Transitions between three swimming gaits in Paramecium escape

Inertial swimming in an Oldroyd-B fluid

The effects of fluid inertia on a self-propelling inextensible waving sheet in an Oldroyd-B fluid are examined. The swimming velocity of the sheet is calculated in the limit in which the amplitude of the waves propagating along the sheet is small relative to the wavelength of the waves. The rate of work done by the sheet is also calculated. It is found that the swimming speed decreases monotonically approaching a limiting value with increasing Reynolds number (R) for a Newtonian fluid. For an Oldroyd-B fluid, the swimming speed increases to a maximum and then decreases asymptotically to a limiting value with increasing R. In contrast, it increases monotonically to a limiting value with increasing R for a Maxwell fluid. The limiting value is highest for the Maxwell fluid and lowest for the Oldroyd-B fluid. The corresponding value for the Newtonian fluid lies in between. The rate of work done by the sheet increases with increasing Reynolds number for all Deborah numbers. However, the energy consumed at a fixed swimming speed is lesser for an Oldroyd-B fluid than that of a Newtonian fluid. These results suggest that contrary to the Newtonian case, the fluid inertia supports the swimming sheet motion in a complex fluid. At a particular Deborah number, the oscillation frequency of the sheet could be adjusted to achieve the maximum speed. Similarly, at a particular frequency of oscillation, the Deborah numbers could be adjusted to achieve the maximum speed. These observations are in sharp contrast with the previous results reported for Newtonian and second-order fluids.

Male Caenorhabditis elegans optimizes avoidance behavior against acute and chronic stress for successful mating with hermaphrodites

The optimization of avoidance behaviors in response to stress is an instinctual life function universally present in animals. In many sexually dimorphic animals, males exhibit higher stress resistance than females, but there have been no reports of comparative studies on stress resistance in sexually dimorphic hermaphrodites capable of reproducing alone. In the present study, we aimed to utilize a reversal/turn behavioral choice to conduct a comparative analysis of optimized avoidance behavior patterns in hermaphrodite and male Caenorhabditis elegans. We found that C. elegans males showed greater resistance to physical movement under acute stress and to lifespan reduction under chronic stress than C. elegans hermaphrodites. Interestingly, males exhibited a stronger avoidance behavior pattern known as "turn" than did the hermaphrodites, even in response to mild acute stress stimuli, to which they responded as if they had been exposed to strong stimuli. Stress conditions can lead to unsuccessful mating in C. elegans, and exaggerated stress avoidance in males may have biological significance for successful mating. This sexual dimorphism in avoidance behavior optimization was attributed to neural circuits downstream of the AIB neurons, the center of turn behavior, suggesting the presence of a novel mechanism distinct from previously reported neural and molecular mechanisms of avoidance behavior optimization.

The power of 810 nm near-infrared photobiomodulation therapy for human asthenozoospermia

Sperm motility is a crucial factor in male fertility. Photobiomodulation (PBM) has been reported to increase sperm motility, but a consistent approach suitable for identifying standardizable protocols is lacking. We collected asthenozoospermic (n = 70) and normozoospermic (n = 20) semen. The asthenozoospermic samples were irradiated with an 810 nm diode laser, in continuous wave mode, at 0.25 W, 0.5 W, 1 W and 2 W for 60 s on a circular area of 1 cm2 through a novel handpiece with an innovative flat-top profile. Sperm motility was assessed immediately, after 30 and 60 min. A sample size calculator, unpaired t-test and one-way ANOVA with post-hoc Tukey HSD tests were used for statistics. One and 2 W were the most effective outputs in increasing progressive motility compared to control (p < 0.001). The maximum effect was immediately after 1 W-PBM (p < 0.001) and decreased after 60 min (p < 0.001). Time physiologically decreased vitality (p < 0.001), but less in the 1 W-PBM samples (p < 0.05). 1 W-PBM did not affect chromatin condensation. Asthenozoospermic samples displayed an impairment of 80% in oxygen consumption and ATP production and a slight inefficiency of oxidative phosphorylation compared to normozoospermic samples (p < 0.001). 1 W-PBM partially restored the functionality of aerobic metabolism (p < 0.001) by recovery of oxidative phosphorylation efficiency. PBM did not affect lactate dehydrogenase (glycolysis pathway). No irradiated samples increased accumulated malondialdehyde, a marker of lipidic peroxidation. In conclusion, PBM improves progressive motility in asthenozoospermia through increased mitochondrial energetic metabolism without harmful oxidative stress.

Biophysics of protist behaviour

Protists, an umbrella term first coined by Ernst Haeckel in 1866, are a vast collection of (primarily unicellular) eukaryotes that are "neither animals nor plants". This basic definition by exclusion has been exercised for centuries, even though recent advances have led to more rigorous taxonomic assignment of various protist groups. Pioneering comparative phylogenetic approaches have been applied to these organisms to reconstruct the deep branches of the eukaryotic tree, revealing essential clues about early eukaryotic evolution. Protists, including amoebae, flagellates, ciliates, and algae, are also vital constituents of global ecosystems, where they appear at the base of food chains, control the relative abundance of other microbes, and participate in global biogeochemical recycling. Due to their typically small size and lack of nervous systems, protists are often associated with the unfortunate label 'primitive'. Yet they exhibit remarkable behavioural sophistication and are able to feed, predate, navigate and interact with their surroundings. Unlike macroscopic animals, many protists reside in a non-intuitive physical regime where viscous forces dominate over inertia, and where they use diverse propulsion and navigation strategies. Interdisciplinary research into these cell-scale phenomena, characterised by a complex interplay of physical forces and mechanical constraints, has significantly advanced the emerging fields of active matter, microhydrodynamics, and non-equilibrium statistical physics. This primer discusses the biophysics of protist behaviour, with a focus on locomotion and feeding. I will highlight the most extensively studied principles and describe some more esoteric behaviours that have not yet been systematically explored.

Enhanced speed of microswimmers adjacent to a rough surface

Increased speed is not only the goal of human sports but also the aim we seek to achieve for artificial microswimmers. Microswimmers driven by various power mechanisms have shown unrivaled advantages in drug delivery and cancer therapy. Attaining high mobility with limited power has been a never-ending motive for researchers. We show the speed of squirmer-type microswimmers can be noticeably enhanced as they are released to move along the surface of a pillar array, which is constructed of multiple pillars of equal sizes and spacing. An additional pressure force arising from the significant low pressure between the swimmers and the surface is likely behind this enhancement. According to their polarity strengths, the speed of the microswimmers can be double or triple (or even more) compared with that in an unbounded environment. In particular, for systems requiring microswimmers moving along a complex path, the transport rate, instead of being slowed down, may be increased owing to the curvatures of the path constructed by the pillar arrays. We reveal two types of motion for microswimmers after increasing the pillar gap: free and forced oscillating. Our study sheds light on the hydrodynamic interactions between squirmer-type microswimmers and a rough wall.

The motion of micro-swimmers over a cavity in a micro-channel

This article combines the lattice Boltzmann method (LBM) with the squirmer model to investigate the motion of micro-swimmers in a channel-cavity system. The study analyses various influential factors, including the value of the squirmer-type factor (β), the swimming Reynolds number (Rep), the size of the cavity, initial position and particle size on the movement of micro-swimmers within the channel-cavity system. We simultaneously studied three types of squirmer models, Puller (β > 0), Pusher (β < 0), and Neutral (β = 0) swimmers. The findings reveal that the motion of micro-swimmers is determined by the value of β and Rep, which can be classified into six distinct motion modes. For Puller and Pusher, when the β value is constant, an increase in Rep will lead to transition in the motion mode. Moreover, the appropriate depth of cavity within the channel-cavity system plays a crucial role in capturing and separating Neutral swimmers. This study, for the first time, explores the effect of complex channel-cavity systems on the behaviour of micro-swimmers and highlights their separation and capture ability. These findings offer novel insights for the design and enhancement of micro-channel structures in achieving efficient separation and capture of micro-swimmers.

Bioelectric control of locomotor gaits in the walking ciliate Euplotes

Diverse animal species exhibit highly stereotyped behavioral actions and locomotor sequences as they explore their natural environments. In many such cases, the neural basis of behavior is well established, where dedicated neural circuitry contributes to the initiation and regulation of certain response sequences. At the microscopic scale, single-celled eukaryotes (protists) also exhibit remarkably complex behaviors and yet are completely devoid of nervous systems. Here, to address the question of how single cells control behavior, we study locomotor patterning in the exemplary hypotrich ciliate Euplotes, a highly polarized cell, which actuates a large number of leg-like appendages called cirri (each a bundle of ∼25-50 cilia) to swim in fluids or walk on surfaces. As it navigates its surroundings, a walking Euplotes cell is routinely observed to perform side-stepping reactions, one of the most sophisticated maneuvers ever observed in a single-celled organism. These are spontaneous and stereotyped reorientation events involving a transient and fast backward motion followed by a turn. Combining high-speed imaging with simultaneous time-resolved electrophysiological recordings, we show that this complex coordinated motion sequence is tightly regulated by rapid membrane depolarization events, which orchestrate the activity of different cirri on the cell. Using machine learning and computer vision methods, we map detailed measurements of cirri dynamics to the cell's membrane bioelectrical activity, revealing a differential response in the front and back cirri. We integrate these measurements with a minimal model to understand how Euplotes-a unicellular organism-manipulates its membrane potential to achieve real-time control over its motor apparatus.

Statistical analysis of organelle movement using state-space models

BACKGROUND

Organelle motility is essential for the correct cellular function of various eukaryotic cells. In plant cells, chloroplasts move towards the intracellular area irradiated by a weak light to maximise photosynthesis. To initiate this process, an unknown signal is transferred from the irradiated area to distant chloroplasts. Quantification of this chloroplast movement has been performed using visual estimations that are analyst-dependent and labour-intensive. Therefore, an objective and faster method is required.

RESULTS

In this study, we developed the cellssm package of R ( https://github.com/hnishio/cellssm.git ), which is a user-friendly tool for state-space modelling to statistically analyse the directional movement of cells or organelles. Our method showed a high accuracy in estimating the start time of chloroplast movement in the liverwort Marchantia polymorpha over a short period. The tool indicated that chloroplast movement accelerates during transport to the irradiated area and that signal transfer speed is uneven within a cell. We also developed a method to estimate the common dynamics among multiple chloroplasts in each cell, which clarified different characteristics among cells.

CONCLUSIONS

We demonstrated that state-space modelling is a powerful method to understand organelle movement in eukaryotic cells. The cellssm package can be applied to various directional movements (both accumulation and avoidance) at cellular and subcellular levels to estimate the true transition of states behind the time-series data.

An electrophysiological and kinematic model of Paramecium, the "swimming neuron"

Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments.

Run-and-Tumble Dynamics and Mechanotaxis Discovered in Microglial Migration

Microglia are resident macrophage cells in the central nervous system that search for pathogens or abnormal neural activities and migrate to resolve the issues. The effective search and targeted motion of macrophages mean dearly to maintaining a healthy brain, yet little is known about their migration dynamics. In this work, we study microglial motion with and without the presence of external mechanostimuli. We discover that the cells are promptly attracted by the applied forces (i.e., mechanotaxis), which is a tactic behavior as yet unconfirmed in microglia. Meanwhile, in both the explorative and the targeted migration, microglia display dynamics that is strikingly analogous to bacterial run-and-tumble motion. A closer examination reveals that microglial run-and-tumble is more sophisticated, e.g., they display a short-term memory when tumbling and rely on active steering during runs to achieve mechanotaxis, probably via the responses of mechanosensitive ion channels. These differences reflect the sharp contrast between microglia and bacteria cells (eukaryotes vs. prokaryotes) and their environments (compact tissue vs. fluid). Further analyses suggest that the reported migration dynamics has an optimal search efficiency and is shared among a subset of immune cells (human monocyte and macrophage). This work reveals a fruitful analogy between the locomotion of 2 remote systems and provides a framework for studying immune cells exploring complex environments.

Nematic order condensation and topological defects in inertial active nematics

Living materials at different length scales manifest active nematic features such as orientational order, nematic topological defects, and active nematic turbulence. Using numerical simulations we investigate the impact of fluid inertia on the collective pattern formation in active nematics. We show that an incremental increase in inertial effects due to reduced viscosity results in gradual melting of nematic order with an increase in topological defect density before a discontinuous transition to a vortex-condensate state. The emergent vortex-condensate state at low enough viscosities coincides with nematic order condensation within the giant vortices and the drop in the density of topological defects. We further show flow field around topological defects is substantially affected by inertial effects. Moreover, we demonstrate the strong dependence of the kinetic energy spectrum on the inertial effects, recover the Kolmogorov scaling within the vortex-condensate phase, but find no evidence of universal scaling at higher viscosities. The findings reveal complexities in active nematic turbulence and emphasize the important cross-talk between active and inertial effects in setting flow and orientational organization of active particles.

Hydrodynamic Behavior of Self-Propelled Particles in a Simple Shear Flow

The hydrodynamic properties of a squirmer type of self-propelled particle in a simple shear flow are investigated using the immersed boundary-lattice Boltzmann method in the range of swimming Reynolds number 0.05 ≤ Re_s ≤ 2.0, flow Reynolds number 40 ≤ Re_p ≤ 160, blocking rate 0.2 ≤ κ ≤ 0.5. Some results are validated by comparing with available other results. The effects of Re_s, Re_p and κ on the hydrodynamic properties of squirmer are discussed. The results show that there exist four distinct motion modes for the squirmer, i.e., horizontal mode, attractive oscillation mode, oscillation mode, and chaotic mode. Increasing Re_s causes the motion mode of the squirmer to change from a constant tumbling near the centerline to a stable horizontal mode, even an oscillatory or appealing oscillatory mode near the wall. Increasing the swimming intensity of squirmer under the definite Re_s will induce the squirmer to make periodic and stable motion at a specific distance from the wall. Increasing Re_p will cause the squirmer to change from a stable swimming state to a spiral motion or continuous rotation. Increasing κ will strengthen the wall’s attraction to the squirmer. Increasing swimming intensity of squirmer will modify the strength and direction of the wall’s attraction to the squirmer if κ remains constant.

Oscillators and servomechanisms in orientation and navigation, and sometimes in cognition

Navigational mechanisms have been characterized as servomechanisms. A navigational servomechanism specifies a goal state to strive for. Discrepancies between the perceived current state and the goal state specify error. Servomechanisms adjust the course of travel to reduce the error. I now add that navigational servomechanisms work with oscillators, periodic movements of effectors that drive locomotion. I illustrate this concept selectively over a vast range of scales of travel from micrometres in bacteria to thousands of kilometres in sea turtles. The servomechanisms differ in sophistication, with some interrupting forward motion occasionally or changing travel speed in kineses and others adjusting the direction of travel in taxes. I suggest that in other realms of life as well, especially in cognition, servomechanisms work with oscillators.

Metachronal motion across scales: current challenges and future directions

Metachronal motion is used across a wide range of organisms for a diverse set of functions. However, despite its ubiquity, analysis of this behavior has been difficult to generalize across systems. Here we provide an overview of known commonalities and differences between systems that use metachrony to generate fluid flow. We also discuss strategies for standardizing terminology and defining future investigative directions that are analogous to other established subfields of biomechanics. Lastly, we outline key challenges that are common to many metachronal systems, opportunities that have arisen due to the advent of new technology (both experimental and computational), and next steps for community development and collaboration across the nascent network of metachronal researchers.

Integrative Neuroscience of Paramecium, a "Swimming Neuron"

Paramecium is a unicellular organism that swims in fresh water by beating thousands of cilia. When it is stimulated (mechanically, chemically, optically, thermally…), it often swims backward then turns and swims forward again. This "avoiding reaction" is triggered by a calcium-based action potential. For this reason, some authors have called Paramecium a "swimming neuron." This review summarizes current knowledge about the physiological basis of behavior of Paramecium.

Changes in geometrical aspects of a simple model of cilia synchronization control the dynamical state, a possible mechanism for switching of swimming gaits in microswimmers

Active oscillators, with purely hydrodynamic coupling, are useful simple models to understand various aspects of motile cilia synchronization. Motile cilia are used by microorganisms to swim and to control the flow fields in their surroundings; the patterns observed in cilia carpets can be remarkably complex, and can be changed over time by the organism. It is often not known to what extent the coupling between cilia is due to just hydrodynamic forces, and neither is it known if it is biological or physical triggers that can change the dynamical collective state. Here we treat this question from a very simplified point of view. We describe three possible mechanisms that enable a switch in the dynamical state, in a simple scenario of a chain of oscillators. We find that shape-change provides the most consistent strategy to control collective dynamics, but also imposing small changes in frequency produces some unique stable states. Demonstrating these effects in the abstract minimal model proves that these could be possible explanations for gait switching seen in ciliated micro organisms like Paramecium and others. Microorganisms with many cilia could in principle be taking advantage of hydrodynamic coupling, to switch their swimming gait through either a shape change that manifests in decreased coupling between groups of cilia, or alterations to the beat style of a small subset of the cilia.

Polarization grating based on diffraction phase microscopy for quantitative phase imaging of paramecia

This study presents a polarization grating based diffraction phase microscopy (PG-DPM) and its application in bio-imaging. Compared with traditional diffraction phase microscopy (DPM) of which the fringe contrast is sample-dependent, the fringe contrast of PG-DPM is adjustable by changing the polarization of the illumination beam. Moreover, PG-DPM has been applied to real-time phase imaging of live paramecia for the first time. The study reveals that paramecium has self-helical forward motion characteristics, or more specifically, 77% clockwise and 23% anti-clockwise rotation when moving forward. We can envisage that PG-DPM will be applied to many different fields.

Active matter therapeutics

Nanotherapies based on micelles, liposomes, polymersomes, nanocapsules, magnetic nanoparticles, and noble metal nanoparticles have been at the forefront of drug delivery in the past few decades. Some of these nanopharmaceuticals have been commercially applied to treat a wide range of diseases, from dry eye syndrome to cancer. However, the majority involve particles that are passive, meaning that they do not change shape, and they lack motility; the static features can limit their therapeutic efficacy. In this review, we take a critical look at an emerging field that seeks to utilize active matter for therapeutics. In this context, active matter can be broadly referred to as micro or nanosized constructs that energetically react with their environment or external fields and translate, rotate, vibrate or change shape. Essentially, the recent literature suggests that such particles could significantly augment present-day drug delivery, by enhancing transport and increasing permeability across anatomical barriers by transporting drugs within solid tumor microenvironments or disrupting cardiovascular plaque. We discuss examples of such particles and link the transport and permeability properties of active matter to potential therapeutic applications in the context of two major diseases, namely cancer and heart disease. We also discuss potential challenges, opportunities, and translational hurdles.

A Light-Driven Microgel Rotor

The current understanding of motility through body shape deformation of micro-organisms and the knowledge of fluid flows at the microscale provides ample examples for mimicry and design of soft microrobots. In this work, a 2D spiral is presented that is capable of rotating by non-reciprocal curling deformations. The body of the microswimmer is a ribbon consisting of a thermoresponsive hydrogel bilayer with embedded plasmonic gold nanorods. Such a system allows fast local photothermal heating and nonreciprocal bending deformation of the hydrogel bilayer under nonequilibrium conditions. It is shown that the spiral acts as a spring capable of large deformations thanks to its low stiffness, which is tunable by the swelling degree of the hydrogel and the temperature. Tethering the ribbon to a freely rotating microsphere enables rotational motion of the spiral by stroboscopic irradiation. The efficiency of the rotor is estimated using resistive force theory for Stokes flow. This research demonstrates microscopic locomotion by the shape change of a spiral and may find applications in the field of microfluidics, or soft microrobotics.

Direct-forcing fictitious domain method for simulating non-Brownian active particles

We present a direct-forcing fictitious domain method for simulating non-Brownian squirmer particles with both the hydrodynamic interactions and collisions being fully resolved. In this method, we solve the particle motion by distributing collocation points inside the particle interior domain that overlay upon a fixed Eulerian mesh. The fluid motions, including those of the "fictitious fluids" being extended into the particle, are solved on the entire computation domain. Pseudo-body forces are used to enforce the fictitious fluids to follow the particle movement. A direct-forcing approach is employed to map physical variables between the overlaid meshes, which does not require additional iterations to achieve convergence. We perform a series of numerical studies at both small and finite Reynolds numbers. First, accuracy of the algorithm is examined in studying benchmark problems of a free-swimming squirmer and two side-by-side squirmers. Then we investigate statistic properties of the quasi-two-dimensional collective dynamics for a monolayer of squirmer particles that are confined on a surface immersed in a bulk flow. Finally, we explore the physical mechanisms of how a freely moving short cylinder interacts with a monolayer of active particles, and find out that the cylinder movement is dominated by collision. We demonstrate that a more directional migration of cylinder can be resultant from an inhomogeneous distribution of active particles around the cylinder that has an anisotropic shape.

Time Irreversibility and Criticality in the Motility of a Flagellate Microorganism

Active living organisms exhibit behavioral variability, partitioning between fast and slow dynamics. Such variability may be key to generating rapid responses in a heterogeneous, unpredictable environment wherein cellular activity effects continual exchanges of energy fluxes. We demonstrate a novel, noninvasive strategy for revealing nonequilibrium control of swimming-specifically, in an octoflagellate microalga. These organisms exhibit surprising features of flagellar excitability and mechanosensitivity, which characterize a novel, time-irreversible "run-stop-shock" motility comprising forward runs, knee-jerk shocks with dramatic beat reversal, and long stops during which cells are quiescent yet continue to exhibit submicron flagellar vibrations. Entropy production, associated with flux cycles arising in a reaction graph representation of the gait-switching dynamics, provides a direct measure of detailed balance violation in this primitive alga.

Reduced-order model for inertial locomotion of a slender swimmer

The inertial locomotion of an elongated model swimmer in a Newtonian fluid is quantified, wherein self-propulsion is achieved via steady tangential surface treadmilling. The swimmer has a length 2l and a circular cross section of longitudinal profile aR(z), where a is the characteristic width of the cross section, R(z) is a dimensionless shape function, and z is a dimensionless coordinate, normalized by l, along the centerline of the body. It is assumed that the swimmer is slender, ε=a/l≪1. Hence, we utilize slender-body theory to analyze the Navier-Stokes equations that describe the flow around the swimmer. Therefrom, we compute an asymptotic approximation to the swimming speed, U, as U/u_{s}=1-β[V(Re)-1/2∫_{-1}^{1}zlnR(z)dz]/ln(1/ε)+O[1/ln^{2}(1/ε)], where u_{s} is the characteristic speed of the surface treadmilling, Re is the Reynolds number based on the body length, and β is a dimensionless parameter that differentiates between "pusher" (propelled from the rear, β<0) and "puller" (propelled from the front, β>0) -type swimmers. The function V(Re) increases monotonically with increasing Re; hence, fluid inertia causes an increase (decrease) in the swimming speed of a pusher (puller). Next, we demonstrate that the power expenditure of the swimmer increases monotonically with increasing Re. Further, the power expenditures of a puller and pusher with the same value of |β| are equal. Therefore, pushers are superior in inertial locomotion as compared to pullers, in that they achieve a faster swimming speed for the same power expended. Finally, it is demonstrated that the flow structure predicted from our reduced-order model is consistent with that from direct numerical simulation of swimmers at intermediate Re.

Microrobotic Platform for Single Motile Microorganism Investigation

We propose a microrobotic platform for single motile microorganism observation and investigation. The platform utilizes a high-speed online vision sensor to realize real-time observation of a microorganism under a microscopic environment with a relatively high magnification ratio. A microfluidic chip was used to limit the vertical movement of the microorganism and reduce the tracking system complexity. We introduce a simple image processing method, which utilizes high-speed online vision characteristics and shows robustness against image noise to increase the overall tracking performance with low computational time consumption. The design also considers the future integration of a stimulation system using microtools. Successful long-time tracking of a freely swimming microorganism inside of a microfluidic chip for more than 30 min was achieved notwithstanding the presence of noises in the environment of the cell. The specific design of the platform, particularly the tracking system, is described, and the performance is evaluated and confirmed through basic experiments. The potential of the platform to apply mechanical stimulation to a freely swimming microorganism is demonstrated by using a 50-µm-thick microtool. The proposed platform can be used for long-term observation and to achieve different kinds of stimulations, which can induce new behavior of the cells and lead to unprecedented discoveries in biological fields.

Photobiomodulation by Infrared Diode Laser: Effects on Intracellular Calcium Concentration and Nitric Oxide Production of Paramecium

In Paramecium, cilia beating is correlated to intracellular calcium concentration ([Ca²⁺ ]i) and nitric oxide (NO) synthesis. Recent findings affirm that photobiomodulation (PBM) can transiently increase the [Ca²⁺ ]i in mammalian cells. In this study, we investigated the effect of both 808 and 980 nm diode laser irradiated with flat-top hand-piece on [Ca²⁺ ]i and NO production of Paramecium primaurelia, to provide basic information for the development of new therapeutic approaches. In the experiments, the laser power in CW varied (0.1; 0.5; 1; and 1.5 W) to generate the following respective fluences: 6.4; 32; 64; and 96 J cm^-2 . The 6.4 J cm^-2 did not induce PBM if irradiated by both 808 and 980 nm diode laser. Conversely, the 32 J cm^-2 fluence had no effect on Paramecium cells if irradiated by the 808 nm laser, while if irradiated by the 980 nm laser induced increment in swimming speed (suggesting an effect on the [Ca²⁺ ]i, NO production, similar to the 64 J cm^-2 with the 808 nm wavelength). The more evident discordance occurred with the 96 J cm^-2 fluence, which had the more efficient effect on PBM among the parameters if irradiated with the 808 nm laser and killed the Paramecium cells if irradiated by the 980 nm laser. Lastly, the 980 nm and 64 or 96 J cm^-2 were the only parameters to induce a release of stored calcium.

Hotspots of boundary accumulation: dynamics and statistics of micro-swimmers in flowing films

Biological flows over surfaces and interfaces can result in accumulation hotspots or depleted voids of microorganisms in natural environments. Apprehending the mechanisms that lead to such distributions is essential for understanding biofilm initiation. Using a systematic framework, we resolve the dynamics and statistics of swimming microbes within flowing films, considering the impact of confinement through steric and hydrodynamic interactions, flow and motility, along with Brownian and run-tumble fluctuations. Micro-swimmers can be peeled off the solid wall above a critical flow strength. However, the interplay of flow and fluctuations causes organisms to migrate back towards the wall above a secondary critical value. Hence, faster flows may not always be the most efficacious strategy to discourage biofilm initiation. Moreover, we find run-tumble dynamics commonly used by flagellated microbes to be an intrinsically more successful strategy to escape from boundaries than equivalent levels of enhanced Brownian noise in ciliated organisms.

Diversity of extracellular proteins during the transition from the ‘proto-apicomplexan’ alveolates to the apicomplexan obligate parasites

The recent completion of high-coverage draft genome sequences for several alveolate protozoans – namely, the chromerids, Chromera velia and Vitrella brassicaformis; the perkinsid Perkinsus marinus; the apicomplexan, Gregarina niphandrodes, as well as high coverage transcriptome sequence information for several colpodellids, allows for new genome-scale comparisons across a rich landscape of apicomplexans and other alveolates. Genome annotations can now be used to help interpret fine ultrastructure and cell biology, and guide new studies to describe a variety of alveolate life strategies, such as symbiosis or free living, predation, and obligate intracellular parasitism, as well to provide foundations to dissect the evolutionary transitions between these niches. This review focuses on the attempt to identify extracellular proteins which might mediate the physical interface of cell–cell interactions within the above life strategies, aided by annotation of the repertoires of predicted surface and secreted proteins encoded within alveolate genomes. In particular, we discuss what descriptions of the predicted extracellular proteomes reveal regarding a hypothetical last common ancestor of a pre-apicomplexan alveolate – guided by ultrastructure, life strategies and phylogenetic relationships – in an attempt to understand the evolution of obligate parasitism in apicomplexans.

Paramecium swimming and ciliary beating patterns: a study on four RNA interference mutations

Paramecium cells swim and feed by beating their thousands of cilia in coordinated patterns. The organization of these patterns and its relationship with cell motility has been the subject of a large body of work, particularly as a model for ciliary beating in human organs where similar organization is seen. However the rapid motion of the cells makes quantitative measurements very challenging. Here we provide detailed measurements of the swimming of Paramecium cells from high-speed video at high magnification, as they move in microfluidic channels. An image analysis protocol allows us to decouple the cell movement from the motion of the cilia, thus allowing us to measure the ciliary beat frequency (CBF) and the spatio-temporal organization into metachronal waves along the cell periphery. Two distinct values of the CBF appear at different regions of the cell: most of the cilia beat in the range of 15 to 45 Hz, while the cilia in the peristomal region beat at almost double the frequency. The body and peristomal CBF display a nearly linear relation with the swimming velocity. Moreover the measurements do not display a measurable correlation between the swimming velocity and the metachronal wave velocity on the cell periphery. These measurements are repeated for four RNAi silenced mutants, where proteins specific to the cilia or to their connection to the cell base are depleted. We find that the mutants whose ciliary structure is affected display similar swimming to the control cells albeit with a reduced efficiency, while the mutations that affect the cilia's anchoring to the cell lead to strongly reduced ability to swim. This reduction in motility can be related to a loss of coordination between the ciliary beating in different parts of the cell.

Somersault of Paramecium in extremely confined environments

We investigate various swimming modes of Paramecium in geometric confinements and a non-swimming self-bending behavior like a somersault, which is quite different from the previously reported behaviors. We observe that Paramecia execute directional sinusoidal trajectories in thick fluid films, whereas Paramecia meander around a localized region and execute frequent turns due to collisions with adjacent walls in thin fluid films. When Paramecia are further constrained in rectangular channels narrower than the length of the cell body, a fraction of meandering Paramecia buckle their body by pushing on the channel walls. The bucking (self-bending) of the cell body allows the Paramecium to reorient its anterior end and explore a completely new direction in extremely confined spaces. Using force deflection method, we quantify the Young's modulus of the cell and estimate the swimming and bending powers exerted by Paramecium. The analysis shows that Paramecia can utilize a fraction of its swimming power to execute the self-bending maneuver within the confined channel and no extra power may be required for this new kind of self-bending behavior. This investigation sheds light on how micro-organisms can use the flexibility of the body to actively navigate within confined spaces.

Effect of 808 nm Diode Laser on Swimming Behavior, Food Vacuole Formation and Endogenous ATP Production of Paramecium primaurelia (Protozoa)

Photobiomodulation (PBM) has been used in clinical practice for more than 40 years. To clarify the mechanisms of action of PBM at cellular and organism levels, we investigated its effect on Paramecium primaurelia (Protozoa) irradiated by an 808 nm infrared diode laser with a flat-top handpiece (1 W in CW). Our results led to the conclusion that: (1) the 808 nm laser stimulates the P. primaurelia without a thermal effect, (2) the laser effect is demonstrated by an increase in swimming speed and in food vacuole formation, (3) the laser treatment affects endogenous adenosine triphosphate (ATP) production in a positive way, (4) the effects of irradiation dose suggest an optimum exposure time of 50 s (64 J cm(-2) of fluence) to stimulate the Paramecium cells; irradiation of 25 s shows no effect or only mild effects and irradiation up to 100 s does not increase the effect observed with 50 s of treatment, (5) the increment of endogenous ATP concentration highlights the positive photobiomodulating effect of the 808 nm laser and the optimal irradiation conditions by the flat-top handpiece.

Density- and trait-mediated effects of a parasite and a predator in a tri-trophic food web

Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density or trait mediated. We studied a tri-trophic food chain comprised of (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum) and (iv) a parasite of the intermediate consumer (Holospora undulata). A fully factorial experimental manipulation of predator and parasite presence/absence was combined with analyses of population dynamics, modelling and analyses of host (Paramecium) morphology and behaviour. Predation and parasitism each reduced the abundance of the intermediate consumer (Paramecium), and parasitism indirectly reduced the abundance of the basal resource (Serratia). However, in combination, predation and parasitism had non-additive effects on the abundance of the intermediate consumer, as well as on that of the basal resource. In both cases, the negative effect of parasitism seemed to be effaced by predation. Infection of the intermediate consumer reduced predator abundance. Modelling and additional experimentation revealed that this was most likely due to parasite reduction of intermediate host abundance (a density-mediated effect), as opposed to changes in predator functional or numerical response. Parasitism altered morphological and behavioural traits, by reducing host cell length and increasing the swimming speed of cells with moderate parasite loads. Additional tests showed no significant difference in Didinium feeding rate on infected and uninfected hosts, suggesting that the combination of these modifications does not affect host vulnerability to predation. However, estimated rates of encounter with Serratia based on these modifications were higher for infected Paramecium than for uninfected Paramecium. A mixture of density-mediated and trait-mediated indirect effects of parasitism on non-host species creates rich and complex possibilities for effects of parasites in food webs that should be included in assessments of possible impacts of parasite eradication or introduction.

Autophoretic locomotion from geometric asymmetry

Among the few methods which have been proposed to create small-scale swimmers, those relying on self-phoretic mechanisms present an interesting design challenge in that chemical gradients are required to generate net propulsion. Building on recent work, we propose that asymmetries in geometry are sufficient to induce chemical gradients and swimming. We illustrate this idea using two different calculations. We first calculate exactly the self-propulsion speed of a system composed of two spheres of unequal sizes but identically chemically homogeneous. We then consider arbitrary, small-amplitude, shape deformations of a chemically homogeneous sphere, and calculate asymptotically the self-propulsion velocity induced by the shape asymmetries. Our results demonstrate how geometric asymmetries can be tuned to induce large locomotion speeds without the need of chemical patterning.

Buckling of a beam extruded into highly viscous fluid

Inspired by microscopic Paramecia which use trichocyst extrusion to propel themselves away from thermal aggression, we propose a macroscopic experiment to study the stability of a slender beam extruded in a highly viscous fluid. Piano wires were extruded axially at constant speed in a tank filled with corn syrup. The force necessary to extrude the wire was measured to increase linearly at first until the compressive viscous force causes the wire to buckle. A numerical model, coupling a lengthening elastica formulation with resistive-force theory, predicts a similar behavior. The model is used to study the dynamics at large time when the beam is highly deformed. It is found that at large time, a large deformation regime exists in which the force necessary to extrude the beam at constant speed becomes constant and length independent. With a proper dimensional analysis, the beam can be shown to buckle at a critical length based on the extrusion speed, the bending rigidity, and the dynamic viscosity of the fluid. Hypothesizing that the trichocysts of Paramecia must be sized to maximize their thrust per unit volume as well as avoid buckling instabilities, we predict that their bending rigidity must be about 3×10^{-9}Nμm^{2}. The verification of this prediction is left for future work.

Evidence for two extremes of ciliary motor response in a single swimming microorganism

Because arrays of motile cilia drive fluids for a range of processes, the versatile mechano-chemical mechanism coordinating them has been under scrutiny. The protist Paramecium presents opportunities to compare how groups of cilia perform two distinct functions, swimming propulsion and nutrient uptake. We present how the body cilia responsible for propulsion and the oral-groove cilia responsible for nutrient uptake respond to changes in their mechanical environment accomplished by varying the fluid viscosity over a factor of 7. Analysis with a phenomenological model of trajectories of swimmers made neutrally buoyant with magnetic forces combined with high-speed imaging of ciliary beating reveal that the body cilia exert a nearly constant propulsive force primarily by reducing their beat frequency as viscosity increases. By contrast, the oral-groove cilia beat at a nearly constant frequency. The existence of two extremes of motor response in a unicellular organism prompts unique investigations of factors controlling ciliary beating.

Hydrodynamic interaction of microswimmers near a wall

The hydrodynamics of an archetypal low-Reynolds number swimmer, called "squirmer," near a wall has been numerically studied. For a single squirmer, depending on the swimming mechanism, three different modes are distinguished: (a) the squirmer escaping from the wall, (b) the squirmer swimming along the wall at a constant distance and orientation angle, and (c) the squirmer swimming near the wall in a periodic trajectory. The role of inertial effects on the near-wall motion of the squirmer is quantified. The dynamics of multiple squirmers swimming between two walls is found to be very different from a single squirmer. Near-wall accumulation of squirmers are observed. At a relatively small concentration c = 0.1, around 60-80% of the squirmers are accumulated near the walls and attraction of pushers and pullers toward the wall is stronger than neutral squirmers. Near-wall squirmers orient normal to the wall, while in the bulk region, the squirmers are mostly oriented parallel to the wall. At a high concentration c = 0.4, the percentage of the near-wall squirmers is around 40%. The orientation angle of squirmers in the bulk region is more uniformly distributed at high concentrations. In the near-wall region, pullers repel each other, while pushers are attracted to each other and form clusters.

Flagellar waveform dynamics of freely swimming algal cells

We present quantitative measurements of time-dependent flagellar waveforms for freely swimming biflagellated algal cells, for both synchronous and asynchronous beating. We use the waveforms in conjunction with resistive force theory as well as a singularity method to predict a cell's time-dependent velocity for comparison with experiments. While net propulsion is thought to arise from asymmetry between the power and recovery strokes, we show that hydrodynamic interactions between the flagella and cell body on the return stroke make an important contribution to enhance net forward motion.

The kinematics of swimming and relocation jumps in copepod nauplii

Copepod nauplii move in a world dominated by viscosity. Their swimming-by-jumping propulsion mode, with alternating power and recovery strokes of three pairs of cephalic appendages, is fundamentally different from the way other microplankters move. Protozoans move using cilia or flagella, and copepodites are equipped with highly specialized swimming legs. In some species the nauplius may also propel itself more slowly through the water by beating and rotating the appendages in a different, more complex pattern. We use high-speed video to describe jumping and swimming in nauplii of three species of pelagic copepods: Temora longicornis, Oithona davisae and Acartia tonsa. The kinematics of jumping is similar between the three species. Jumps result in a very erratic translation with no phase of passive coasting and the nauplii move backwards during recovery strokes. This is due to poorly synchronized recovery strokes and a low beat frequency relative to the coasting time scale. For the same reason, the propulsion efficiency of the nauplii is low. Given the universality of the nauplius body plan, it is surprising that they seem to be inefficient when jumping, which is different from the very efficient larger copepodites. A slow-swimming mode is only displayed by T. longicornis. In this mode, beating of the appendages results in the creation of a strong feeding current that is about 10 times faster than the average translation speed of the nauplius. The nauplius is thus essentially hovering when feeding, which results in a higher feeding efficiency than that of a nauplius cruising through the water.

Hydrodynamic synchronization of nonlinear oscillators at low Reynolds number

We introduce a generic model of a weakly nonlinear self-sustained oscillator as a simplified tool to study synchronization in a fluid at low Reynolds number. By averaging over the fast degrees of freedom, we examine the effect of hydrodynamic interactions on the slow dynamics of two oscillators and show that they can lead to synchronization. Furthermore, we find that synchronization is strongly enhanced when the oscillators are nonisochronous, which on the limit cycle means the oscillations have an amplitude-dependent frequency. Nonisochronity is determined by a nonlinear coupling α being nonzero. We find that its (α) sign determines if they synchronize in phase or antiphase. We then study an infinite array of oscillators in the long-wavelength limit, in the presence of noise. For α>0, hydrodynamic interactions can lead to a homogeneous synchronized state. Numerical simulations for a finite number of oscillators confirm this and, when α<0, show the propagation of waves, reminiscent of metachronal coordination.

Calcium signaling in closely related protozoan groups (Alveolata): non-parasitic ciliates (Paramecium, Tetrahymena) vs. parasitic Apicomplexa (Plasmodium, Toxoplasma)

The importance of Ca2+-signaling for many subcellular processes is well established in higher eukaryotes, whereas information about protozoa is restricted. Recent genome analyses have stimulated such work also with Alveolates, such as ciliates (Paramecium, Tetrahymena) and their pathogenic close relatives, the Apicomplexa (Plasmodium, Toxoplasma). Here we compare Ca2+ signaling in the two closely related groups. Acidic Ca2+ stores have been characterized in detail in Apicomplexa, but hardly in ciliates. Two-pore channels engaged in Ca2+-release from acidic stores in higher eukaryotes have not been stingently characterized in either group. Both groups are endowed with plasma membrane- and endoplasmic reticulum-type Ca2+-ATPases (PMCA, SERCA), respectively. Only recently was it possible to identify in Paramecium a number of homologs of ryanodine and inositol 1,3,4-trisphosphate receptors (RyR, IP3R) and to localize them to widely different organelles participating in vesicle trafficking. For Apicomplexa, physiological experiments suggest the presence of related channels although their identity remains elusive. In Paramecium, IP3Rs are constitutively active in the contractile vacuole complex; RyR-related channels in alveolar sacs are activated during exocytosis stimulation, whereas in the parasites the homologous structure (inner membrane complex) may no longer function as a Ca2+ store. Scrutinized comparison of the two closely related protozoan phyla may stimulate further work and elucidate adaptation to parasitic life. See also "Conclusions" section.

The computational worm: spatial orientation and its neuronal basis in C. elegans

Spatial orientation behaviors in animals are fundamental for survival but poorly understood at the neuronal level. The nematode Caenorhabditis elegans orients to a wide range of stimuli and has a numerically small and well-described nervous system making it advantageous for investigating the mechanisms of spatial orientation. Recent work by the C. elegans research community has identified essential computational elements of the neural circuits underlying two orientation strategies that operate in five different sensory modalities. Analysis of these circuits reveals novel motifs including simple circuits for computing temporal derivatives of sensory input and for integrating sensory input with behavioral state to generate adaptive behavior. These motifs constitute hypotheses concerning the identity and functionality of circuits controlling spatial orientation in higher organisms.