Physiological adaptation in flagellar architecture improves Vibrio alginolyticus chemotaxis in complex environments

Bacteria navigate natural habitats with a wide range of mechanical properties, from the ocean to the digestive tract and soil, by rotating helical flagella like propellers. Species differ in the number, position, and shape of their flagella, but the adaptive value of these flagellar architectures is unclear. Many species traverse multiple types of environments, such as pathogens inside and outside a host. We investigate the hypothesis that flagellar architectures mediate environment-specific benefits in the marine pathogen Vibrio alginolyticus which exhibits physiological adaptation to the mechanical environment. In addition to its single polar flagellum, the bacterium produces lateral flagella in environments that differ mechanically from water. These are known to facilitate surface motility and attachment. We use high-throughput 3D bacterial tracking to quantify chemotactic performance of both flagellar architectures in three archetypes of mechanical environments relevant to the bacterium's native habitats: water, polymer solutions, and hydrogels. We reveal that lateral flagella impede chemotaxis in water by lowering the swimming speed but improve chemotaxis in both types of complex environments. Statistical trajectory analysis reveals two distinct underlying behavioral mechanisms: In viscous solutions of the polymer PVP K90, lateral flagella increase the swimming speed. In agar hydrogels, lateral flagella improve overall chemotactic performance, despite lowering the swimming speed, by preventing trapping in pores. Our findings show that lateral flagella are multipurpose tools with a wide range of applications beyond surfaces. They implicate flagellar architecture as a mediator of environment-specific benefits and point to a rich space of bacterial navigation behaviors in complex environments.

High-resolution and high-speed 3D tracking of microrobots using a fluorescent light field microscope

Background

Imaging and tracking are crucial for microrobots which navigate through complex 3D environments. Fluorescent imaging (FI) by microscope offers a high-resolution and high-sensitive imaging method to study the property of microrobots. However, conventional microscope suffers from shallow depth of field (DOF) and lacks 3D imaging capability.

Methods

We proposed a high-resolution and high-speed 3D tracking method for microrobots based on a fluorescent light field microscope (FLFM). We designed the FLFM system according to the size of a representative helical microrobot (150 μm body length, 50 μm screw diameter), and studied the system's performance. We also proposed a 3D tracking algorithm for microrobots using digital refocusing.

Results

We validated the method by simulations and built an FLFM system to perform the tracking experiments of microrobots with representative size. Our 3D tracking method achieves a 30 fps data acquisition rate, 10 μm lateral resolution and approximately 40 μm axial resolution over a volume of 1,200×1,200×326 μm³. Results indicate that the accuracy of the method can reach about 9 μm.

Conclusions

Compared with the FI by a conventional microscope, the FLFM-based method gains wider DOF and 3D imaging capability with a single-shot image. The tracking method succeeds in providing the trajectory of the microrobot with a good lateral resolution.

Sensor Fusion with Asynchronous Decentralized Processing for 3D Target Tracking with a Wireless Camera Network

We present a method to acquire 3D position measurements for decentralized target tracking with an asynchronous camera network. Cameras with known poses have fields of view with overlapping projections on the ground and 3D volumes above a reference ground plane. The purpose is to track targets in 3D space without constraining motion to a reference ground plane. Cameras exchange line-of-sight vectors and respective time tags asynchronously. From stereoscopy, we obtain the fused 3D measurement at the local frame capture instant. We use local decentralized Kalman information filtering and particle filtering for target state estimation to test our approach with only local estimation. Monte Carlo simulation includes communication losses due to frame processing delays. We measure performance with the average root mean square error of 3D position estimates projected on the image planes of the cameras. We then compare only local estimation to exchanging additional asynchronous communications using the Batch Asynchronous Filter and the Sequential Asynchronous Particle Filter for further fusion of information pairs' estimates and fused 3D position measurements, respectively. Similar performance occurs in spite of the additional communication load relative to our local estimation approach, which exchanges just line-of-sight vectors.

Daphnia magna trade-off safety from UV radiation for food

Research on diel vertical migration (DVM) is generally conducted at the population level, whereas few studies have focused on how individual animals behaviorally respond to threats when also having access to foraging opportunities. We utilized a 3D tracking platform to record the swimming behavior of Daphnia magna exposed to ultraviolet radiation (UVR) in the presence or absence of a food patch. We analyzed the vertical position of individuals before and during UVR exposure and found that the presence of food reduced the average swimming depth during both sections of the trial. Since UVR is a strong driver of zooplankton behavior, our results highlight that biotic factors, such as food patches, have profound effects on both the amplitude and the frequency of avoidance behavior. In a broader context, the trade-off between threats and food adds to our understanding of the strength and variance of behavioral responses to threats, including DVM.

In vivo dynamic 3D imaging of oocytes and embryos in the mouse oviduct

Developmental biologists have always relied on imaging to shed light on dynamic cellular events. However, processes such as mammalian fertilization and embryogenesis are generally inaccessible for direct imaging. In consequence, how the oviduct (fallopian tube) facilitates the transport of gametes and preimplantation embryos continues to be unanswered. Here we present a combination of intravital window and optical coherence tomography for dynamic, volumetric, in vivo imaging of oocytes and embryos as they are transported through the mouse oviduct. We observed location-dependent circling, oscillating, and long-distance bi-directional movements of oocytes and embryos that suggest regulatory mechanisms driving transport and question established views in the field. This in vivo imaging approach can be combined with a variety of genetic and pharmacological manipulations for live functional analysis, bringing the potential to investigate reproductive physiology in its native state.

Wang and Larina present in vivo volumetric imaging of oocytes and embryos as they are transported through the mouse oviduct with optical coherence tomography and an intravital microscopy. The study reveals complex dynamics of oocytes and embryos that suggest a regulatory role of cilia and oviductal contractions in driving the transport.

Vision-Based Hybrid Controller to Release a 4-DOF Parallel Robot from a Type II Singularity

The high accuracy and dynamic performance of parallel robots (PRs) make them suitable to ensure safe operation in human–robot interaction. However, these advantages come at the expense of a reduced workspace and the possible appearance of type II singularities. The latter is due to the loss of control of the PR and requires further analysis to keep the stiffness of the PR even after a singular configuration is reached. All or a subset of the limbs could be responsible for a type II singularity, and they can be detected by using the angle between two output twist screws (OTSs). However, this angle has not been applied in control because it requires an accurate measure of the pose of the PR. This paper proposes a new hybrid controller to release a 4-DOF PR from a type II singularity based on a real time vision system. The vision system data are used to automatically readapt the configuration of the PR by moving the limbs identified by the angle between two OTSs. This controller is intended for a knee rehabilitation PR, and the results show how this release is accomplished with smooth controlled movements where the patient’s safety is not compromised.

Mosquito Host Seeking in 3D Using a Versatile Climate-Controlled Wind Tunnel System

Future anthropogenic climate change is predicted to impact sensory-driven behaviors. Building on recent improvements in computational power and tracking technology, we have developed a versatile climate-controlled wind tunnel system, in which to study the effect of climate parameters, including temperature, precipitation, and elevated greenhouse gas levels, on odor-mediated behaviors in insects. To establish a baseline for future studies, we here analyzed the host-seeking behavior of the major malaria vector mosquito, Anopheles gambiae sensu strico, to human odor and carbon dioxide (CO₂), under tightly controlled climatic conditions, and isolated from potential background contamination by the presence of an experimenter. When presented with a combination of human foot odor and CO₂ (case study I), mosquitoes engaged in faster crosswind flight, spent more time in the filamentous odor plume and targeted the odor source more successfully. In contrast, female An. gambiae s. s. presented with different concentrations of CO₂ alone, did not display host-seeking behavior (case study II). These observations support previous findings on the role of human host-associated cues in host seeking and confirm the role of CO₂ as a synergist, but not a host-seeking cue on its own. Future studies are aimed at investigating the effect of climate change on odor-mediated behavior in mosquitoes and other insects. Moreover, the system will be used to investigate detection and processing of olfactory information in various behavioral contexts, by providing a fine-scale analysis of flight behavior.

Transfer Entropy Analysis of Interactions between Bats Using Position and Echolocation Data

Many animal species, including many species of bats, exhibit collective behavior where groups of individuals coordinate their motion. Bats are unique among these animals in that they use the active sensing mechanism of echolocation as their primary means of navigation. Due to their use of echolocation in large groups, bats run the risk of signal interference from sonar jamming. However, several species of bats have developed strategies to prevent interference, which may lead to different behavior when flying with conspecifics than when flying alone. This study seeks to explore the role of this acoustic sensing on the behavior of bat pairs flying together. Field data from a maternity colony of gray bats (Myotis grisescens) were collected using an array of cameras and microphones. These data were analyzed using the information theoretic measure of transfer entropy in order to quantify the interaction between pairs of bats and to determine the effect echolocation calls have on this interaction. This study expands on previous work that only computed information theoretic measures on the 3D position of bats without echolocation calls or that looked at the echolocation calls without using information theoretic analyses. Results show that there is evidence of information transfer between bats flying in pairs when time series for the speed of the bats and their turning behavior are used in the analysis. Unidirectional information transfer was found in some subsets of the data which could be evidence of a leader-follower interaction.

High-resolution, non-invasive animal tracking and reconstruction of local environment in aquatic ecosystems

BACKGROUND

Acquiring high resolution quantitative behavioural data underwater often involves installation of costly infrastructure, or capture and manipulation of animals. Aquatic movement ecology can therefore be limited in taxonomic range and ecological coverage.

METHODS

Here we present a novel deep-learning based, multi-individual tracking approach, which incorporates Structure-from-Motion in order to determine the 3D location, body position and the visual environment of every recorded individual. The application is based on low-cost cameras and does not require the animals to be confined, manipulated, or handled in any way.

RESULTS

Using this approach, single individuals, small heterospecific groups and schools of fish were tracked in freshwater and marine environments of varying complexity. Positional tracking errors as low as 1.09 ± 0.47 cm (RSME) in underwater areas up to 500 m2 were recorded.

CONCLUSIONS

This cost-effective and open-source framework allows the analysis of animal behaviour in aquatic systems at an unprecedented resolution. Implementing this versatile approach, quantitative behavioural analysis can be employed in a wide range of natural contexts, vastly expanding our potential for examining non-model systems and species.

Nanoscale Resolution 3D Snapshot Particle Tracking by Multifocal Microscopy

Accurate, precise, and rapid particle tracking in three dimensions remains a challenge; yet, its achievement will significantly enhance our understanding of living systems. We developed a multifocal microscopy (MFM) that allows snapshot acquisition of the imaging data, and an associated image processing approach, that together allow simultaneous 3D tracking of many fluorescent particles with nanoscale resolution. The 3D tracking was validated by measuring a known trajectory of a fluorescent bead with an axial accuracy of 19 nm through an image depth (axial range) of 3 μm and 4 nm precision of axial localization through an image depth of 4 μm. A second test obtained a uniform axial probability distribution and Brownian dynamics of beads diffusing in solution. We also validated the MFM approach by imaging fluorescent beads immobilized in gels and comparing the 3D localizations to their "ground truth" positions obtained from a confocal microscopy z-stack of finely spaced images. Finally, we applied our MFM and image processing approach to obtain 3D trajectories of insulin granules in pseudoislets of MIN6 cells to demonstrate its compatibility with complex biological systems. Our study demonstrates that multifocal microscopy allows rapid (video rate) and simultaneous 3D tracking of many "particles" with nanoscale accuracy and precision in a wide range of systems, including over spatial scales relevant to whole live cells.

Single-Particle Dynamic Light Scattering: Shapes of Individual Nanoparticles

Metallic nanoparticles (MNPs) are prevalent in modern nanotechnologies due to their unique optical properties, chemical and photostability, and ease of manipulation. In particular, many recent advances have highlighted the importance of fundamentally understanding dynamic reconfiguration in MNP morphologies and compositions. Techniques to measure the shape of a single particle are lacking, however, often requiring immobilization, extensive numerical simulations, and irreversible alterations of the particle or its environment. In this work, we introduce "single-particle dynamic light scattering" (SP-DLS) as a far-field technique capable of analyzing the shape of individual, freely diffusing MNPs. Assuming symmetric-top rotors for MNPs and passively confining them to the focal volume of a dark-field microscope for long-term observation, we directly relate polarization dynamic fluctuations in the scattered light to the relative difference between the nondegenerate axes of individual particles. Our results show remarkable agreement with transmission electron microscopy analyses of the same population and allow for unprecedented measurements of the extent of prolate or oblate asphericity of nominally spherical MNPs in solution where the current implementation affords an asphericity detection limit of ∼2.5% assuming a 10% relative error. SP-DLS should serve as a powerful, nondestructive technique for characterizing the shapes of individual MNPs and other nanostructures.

A system for the real-time tracking of operant behavior as an application of 3D camera

The capacity of 3D cameras to measure many different aspects of behavior (e.g., velocity, pattern, and posture) could contribute to the understanding of behavior. The present article describes a system for the real-time tracking of operant behavior, which is applicable to other domains of behavioral science as well. Methods for real-time 3D tracking of animal behavior are described, along with sample C++ programs. A demonstration using one zebrafish as a subject indicated that the present system successfully tracked the 3D motion of the fish. Moreover, the acquisition of a target response (i.e., approach to a corner of the aquarium) was demonstrated with the arrangement of a reinforcement contingency at the corner in the absence of a traditional, salient operandum. The system offers the capacity to characterize more completely ongoing behavior in learning tasks across a range of species than simply performance of discrete operant responses. The system also is capable of tracking multiple individuals simultaneously so it is possible both to study social interactions and arrange contingencies for engaging in social behavior. Other possible applications of 3D cameras are discussed.

A Method to Track Targets in Three-Dimensional Space Using an Imaging Sonar

This paper introduces a methodology applying an imaging sonar for three-dimensional (3D) target tracking underwater. The key process in this work involves obtaining the target’s position in space using two images of the same scene, acquired by an adaptive resolution imaging sonar (ARIS) at different positions. A data association algorithm was designed to connect the same target in image sequences. The goal of this work was to track multiple targets in 3D space. The ARIS provides sequences of bi-dimensional images from the backscattered energy according to the range and azimuth. The challenge involved determining the missing elevation information for the observed object within the sonar detection range. By computing the geometrical transformation between the acquisition planar images and the cubical space, using only the sonar information that included the posture and moving speed of the ARIS, the target’s elevation information was obtained. To evaluate the performance of the proposed method, an indoor experiment was conducted using the ARIS. On the basis of the experimental results, we confirmed that the proposed method effectively obtained the target’s position in 3D space. A moving target simulation was also conducted, and the results showed that this method was effective for moving targets. Finally, a field experiment was performed to obtain the vertical distribution and track the 3D trajectories of fish.

Measuring Microtubule Supertwist and Defects by Three-Dimensional-Force-Clamp Tracking of Single Kinesin-1 Motors

Three-dimensional (3D) nanometer tracking of single biomolecules provides important information about their biological function. However, existing microscopy approaches often have only limited spatial or temporal precision and do not allow the application of defined loads. Here, we developed and applied a high-precision 3D-optical-tweezers force clamp to track in vitro the 3D motion of single kinesin-1 motor proteins along microtubules. To provide the motors with unimpeded access to the whole microtubule lattice, we mounted the microtubules on topographic surface features generated by UV-nanoimprint lithography. Because kinesin-1 motors processively move along individual protofilaments, we could determine the number of protofilaments the microtubules were composed of by measuring the helical pitches of motor movement on supertwisted microtubules. Moreover, we were able to identify defects in microtubules, most likely arising from local changes in the protofilament number. While it is hypothesized that microtubule supertwist and defects can severely influence the function of motors and other microtubule-associated proteins, the presented method allows for the first time to fully map the microtubule lattice in situ. This mapping allows the correlation of motor-filament interactions with the microtubule fine-structure. With the additional ability to apply loads, we expect our 3D-optical-tweezers force clamp to become a valuable tool for obtaining a wide range of information from other biological systems, inaccessible by two-dimensional and/or ensemble measurements.

Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding

The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3–45 s lifetimes, the ESCRT-III assemblies accumulated 75–200 Snf7 and 15–50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission.

3D motion of vesicles along microtubules helps them to circumvent obstacles in cells

Vesicle transport is regulated at multiple levels, including regulation by scaffolding proteins and the cytoskeleton. This tight regulation is essential, since slowing or stoppage of transport can cause accumulation of obstacles and has been linked to diseases. Understanding the mechanisms by which transport is regulated as well as how motor proteins overcome obstacles can give important clues as to how these mechanisms break down in disease states. Here, we describe that the cytoskeleton architecture impacts transport in a vesicle-size-dependent manner, leading to pausing of vesicles larger than the separation of the microtubules. We further develop methods capable of following 3D transport processes in living cells. Using these methods, we show that vesicles move using two different modes along the microtubule. Off-axis motion, which leads to repositioning of the vesicle in 3D along the microtubule, correlates with the presence of steric obstacles and may help in circumventing them.

Seeing is believing: the nocturnal malarial mosquito Anopheles coluzzii responds to visual host-cues when odour indicates a host is nearby

Background

The immediate aim of our study was to analyse the behaviour of the malarial mosquito Anopheles coluzzii (An. gambiae species complex) near a human host with the ultimate aim of contributing to our fundamental understanding of mosquito host-seeking behaviour and the overall aim of identifying behaviours that could be exploited to enhance sampling and control strategies.

Results

Based on 3D video recordings of individual host-seeking females in a laboratory wind-tunnel, we found that despite being a nocturnal species, An. coluzzii is highly responsive to a visually conspicuous object, but only in the presence of host-odour. Female mosquitoes approached and abruptly veered away from a dark object, which suggests attraction to visual cues plays a role in bringing mosquitoes to the source of host odour. It is worth noting that the majority of our recorded flight tracks consisted of highly stereotyped ‘dipping’ sequences near the ground, which have been mentioned in the literature, but never before quantified.

Conclusions

Our quantitative analysis of female mosquito flight patterns within ~1.5 m of a host has revealed highly relevant information about responsiveness to visual objects and flight height that could revolutionise the efficacy of sampling traps; the capturing device of a trap should be visually conspicuous and positioned near the ground where the density of host-seeking mosquitoes would be greatest. These characteristics are not universally present in current traps for malarial mosquitoes. The characterisation of a new type of flight pattern that is prevalent in mosquitoes suggests that there is still much that is not fully understood about mosquito flight behaviour.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1609-z) contains supplementary material, which is available to authorized users.

Live Imaging of Border Cell Migration in Drosophila

Border cells are a cluster of cells that migrate from the anterior tip of the Drosophila egg chamber to the border of the oocyte in stage 9. They serve as a useful model to study collective cell migration in a native tissue environment. Here we describe a protocol for preparing ex vivo egg chamber cultures from transgenic flies expressing fluorescent proteins in the border cells, and using confocal microscopy to take a multi-positional time-lapse movie. We include an image analysis method for tracking border cell cluster dynamics as well as tracking individual cell movements.

Tracking the startle response of guppies Poecilia reticulata in three dimensions

A three-dimensional analysis of startle behaviours of guppies Poecilia reticulata, in dyads or alone, from two populations that show distinct differences in shoaling behaviour was performed. During the first few seconds after a startling stimulus, changes in behaviour, which could be critical if an individual is to survive a predatory attack, and the interactions between pairs of P. reticulata were examined. The enhanced social interactions immediately after the stimulus, as a proxy for shoaling behaviour, and their dissipation were quantified. Social (individuals tested in dyads) v. asocial (tested alone) responses to the startling stimulus were also compared. The three-dimensional reconstruction, from a two-camera, high-frame-rate tracking system allowed for the tracking of the individuals' speed and speed recovery and, for P. reticulata in dyads, interindividual distance and orientation. For the dyads from the high-predation population, the closer the individuals were to each other, the more likely they were to be parallel, but no correlation was found for the low-predation P. reticulata. The startle response of P. reticulata comprised the following sequence: freezing, darting and skittering and recovery to pre-stimulus swimming behaviour. Upon repeated encounters with the stimulus, a reduced shoaling and startle response was observed, although the rate of reduction was faster in P. reticulata from the high-predation population than those from the low-predation population. The results are discussed in light of what is known about the anti-predator behaviour of this species.

Label-Free Tracking of Single Organelle Transportation in Cells with Nanometer Precision Using a Plasmonic Imaging Technique

Imaging and tracking of nano- and micrometer-sized organelles in cells with nanometer precision is crucial for understanding cellular behaviors at the molecular scale. Because of the fast intracellular dynamic processes, the imaging and tracking method must also be fast. In addition, to ensure that the observed dynamics is relevant to the native functions, it is critical to keep the cells under their native states. Here, a plasmonics-based imaging technique is demonstrated for studying the dynamics of organelles in 3D with high localization precision (5 nm) and temporal (10 ms) resolution. The technique is label-free and can track subcellular structures in the native state of the cells. Using the technique, nanometer steps of organelle (e.g., mitochondria) transportation are observed along neurite microtubules in primary neurons, and the 3D structure of neurite microtubule bundles is reconstructed at the nanometer scale from the tracks of the moving organelles.

Barnacle cyprid motility and distribution in the water column as an indicator of the settlement-inhibiting potential of nontoxic antifouling chemistries

Testing of new coatings to control fouling frequently involves single-species laboratory bioassays. Barnacle cyprids are among the most widely used model organisms in marine biofouling research, and surfaces that inhibit their settlement are considered to be promising candidates for new coating concepts. An analysis of motility parameters (mean velocity and swimming area coefficient) and distribution of cyprids of Balanus amphitrite in different swimming regions in the vicinity of model surfaces (self-assembled monolayers) is presented. The data are correlated with the settlement preferences of cyprids on these surfaces. Cyprids were predominantly found in interfacial regions and the transition frequencies between swimming regions of different depths were determined.

High-precision, three-dimensional tracking of mouse whisker movements with optical motion capture technology

The mystacial vibrissae or whiskers in rodents are sensitive tactile hairs emerging from both sides of the face. Rats and mice actively move these whiskers during exploration. The neuronal mechanisms controlling whisker movements and the sensory representation of whisker tactile information are widely studied as a model for sensorimotor processing in mammals. Studies of the natural whisker movement patterns during exploration and tactile examination are still in their early stages. Tracking the movements of whiskers is technically challenging as they move relatively fast and are very thin, particularly in mice. Existing systems detect light-beam interruptions by the whiskers or use high-speed video to track whisker movements in one or two-dimensions. Here we describe a method for tracking the movements of mouse whiskers in three-dimensions (3D) using optical motion capture technology (OMCT). OMCT tracks the movements of small retro-reflective markers attached to whiskers of a head-fixed mouse with a spatial resolution of <0.5 mm in all 3D and a temporal resolution of 5 ms (200 fps). The system stores the 3D coordinates of the marker's trajectories onto hard disk allowing a detailed analysis of movement trajectories bilateral coordination. The described method currently uses the minimum of two tracking cameras, which requires head-fixation for reliable tracking.

Stereo vision tracking of multiple objects in complex indoor environments

This paper presents a novel system capable of solving the problem of tracking multiple targets in a crowded, complex and dynamic indoor environment, like those typical of mobile robot applications. The proposed solution is based on a stereo vision set in the acquisition step and a probabilistic algorithm in the obstacles position estimation process. The system obtains 3D position and speed information related to each object in the robot’s environment; then it achieves a classification between building elements (ceiling, walls, columns and so on) and the rest of items in robot surroundings. All objects in robot surroundings, both dynamic and static, are considered to be obstacles but the structure of the environment itself. A combination of a Bayesian algorithm and a deterministic clustering process is used in order to obtain a multimodal representation of speed and position of detected obstacles. Performance of the final system has been tested against state of the art proposals; test results validate the authors’ proposal. The designed algorithms and procedures provide a solution to those applications where similar multimodal data structures are found.