving a departmental colloquium detailing the efforts of the entire group over the past seven years. So many great stories to tell, so little time! Come hear about active-feedback tracking of single molecules, viruses, growing polymers, lipid nanoparticles, and much more! The talk will be held in the Bonk Lecture Hall starting at 2:30 PM on May the Fourth, 2022. There will be a cocktail reception to follow.

https://chem.duke.edu/events/chemistry-faculty-colloquium-featuring-professor-kevin-welsher-locking-single-molecules-and

Congratulations to Yuxin for passing his preliminary exam with a wonderful talk! Yuxin now embarks on a long journey to capture the dynamics of nanoscale carriers in the extracellular space. Way to go, Yuxin!