Mucin Promotes Bacterial Swarming by Making the Agar Surface More Slippery.

When inoculated on the surface of soft agar containing nutrients, many species of motile bacteria can grow into a dense population and spread across the surface by a form of motility called swarming. We study the swarming behavior of sp. SM3, a species of bacteria that exhibits a swarm-dependent reduction in symptoms associated with inflammatory bowel disease (IBD).

Rapid growth rate of Enterobacter sp. SM3 determined using several methods.

Background: Bacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and  Staphylococcus aureus.

Run-and-tumble kinematics of Enterobacter Sp. SM3.

The recent discovery of the peritrichous, swarm-competent bacterium Enterobacter sp. SM3 has offered a new opportunity to investigate the connection between bacterial swimming and swarming. Here, we report the run-and-tumble behavior of SM3 as planktonic swimming cells and as swarming cells diluted in liquid medium, drawing comparison between the two states.

Enterobacter sp. Strain SM1_HS2B Manifests Transient Elongation and Swimming Motility in Liquid Medium.

Many species of bacteria change their morphology and behavior under external stresses. In this study, we report transient elongation and swimming motility of a novel Enterobacter sp. strain, SM1_HS2B, in liquid broth under a standard growth condition.

An Inexpensive Imaging Platform to Record and Quantitate Bacterial Swarming.

Bacterial swarming refers to a rapid spread, with coordinated motion, of flagellated bacteria on a semi-solid surface (Harshey, 2003). There has been extensive study on this particular mode of motility because of its interesting biological and physical relevance, ., enhanced antibiotic resistance (Kearns, 2010) and turbulent collective motion ( Steager , 2008 ).

Confinement discerns swarmers from planktonic bacteria.

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper-flagellation have been shown to accompany the swarming phenotype.

Bacterial Swarmers Enriched During Intestinal Stress Ameliorate Damage.

Background And Aims: Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. This study aims to define a role for bacterial swarmers in amelioration of intestinal stress.

Methods: We developed a polymicrobial plate agar assay to detect swarming and screened mice and humans with intestinal stress and inflammation.

An expanding bacterial colony forms a depletion zone with growing droplets.

Many species of bacteria have developed effective means to spread on solid surfaces. This study focuses on the expansion of Pseudomonas aeruginosa on an agar gel surface under conditions of minimal evaporation. We report the occurrence and spread of a depletion zone within an expanded colony, where the bacteria laden film becomes thinner.

Discovery of oscillations in rotational speed of body-tethered Caulobacter crescentus.

Swarmer cells of Caulobacter crescentus have been found to tether to glass at a point on the cell body. The rolling of the freely rotating flagellum near the glass surface causes the cell body to rotate. We describe the discovery of damped oscillations in the rotational speed of these cell bodies.

Orbiting of Flagellated Bacteria within a Thin Fluid Film around Micrometer-Sized Particles.

Bacterial motility under confinement is relevant to both environmental control and the spread of infection. Here, we report observations on Escherichia coli, Enterobacter sp., Pseudomonas aeruginosa, and Bacillus subtilis when they are confined within a thin layer of water around dispersed micrometer-sized particles sprinkled over a semisolid agar gel.

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores.

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters.

Capillary flow and mechanical buckling in a growing annular bacterial colony.

A growing bacterial colony is a dense suspension of an increasing number of cells capable of individual as well as collective motion. After inoculating Pseudomonas aeruginosa over an annular area on an agar plate, we observe the growth and spread of the bacterial population, and model the process by considering the physical effects that account for the features observed. Over a course of 10-12 hours, the majority of bacteria migrate to and accumulate at the edges.

Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer.

We report measurements and analyses of nanopore translocations by fd and M13, two related strains of filamentous virus that are identical except for their charge densities. The standard continuum theory of electrokinetics greatly overestimates the translocation speed and the conductance associated with counterions for both viruses. Furthermore, fd and M13 behave differently from one another, even translocating in opposite directions under certain conditions.

Influence of Physical Effects on the Swarming Motility of Pseudomonas aeruginosa.

Many species of bacteria can spread over a moist surface via a particular form of collective motion known as "surface swarming". This form of motility is typically studied by inoculating bacteria on a gel formed by 0.4-1.

Measurements of fluid viscosity using a miniature ball drop device.

This paper describes measurement of fluid viscosity using a small ball drop device. It requires as little as 100 μl of fluid. Each measurement can be performed in seconds.

The Aerotactic Response of Caulobacter crescentus.

Many motile microorganisms are able to detect chemical gradients in their surroundings to bias their motion toward more favorable conditions. In this study, we observe the swimming patterns of Caulobacter crescentus, a uniflagellated bacterium, in a linear oxygen gradient produced by a three-channel microfluidic device. Using low-magnification dark-field microscopy, individual cells are tracked over a large field of view and their positions within the oxygen gradient are recorded over time.

Flagellar Motor Switching in Caulobacter Crescentus Obeys First Passage Time Statistics.

A Caulobacter crescentus swarmer cell is propelled by a helical flagellum, which is rotated by a motor at its base. The motor alternates between rotating in clockwise and counterclockwise directions and spends variable intervals of time in each state. We measure the distributions of these intervals for cells either free swimming or tethered to a glass slide.

Describing directional cell migration with a characteristic directionality time.

Many cell types can bias their direction of locomotion by coupling to external cues. Characteristics such as how fast a cell migrates and the directedness of its migration path can be quantified to provide metrics that determine which biochemical and biomechanical factors affect directional cell migration, and by how much. To be useful, these metrics must be reproducible from one experimental setting to another.

Altered motility of Caulobacter Crescentus in viscous and viscoelastic media.

Background: Motility of flagellated bacteria depends crucially on their organelles such as flagella and pili, as well as physical properties of the external medium, such as viscosity and matrix elasticity. We studied the motility of wild-type and two mutant strains of Caulobacter crescentus swarmer cells in two different types of media: a viscous and hyperosmotic glycerol-growth medium mixture and a viscoelastic growth medium, containing polyethylene glycol or polyethylene oxide of different defined sizes.

Results: For all three strains in the medium containing glycerol, we found linear drops in percentage of motile cells and decreases in speed of those that remained motile to be inversely proportional to viscosity.

Osmotic pressure in a bacterial swarm.

Using Escherichia coli as a model organism, we studied how water is recruited by a bacterial swarm. A previous analysis of trajectories of small air bubbles revealed a stream of fluid flowing in a clockwise direction ahead of the swarm. A companion study suggested that water moves out of the agar into the swarm in a narrow region centered ∼ 30 μm from the leading edge of the swarm and then back into the agar (at a smaller rate) in a region centered ∼ 120 μm back from the leading edge.

Helical motion of the cell body enhances Caulobacter crescentus motility.

We resolve the 3D trajectory and the orientation of individual cells for extended times, using a digital tracking technique combined with 3D reconstructions. We have used this technique to study the motility of the uniflagellated bacterium Caulobacter crescentus and have found that each cell displays two distinct modes of motility, depending on the sense of rotation of the flagellar motor. In the forward mode, when the flagellum pushes the cell, the cell body is tilted with respect to the direction of motion, and it precesses, tracing out a helical trajectory.

Stiff filamentous virus translocations through solid-state nanopores.

The ionic conductance through a nanometer-sized pore in a membrane changes when a biopolymer slides through it, making nanopores sensitive to single molecules in solution. Their possible use for sequencing has motivated numerous studies on how DNA, a semi-flexible polymer, translocates nanopores. Here we study voltage-driven dynamics of the stiff filamentous virus fd with experiments and simulations to investigate the basic physics of polymer translocations.

Technical advance: introducing a novel metric, directionality time, to quantify human neutrophil chemotaxis as a function of matrix composition and stiffness.

A direct consequence of cellular movement and navigation, migration incorporates elements of speed, direction, and persistence of motion. Current techniques to parameterize the trajectory of a chemotaxing cell most commonly pair migration speed with some measure of persistence by calculating MSD, RMS speed, TAD, and/or CI. We address inherent limitations in TAD and CI for comparative analysis by introducing two new analytical tools to quantify persistence: directionality index and directionality time.

Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization.

The separation of target nucleic acid sequences from biological samples has emerged as a significant process in today's diagnostics and detection strategies. In addition to the possible clinical applications, the fundamental understanding of target and sequence specific hybridization on surface modified magnetic beads is of high value. In this paper, we describe a novel microfluidic platform that utilizes a mobile magnetic field in static microfluidic channels, where single stranded DNA (ssDNA) molecules are isolated via nucleic acid hybridization.