arXiv subjects

Joshua W. Shaevitz

Publications and source records attributed to Joshua W. Shaevitz.

At least 19 recordsLinked to original sources

arXiv2024

The time is ripe to reverse engineer an entire nervous system: simulating behavior from neural interactions

Just like electrical engineers understand how microprocessors execute programs in terms of how transistor currents are affected by their inputs, neuroscientists want to understand behavior production in terms of how neuronal outputs are affected by their inputs and internal states. This dependency of neuronal outputs on inputs can be described by a state-dependent input-output (IO)-function. However, to reliably identify these IO-functions, we need to perturb each input and combinations of inputs while observing all the outputs. Here, we argue that such completeness is possible in C. elegans; a complete description that goes all the way from the activity of every neuron to predict behavior. The established and growing toolkit of optophysiology can non-invasively capture and control every neuron's activity and scale to countless experiments. The information from many such experiments can be pooled while capturing the inter-individual variability because neuronal identity and function are largely conserved across individuals. Just like electrical engineers use transistor IO-functions to simulate program execution, we argue that neuronal IO-functions could be used to simulate the impressive breadth of brain states and behaviors of C. elegans.

q-bio.NC↗

arXiv2023

Capturing continuous, long timescale behavioral changes in $\textit{Drosophila melanogaster}$ postural data

Animal behavior spans many timescales, from short, seconds-scale actions to circadian rhythms over many hours to life-long changes during aging. Most quantitative behavior studies have focused on short-timescale behaviors such as locomotion and grooming. Analysis of these data suggests there exists a hierarchy of timescales; however, the limited duration of these experiments prevents the investigation of the full temporal structure. To access longer timescales of behavior, we continuously recorded individual $\textit{Drosophila melanogaster}$ at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural data set for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct circadian patterns in all of our stereotyped behavior and also see changes in behavior over the course of the experiment as the flies weaken and die.

physics.bio-ph↗

arXiv2023

Local polar order controls mechanical stress and triggers layer formation in developing Myxococcus xanthus colonies

Colonies of the social bacterium Myxococcus xanthus go through a morphological transition from a thin colony of cells to three-dimensional droplet-like fruiting bodies as a strategy to survive starvation. The biological pathways that control the decision to form a fruiting body have been studied extensively. However, the mechanical events that trigger the creation of multiple cell layers and give rise to droplet formation remain poorly understood. By measuring cell orientation, velocity, polarity, and force with cell-scale resolution, we reveal a stochastic local polar order in addition to the more obvious nematic order. Average cell velocity and active force at topological defects agree with predictions from active nematic theory, but their fluctuations are anomalously large due to polar active forces generated by the self-propelled rod-shaped cells. We find that M. xanthus cells adjust their reversal frequency to tune the magnitude of this local polar order, which in turn controls the mechanical stresses and triggers layer formation in the colonies.

cond-mat.soft↗

arXiv2023

Long time scales, individual differences, and scale invariance in animal behavior

The explosion of data on animal behavior in more natural contexts highlights the fact that these behaviors exhibit correlations across many time scales. But there are major challenges in analyzing these data: records of behavior in single animals have fewer independent samples than one might expect; in pooling data from multiple animals, individual differences can mimic long-ranged temporal correlations; conversely long-ranged correlations can lead to an over-estimate of individual differences. We suggest an analysis scheme that addresses these problems directly, apply this approach to data on the spontaneous behavior of walking flies, and find evidence for scale invariant correlations over nearly three decades in time, from seconds to one hour. Three different measures of correlation are consistent with a single underlying scaling field of dimension $Δ= 0.180\pm 0.005$.

q-bio.NC↗

arXiv2021

Rheological dynamics of active Myxococcus xanthus populations during development

The bacterium Myxoccocus xanthus produces multicellular protective droplets called fruiting bodies when starved. These structures form initially through the active dewetting of cells into surface-bound droplets, where substantial flows of the material are needed as the fruiting bodies grow and become round. These dynamics are followed by a primitive developmental process in which the fluid-like droplets of motile cells mature into mechanically-resilient mounds of non-motile spores that can resist significant mechanical perturbation from the external environment. To date, the mechanical properties of fruiting bodies and the changes in cellular behavior that lead to maturation have not been studied. We use atomic force microscopy to probe the rheology of droplets throughout their development and find that relaxation occurs on two time scales, $\sim$1~s and $\sim$100~s. We use a two-element Maxwell-Wiechert model to quantify the viscoelastic relaxation and find that at early developmental times, cellular motility is responsible for the flow of the material but that this flow ceases when cells stop moving and become nonmotile spores. Later in development there is a dramatic increase in the modulus of the droplet as cells sporulate and the fruiting body matures, resulting in a mostly elastic structure that can protect spores from harsh environmental insult.

physics.bio-ph↗

arXiv2021

Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster

Aging affects almost all aspects of an organism -- its morphology, its physiology, its behavior. Isolating which biological mechanisms are regulating these changes, however, has proven difficult, potentially due to our inability to characterize the full repertoire of an animal's behavior across the lifespan. Using data from fruit flies (D. melanogaster) we measure the full repertoire of behaviors as a function of age. We observe a sexually dimorphic pattern of changes in the behavioral repertoire during aging. Although the stereotypy of the behaviors and the complexity of the repertoire overall remains relatively unchanged, we find evidence that the observed alterations in behavior can be explained by changing the fly's overall energy budget, suggesting potential connections between metabolism, aging, and behavior.

q-bio.QM↗

arXiv2021

Topological defects promote layer formation in Myxococcus xanthus colonies

The soil bacterium Myxococcus xanthus lives in densely packed groups that form dynamic three-dimensional patterns in response to environmental changes, such as droplet-like fruiting bodies during starvation. The development of these multicellular structures begins with the sequential formation of cell layers in a process that is poorly understood. Using confocal three-dimensional imaging, we find that motile rod-shaped M. xanthus cells are densely packed and aligned in each layer, forming an active nematic liquid crystal. Cell alignment is nearly perfect throughout the population except at point defects that carry half-integer topological charge. We observe that new cell layers preferentially form at the position of +1/2 defects, whereas holes preferentially open at -1/2 defects. To explain these findings, we model the bacterial colony as an extensile active nematic fluid with anisotropic friction. In agreement with our experimental measurements, this model predicts an influx of cells toward +1/2 defects, and an outflux of cells from -1/2 defects. Our results suggest that cell motility and mechanical cell-cell interactions are sufficient to promote the formation of cell layers at topological defects, thereby seeding fruiting bodies in colonies of M. xanthus.

physics.bio-ph↗

arXiv2021

Low-Reynolds-number, bi-flagellated Quincke swimmers with multiple forms of motion

In the limit of zero Reynolds number (Re), swimmers propel themselves exploiting a series of non-reciprocal body motions. For an artificial swimmer, a proper selection of the power source is required to drive its motion, in cooperation with its geometric and mechanical properties. Although various external fields (magnetic, acoustic, optical, etc.) have been introduced, electric fields are rarely utilized to actuate such swimmers experimentally in unbounded space. Here we use uniform and static electric fields to demonstrate locomotion of a bi-flagellated sphere at low Re via Quincke rotation. These Quincke swimmers exhibit three different forms of motion, including a self-oscillatory state due to elasto-electro-hydrodynamic interactions. Each form of motion follows a distinct trajectory in space. Our experiments and numerical results demonstrate a new method to generate, and potentially control, the locomotion of artificial flagellated swimmers.

cond-mat.soft↗

arXiv2020

Exploring a strongly non-Markovian animal behavior

A freely walking fly visits roughly 100 stereotyped states in a strongly non-Markovian sequence. To explore these dynamics, we develop a generalization of the information bottleneck method, compressing the large number of behavioral states into a more compact description that maximally preserves the correlations between successive states. Surprisingly, preserving these short time correlations with a compression into just two states captures the long ranged correlations seen in the raw data. Having reduced the behavior to a binary sequence, we describe the distribution of these sequences by an Ising model with pairwise interactions, which is the maximum entropy model that matches the two-point correlations. Matching the correlation function at longer and longer times drives the resulting model toward the Ising model with inverse square interactions and near zero magnetic field. The emergence of this statistical physics problem from the analysis real data on animal behavior is unexpected.

q-bio.NC↗

arXiv2020

A hydrodynamic instability drives protein droplet formation on microtubules to nucleate branches

Liquid-liquid phase separation occurs not only in bulk liquid, but also on surfaces. In physiology, the nature and function of condensates on cellular structures remain unexplored. Here, we study how the condensed protein TPX2 behaves on microtubules to initiate branching microtubule nucleation, which is critical for spindle assembly in eukaryotic cells. Using fluorescence, electron, and atomic force microscopies and hydrodynamic theory, we show that TPX2 on a microtubule reorganizes according to the Rayleigh-Plateau instability, like dew droplets patterning a spider web. After uniformly coating microtubules, TPX2 forms regularly spaced droplets from which branches nucleate. Droplet spacing increases with greater TPX2 concentration. A stochastic model shows that droplets make branching nucleation more efficient by confining the space along the microtubule where multiple necessary factors colocalize to nucleate a branch.

physics.bio-ph↗

arXiv2020

Localization precision in chromatic multifocal imaging

Multifocal microscopy affords fast acquisition of microscopic 3D images. This is made possible using a multifocal grating optic, however this induces chromatic dispersion effects into the point spread function impacting image quality and single-molecule localization precision. To minimize this effect, researchers use narrow-band emission filters. However, the choice of optimal emission filter bandwidth in such systems is, thus far, unclear. This work presents a theoretical framework to investigate how the localization precision of a point emitter is affected by the emission filter bandwidth. We calculate the Cramér-Rao lower bound for the 3D position of a single emitter imaged using a chromatic multifocal microscope. Results show that the localization precision improves with broader emission filter bandwidth due to increased photon throughput, despite a larger chromatic dispersion. This study provides a framework for optimally designing chromatic multifocal optics and serves as a theoretical foundation for interpretting results.

physics.optics↗

arXiv2019

Uniform intensity in multifocal microscopy using a spatial light modulator

Multifocal microscopy (MFM) offers high-speed three-dimensional imaging through the simultaneous image capture from multiple focal planes. Conventional MFM systems use a fabricated grating in the emission path for a single emission wavelength band and one set of focal plane separations. While a Spatial Light Modulator (SLM) can add more flexibility, the relatively small number of pixels in the SLM chip, cross-talk between the pixels, and aberrations in the imaging system can produce non-uniform intensity in the different axially separated image planes. We present an in situ iterative SLM calibration algorithm that overcomes these optical- and hardware-related limitations to deliver near-uniform intensity across all focal planes. Using immobilized gold nanoparticles under darkfield illumination, we demonstrate superior intensity evenness compared to current methods. We also demonstrate applicability across emission wavelengths, axial plane separations, imaging modalities, SLM settings, and different SLM manufacturers. Therefore, our microscope design and algorithms provide an alternative to fabricated gratings in MFM, as they are relatively simple and could find broad applications in the wider research community.

physics.bio-ph↗

arXiv2019

A self-driven phase transition drives Myxococcus xanthus fruiting body formation

Combining high-resolution single cell tracking experiments with numerical simulations, we show that starvation-induced fruiting body (FB) formation in Myxococcus xanthus is a phase separation driven by cells that tune their motility over time. The phase separation can be understood in terms of cell density and a dimensionless Peclet number that captures cell motility through speed and reversal frequency. Our work suggests that M. xanthus take advantage of a self-driven non-equilibrium phase transition that can be controlled at the single cell level.

physics.bio-ph↗

arXiv2017

Collective force generation by groups of migrating bacteria

From biofilm and colony formation in bacteria to wound healing and embryonic development in multicellular organisms, groups of living cells must often move collectively. While considerable study has probed the biophysical mechanisms of how eukaryotic cells generate forces during migration, little such study has been devoted to bacteria, in particular with regard to the question of how bacteria generate and coordinate forces during collective motion. This question is addressed here for the first time using traction force microscopy. We study two distinct motility mechanisms of Myxococcus xanthus, namely twitching and gliding. For twitching, powered by type-IV pilus retraction, we find that individual cells exert local traction in small hotspots with forces on the order of 50 pN. Twitching of bacterial groups also produces traction hotspots, however with amplified forces around 100 pN. Although twitching groups migrate slowly as a whole, traction fluctuates rapidly on timescales <1.5 min. Gliding, the second motility mechanism, is driven by lateral transport of substrate adhesions. When cells are isolated, gliding produces low average traction on the order of 1 Pa. However, traction is amplified in groups by a factor of ~5. Since advancing protrusions of gliding cells push on average in the direction of motion, we infer a long-range compressive load sharing among sub-leading cells. Together, these results show that the forces generated during twitching and gliding have complementary characters and both forces are collectively amplified in groups.

physics.bio-ph↗

arXiv2016

Automatically tracking neurons in a moving and deforming brain

Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must be tracked in 3D over time to accurately extract single neuron activity traces. Recordings from small invertebrates like C. elegans are especially challenging because they undergo very large brain motion and deformation during animal movement. Here we present an automated computer vision pipeline to reliably track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. 3D volumetric fluorescent images of the animal's brain are straightened, aligned and registered, and the locations of neurons in the images are found via segmentation. Each neuron is then assigned an identity using a new time-independent machine-learning approach we call Neuron Registration Vector Encoding. In this approach, non-rigid point-set registration is used to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. The way each neuron matches with the references defines a feature vector which is clustered to assign an identity to each neuron in each volume. Finally, thin-plate spline interpolation is used to correct errors in segmentation and check consistency of assigned identities. The Neuron Registration Vector Encoding approach proposed here is uniquely well suited for tracking neurons in brains undergoing large deformations. When applied to whole-brain calcium imaging recordings in freely moving C. elegans, this analysis pipeline located 150 neurons for the duration of an 8 minute recording and consistently found more neurons more quickly than manual or semi-automated approaches.

q-bio.NC↗

arXiv2016

An Unsupervised Method for Quantifying the Behavior of Interacting Individuals

Social behaviors involving the interaction of multiple individuals are complex and frequently crucial for an animal's survival. These interactions, ranging across sensory modalities, length scales, and time scales, are often subtle and difficult to quantify. Contextual effects on the frequency of behaviors become even more difficult to quantify when physical interaction between animals interferes with conventional data analysis, e.g. due to visual occlusion. We introduce a method for quantifying behavior in courting fruit flies that combines high-throughput video acquisition and tracking of individuals with recent unsupervised methods for capturing an animal's entire behavioral repertoire. We find behavioral differences in paired and solitary flies of both sexes, identifying specific behaviors that are affected by social and spatial context. Our pipeline allows for a comprehensive description of the interaction between multiple individuals using unsupervised machine learning methods, and will be used to answer questions about the depth of complexity and variance in fruit fly courtship.

physics.bio-ph↗

arXiv2016

Predictability and hierarchy in Drosophila behavior

Even the simplest of animals exhibit behavioral sequences with complex temporal dynamics. Prominent amongst the proposed organizing principles for these dynamics has been the idea of a hierarchy, wherein the movements an animal makes can be understood as a set of nested sub-clusters. Although this type of organization holds potential advantages in terms of motion control and neural circuitry, measurements demonstrating this for an animal's entire behavioral repertoire have been limited in scope and temporal complexity. Here, we use a recently developed unsupervised technique to discover and track the occurrence of all stereotyped behaviors performed by fruit flies moving in a shallow arena. Calculating the optimally predictive representation of the fly's future behaviors, we show that fly behavior exhibits multiple time scales and is organized into a hierarchical structure that is indicative of its underlying behavioral programs and its changing internal states.

physics.bio-ph↗

arXiv2015

MreB helical pitch angle determines cell diameter in Escherichia coli

Bacteria have remarkably robust cell shape control mechanisms. For example, cell diameter only varies by a few percent across a population. MreB is necessary for establishment and maintenance of rod shape although the mechanism of shape control remains unknown. We perturbed MreB in two complimentary ways to produce steady-state cell diameters over a wide range, from 790+/-30 nm to 1700+/-20 nm. To determine which properties of MreB are important for diameter control, we correlated structural characteristics of fluorescently-tagged MreB polymers with cell diameter by simultaneously analyzing 3-dimensional images of MreB and cell shape. Our results indicate that the pitch angle of MreB inversely correlates with cell diameter. Other correlations are not found to be significant. These results demonstrate that the physical properties of MreB filaments are important for shape control and support a model in which MreB dictates cell diameter and organizes cell wall growth to produce a chiral cell wall.

physics.bio-ph↗