Collaborative Projects
Our lab is involved in a number of collaborative projects focused on biological applications of microscopy and the development
of new optical imaging techniques and instrumentation. Here are some of our current and previous collaborative projects:
Imaging transcription at the heat shock locus in Drosophila:
We have collaborated for more than 20 years with the laboratory of Professor John Lis at Cornell on imaging projects in which we track the dynamics of Pol II and transcription factors (TFs) in the polytene chromsomes of the Drosophila salivary glands during the heat shock response. We are continuing these investigations in a project with a Biophysics student (James Borovilas) who has now developed a way to micro-inject small to medium sized molecules into the salivary gland cells. This has always been a challenge due to the complicated morphology and sticky nature of the glands, but we are now able get small molecule inhibitors and inhibitory RNA aptamers into the nuclei of cells in the salivary gland, and visualize transcription after heat shock using confocal and two-photon microscopy. This enables us to interfere with any TF we have inhibitors or modulators for, and catalog the effect on transcriptional dynamics.
We have collaborated for more than 20 years with the laboratory of Professor John Lis at Cornell on imaging projects in which we track the dynamics of Pol II and transcription factors (TFs) in the polytene chromsomes of the Drosophila salivary glands during the heat shock response. We are continuing these investigations in a project with a Biophysics student (James Borovilas) who has now developed a way to micro-inject small to medium sized molecules into the salivary gland cells. This has always been a challenge due to the complicated morphology and sticky nature of the glands, but we are now able get small molecule inhibitors and inhibitory RNA aptamers into the nuclei of cells in the salivary gland, and visualize transcription after heat shock using confocal and two-photon microscopy. This enables us to interfere with any TF we have inhibitors or modulators for, and catalog the effect on transcriptional dynamics.
Zobeck, K.L., M.S. Buckley, W.R. Zipfel, and J.T. Lis, Recruitment Timing and Dynamics of Transcription Factors
at the Hsp70 Loci in Living Cells. Molecular Cell, 2010. 40(6): p. 965-975.
Buckley, M.S., H. Kwak, W.R. Zipfel, and J.T. Lis, Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation. Genes & Development, 2014. 28(1): p. 14-19.
Versluis P, Graham TGW, Eng V, Ebenezer J, Darzacq X, Zipfel WR, Lis JT. Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation. Mol Cell. 2024 Aug 8;84(15):2856-2869.e9. doi: 10.1016/j.molcel.2024.07.009. PMID: 39121843; PMCID: PMC11486293.
Buckley, M.S., H. Kwak, W.R. Zipfel, and J.T. Lis, Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation. Genes & Development, 2014. 28(1): p. 14-19.
Versluis P, Graham TGW, Eng V, Ebenezer J, Darzacq X, Zipfel WR, Lis JT. Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation. Mol Cell. 2024 Aug 8;84(15):2856-2869.e9. doi: 10.1016/j.molcel.2024.07.009. PMID: 39121843; PMCID: PMC11486293.
Scanning Angle Interference microscopy (SAIM):
In this collaborative project with Matt Paszek’s lab, we constructed a hardware platform that significantly expanded the capabilities of Scanning Angle Interference Microscopy (SAIM) by combining my lab’s existing circularly scanned TIRF hardware with SAIM. SAIM combines interferometry and fluorescence microscopy into an imaging modality capable of imaging fluorescently labeled structures in living cells with 10-nm axial resolution.
In this collaborative project with Matt Paszek’s lab, we constructed a hardware platform that significantly expanded the capabilities of Scanning Angle Interference Microscopy (SAIM) by combining my lab’s existing circularly scanned TIRF hardware with SAIM. SAIM combines interferometry and fluorescence microscopy into an imaging modality capable of imaging fluorescently labeled structures in living cells with 10-nm axial resolution.
Colville M, Park, S, Zipfel, WR, Paszek, MJ “High-speed device synchronization in optical microscopy with an
open-source hardware control platform” Sci Rep 9, 12188 (2019). https://doi.org/10.1038/s41598-019-48455-z
Colville M, Park S, Singh A, Paszek M, Zipfel WR. Azimuthal Beam Scanning Microscope Design and Implementation
for Axial Localization with Scanning Angle Interference Microscopy. Methods Mol Biol. 2022; 2393:127-152.
doi: 10.1007/978-1-0716-1803-5_7. PMID: 34837177.
Deep UV imaging of electrospray plumes:
Satellite propulsion systems can be constructed using electrospray thrusters with ionic liquids as propellants. An electric field is applied to the ionic liquid, creating a "Taylor cone" at the emitter tip, where ions are directly extracted and accelerated, providing thrust. In a collaboration with Elaine Petro's lab in Mechanical Engineering at Cornell, we are devising ways to image the ionic plume in order to optimize the design of the electrospray thrusters. Using a 265 nm bright LED and a deep UV sensitive EM-CCD we are able to visualize this propulsion plume, enabling new electrospray designs to be evaluated.
Satellite propulsion systems can be constructed using electrospray thrusters with ionic liquids as propellants. An electric field is applied to the ionic liquid, creating a "Taylor cone" at the emitter tip, where ions are directly extracted and accelerated, providing thrust. In a collaboration with Elaine Petro's lab in Mechanical Engineering at Cornell, we are devising ways to image the ionic plume in order to optimize the design of the electrospray thrusters. Using a 265 nm bright LED and a deep UV sensitive EM-CCD we are able to visualize this propulsion plume, enabling new electrospray designs to be evaluated.
Shadow Moire Profilimetrty Imaging system for the CCMR:
In a new project with the Cornell Center for Materials Research (CCMR), we are building a Shadow Moire Profilimetry system to enable high resolution surface profiling of materials. This system will be used by CCMR members to evaluate the surface profiles of materials and devices they are developing, and will be available as a shared resource for the CCMR community.
In a new project with the Cornell Center for Materials Research (CCMR), we are building a Shadow Moire Profilimetry system to enable high resolution surface profiling of materials. This system will be used by CCMR members to evaluate the surface profiles of materials and devices they are developing, and will be available as a shared resource for the CCMR community.