Swimming Behavior In Response Research Articles

Relationships among the fish passage efficiency, fish swimming behavior, and hydraulic properties in a vertical‐slot fishway

AbstractThree‐dimensional hydrodynamic numerical simulation and laboratory fish‐passage experiment with juvenile grass carp (Ctenopharyngodon idella) were used to systematically estimate hydrodynamic parameters, fish passage efficiency, fish swimming behavior, and fish swimming trajectories in a vertical‐slot fishway (VSF) under five different flow discharges. The spatial‐mean time‐averaged velocity magnitude along the slot section determined passage success rate. The absolute value of the time‐averaged Reynolds‐shear‐stress component in the X–Y direction played a decisive role in selecting the swimming path. In addition, fish energy expenditure along the mean‐50% swimming route indicated that higher mainstream velocity did not necessarily signify larger energy consumption, because successfully‐migrating fish selected the relatively lower velocity zone during the migration process. Our findings for fish swimming behavior in response to velocity and turbulence can be used to develop high‐efficiency fishways for grass carps or other species with similar traits.

Early warning through video monitoring: Dissolved hydrogen sulphide (H2S) affects Atlantic salmon swimming behavior in recirculating aquaculture systems

Hydrogen sulphide (H2S) poses a major threat in marine land-based recirculating aquaculture systems (RAS) leading to acute mortality in sensitive fish species such as Atlantic salmon (Salmo salar). To date, little is known about the effects of H2S on the physiology and behavior of the species. The present study analyzed Atlantic salmon swimming behavior in response to H2S in a controlled trial. The setup consisted of two Recirculating Aquaculture Systems (RAS) in parallel. The control RAS comprised of one fish tank (800 L, 10 kg fish/m3 (≈ 70 fish)), while the exposure RAS included two fish tanks (800 L; 10 and 30 kg fish/ m3 (≈ 70 and 200 fish)). Swimming behavior was monitored via a submerged custom-built stereo camera system and an overhead surveillance camera. Fish (smolt, ≈ 114 g) were exposed once a day for 10 consecutive days to increasing H2S concentrations, from ≈ 1- up to ≈ 68 μg/L (2 μM). Continuous measurements of dissolved H2S, O2 and CO2 were taken using a real-time monitoring system. Three swimming parameters were extrapolated from video recordings using machine learning algorithms: i) speed, ii) pattern (representing whether the fish swim in a straight or zigzagging direction) and iii) dispersion (indicative of schooling behavior). The results showed that fish reacted rapidly to H2S, with a stress response characterized by faster swimming speed, erratic pattern, and loss of schooling behavior. The response was concentration-dependent, increasing linearly up to 30–40 μg/L, above which a clear threshold was observed. Notably, concentrations around 40–50 μg/L, induced significantly greater behavioral changes compared to lower concentrations, and further increases in H2S did not lead to additional changes in behavior. Swimming parameters quickly returned to basal levels, comparable to the one's prior exposure, once H2S was no longer present in the water. This study provides new insights on the sensitivity of Atlantic salmon to acute H2S exposure and highlights the potential behind the use of machine vision as an early warning tool for poor water quality in RAS.

Evaluation of Volitional Swimming Behavior of Schizothorax prenanti Using an Open-Channel Flume with Spatially Heterogeneous Turbulent Flow.

Simple SummaryA lack of information on fish volitional swimming behavior in response to various instream flow conditions may inhibit the development of an effective fishway. In this study, Schizothorax prenanti, Tchang, 1930 (S. prenanti), an endemic species in the Jinsha river basin, was tested for volitional swimming behavior in a self-designed open-channel flume. Quantified indices, describing preferred hydraulic characteristics, swimming strategies, and swimming speeds, were collected to analyze fish behavioral responses to turbulent flow. The results showed that S. prenanti preferred to select regions with low flow velocities (0.25–0.50 m/s) and turbulent kinetic energy (<0.05 m2/s2) and employed steady swimming behavior to search for flow velocities lower than the average current to conserve energy in low- and moderate-flow regimes. Additionally, the average and maximum burst speeds of S. prenanti were 2.63 ± 0.37 and 3.49 m/s, respectively. The aim of this study was to apply fish volitional swimming behavior data on the the design and optimization of fishways for specific target species, as well as a novel test method for other migratory fish species.Effective fishway design requires knowledge of fish swimming behavior in streams and channels. Appropriate tests with near-natural flow conditions are required to assess the interaction between fish behavior and turbulent flows. In this study, the volitional swimming behavior of S. prenanti was tested and quantified in an open-channel flume with three (low, moderate, and high) flow regimes. The results showed that, when confronted with alternative flow regimes, S. prenanti preferred to select regions with low flow velocities (0.25–0.50 m/s) and turbulent kinetic energy (<0.05 m2/s2) for swimming, while avoiding high-turbulence areas. Moreover, S. prenanti primarily employed steady swimming behavior to search for flow velocities lower than the average current to conserve energy in low- and moderate-flow regimes. It is hypothesized that in regions with higher flow velocities, fish may change their swimming strategy from energy conservation to time conservation. Additionally, the average and maximum burst speeds of S. prenanti were 2.63 ± 0.37 and 3.49 m/s, respectively, which were 2.21- and 2.28-fold higher than the average (1.19 m/s) and maximum (1.53 m/s) burst speeds estimated from the enclosed swim chamber for fish of similar length. This study contributes a novel research approach that provides more reliable information about fish volitional swimming behavior in natural habitats, as well as recommendations for hydraulic criteria for fishways and the identification of barriers to fish migrations.

Phototactic responses in four monogenean oncomiracidia.

Phototaxis is the common behavioral response exhibited by the oncomiracidia of various monogeneans. However, the changes in the oncomiracidial swimming behavior in response to light cues are not well understood. Here, we investigated the light responses of four monogeneans that are important pathogens in mariculture, namely Benedenia epinepheli, Benedenia seriolae, Neobenedenia girellae, and Heteraxine heterocerca. The swimming trajectory and speed of oncomiracidia of each species were assessed in a glass Petri dish with an LED light placed adjacent to it, based on three different light responses: LED light in the off position (normal swimming), LED light in the on position (phototactic behavior), and immediately (< 5s) after switching the LED light off (photophobic behavior). The oncomiracidia of all four species exhibited positive phototactic and photophobic responses; however, the change in swimming speed between each response differed among the species. The oncomiracidia of three species (B. epinepheli, N. girellae, and H. heterocerca) exhibited high swimming speed, as a phototactic response; in contrast, the oncomiracidia of B. seriolae exhibited reduced swimming speed when moving toward the light source. Benedenia epinepheli and H. heterocerca exhibited the highest swimming speed during the phototaxis phase, whereas B. seriolae and N. girellae exhibited the highest swimming speed during the photophobic phase. These light responses are considered adaptive traits to increase the chance of encountering and infecting suitable hosts in nature, and such responses could potentially be applied to the control of parasite infections in aquaculture.

Schizothorax prenanti swimming behavior in response to different flow patterns in vertical slot fishways with different slot positions

Fish swimming behavior is a critical parameter for the design of vertical slot fishways. Although Schizothorax prenanti is a significant reproductive potamodromous migratory fish species in the upper reaches of the rivers in Southwest China, its swimming behavior has not been extensively researched. Therefore, in this study, a comparative experiment was conducted in vertical slot fishways to analyze the behavior of Schizothorax prenanti in response to different flow patterns, with respect to different slot positions. The experimental model was designed with a length scale of 1:4, and a method for selecting the appropriate fish size in the scaled physical model was proposed. Based on these experiments, it was found that the typical upstream trajectories of Schizothorax prenanti are traceable to the sidewall of the pool, which are characterized by low velocity and turbulent kinetic energy (TKE). The hydraulic variables exhibited an asymmetric distribution within the vertical slot, and the fish were found to pass through the area with the lowest velocity and TKE. A flow pattern with a guide wall length-to-pool width ratio of P/B = 0.25, in which Schizothorax prenanti can immediately find the sidewall, is suitable for fish migration. Therefore, this is the recommended value for the construction of effective vertical-slot fishway structures.

TaxisPy: A Python-based software for the quantitative analysis of bacterial chemotaxis

Several species of bacteria are able to modify their swimming behavior in response to chemical attractants or repellents. Methods for the quantitative analysis of bacterial chemotaxis such as quantitative capillary assays are tedious and time-consuming. Computer-based video analysis of swimming bacteria represents a valuable method to directly assess their chemotactic response. Even though multiple studies have used this approach to elucidate various aspects of bacterial chemotaxis, to date, no computer software for such analyses is freely available. Here, we introduce TaxisPy, a Python-based software for the quantitative analysis of bacterial chemotaxis. The software comes with an intuitive graphical user interface and can be accessed easily through Docker on any operating system. Using a video of freely swimming cells as input, TaxisPy estimates the culture's average tumbling frequency over time. We demonstrate the utility of the software by assessing the effect of different concentrations of the attractant shikimate on the swimming behavior of Pseudomonas putida F1 and by capturing the adaptation process that Escherichia coli undergoes after being exposed to l-aspartate.

Differential responses of larval zebrafish to the fungicide propamocarb: Endpoints at development, locomotor behavior and oxidative stress

The fungicide propamocarb (PM) is widely used to protect cucumbers, tomatoes and other plants from pathogens. According to previous studies, PM could be detected in the aquatic system in some area. However, the toxic effects of PM on zebrafish received very limited attention. In this study, we examined the toxic effects of various concentration of PM on the endpoints of development, locomotor behavior and oxidative stress in larval zebrafish. It was observed that PM exposure delayed embryonic development, inhibited hatchability at 60 and 72 h postfertilization and increased heart rate. After PM exposure, the larval zebrafish showed abnormal free swimming behavior and the swimming behavior in response to light-dark transition, indicating that PM had the potential to induce neurotoxicity. Moreover, PM exposure also affected the enzymatic activity of acetylcholinesterase and dopamine and the transcriptional level of genes related to neurotoxicity. In addition, PM exposure not only affects catalase (CAT), glutathione peroxidase (GPX), and glutathione S-transferase (GST) activity but also affects the transcription level of various genes. We believed that PM induced oxidative stress was also a possible reason to cause neurotoxicity in larval zebrafish. In summary, our results suggested that PM could disturb the endpoints at development, locomotor behavior and oxidative stress in larval zebrafish.

Effects of embryonic propofol exposure on axonal growth and locomotor activity in zebrafish.

Prenatal propofol exposure induced neurotoxicity in the developing brains and led to persistent learning deficits in the offspring. Our goal was to use zebrafish to explore whether the decline in learning and memory was correlated with inhibition of neuronal growth after propofol exposure. Zebrafish embryos at 6 hours postfertilization (hpf) were exposed to control or 1, 2 or 4 μg/mL propofol until 48 hpf. Spontaneous locomotor activity and swimming behavior in response to dark-to-light photoperiod stimulation were studied in zebrafish larvae at 6 days postfertilization (dpf). The adaptability to repeated stimulation was used to indicate learning and memory function of larvae. Transgenic NBT line zebrafish was used to quantitate the effect of propofol on motor neuronal growth of embryos in vivo. Six dpf transgenic zebrafish larvae went through photoperiod stimulation after their neuronal length had been analyzed during the embryonic period. Our data indicate that embryonic exposure to 1, 2 and 4 μg/mL propofol had no adverse effect on spontaneous movement in zebrafish larvae, but 2 and 4 μg/mL propofol significantly impaired the learning and memory function of larvae. Moreover, propofol significantly inhibited axonal growth of motor neurons during the embryonic stage, which was correlated with learning and memory deficiency in larvae. Our findings demonstrate that the neuronal growth was correlated with learning and memory function, indicating the relevance of zebrafish as a new model to explore the mechanisms through which propofol induces long-term learning and memory impairment.

Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor

Flagellated bacteria modulate their swimming behavior in response to environmental cues through the CheA/CheY signaling pathway. In addition to responding to external chemicals, bacteria also monitor internal conditions that reflect the availability of oxygen, light, and reducing equivalents, in a process termed “energy taxis.” In Escherichia coli, the transmembrane receptor Aer is the primary energy sensor for motility. Genetic and physiological data suggest that Aer monitors the electron transport chain through the redox state of its FAD cofactor. However, direct biochemical data correlating FAD redox chemistry with CheA kinase activity have been lacking. Here, we test this hypothesis via functional reconstitution of Aer into nanodiscs. As purified, Aer contains fully oxidized FAD, which can be chemically reduced to the anionic semiquinone (ASQ). Oxidized Aer activates CheA, whereas ASQ Aer reversibly inhibits CheA. Under these conditions, Aer cannot be further reduced to the hydroquinone, in contrast to the proposed Aer signaling model. Pulse ESR spectroscopy of the ASQ corroborates a potential mechanism for signaling in that the resulting distance between the two flavin-binding PAS (Per-Arnt-Sim) domains implies that they tightly sandwich the signal-transducing HAMP domain in the kinase-off state. Aer appears to follow oligomerization patterns observed for related chemoreceptors, as higher loading of Aer dimers into nanodiscs increases kinase activity. These results provide a new methodological platform to study Aer function along with new mechanistic details into its signal transduction process.

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors.

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis.

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors.

Isolating the hydrodynamic triggers of the dive response in eastern oyster larvae

AbstractUnderstanding the behavior of larval invertebrates during planktonic and settlement phases remains an open and intriguing problem in larval ecology. Larvae modify their vertical swimming behavior in response to water column cues to feed, avoid predators, and search for settlement sites. The larval eastern oyster (Crassostrea virginica) can descend in the water column via active downward swimming, sinking, or “diving,” which is a flick and retraction of the ciliated velum to propel a transient downward acceleration. Diving may play an important role in active settlement, as diving larvae move rapidly downward in the water column and may regulate their proximity to suitable settlement sites. Alternatively, it may function as a predator‐avoidance escape mechanism. We examined potential hydrodynamic triggers to this behavior by observing larval oysters in a grid‐stirred turbulence tank. Larval swimming was recorded for two turbulence intensities and flow properties around each larva were measured using particle image velocimetry. The statistics of flow properties likely to be sensed by larvae (fluid acceleration, deformation, vorticity, and angular acceleration) were compared between diving and non‐diving larvae. Our analyses showed that diving larvae experienced high average flow accelerations in short time intervals (approximately 1–2 s) prior to dive onset, while accelerations experienced by non‐diving larvae were significantly lower. Further, the probability that larvae dove increased with the fluid acceleration they experienced. These results indicate that oyster larvae actively respond to hydrodynamic signals in the local flow field, which has ecological implications for settlement and predator avoidance.

Analysis of Skeletal Muscle Defects in Larval Zebrafish by Birefringence and Touch-evoke Escape Response Assays

Zebrafish (Danio rerio) have become a particularly effective tool for modeling human diseases affecting skeletal muscle, including muscular dystrophies, congenital myopathies, and disruptions in sarcomeric assembly, due to high genomic and structural conservation with mammals. Muscular disorganization and locomotive impairment can be quickly assessed in the zebrafish over the first few days post-fertilization. Two assays to help characterize skeletal muscle defects in zebrafish are birefringence (structural) and touch-evoked escape response (behavioral). Birefringence is a physical property in which light is rotated as it passes through ordered matter, such as the pseudo-crystalline array of muscle sarcomeres. It is a simple, noninvasive approach to assess muscle integrity in translucent zebrafish larvae early in development. Wild-type zebrafish with highly organized skeletal muscle appear very bright amidst a dark background when visualized between two polarized light filters, whereas muscle mutants have birefringence patterns specific to the primary muscular disorder they model. Zebrafish modeling muscular dystrophies, diseases characterized by myofiber degeneration followed by repeated rounds of regeneration, exhibit degenerative dark patches in skeletal muscle under polarized light. Nondystrophic myopathies are not associated with necrosis or regenerative changes, but result in disorganized myofibers and skeletal muscle weakness. Myopathic zebrafish typically show an overall reduction in birefringence, reflecting the disorganization of sarcomeres. The touch-evoked escape assay involves observing an embryo's swimming behavior in response to tactile stimulation. In comparison to wild-type larvae, mutant larvae frequently display a weak escape contraction, followed by slow swimming or other type of impaired motion that fails to propel the larvae more than a short distance. The advantage of these assays is that disease progression in the same fish type can be monitored in vivo for several days, and that large numbers of fish can be analyzed in a short time relative to higher vertebrates.

Three dimensional observation of salinity-induced changes in the swimming behavior of the estuarine calanoid copepod Pseudodiaptomus annandalei

Salinity is a major parameter in the ecology of estuarine copepods. However, its effects on swimming behavior are relatively unclear. The study of copepod swimming behavior requires a sufficient number of long and simultaneous trajectories to form a reliable basis for statistical analysis. Using a three-dimensional particle tracking technique, we observed changes in Pseudodiaptomus annandalei swimming behavior in response to a realistic salinity variation. The three adult states i.e. males, females and ovigerous females were actively swimming over the experimental range of salinity. However, an increase in salinity from 5 to 25 caused a decrease in ovigerous female speed and activity. In males and females, swimming speeds were higher at medium salinities and lower at salinities 5 and 25. Slower or faster swimming speeds were explained by variations in frequencies of resting periods (below 1mm/s), slow swimming (between 1 and 8mm/s) and fast swimming (above 8mm/s). Swimming state residence times varied in concordance. Longer durations of resting periods were observed at slow swimming speeds, together with shorter durations of periods of slow and fast swimming. The degree of space occupation of trajectories was estimated through their fractal dimension and was unaffected by salinity. The relative importance of extreme events i.e. large amplitudes of velocity and acceleration indicated intermittency in behavior. Overall, our results show an optimal salinity for swimming activity and highlight differences between adult states. Results add insight into how salinity may influence copepod swimming behavior. Redirection of energy from swimming to osmoregulation when salinity diverges from the optimal range of the species is a possible explanation. Further tests on total metabolism are warranted to confirm this hypothesis.

Computational and Experimental Analyses Reveal the Essential Roles of Interdomain Linkers in the Biological Function of Chemotaxis Histidine Kinase CheA

A two-component signal transduction pathway underlies the phenomenon of bacterial chemotaxis that allows bacteria to modulate their swimming behavior in response to environmental stimuli. The dimeric five-domain histidine kinase, CheA, plays a central role in the pathway, converting sensory signals to a chemical signal via trans-autophosphorylation between the P1 and P4 domains. This autophosphorylation is regulated via the networked interactions among the P5 domain of CheA, CheW, and chemoreceptors. Despite a wealth of structural information about these components and their interactions, the key question of how the kinase activity of the catalytic P4 domain is regulated by the signal received from the regulatory P5 domain remains poorly understood. We performed replica exchange molecular dynamics simulations on the CheA kinase core and found that while individual domains maintained their structural fold, these domains exhibited a variety of interdomain orientations due to two interdomain linkers. A partially populated conformation that adopts an interdomain arrangement is suitable for building a functional ternary complex. An allosteric network derived from this structural model implies critical roles for two linkers in CheA's activity. The biochemical and biological functions of these linkers were assigned via a series of biochemical and genetic assays that show the P4-P5 linker controls the activation of CheA and the P3-P4 linker controls both the basal autophosphorylation activity and the activation of CheA. These results reveal the functional dependence between the two linkers and the essential role of the linkers in passing signal information from one domain to another.

CheA–Receptor Interaction Sites in Bacterial Chemotaxis

In bacterial chemotaxis, transmembrane chemoreceptors, the CheA histidine kinase, and the CheW coupling protein assemble into signaling complexes that allow bacteria to modulate their swimming behavior in response to environmental stimuli. Among the protein-protein interactions in the ternary complex, CheA-CheW and CheW-receptor interactions were studied previously, whereas CheA-receptor interaction has been less investigated. Here, we characterize the CheA-receptor interaction in Thermotoga maritima by NMR spectroscopy and validate the identified receptor binding site of CheA in Escherichia coli chemotaxis. We find that CheA interacts with a chemoreceptor in a manner similar to that of CheW, and the receptor binding site of CheA's regulatory domain is homologous to that of CheW. Collectively, the receptor binding sites in the CheA-CheW complex suggest that conformational changes in CheA are required for assembly of the CheA-CheW-receptor ternary complex and CheA activation.

BDE-47 disrupts axonal growth and motor behavior in developing zebrafish

Polybrominated diphenyl ethers (PBDEs) are ubiquitous environmental pollutants detected in a wide variety of environmental matrixes and pose a significant public health concern. 2,2′,4,4′-Tetrabromodiphenyl ether (BDE-47) is one of the most predominant PBDE congeners in environmental media, biota and human tissues. However, few studies have explored the BDE-47 developmental neurotoxicity and underlying mechanisms. In this study, zebrafish (Danio rerio) embryos were waterborne exposed to BDE-47 at 1.25, 5, 20μM starting from 6h post-fertilization (hpf). Motor behavior development and swimming behavior in response to light-to-dark photoperiod stimulation were studied at various developmental stages. Our data indicate that BDE-47 exposure significantly affected spontaneous movement, decreased touch response and free swimming speed, altered larvae swimming behavior in response to light stimulation in developing zebrafish. Consistent with these motor deficits, BDE-47 significantly inhibited axonal growth of primary and secondary motor neurons during the early developmental stages, suggesting the functional relevance of structural changes. Our findings demonstrate that the altered patterns of neuronal connectivity may contribute to motor behavior deficits, indicating the relevance of zebrafish as a model for studying toxicant developmental neurotoxicity.

Disruption of Eaat2b, a glutamate transporter, results in abnormal motor behaviors in developing zebrafish

Analysis of zebrafish mutants that have defects in motor behavior can allow entrée into the hindbrain and spinal cord networks that control locomotion. Here, we report that zebrafish techno trousers ( tnt) locomotor mutants harbor a mutation in slc1a2b, which encodes Eaat2b, a plasma membrane glutamate transporter. We used tnt mutants to explore the effects of impaired glutamate transporter activity on locomotor network function. Wild-type larvae perform robust swimming behavior in response to touch stimuli at two and four days after fertilization. In contrast, tnt mutant larvae demonstrate aberrant, exaggerated body bends beginning two days after fertilization and they are almost paralyzed four days after fertilization. We show that slc1a2b is expressed in glial cells in a dynamic fashion across development, which may explain the abnormal sequence of motor behaviors demonstrated by tnt mutants. We also show that tnt larvae demonstrate enhanced excitation of neurons, consistent with the predicted effects of excessive glutamate. These findings illustrate the dynamic regulation and importance of glutamate transporters during development. Since glutamate toxicity caused by EAAT2 dysfunction is thought to promote several different neurological disorders in humans, including epilepsy and neurodegenerative diseases, tnt mutants hold promise as a new tool to better understand these pathologies.

An Agent-Based Model of Signal Transduction in Bacterial Chemotaxis

We report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimuli. Agent-based modeling is a stochastic and bottom-up approach, where individual components of the modeled system are explicitly represented, and bulk properties emerge from their movement and interactions. We present the Chemoscape model: a collection of agents representing both fixed membrane-embedded and mobile cytoplasmic proteins, each governed by a set of rules representing knowledge or hypotheses about their function. When the agents were placed in a simulated cellular space and then allowed to move and interact stochastically, the model exhibited many properties similar to the biological system including adaptation, high signal gain, and wide dynamic range. We found the agent based modeling approach to be both powerful and intuitive for testing hypotheses about biological properties such as self-assembly, the non-linear dynamics that occur through cooperative protein interactions, and non-uniform distributions of proteins in the cell. We applied the model to explore the role of receptor type, geometry and cooperativity in the signal gain and dynamic range of the chemotactic response to environmental stimuli. The model provided substantial qualitative evidence that the dynamic range of chemotactic response can be traced to both the heterogeneity of receptor types present, and the modulation of their cooperativity by their methylation state.

Impacts of biochemical cues on horizontal swimming behavior of individual crab larvae

To determine if larval crabs alter their horizontal swimming behavior in response to biochemical cues in the water, fiddler crab (Uca pugnax) and blue crab (Callinectes sapidus) megalopae were video recorded in a laminar-flow flume while putative cues were introduced and allowed to establish a gradient in the flow field. Changes in horizontal orientation, distribution, and swimming velocity were observed for six different cue treatments. Overall results show that crab megalopae can detect biochemical cues in ambient water and that they adjust their horizontal swimming behavior in response to these cues. The dominant response was a change in swimming velocity in the presence of a cue. While this response may affect the dynamics of larval patches, it is not clear if swimming in the horizontal plane has a substantial effect on the spatial aggregation of the larvae in the field.