Single Molecule Biophysics Laboratory
About
About
We are a multidisciplinary research group. Our vision is to develop better imaging and analysis tools to understand important biological processes. Members in our group will learn independent thinking, single-molecule instrumentation, rigorous data analysis, simulation, molecular biology, and cutting edge imaging for biomedical applications. Soft skills such as grant writing, multi-tasking, presentation, and interpersonal communications will be necessary part of our collective development.
Two primary research directions are:
- Collagen fibril degradation by matrix metalloproteases.
- Applications of matrix metalloproteases beyond collagen.
Recent Publications
Recent Publications
1. Lokender Kumar, Warren Colomb, John Czerski, Christopher Cox, and Susanta K. Sarkar,
“Efficient protease based purification of recombinant matrix metalloproteinase-1 in E. coli”, Protein Expression and Purification, 148, 59-67, 2018. MMP1 purification. Patent filed
2. John Czerski, Warren Colomb, Frank Cannataro, and Susanta K. Sarkar, “Spectroscopic
identification of fluorophores at single molecule level using photoluminescence excitation spectra”, Journal of microscopy, 270(3), 261-271, 2018. Spectroscopic identification of single molecules.
3. Warren Colomb, John Czerski, Jaydeep Sau, and Susanta K. Sarkar, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers”, Journal of Microscopy, 266(3), 298-306, 2017. FNDs as fiducial markers.
4. W. Colomb and Susanta K. Sarkar, “Extracting Physics of Life at the Molecular Level: A Review of Single-molecule Data Analyses”, Physics of Life Reviews, 13, 107-137, 2015.
Data analysis.
Facilities
Facilities
MICROSCOPY We build our own microscopes! We have three highly modular microscopes with extensive experimental capabilities: a Total Internal Reflection Fluorescence Microscope (TIRFM) for single molecule studies, a light sheet microscope to image 5 mm or more thick samples, and a multiphoton microscope for time resolved two-photon imaging. Journal of microscopy, 270(3), 261-271, 2018. Journal of microscopy, 270(3), 261-271, 2018.
MOLECULAR BIOLOGY We purify and characterize our own proteins! We have complete facility for E. coli based molecular biology and protein purification including autoclave, shaker, AKTA FPLC, SORVALL centrifuge, -80 freezer, -20 freezer, 4 degree refrigerator, cell disruptor, micro-centrifuge, fumehood, two-stage water deionizer, PCR, nanodrop, and ice maker. Protein Expression and Purification, 148, 59-67, 2018.
COMPUTATION We develop our own analyses and simulations! We have multiple high end computers for data analysis and simulations (12 core/24 thread, 512 MB SSD, 64 GB RAM). Physics of Life Reviews, 13, 107-137, 2015.
BEYOND COLLAGEN DEGRADATION Our multidisciplinary research laboratory allows for exploration of transformative research ideas because we do core sample preparations, experiments, and analyses ourselves.
Lokender Kumar et al. Matrix metalloproteases-1 inhibits and eradicates Enterococcus faecalis biofilms. (Submitted 2018).
Patent filed.
