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In the last quarter century, biologists have made great strides towards understanding biology at the molecular scale. The human genome has been sequenced and the structures of many proteins, the molecular machines responsible for the function and structure of cells, have been solved. Single-molecule techniques and advances in microscopy have significantly changed the way in which biologists ask and answer questions. As biological measurements and techniques have become increasingly quantitative, they have allowed biologists to ask ever more quantitative questions: How do the molecular machines, which comprise the cell, function microscopically? Can we understand the design principles that govern the structure and function of biological systems on a microscopic scale? What role does the chaotic microscopic environment play in cellular function? One outcome of this new generation of quantitative biological questions is the need to greet quantitative experiments with models at a higher level of abstraction than the traditional cartoons of molecular biology. Our work centers on the interface between mathematical models of biological systems and this new generation of quantitative biological experiments.

Interested in Quantitative or Physical Biology?:

Join us for espresso any day at 10 AM in Physics and Astronomy B031!

 

Bacterial ultrastructure:
One of the most aesthetically appealing problems in biology is elucidating the mechanisms that give rise to spatial organization in biological systems. Far from being well-mixed, almost all biological systems exhibit precise spatial and temporal control of protein, mRNA, and DNA concentration, demonstrating that cells measure distance and detect proximity with a molecular-scale tool kit. Although these phenomena have traditionally been studied in the context of the detailed expression patterning in development, recent exciting results (including our own work, Wiggins, et al. PNAS, 2009) reveal that precise spatial organization is the rule rather than the exception in the bacterial cell.
Chromosome structure and dynamics:
The mechanisms by which the prokaryotic cell organizes and segregates its chromosome remain largely unknown in spite of a long standing appreciation of the importance of these processes. The Wiggins lab has been investigating the physical structure, organization, and dynamics of the prokaryotic chromosome by exploiting three complementary approaches: live-cell imaging, in vitro single-molecule experiments investigating proteins-DNA interactions, and biophysical modeling.
DNA chain statistics for biological applications:

What role does DNA statistics play in transcriptional regulation? Given the genomic locations of gene regulatory sequences relative to the promoter, what is their relative importance? (See description above.) The Wiggins lab is currently working on practical computational tools for biologist to help answer these questions quantitatively. More information on this soon!
Bacterial interactions & cooperativity: Although usually considered relatively simple single-celled organisms, bacteria have developted a number of complex mechanisms to interact with their neighbors. Many of these systems are thought to be triggered by physical mechanisms, such as cell-to-cell contact or surface sensing, but the biophysical processes that are responsible for this regulation remain largely a mystery. We are working in collaboration with the Mougous Lab to quantitatively characterize the dynamics of one of these inter-cellular systems, the Type VI secretion system.
Membranes, geometry & force:
We have proposed that in some biological contexts it is possible to deduce the forces applied to a membrane from its conformation, captured via cryo electron microscopy tomograms (three dimensional reconstructions). We are currently experimenting with this new technique in in vitro experiments.

Lab Microscopes:

For more information on using the microscopes or for collaboration requestions, please contact a lab member.

"Super-Scope": This is a home-brew Single-molecule TIRF, autofocus, super-resolution, Dualview scope. The microscope is controled using the micromanager software package. It has the following laser excitation lines: 561, 488, and 405. It has a perfect focus like autofocus, an Andor EMCCD camera and an AOTF.
"Scot-o-scope" features a dual-beam optical trap with force detection, and GFP/mCherry fluorescence. This scope is controled by micromanager and labview. Imaging from a Princeton Instruments MicroMax camera

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"Octoscope" is a commerical Nikon Eclipse Ti, with an arc-lamp, environmental chamber, perfect focus, a motorized stage, and imaging using either the Coolsnap HQ2 or K4 camera. This scope currently has filter sets for mCherry, dsRed, YFP, GFP, CFP, and DAPI and is used principly for multi-hour timelapse and high-throughput imaging. We use the Elements software package to control this scope. Objectives: 100x Ph3 1.4 NA, 60x Ph3 1.4 NA.

"Zeiss" is an old Axioplan II Zeiss scope controlled by micromaganger. This scope uses a Photometrics FX cooled CCD camera, 100x Phase3 objective, and has a motorized z-drive, objective turret, and filter wheel.

Lab Software:

These software packages are written and maintained by the lab. More information on request.:

SuperSegger/TrackOpti is a matlab-based second generation, trainable cell segmentation algorithm for segmenting Ecoli timelapse movie, quantifying fluorescence and tracking foci.
Wormulator is a DNA statistics calculator that can be used with a web-based interface.

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Trace is a matlab-based polymer tracking software package which we have used for tracing DNA contours.