Biology subjects

Shaevitz, J. W.

Publications and source records attributed to Shaevitz, J. W..

At least 19 recordsLinked to original sources

bioRxiv2026

Learning fly pose from vision-language annotations

Animal pose estimation typically requires manual annotation of body parts to train neural networks for each new recording system or environmental condition. Here we use a general-purpose vision-language model (VLM) to generate annotations in multi-animal recordings of fruit flies (Drosophila melanogaster). Initial annotations follow written anatomical descriptions and are reviewed by an independent VLM session using neighboring video frames. On 120 held-out fly images, AI annotations had a median distance of 2.28 pixels from human labels, with 84.0% agreement within eight pixels, averaged across landmark types. The comparison included 10 landmarks, with head and eyes analyzed separately because of systematic differences in placement. Review improved agreement primarily at the feet, with the largest remaining discrepancies at positions with limited visual evidence. Visual inspection revealed cases in which the AI annotations were more anatomically accurate than those of an experienced human annotator, particularly at the feet. A convolutional network trained using SLEAP on 300 AI-annotated fly images showed similar agreement with human labels and closely reproduced the AI annotations on held-out images, with a median distance of 1.56 pixels. We also applied the procedure to recordings from another laboratory, using new AI annotations to train a separate pose network. Although VLM annotation required minutes per fly, the trained networks enabled pose estimation throughout more than 700,000 frames. These results demonstrate that VLM annotations can support fast animal pose estimation without manually labeled training images.

animal behavior and cognition↗

bioRxiv2026

Capillary bundling of microtubules by condensates

The cytoskeleton organizes the cellular interior using cytoskeletal filaments that rely on bundling, usually executed by stable and ordered crosslinking proteins. Bundling often requires protein complexes with at least two defined microtubule binding regions, as present in many molecular motors. Here, we establish a mechanism of microtubule bundling based on capillary forces, analogous to how wet hair sticks together. We show using in vitro experiments and theory that condensates can bundle microtubules through capillary forces, wherein liquid-like capillary bridges form between microtubules and adhere them together through interfacial and wetting forces. We quantify the structure and dynamics of these capillary bundles using total internal reflection fluorescence microscopy, and directly measure the charge-dependent interfacial tensions of condensates on microtubules using atomic force microscopy. Lastly, we show that these capillary bridges provide viscous resistance to motor-driven microtubule sliding that is insensitive to the bulk protein concentration. Taken together, we provide a novel mechanism for how cytoskeletal filaments bundle: through condensate-mediated capillary forces.

biophysics↗

bioRxiv2025

Active surface waves drive rippling in Myxococcus xanthus colonies

During periods of predation or starvation, populations of the gliding bacterium Myxococcus xan-thus self-organize into striking wave-like structures termed ripples. This phenomenon was thought to arise from wave collisions triggering synchronized reversals of cell motility. However, using three-dimensional microscopy, we find no evidence for such synchronization during rippling. Instead, we show that ripples are surface waves with a period of [~] 20 min, wavelength of [~] 100 {micro}m and an amplitude of 6 to 20 cell widths at the top of a thick film of cells, akin to surface waves seen in fluids. We propose a physical model of rippling as surface waves of an active nematic liquid crystal. Two key predictions of this model are verified experimentally: the rippling wavelength increases with the surface tension at the film-air interface, and it decreases with substrate stiffness, which regulates the availability of water coating the bacterial film. These findings reveal the physical basis of rippling and highlight the role of active surface waves in shaping collective biological behavior.

biophysics↗

bioRxiv2025

Soil texture regulates bacterial motility and chemotactic recruitment to plant roots

Soil microbial communities regulate critical ecological processes, including nutrient cycling, carbon sequestration, and plant growth. However, due to the opacity and structural complexity of soil, how physical constraints imposed by pore geometry in-fluence bacterial motility and chemotactic recruitment to plant roots remains poorly understood. We use a transparent soil mimic composed of cryolite grains that replicate the structural characteristics of natural soils while enabling direct visualization of bacterial dynamics. Using Escherichia coli as a model bacterium, we combine macroscopic spreading assays with microscopic tracking of cellular trajectories to characterize how soil texture affects motility across pore scales. We find that bacterial motility shifts from run-and-tumble behavior in large, open pores to frequent trapping in smaller, more confined spaces. This transition is governed by the pore size distribution and leads to reduced effective diffusivity and slower population-scale spreading. Moreover, pore-scale confinement hinders the chemotactic recruitment of bacteria to Arabidopsis thaliana roots: recruitment is robust in sandy and loamy soils but negligible in highly confining textures. Our results establish soil texture as a critical factor regulating microbial dynamics and ecological interactions in the rhizosphere. This mechanistic understanding complements genomic surveys by identifying physical confinement as an ecological filter that shapes root-associated microbiomes. These findings highlight the essential and previously underappreciated role of soil texture, suggesting new strategies for managing microbial communities to promote plant health and sustainable agriculture.

biophysics↗

bioRxiv2025

3D Agent-based modeling without chemical signaling recreatescollective behaviors seen in Myxococcus xanthus colonies

Myxococcus xanthus is a soil-dwelling bacterium that lives in dense populations of millions of cells and displays an array of collective behaviors and macroscopic patterns in response to environmental conditions. The transitions between macroscopic patterns formed by this species are driven by changes in cell motility such as increasing Peclet number via increasing cell speed and reversal period. While cells are capable of passing contact-mediated signals that can trigger reversal events, we set out to study which aspects of M. xanthus collective behavior may be driven by simple individual cell behavior changes in the absence of cell signaling. We do this through 3D agent-based simulations with a bead-spring chain model. We find that when tuned to match single cell properties, this model captures multicellular structures observed at both intermediate and global scales in M. xanthus experiments. Increasing cell speed and reversal period together (as cells do when they starve), maintains a constant overall nematic structure in the population, while significantly increasing the net flow into and out of topological defects, which drives an increased aggregation that leads to fruiting body formation during starvation.

biophysics↗

bioRxiv2024

Sensing the shape of a surface by intracellular filaments

Understanding the mechanisms that dictate the localization of cytoskeletal filaments is crucial for elucidating cell shape regulation in prokaryotes. The actin homolog MreB plays a pivotal role in maintaining the shape of many rod-shaped bacteria such as Escherichia coli by directing cell-wall synthesis according to local curvature cues. However, the basis of MreBs curvature-dependent localization has remained elusive. Here, we develop a biophysical model for the energetics of filament binding to a surface that integrates the complex interplay between filament twist and bending and the two-dimensional surface geometry. Our model predicts that the spatial localization of a filament like MreB with substantial intrinsic twist is governed by both the mean and Gaussian curvatures of the cell envelope, which strongly covary in rod-shaped cells. Using molecular dynamics simulations to estimate the mechanical properties of MreB filaments, we show that their thermodynamic preference for regions with lower mean and Gaussian curvatures matches experimental observations for physiologically relevant filament lengths of [~]50 nm. We find that the experimentally measured statistical curvature preference is maintained in the absence of filament motion and after a cycle of depolymerization, repolymerization, and membrane rebinding, indicating that equilibrium energetics can explain MreB localization. These findings provide critical insights into the physical principles underlying cytoskeletal filament localization, and suggest new design principles for synthetic shape sensing nanomaterials. Significance statementThe protein MreB, a homolog of eukaryotic actin, regulates the shape of bacteria like Escherichia coli by guiding new cell-wall insertion based on local curvature cues. However, the mechanism by which a nanometer-scale MreB filament "senses" the micron-scale curvature of the cell wall has remained a mystery. We introduce a biophysical model of the energetics of twisted and bent filaments bound to curved surfaces, which predicts that localization of filaments like MreB is sensitive to both mean and Gaussian curvature. The model captures experimentally measured curvature enrichment patterns and explains how MreB naturally localizes to saddle-shaped regions without energy-consuming processes. Beyond cell shape regulation, our work suggests design principles for synthetic systems that can sense and respond to surface shape.

biophysics↗

bioRxiv2024

Capillary interactions drive the self-organization of bacterial colonies

Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.

biophysics↗

bioRxiv2024

Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells

The crowded bacterial cytoplasm is comprised of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-2160 to +1800 e) in live Escherichia coli cells. To probe intermolecular details at spatial and temporal resolutions beyond experimental limits, we also developed a colloidal whole-cell model that explicitly represents the size and charge of cytoplasmic macromolecules and the porous structure of the bacterial nucleoid. Combining these techniques, we show that bGEMs spatially segregate by size, with small 20-nm particles enriched inside the nucleoid, and larger and/or positively charged particles excluded from this region. Localization is driven by entropic and electrostatic forces arising from cytoplasmic polydispersity, nucleoid structure, geometrical confinement, and interactions with other biomolecules including ribosomes and DNA. We observe that at the timescales of traditional single molecule tracking experiments, motion appears sub-diffusive for all particle sizes and charges. However, using computer simulations with higher temporal resolution, we find that the apparent anomalous exponents are governed by the region of the cell in which bGEMs are located. Molecular motion does not display anomalous diffusion on short time scales and the apparent sub-diffusion arises from geometrical confinement within the nucleoid and by the cell boundary.

biophysics↗

bioRxiv2023

Integrin-like adhesin CglD confers traction and stabilizes bacterial focal adhesions involved in myxobacterial gliding motility

AO_SCPLOWBSTRACTC_SCPLOWIntegrins are crucial for eukaryotic cell attachment and motility within the extracellular matrix (ECM) via focal-adhesion formation, with their evolutionary emergence important for the development of multicellularity. Intriguingly, single gliding cells of the predatory deltaproteobacterium Myxococcus xanthus form bacterial focal-adhesion (bFA) sites; therein, helically-trafficked motors become immobilized at anchored locations through Glt apparatus association with cell-surface integrin I-domain-like adhesin CglB. Using traction-force, bead-force, and total internal reflection-fluorescence microscopies combined with biochemical approaches, we herein identify the von Willebrand A domain-containing cell-surface lipoprotein CglD to be a {beta}-integrin-like outer-membrane lipoprotein that functionally associates with and anchors the trans-envelope Glt-CglB gliding apparatus, stabilizing and efficiently anchoring this assembly at bFAs. Calcium dependence governs CglD importance, consistent with its integrated ECM eukaryotic cartilage oligomeric matrix protein domains. CglD thus confers mechanosensory and mechanotransductory capabilities to the gliding apparatus, helping explain bFA-mediated trans-envelope force transduction, from inner-membrane-embedded motors to the cell surface.

microbiology↗

bioRxiv2022

NAPS: Integrating pose estimation and tag-based tracking

O_LISignificant advances in computational ethology have allowed the quantification of behavior in unprecedented detail. Tracking animals in social groups, however, remains challenging as most existing methods can either capture pose or robustly retain individual identity over time but not both. C_LIO_LITo capture finely resolved behaviors while maintaining individual identity, we built NAPS (NAPS is ArUco Plus SLEAP), a hybrid tracking framework that combines state-of-the-art, deep learning-based methods for pose estimation (SLEAP) with unique markers for identity persistence (ArUco). We show that this framework allows the exploration of the social dynamics of the common eastern bumblebee (Bombus impatiens). C_LIO_LIWe provide a stand-alone Python package for implementing this framework along with detailed documentation to allow for easy utilization and expansion. We show that NAPS can scale to long timescale experiments at a high frame rate and that it enables the investigation of detailed behavioral variation within individuals in a group. C_LIO_LIExpanding the toolkit for capturing the constituent behaviors of social groups is essential for understanding the structure and dynamics of social networks. NAPS provides a key tool for capturing these behaviors and can provide critical data for understanding how individual variation influences collective dynamics. C_LI

animal behavior and cognition↗

bioRxiv2022

Acentrosomal spindles assemble from branching microtubule nucleation near chromosomes

Microtubules are generated at centrosomes, chromosomes, and within spindles during cell division. Whereas microtubule nucleation at the centrosome is well characterized, much remains unknown about where, when, and how microtubules are nucleated at chromosomes. To address these questions, we reconstituted microtubule nucleation from purified chromosomes in meiotic Xenopus egg extract and found that chromosomes alone can form spindles. We visualized microtubule nucleation at chromosomes using total internal reflection fluorescence microscopy to find that this occurs through branching microtubule nucleation. The initial branches nucleate near and towards kinetochores, helping explain how kinetochores might be efficiently captured. By depleting molecular motors, we find that the organization of the resultant polar branched networks is consistent with a theoretical model where the effectors for branching nucleation are released by chromosomes, forming a concentration gradient around them that spatially biases branching nucleation. In the presence of motors, these branched networks are organized into multipolar spindles.

biophysics↗

bioRxiv2021

Isolation disrupts social interactions and destabilizes brain development in bumblebees

Social isolation, particularly in early life, leads to deleterious physiological and behavioral outcomes. Few studies, if any, have been able to capture the behavioral and neurogenomic consequences of early life social isolation together in a single social animal system. Here, we leverage new high-throughput tools to comprehensively investigate the impact of isolation in the bumblebee (Bombus impatiens) from behavioral, molecular, and neuroanatomical perspectives. We reared newly emerged bumblebees either in complete isolation, small groups, or in their natal colony, and then analyzed their behaviors while alone or paired with another bee. We find that when alone, individuals of each rearing condition show distinct behavioral signatures. When paired with a conspecific, bees reared in small groups or in the natal colony express similar behavioral profiles. Isolated bees, however, showed increased social interactions. To identify the neurobiological correlates of these differences, we quantified brain gene expression and measured the volumes of key brain regions for a subset of individuals from each rearing condition. Overall, we find that isolation increases social interactions and disrupts gene expression and brain development. Limited social experience in small groups is sufficient to preserve typical patterns of brain development and social behavior.

animal behavior and cognition↗

bioRxiv2021

Cerebellar contributions to a brainwide network for flexible behavior

The cerebellum regulates nonmotor behavior, but the routes by which it exerts its influence are not well characterized. Here we report a necessary role for the posterior cerebellum in guiding a reversal learning task, acting through a network of diencephalic and neocortical structures. After chemogenetic inhibition of Purkinje cells in lobule VI or crus I, mice could learn a water Y-maze task but were impaired in their ability to reverse their initial choice. To map targets of perturbation, we imaged c-Fos activation in cleared whole brains using light-sheet microscopy. Reversal learning activated diencephalic regions and associative neocortical regions. Distinctive subsets of structures were altered by perturbation of lobule VI (including thalamus and habenula) and crus I (including hypothalamus and prelimbic/orbital cortex), and both perturbations influenced anterior cingulate and infralimbic cortex. To identify functional networks, we used correlated variation in c-Fos activation within each test group. Lobule VI inactivation weakened within-thalamus correlations, while crus I inactivation divided neocortical activity into well-separated sensorimotor and associative subnetworks. In both groups, high-throughput automated analysis of complex whole-body movement revealed deficiencies in across-day adaptation to an open field environment. Neither perturbation affected gait, within-day open-field adaptation, or location preference. Taken together, these experiments reveal brainwide systems for cerebellar influence that can affect multiple flexible responses. Significance statementThe cerebellum, a part of all vertebrate brains, provides feedback to the rest of the brain on a split-second basis in response to unexpected events. The consequent changes can range from minute adjustments in movement to broad changes in behavior. In mice, we investigated cerebellar regions that help guide flexible behavior. Inactivation of these regions prevented mice from responding flexibly to a changing Y-shaped maze. We used light-sheet microscopy of c-fos protein expression to map brainwide effects of different stages of learning and cerebellar inactivation. Inactivation caused changes in thalamocortical activity that were similar in pattern, but opposite in sign, from normal learning. Lobule VI inactivation weakened thalamic functional networks, while crus I inactivation divided sensorimotor from associative neocortical networks. The same inactivation also impaired multiday adaptation to an open arena, as tracked using machine vision. Our work shows how the cerebellums influence over flexible response can be mediated by a widespread brain network.

neuroscience↗

bioRxiv2021

Pseudomonas aeruginosa differentiates substrate rigidity using retraction of type IV pili

The ability of eukaryotic cells to differentiate substrate stiffness is fundamental for many processes such as the development of stem cells into mature tissue. Here, we establish that bacteria feel their microenvironment in a similar manner. We show that Pseudomonas aeruginosa actively probes and measures substrate stiffness using type IV pili (TFP). The activity of the major virulence factor regulator Vfr is peaked with stiffness in a physiologically important range between 0.1 kPa (mucus) and 1000 kPa (cartilage). The local concentration of PilA at the base of dynamic TFP changes during extension and retraction in a surface dependent manner due to slow PilA diffusion in the cell membrane. Traction force measurements reveal that TFP retraction deforms even stiff substrates. Modeling of the measured substrate deformation and optical tweezers experiments suggest that TFP adhere at the tip only. Informed by these experimental results, we developed a model that describes substrate stiffness dependent dynamics of the polar PilA concentration which are quantitatively consistent with the transcriptional response to stiffness. Manipulating the ATPase activity of the TFP motors changes the TFP extension and retraction velocities and consequently the PilA concentration dynamics in a manner that is predictive of the experimental stiffness response. This work points to the use of a competition between PilA diffusion and TFP extension-retraction as a molecular shear rheometer. Our results highlight that stiffness sensing is a conserved property between the kingdoms of life.

microbiology↗

bioRxiv2021

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 animals 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 flys overall energy budget, suggesting potential connections between metabolism, aging, and behavior.

animal behavior and cognition↗

bioRxiv2021

Deep behavioral phenotyping of mouse autism models using open-field behavior

AO_SCPLOWBSTRACTC_SCPLOWAutism is noted for both its genotypic and phenotypic diversity. Repetitive action, resistance to environmental change, and motor disruptions vary from individual to individual. In animal models, conventional behavioral phenotyping captures such fine-scale variations incompletely. Here we use advances in computer vision and deep learning to develop a framework for characterizing mouse behavior on multiple time scales using a single popular behavioral assay, the open field test. We observed male and female C57BL/6J mice to develop a dynamic baseline of adaptive behavior over multiple days. We then examined two rodent models of autism, a cerebellum-specific model, L7-Tsc1, and a whole-brain knockout model, Cntnap2. Both Cntnap2 knockout and L7-Tsc1 mutants showed forelimb lag during gait. L7-Tsc1 mutants showed complex defects in multi-day adaptation, lacking the tendency of wild-type mice to spend progressively more time in corners of the arena. In L7-Tsc1 mutant mice, failure-to-adapt took the form of maintained ambling, turning, and locomotion, and an overall decrease in grooming. Adaptation in Cntnap2 knockout mice more broadly resembled that of wild-type. L7-Tsc1 mutant and Cntnap2 knockout mouse models showed different patterns of behavioral state occupancy. Our automated pipeline for deep phenotyping successfully captures model-specific deviations in adaptation and movement as well as differences in the detailed structure of behavioral dynamics.

neuroscience↗

bioRxiv2020

Novel mechanisms of type IV pilus regulation in Acinetobacter baylyi

Bacteria use extracellular appendages called type IV pili (T4P) for diverse behaviors including DNA uptake, surface sensing, virulence, protein secretion, and twitching motility1. Dynamic extension and retraction of T4P is essential for their function, yet little is known about the mechanisms controlling these dynamics or the extent to which their regulation is conserved across bacterial species. Here, we develop Acinetobacter baylyi as a new model to study T4P by employing a recently developed pilus labeling method2,3. Our findings overturn the current dogma that T4P extension occurs through the action of a single, highly conserved motor, PilB, by showing that T4P synthesis in A. baylyi is dependent on an additional, phylogenetically distinct motor, TfpB. Furthermore, we uncover an inhibitor of T4P extension that specifically binds to and inhibits PilB but not TfpB. These results expand our understanding of T4P regulation and highlight how inhibitors might be exploited to inhibit T4P synthesis.

microbiology↗

bioRxiv2020

SLEAP: Multi-animal pose tracking

The desire to understand how the brain generates and patterns behavior has driven rapid methodological innovation to quantify and model natural animal behavior. This has led to important advances in deep learning-based markerless pose estimation that have been enabled in part by the success of deep learning for computer vision applications. Here we present SLEAP (Social LEAP Estimates Animal Poses), a framework for multi-animal pose tracking via deep learning. This system is capable of simultaneously tracking any number of animals during social interactions and across a variety of experimental conditions. SLEAP implements several complementary approaches for dealing with the problems inherent in moving from single-to multi-animal pose tracking, including configurable neural network architectures, inference techniques, and tracking algorithms, enabling easy specialization and tuning for particular experimental conditions or performance requirements. We report results on multiple datasets of socially interacting animals (flies, bees, and mice) and describe how dataset-specific properties can be leveraged to determine the best configuration of SLEAP models. Using a high accuracy model (<2.8 px error on 95% of points), we were able to track two animals from full size 1024 x 1024 pixel frames at up to 320 FPS. The SLEAP framework comes with a sophisticated graphical user interface, multi-platform support, Colab-based GPU-free training and inference, and complete tutorials available, in addition to the datasets, at sleap.ai.

animal behavior and cognition↗