In bacteria, chromosomal architecture shows strong spatial and temporal organization, and regulates key cellular functions, such as transcription. Tracking the motion of chromosomal loci at short timescales provides information related to both the physical state of the nucleo-protein complex and its local environment, independent of large-scale motions related to genome segregation. Here we investigate the short-time (0.1-10 s) dynamics of fluorescently labelled chromosomal loci in Escherichia coli at different growth rates. At these timescales, we observe for the first time a dependence of the loci's apparent diffusion on both their subcellular localization and chromosomal coordinate, and we provide evidence that the properties of the chromosome are similar in the tested growth conditions. Our results indicate that either non-equilibrium fluctuations due to enzyme activity or the organization of the genome as a polymer-protein complex vary as a function of the distance from the origin of replication.

We systematically investigate droplet movement, coalescence, and splitting on an open hydrophobic surface. These processes are actuated by magnetic beads internalized in an oil-coated aqueous droplet using an external magnet. Results are organized into an 'operating diagram' that describes regions of droplet stable motion, breakage, and release from the magnet. The results are explained theoretically with a simple model that balances magnetic, friction, and capillary-induced drag forces and includes the effects of particle type, droplet size, surrounding oil layer, surface tension, and viscosity. Finally, we discuss the implications of the results for the design of magnet-actuated droplet systems for applications such as nucleic acid purification, immunoassay and drug delivery.

We designed a microfluidic chemostat consisting of 600 sub-micron trapping/growth channels connected to two feeding channels. The microchemostat traps E. coli cells and forces them to grow in lines for over 50 generations. Excess cells, including the mother cells captured at the start of the process, are removed from both ends of the growth channels by the media flow. With the aid of time-lapse microscopy, we have monitored dynamic properties such as growth rate and GFP expression at the single-cell level for many generations while maintaining a population of bacteria of similar age. We also use the microchemostat to show how the population responds to dynamic changes in the environment. Since more than 100 individual bacterial cells are aligned and immobilized in a single field of view, the microchemostat is an ideal platform for high-throughput intracellular measurements. We demonstrate this capability by tracking with sub-diffraction resolution the movements of fluorescently tagged loci in more than one thousand cells on a single device. The device yields results comparable to conventional agar microscopy experiments with substantial increases in throughput and ease of analysis.

The physical nature of the bacterial chromosome has important implications for its function. Using high-resolution dynamic tracking, we observe the existence of rare but ubiquitous 'rapid movements' of chromosomal loci exhibiting near-ballistic dynamics. This suggests that these movements are either driven by an active machinery or part of stress-relaxation mechanisms. Comparison with a null physical model for subdiffusive chromosomal dynamics shows that rapid movements are excursions from a basal subdiffusive dynamics, likely due to driven and/or stress-relaxation motion. Additionally, rapid movements are in some cases coupled with known transitions of chromosomal segregation. They do not co-occur strictly with replication, their frequency varies with growth condition and chromosomal coordinate, and they show a preference for longitudinal motion. These findings support an emerging picture of the bacterial chromosome as off-equilibrium active matter and help developing a correct physical model of its in vivo dynamic structure.

Microfluidic devices integrating membrane-based sample preparation with electrophoretic separation are demonstrated. These multilayer devices consist of 10 nm pore diameter membranes sandwiched between two layers of PDMS substrates with embedded microchannels. Because of the membrane isolation, material exchange between two fluidic layers can be precisely controlled by applied voltages. More importantly, since only small molecules can pass through the nanopores, the integrated membrane can serve as a filter or a concentrator prior to microchip electrophoresis under different design and operation modes. As a filter, they can be used for separation and selective injection of small analytes from sample matrix. This has been effectively applied in rapid determination of reduced glutathione in human plasma and red blood cells without any off-chip deproteinization procedure. Alternatively, in the concentrator mode, they can be used for online purification and preconcentration of macromolecules, which was illustrated by removing primers and preconcentrating the product DNA from a PCR product mixture.