Quorum Sensing Antagonism from Marine Organisms

With the global emergence of multiresistant bacteria there is an increasing demand for development of new treatments to combat pathogens. Bacterial cell–cell communication [quorum sensing (QS)] regulates expression of virulence factors in a number of bacterial pathogens and is a new promising target for the control of infectious bacteria. We present the results of screening of 284 extracts of marine organisms from the Great Barrier Reef, Australia, for their inhibition of QS. Of the 284 extracts, 64 (23%) were active in a general, LuxR-derived QS screen, and of these 36 (56%) were also active in a specific Pseudomonas aeruginosa QS screen. Extracts of the marine sponge Luffariella variabilis proved active in both systems. The secondary metabolites manoalide, manoalide monoacetate, and secomanoalide isolated from the sponge showed strong QS inhibition of a lasB::gfp(ASV) fusion, demonstrating the potential for further identification of specific QS antagonists from marine organisms.     

Mucin Biopolymers Prevent Bacterial Aggregation by Retaining Cells in the Free-Swimming State

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Highlights? Mucin biopolymers reduce bacterial adhesion to underlying substrates ? Bacterial motility is maintained or increased in the presence of mucins ? Mucins block aggregate formation by motile bacteria ? Immotile Pseudomonas aeruginosa can form alginate and Psl-dependent flocs in mucus     

Measuring the Three-Dimensional Kinematics of a Free-Swimming Koi Carp by Video Tracking Method

A video tracking system for measuring three-dimensional kinematics of a free-swimming fish is presented. The tracking is accomplished by simultaneously taking images from the ventral view and the lateral view of the fish with two cameras mounted on two computer-controlled and mutually orthogonal translation stages. Compared to the previous system we reported, the time resolution is greatly improved. A koi carp is selected for the experiment. By processing the images caught by the video tracking system, the three-dimensional kinematics of the koi carp during a continuous swimming containing several moderate maneuvers are obtained. In particular, the pitching motion of fish body and the tail motion, including lateral excursion, variation in tail height and torsion, are revealed for burst-and-coast swimming and turning maneuver. The error analysis is also provided for the measurement results.     

Interactions between Seagrass Complexity,Hydrodynamic Flow and Biomixing Alter Food Availability for Associated Filter-Feeding Organisms

Seagrass shoots interact with hydrodynamic forces and thereby a positively or negatively influence the survival of associated species. The modification of these forces indirectly alters the physical transport and flux of edible particles within seagrass meadows, which will influence the growth and survivorship of associated filter-feeding organisms. The present work contributes to gaining insight into the mechanisms controlling the availability of resources for filter feeders inhabiting seagrass canopies, both from physical (influenced by seagrass density and patchiness) and biological (regulated by filter feeder density) perspectives. A factorial experiment was conducted in a large racetrack flume, which combined changes in hydrodynamic conditions, chlorophyll a concentration in the water and food intake rate (FIR) in a model active filter-feeding organism (the cockle). Results showed that seagrass density and patchiness modified both hydrodynamic forces and availability of resources for filter feeders. Chlorophyll a water content decreased to 50% of the initial value when densities of both seagrass shoots and cockles were high. Also, filter feeder density controlled resource availability within seagrass patches, depending on its spatial position within the racetrack flume. Under high density of filter-feeding organisms, chlorophyll a levels were lower between patches. This suggests that the pumping activity of cockles (i.e. biomixing) is an emergent key factor affecting both resource availability and FIR for filter feeders in dense canopies. Applying our results to natural conditions, we suggest the existence of a direct correlation between habitat complexity (i.e. shoot density and degree of patchiness) and filter feeders density. Fragmented and low-density patches seem to offer both greater protection from hydrodynamic forces and higher resource availability. In denser patches, however, resources are allocated mostly within the canopy, which would benefit filter feeders if they occurred at low densities, but would be limiting when filter feeder were at high densities.     

Collective Response of Zebrafish Shoals to a Free-Swimming Robotic Fish

In this work, we explore the feasibility of regulating the collective behavior of zebrafish with a free-swimming robotic fish. The visual cues elicited by the robot are inspired by salient features of attraction in zebrafish and include enhanced coloration, aspect ratio of a fertile female, and carangiform/subcarangiform locomotion. The robot is autonomously controlled with an online multi-target tracking system and swims in circular trajectories in the presence of groups of zebrafish. We investigate the collective response of zebrafish to changes in robot speed, achieved by varying its tail-beat frequency. Our results show that the speed of the robot is a determinant of group cohesion, quantified through zebrafish nearest-neighbor distance, which increases with the speed of the robot until it reaches . We also find that the presence of the robot causes a significant decrease in the group speed, which is not accompanied by an increase in the freezing response of the subjects. Findings of this study are expected to inform the design of experimental protocols that leverage the use of robots to study the zebrafish animal model.     

Scaling in Free-Swimming Fish and Implications for Measuring Size-at-Time in the Wild

This study was motivated by the need to measure size-at-age, and thus growth rate, in fish in the wild. We postulated that this could be achieved using accelerometer tags based first on early isometric scaling models that hypothesize that similar animals should move at the same speed with a stroke frequency that scales with length^-1, and second on observations that the speed of primarily air-breathing free-swimming animals, presumably swimming ‘efficiently’, is independent of size, confirming that stroke frequency scales as length^-1. However, such scaling relations between size and swimming parameters for fish remain mostly theoretical. Based on free-swimming saithe and sturgeon tagged with accelerometers, we introduce a species-specific scaling relationship between dominant tail beat frequency (TBF) and fork length. Dominant TBF was proportional to length^-1 (r² = 0.73, n = 40), and estimated swimming speed within species was independent of length. Similar scaling relations accrued in relation to body mass^-0.29. We demonstrate that the dominant TBF can be used to estimate size-at-time and that accelerometer tags with onboard processing may be able to provide size-at-time estimates among free-swimming fish and thus the estimation of growth rate (change in size-at-time) in the wild.     

Directional prediction by the saccadic system

One popular and fruitful approach to understanding what influences the decision of where to look next has been to present targets in a series of trials either to the right or left of a central fixation point and examine sequential effects on saccadic latency. However, there is a problem with this paradigm: Every saccade to a target is necessarily followed by an equal and opposite movement back to the center, yet the potentially confounding influence of this refixation saccade is rarely considered. Here, we introduce a novel random-walk paradigm that eliminates this difficulty. Each successive target appears to the left or right of the previous one, allowing us to study long sequences of saccades uncontaminated by refixations. This exposes a new stimulus-history effect, which is remarkably prolonged and relates primarily to movement direction: A saccade reduces the latency for subsequent movements made in the same direction and retards those in the opposite direction. Although in conventional refixation paradigms this effect cancels out, it is of particular significance in the real world--where our fixation point shifts constantly with the object of interest--and reflects a prediction of the way that real objects typically move.     

Interaction of Motility,Directional Sensing,and Polarity Modules Recreates the Behaviors of Chemotaxing Cells

Chemotaxis involves the coordinated action of separable but interrelated processes: motility, gradient sensing, and polarization. We have hypothesized that these are mediated by separate modules that account for these processes individually and that, when combined, recreate most of the behaviors of chemotactic cells. Here, we describe a mathematical model where the modules are implemented in terms of reaction-diffusion equations. Migration and the accompanying changes in cellular morphology are demonstrated in simulations using a mechanical model of the cell cortex implemented in the level set framework. The central module is an excitable network that accounts for random migration. The response to combinations of uniform stimuli and gradients is mediated by a local excitation, global inhibition module that biases the direction in which excitability is directed. A polarization module linked to the excitable network through the cytoskeleton allows unstimulated cells to move persistently and, for cells in gradients, to gradually acquire distinct sensitivity between front and back. Finally, by varying the strengths of various feedback loops in the model we obtain cellular behaviors that mirror those of genetically altered cell lines.     

Directional encoding by fish auditory systems

This paper reviews and discusses several investigations of the peripheral neural code for the directional axis of acoustical particle motion in the saccule of two fishes: goldfish (Carassius auratus) and toadfish (Opsanus tau). Most saccular afferents are directional in the manner of hair cells, having a cosine-shaped directional response pattern. The saccular sensory epithelia are orientated almost vertically in a parasagittal plane. In the horizontal plane, these epithelia are orientated obliquely with respect to the midline. Hair-cell stereocilia project perpendicularly. Thus, directional response patterns of saccular afferents tend to be orientated in azimuth parallel to the orientation of the epithelia in the head. The oblique angle of the toadfish saccule is greater than that of the goldfish, and the range of best directions in the horizontal plane for each species reflects those differing orientations. The azimuth of acoustical particle motion could be computed by comparing the relative activation of the two saccules, as is the case for the ears of most terrestrial vertebrates. The spatial patterns of saccular hair-cell orientation of most fishes thus appear to have little function in azimuthal source location, but for toadfish are probably most important for determining the elevation of monopole sources.     

Real-Time Localization of Moving Dipole Sources for Tracking Multiple Free-Swimming Weakly Electric Fish

In order to survive, animals must quickly and accurately locate prey, predators, and conspecifics using the signals they generate. The signal source location can be estimated using multiple detectors and the inverse relationship between the received signal intensity (RSI) and the distance, but difficulty of the source localization increases if there is an additional dependence on the orientation of a signal source. In such cases, the signal source could be approximated as an ideal dipole for simplification. Based on a theoretical model, the RSI can be directly predicted from a known dipole location; but estimating a dipole location from RSIs has no direct analytical solution. Here, we propose an efficient solution to the dipole localization problem by using a lookup table (LUT) to store RSIs predicted by our theoretically derived dipole model at many possible dipole positions and orientations. For a given set of RSIs measured at multiple detectors, our algorithm found a dipole location having the closest matching normalized RSIs from the LUT, and further refined the location at higher resolution. Studying the natural behavior of weakly electric fish (WEF) requires efficiently computing their location and the temporal pattern of their electric signals over extended periods. Our dipole localization method was successfully applied to track single or multiple freely swimming WEF in shallow water in real-time, as each fish could be closely approximated by an ideal current dipole in two dimensions. Our optimized search algorithm found the animal’s positions, orientations, and tail-bending angles quickly and accurately under various conditions, without the need for calibrating individual-specific parameters. Our dipole localization method is directly applicable to studying the role of active sensing during spatial navigation, or social interactions between multiple WEF. Furthermore, our method could be extended to other application areas involving dipole source localization.     

Organisms in evolution

Organisms constitute one of the most remarkable features of our living world. However, they have not yet received any accepted characterization within the framework of the evolutionary theory. The reasons for this contrast between the saliency of organisms in the biological landscape and their theoretical status are multiple and they are analyzed in the first part of this paper. Starting from this contrast, I argue for a theoretically grounded concept of organism within the framework of evolutionary theory itself. To this effect I argue that the theory of major transitions in evolution (Maynard Smith and Szathmáry 1995; Michod 1999) provides us with the theoretical basis for an understanding of the individuality of organisms and I propose a first characterization of organisms as evolutionary units structured by a division of reproductive labor among their parts. I also discuss one of the most important implications of this definition, namely that some colonial entities are to be counted as superorganisms. Finally, I show that though theoretically satisfying, this definition does not suffice in order fully to individuate the organisms and superorganisms in practice. To this end, physiology is needed, because it offers us some criteria for their individuation in ecological space. These criteria, however, are not immune to errors through misidentification and their shortcomings are discussed in the last section. In conclusion, I emphasize the positive implications of these criteria concerning the ecological significance of organisms.     

Circadian Rhythm of Pattern Formation in Populations of a Free-Swimming Organism,Tetrahymena*

SYNOPSIS. In a preliminary search for a phototactic response in Tetrahymena, we discovered instead an autotactic phenomenon of pattern formation produced by motile free-swimming cells in a dense culture. This pattern of cell aggregation is remarkably similar to the Bénard-cell patterns of classical physical chemistry, and reminiscent of the streaming patterns of motile microorganisms. In a study of light effects on the rate of pattern formation, we found that it has an endogenous circadian component, and is strongly dependent on cell concentration.     

Optimal Census by Quorum Sensing

Quorum sensing is the regulation of gene expression in response to changes in cell density. To measure their cell density, bacterial populations produce and detect diffusible molecules called autoinducers. Individual bacteria internally represent the external concentration of autoinducers via the level of monitor proteins. In turn, these monitor proteins typically regulate both their own production and the production of autoinducers, thereby establishing internal and external feedbacks. Here, we ask whether feedbacks can increase the information available to cells about their local density. We quantify available information as the mutual information between the abundance of a monitor protein and the local cell density for biologically relevant models of quorum sensing. Using variational methods, we demonstrate that feedbacks can increase information transmission, allowing bacteria to resolve up to two additional ranges of cell density when compared with bistable quorum-sensing systems. Our analysis is relevant to multi-agent systems that track an external driver implicitly via an endogenously generated signal.