POVRay Bug
Biophysical Imaging & Spectroscopy


(Click on the 'Layman's summary' links for a one-paragraph summary of the paper)

  • High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms, L. G. Wilson, L. M. Carter and S. E. Reece, Proc. Natl. Acad. Sci. USA 110(47) 18769-18774 (2013).
    [ Layman's summary ]
    In this paper, we use high-speed holographic microscopy to investigate how rodent malaria (Plasmodium berghei) microgametes swim. This stage of the Plasmodium life cycle takes place inside the midgut of a mosquito, and is relatively poorly understood. At the heart of the microgamete is an axoneme, a cylindrical structure that's found throughout the eukaryotic kingdom: plants, animals, fungi and single celled organisms like protozoa. In many cases, these whip-like structures beat to propel cells around (e.g. single-celled Paramecium, the flagella of animal and plant sperm cells) or to pump fluid (e.g. cilia in the lungs and brain of humans). Although we know the protein components of these structures, the way these components interact is not well known. Our work sheds new light on this problem by measuring the three-dimensional shape of a beating flagellum for the first time. We find that the microgametes display a wide variety of wave shapes over time, but some overarching features present themselves. In particular, although the waveforms are varied, they alternate in time between left-handed and right-handed shapes (think of left- and right-handed screw threads). This was somewhat unexpected because the axoneme has a handedness built in. Although waveforms of both handedness have been observed before, it has always been in flagella that are attached to something; a cell body or epithelial tissue. Because the malaria microgametes are naturally occurring, free-swimming flagella, they make an ideal model system for understanding the physics of microswimmers.
  • Differential Dynamic Microscopy: A High-Throughput Method for Characterizing the Motility of Microorganisms, V.A. Martinez, R. Besseling, O.A. Croze, J. Tailleur, M. Reufer, J. Schwarz-Linek, L.G. Wilson, M.A. Bees and W.C.K. Poon, Biophys. J. 103 1637-1647 (2012).
    [ Layman's summary ]
    This paper is an in-depth investigation of the use of Differential Dynamic Microscopy (DDM - see below) to measure swimming speeds of microorganisms. DDM is a powerful way of looking at the swimming behavior of large groups of cells at the same time; this is potentially important for understanding how pathogenic bacteria invade the human body. In particular, we study two types of E. coli bacteria: the regular wild type, which exhibits a 'random walk' swimming behavior made up of straight runs and tumbles that re-orient the cell; and mutant variety that does not tumble, simply running in straight lines. We also examine the swimming behavior of a type of algae - Chlamydomonas reinhardtii. This species displays a very different swimming behavior, getting around by a 'breast stroke' motion that results in spiralling paths. In an important proof-of-concept, we compare results from DDM and traditional video cell-tracking methods of measuring swimming speed.
  • 3D Localization of weak scatterers in digital holographic microscopy using Rayleigh-Sommerfeld back-propagation, Laurence Wilson and Rongjing Zhang, Opt. Express 20 16735-16744 (2012).
    [ Layman's summary ]
    In this paper we demonstrate a method for measuring the position of objects ('localizing' objects) in reconstructed holographic data. To make the hologram, the microscope lighting is set up in a particular way, and pictures of our specimen are taken using a standard digital camera. The trick is to apply a computer algorithm to these images, in order to 'refocus' them. Because we can refocus the image to any point we like, we need only take one image in order to capture the whole 3D volume. We typically use an algorithm adapted from David Grier's Rayleigh-Sommerfeld method (see references in the paper) to achieve this. The difficulty is then in analyzing this data; how do we measure things in 3D? We use a simple trick to make this work, based on observations in the microscope. Very small, transparent objects have a particular appearance in the microscope. If they are out of focus in one direction, their blurred image appears light in the center. If we bring them into good focus, they seem to disappear, and if we continue refocusing in the same direction, the objects start to look dark in the center. By picking out regions in 3D where objects go from light to dark, we can measure their position in 3D. This trick is related to one used in optical tweezers (see below) for measuring the position of a trapped particle. Here, we show some of the math to back this up, and also that you can measure the shape of extended objects in this way, by measuring when different parts are 'in focus'. This is a significant advance on previous methods, and led to our later work on malaria.
  • Microrheology and the fluctuation theorem in dense colloids, L. G. Wilson, A. W. Harrison, W. C. K. Poon and A. M. Puertas, EPL 93 58007 (2011).
    [ Layman's summary ]
    This paper uses simulations to get more insight into what's happening in our microscopic measurements of viscosity and elasticity ('microrheology') in a suspension of hard spherical particles, around 1.5 μm in diameter. As mentioned in other summaries, this technique will be important for understanding the physical behavior of complex substances that are too expensive or difficult to produce in large quantities - particularly biological samples like cells or protein solutions. We pick up small particles using a focused laser beam (optical tweezers) and pull them through a sample to measure its response to an imposed force. A powerful simulation technique is used to relate the behavior of small samples (50 μl) with that of macroscopic samples (50 ml). In particular, the results are analyzed in terms of an effective temperature and the fluctuation theorem. The latter describes a curious effect whereby sometimes the microscopic thermal motion of molecules (Brownian motion) can give our probe a helping 'kick' in the right direction.
  • Differential Dynamic Microscopy of Bacterial Motility, L.G. Wilson, V.A. Martinez, J. Schwarz-Linek, J. Tailleur, G. Bryant, P. N. Pusey, and W. C. K. Poon, Phys. Rev. Lett. 106 018101 (2011).
    [ Layman's summary ]
    Here, we demonstrate how a new technique, Differential Dynamic Microscopy (DDM) can be used to measure the swimming speed of bacteria. This powerful new technique marries two different ideas: video microscopy and scattering methods. In a scattering experiments, a beam of radiation (light, neutrons, x-rays) passes through a sample and is scattered. By looking at the scattering pattern, we can say something about the average structure in the sample. As an example, x-ray crystallography is routinely used to determine the structure of proteins. If objects in our sample are moving around, the scattering pattern will fluctuate. If we know the size of the structure, and the time scale of these fluctuations, we know how fast things in the sample are moving (distance/time=speed, roughly speaking). Scattering patterns can be a bit counterintuitive; small objects have a large scattering pattern, and vice versa. It's therefore relatively easy to measure the scattering from small objects, up to a point, but hard to measure scattering from large ones. DDM gets around this problem with a clever twist: we image objects directly, and calculate the scattering pattern. This lets us measure average quantities from a bacterial population, rapidly. Specifically, we obtain: the average and spread in swimming speed in bacteria; the fraction of the population that are swimming; and how fast the non-swimmers are diffusing around by Brownian motion. It turns out that a higher fraction of swimmers means that non-swimmers move further in a shorter time - they're getting 'pushed about' by the swimmers.
  • Small-world rheology: an introduction to probe-based active microrheology, L.G. Wilson and W.C.K. Poon, Phys. Chem. Chem. Phys. 13 10617-10630 (2011).
    [ Layman's summary ]
    This paper is a mini-review of some 'active' microrheology. In this method, tools like optical or magnetic tweezers are used to push microscopic probes through a sample, or 'wiggle' them locally. By measuring how the particle moves, the idea is to work out the material's bulk properties like viscosity and elasticity. This has the potential to be extremely useful in cases where the material of interest is expensive or difficult to synthesize; biological polymer or protein solutions for pharmacology, for example. We review experimental techniques, and outline some key results and challenges for the future. In particular, we describe limits to the methods that should help experimentalists choose the right probes/experimental geometry for their system.
  • Polymer-induced phase separation in Escherichia coli suspensions, J. Schwarz-Linek, A. Winkler, L.G. Wilson, N.T. Pham, T. Schilling and W.C.K. Poon, Soft Matter 6, p.4540--4549, (2010).
    [ Layman's summary ]
    Here we look at the biologically important phenomenon of bacterial aggregation. When bacteria invade a host, they often transform into a protective form known as a biofilm, a group of cells bound together by a gunk of polymers and proteins. We model this behavior, both in simulation and experiment. In particular, we had hypothesized that the amount of salt in the sample solution could determine whether or not cells can aggregate. In the absence of salts, objects that have the same surface charge (like bacteria) should repel each other. Adding salt 'screens' this interaction and lets cells get close to each other. We study the aggregation of non-swimming cells over a range of polymer concentrations, and speculate as to how swimming might change this behavior.
  • Polymer-induced phase separation in suspensions of bacteria, J. Schwarz-Linek, G. Dorken, A. Winkler, L.G. Wilson, N.T. Pham, C.E. French, T. Schilling and W. C. K. Poon, EPL 89, p.68003, (2010).
    [ Layman's summary ]
    When bacteria invade a host, they often transform into a self-protective form known as a biofilm, a group of cells bound together by a gunk of polymers and proteins. We model this behavior, both in simulation and experiment. Previous studies had suggested that biofilms stick together because the polymers they give off are inherently 'sticky'. We were unsure about this, as previous physical chemistry work had shown that colloidal particles (with diameters around 1 μm) aggregate due a phenomenon known as the depletion interaction. When we mix polymers and small particles such as bacterial cells in water, the cells and polymers jostle each other as they're kicked around by Brownian motion - the thermal motion of water molecules. If two cells get close that there's no room between them for a polymer molecule, they're being jostled by polymers from the outside, but not from within the gap between cells. This has the effect of forcing cells together. We show that this effect (which has a curious analogue known as the Casimir effect in quantum physics) could have an important role in biofilm formation.
  • Passive and Active Microrheology of Hard-Sphere Colloids, L. G. Wilson, A. W. Harrison, A. B. Schofield, J. Arlt and W. C. K. Poon, J. Phys. Chem. B 113, p.3806--3812, (2009).
    [ Layman's summary ]
    This paper describes our investigation of the small-scale viscous and elastic behavior (or 'microrheology') of a sample, using optical tweezers. Microrheology gives us the opportunity to study the physical properties of substances that are either too expensive or too difficult to produce in large quantities. Our study compares the behavior of a model system - a suspension of micrometer-sized spheres. This type of system has been studied for some time, and is well characterized. It's interesting that a suspension as simple as this already shows complicated flow behavior. The viscosity we measure depends on flow speed, like in a cornstarch/water mixture (Youtube has many videos of people playing with this substance!) We compare macroscopic measurements in the literature with our own microscopic measurements, to see whether they find the same answers. We try two types of measurement: passive and active. In the passive case, we trap a particle using optical tweezers and observe its thermal position fluctuations, finding good agreement with comparable light-scattering studies. Things are a little more subtle in the active case. Here, we trap a probe particle, but this time pull it through its surroundings, and measure the forces it experiences. Again, the viscosity measured seems to depend strongly on measurement protocol. We find that the micro-viscosity is lower than the bulk viscosity measured in flowing suspensions, but about the same as the viscosity obtained when the bulk sample is subjected to small-scale oscillating flow. This is a good example of the rich, and sometimes unpredictable flow behavior of complex fluids.
  • Linear and nonlinear microrheology of dense colloidal suspensions, Laurence Wilson, Rut Besseling, Jochen Arlt, and Wilson C. K. Poon, Proc. SPIE, 6326, p.U441--U450, (2006).
    [ Layman's summary ]
    These conference proceedings deal with our optical tweezers methods for investigating the viscous and elastic behavior of complex fluids, and include some preliminary results (later published in J. Phys. Chem. B)
  • Force measurement in colloidal glasses using optical tweezers, L. Wilson, R. Besseling, J. Arlt, W.C.K. Poon, Proc. SPIE, 5930, p. 593016, (2005).
    [ Layman's summary ]
    These conference proceedings deal with our optical tweezers setup for measuring the viscous and elastic behavior of complex fluids, focusing more on instrumentation.
  • Spherical aberration correction for optical tweezers, E. Theofanidou, L. Wilson, W.J. Hossack and J. Arlt, Opt. Commun. 236, p.145--150, (2004).
    [ Layman's summary ]
    In this paper, we examine aberration correction for an optical tweezers system. Although modern microscope lenses are well designed, they don't work perfectly in all situations. Some high magnification lenses require a layer of oil or water between them and the sample in order to work properly. In the case of an oil immersion lens, this can lead to image degradation when looking into water, due to index of refraction mismatches going from oil to glass to water. In essence, light passing through the lens isn't being focused optimally. This aberration also affects optical tweezers systems, as they require a tight laser focus in order to work correctly. If the laser focus is poor, the trap will be weak or unstable. To mitigate this effect, we use an electrically-addressed deformable mirror to reshape the laser beam on the way into the sample. We test the quality of focus by trapping a polystyrene particle that is fluroescently dyed. The more sharply the laser is focused, the brighter the particle fluorescence, so we use this as a figure of merit to assess different aberration correction schemes.