Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

Modelling bacterial behaviour close to a no-slip plane boundary: the influence of bacterial geometry

We describe a boundary-element method used to model the hydrodynamics of a bacterium propelled by a single helical flagellum. Using this model, we optimize the power efficiency of swimming with respect to cell body and flagellum geometrical parameters, and find that optima for swimming in unbounded fluid and near a no-slip plane boundary are nearly indistinguishable. We also consider the novel optimization objective of torque efficiency and find a very different optimal shape. Excluding effects such as Brownian motion and electrostatic interactions, it is demonstrated that hydrodynamic forces may trap the bacterium in a stable, circular orbit near the boundary, leading to the empirically observable surface accumulation of bacteria. Furthermore, the details and even the existence of this stable orbit depend on geometrical parameters of the bacterium, as described in this article. These results shed some light on the phenomenon of surface accumulation of micro-organisms and offer hydrodynamic explanations as to why some bacteria may accumulate more readily than others based on morphology

Towards Synthetic Life: Establishing a Minimal Segrosome for the Rational Design of Biomimetic Systems

DNA segregation is a fundamental life process, crucial for renewal, reproduction and propagation of all forms of life. Hence, a dedicated segregation machinery, a segrosome, must function reliably also in the context of a minimal cell. Conceptionally, the development of such a minimal cell follows a minimalistic approach, aiming at engineering a synthetic entity only consisting of the essential key elements necessary for a cell to survive. In this thesis, various prokaryotic segregation systems were explored as possible candidates for a minimal segrosome. Such a minimal segrosome could be applied for the rational design of biomimetic systems including, but not limited to, a minimal cell. DNA segregation systems of type I (ParABS) and type II (ParMRC) were compared for ensuring genetic stabilities in vivo using vectors derived from the natural secondary chromosome of Vibrio cholerae. The type II segregation system R1-ParMRC was chosen as the most promising candidate for a minimal segrosome, and it was characterized and reconstituted in vitro. This segregation system was encapsulated into biomimetic micro-compartments and its lifetime prolonged by coupling to ATP-regenerating as well as oxygen-scavenging systems. The segregation process was coupled to in vitro DNA replication using DNA nanoparticles as a mimic of the condensed state of chromosomes. Furthermore, another type II segregation system originating from the pLS20 plasmid from Bacillus subtilis (Alp7ARC) was reconstituted in vitro as a secondary orthogonal segrosome. Finally, a chimeric RNA segregation system was engineered that could be applied for an RNA-based protocell. Overall, this work demonstrates successful bottom-up assemblies of functional molecular machines that could find applications in biomimetic systems and lead to a deeper understanding of living systems

Cytoskeleton and Cell Motility

The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms. Bacterial motility as well as the composition of the prokaryotic cytoskeleton is only briefly mentioned. The article is organized as follows. In Section III, I first present an overview of the diversity of cellular motility mechanisms, which might at first glance be categorized into two different types of behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis - or cell division - as well as other extensions of cell motility that rely on the same essential machinery are briefly sketched. In Section IV, I introduce the molecular machinery that underlies cell motility - the cytoskeleton - as well as its interactions with the external environment of the cell and its main regulatory pathways. Sections IV D to IV F are more detailed in their biochemical presentations; readers primarily interested in the theoretical modeling of cell motility might want to skip these sections in a first reading. I then describe the motility mechanisms that rely essentially on polymerization-depolymerization dynamics of cytoskeleton filaments in Section V, and the ones that rely essentially on the activity of motor proteins in Section VI. Finally, Section VII is devoted to the description of the integrated approaches that have been developed recently to try to understand the cooperative phenomena that underly self-organization of the cell cytoskeleton as a whole.Comment: 31 pages, 16 figures, 295 reference

Predicting chemical environments of bacteria from receptor signaling

Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber's law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine.Comment: DG and GM contributed equally to this wor

Linear scanning ATR-FTIR for chemical mapping and high-throughput studies of Pseudomonas sp. biofilms in microfluidic channels

A fully automated linear scanning attenuated total reflection (ATR) accessory is presented for Fourier transform infrared (FTIR) spectroscopy. The approach is based on the accurate displacement of a multi-bounce ATR crystal relative to a stationary infrared beam. To ensure accurate positioning and to provide a second sample characterization mode, a custom-built microscope was integrated into the system and the computerized work flow. Custom software includes automated control and measurement routines with a straightforward user interface for selecting parameters and monitoring experimental progress. This cost-effective modular system can be implemented on any research-grade spectrometer with a standard sample compartment for new bioanalytical chemistry studies. The system was validated and optimized for use with microfluidic flow cells containing growing Pseudomonas sp. bacterial biofilms. The complementarity among the scan positioning accuracy, measurement spatial resolution and the microchannel dimensions paves the way for parallel biological assays with real-time control over environmental parameters and minimal manual labor. By rotating the channel orientation relative to the beam path, the system could also be used for acquisition of linear biochemical maps and stitched microscope images along the channel length.Comment: 9 pages, 6 figure

Rapid rotation of micron and submicron dielectric particles measured using optical tweezers

We demonstrate the use of a laser trap (‘optical tweezers’) and back-focal-plane position detector to measure rapid rotation in aqueous solution of single particles with sizes in the vicinity of 1 μm. Two types of rotation were measured: electrorotation of polystyrene microspheres and rotation of the flagellar motor of the bacterium Vibrio alginolyticus. In both cases, speeds in excess of 1000 Hz (rev s−1) were measured. Polystyrene beads of diameter about 1 μm labelled with smaller beads were held at the centre of a microelectrode array by the optical tweezers. Electrorotation of the labelled beads was induced by applying a rotating electric field to the solution using microelectrodes. Electrorotation spectra were obtained by varying the frequency of the applied field and analysed to obtain the surface conductance of the beads. Single cells of V. alginolyticus were trapped and rotation of the polar sodium-driven flagellar motor was measured. Cells rotated more rapidly in media containing higher concentrations of Na+, and photodamage caused by the trap was considerably less when the suspending medium did not contain oxygen. The technique allows single-speed measurements to be made in less than a second and separate particles can be measured at a rate of several per minute

In-channel experiments on vertical swimming with bacteria-like robots

Bio-inspired micro-robots are of great importance as to implement versatile microsystems for a variety of in vivo and in vitro applications in medicine and biology. Accurate models are necessary to understand the swimming and rigidbody dynamics of such systems. In this study, a series of experiments are conducted with a two-link cm-scale bioinspired robot moving vertically without a tether, in siliconefilled narrow cylindrical glass channels. Swimming velocities are obtained for a set of varying tail and wave geometries, and employed to validate a resistive force theory (RFT) model using modified resistance coefficients based on measured forward velocity and body rotation rates