A lexical approach for identifying behavioural action sequences

Animals display characteristic behavioural patterns when performing a task, such as the spiraling of a soaring bird or the surge-and-cast of a male moth searching for a female. Identifying such recurring sequences occurring rarely in noisy behavioural data is key to understanding the behavioural response to a distributed stimulus in unrestrained animals. Existing models seek to describe the dynamics of behaviour or segment individual locomotor episodes rather than to identify the rare and transient sequences of locomotor episodes that make up the behavioural response. To fill this gap, we develop a lexical, hierarchical model of behaviour. We designed an unsupervised algorithm called “BASS” to efficiently identify and segment recurring behavioural action sequences transiently occurring in long behavioural recordings. When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts. Applied to a novel chemotaxis assay, BASS uncovers chemotactic strategies deployed by zebrafish to avoid aversive cues consisting of sequences of fast large-angle turns and burst swims. In a simulated dataset of soaring gliders climbing thermals, BASS finds the spiraling patterns characteristic of soaring behaviour. In both cases, BASS succeeds in identifying rare action sequences in the behaviour deployed by freely moving animals. BASS can be easily incorporated into the pipelines of existing behavioural analyses across diverse species, and even more broadly used as a generic algorithm for pattern recognition in low-dimensional sequential data.

A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.

Recent Developments in Bacterial Chemotaxis Analysis Based on the Microfluidic System

Bacterial motility in response to chemicals, also called bacterial chemotaxis, is a critical ability to search for the optimal environment to ensure the survival of bacterial species. Recent advances in microbiology have allowed the engineering of bacterial chemotactic properties. Conventional methods for characterizing bacterial motility are not able to fully monitor chemotactic behavior. Developments in microfluidic technology have enabled the designing of new experimental protocols in which spatiotemporal control of the cellular microenvironment can be achieved, and in which bacterial motility can be precisely and quantitatively measured and compared. This review provides an overview of recent developments of and new insights into microfluidic systems for chemotaxis assay.

A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.

A lexical approach for identifying behavioral action sequences

Animals display characteristic behavioral patterns when performing a task, such as the spiraling of a soaring bird or the surge-and-cast of a male moth searching for a female. Identifying such conserved patterns occurring rarely in noisy behavioral data is key to understanding the behavioral response to a distributed stimulus in unrestrained animals. Existing models seek to describe the dynamics of behavior or segment individual locomotor episodes rather than to identify occasional, transient irregularities that make up the behavioral response. To fill this gap, we develop a lexical, hierarchical model of behavior. We designed an unsupervised algorithm called “BASS” to efficiently identify and segment conserved behavioral action sequences transiently occurring in long behavioral recordings. When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts. Applied to a novel chemotaxis assay, BASS uncovers conserved chemotactic strategies deployed by zebrafish to avoid aversive cues consisting of sequences of fast large-angle turns and burst swims. In a simulated dataset of soaring gliders climbing thermals, BASS finds the spiralling patterns characteristic of soaring behavior. In both cases, BASS succeeds in identifying action sequences that are highly conserved but transient in the behavior deployed by freely moving animals. BASS can be easily incorporated into the pipelines of existing behavioral analyses across diverse species, and even more broadly used as a generic algorithm for pattern recognition in low-dimensional sequential data.

Cellular Response of Neutrophils to Bismuth Subnitrate and Micronized Keratin Products In Vitro

The aim of this study was to assess the effect of bismuth subnitrate and micronized keratin on bovine neutrophils in vitro. We hypothesized that recruitment and activation of neutrophils into the teat canal and sinus are the mechanisms of action of bismuth subnitrate and keratin-based teat sealant formulations. To test this, a chemotaxis assay (Experiment 1) and a myeloperoxidase (MPO) assay (Experiment 2) were conducted in vitro. Blood was sampled from 12 mid-lactation dairy cows of variable ages. Neutrophils were extracted and diluted to obtain cell suspensions of approximately 106 cells/mL. In Experiment 1, test substances were placed in a 96-well plate, separated from the cell suspension by a 3 µm pore membrane and incubated for 3 h to allow neutrophils to migrate through the membrane. In Experiment 2, neutrophils were exposed to the test products and the amount of MPO released was measured by optical density. Results showed that neutrophils were not activated by bismuth or keratin products (p < 0.05) in all of the tests performed. These results suggest that the mechanisms of action of bismuth subnitrate and keratin-based teat sealants do not rely on neutrophil recruitment and activation in the teat canal and sinus after treatment.

A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms

How bacteria navigate environmental chemical gradients has implications ranging from health to climate science. The underlying behavioral mechanisms are unknown for most species due to a lack in techniques bridging scales from individual 3D motility behavior to the statistical power required to assess the resulting performance. We present the first demonstration of such a multiscale 3D chemotaxis assay and reveal that Caulobacter crescentus chemotaxis breaks with the Escherichia coli paradigm.

Multiplexed end-point microfluidic chemotaxis assay using centrifugal alignment

We used centrifugal cell alignment to develop a multiplexed end-point chemotaxis assay scalable for high-throughput applications.