The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal's position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal's position and orientation. Custom software tracks the 3D position of the animal's head in real time and two feedback loops adjust a motorized stage and objective to keep the animal's head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal's behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion.calcium imaging | large-scale recording | behavior | C. elegans | microscopy H ow do patterns of neural activity generate an animal's behavior? To answer this question, it is important to develop new methods for recording from large populations of neurons in animals as they move and behave freely. The collective activity of many individual neurons appears to be critical for generating behaviors including arm reach in primates (1), song production in zebrafinch (2), the choice between swimming or crawling in leech (3), and decision-making in mice during navigation (4). New methods for recording from larger populations of neurons in unrestrained animals are needed to better understand neural coding of these behaviors and neural control of behavior more generally.Calcium imaging has emerged as a promising technique for recording dynamics from populations of neurons. Calcium-sensitive proteins are used to visualize changes in intracellular calcium levels in neurons in vivo which serve as a proxy for neural activity (5). To resolve the often weak fluorescent signal of an individual neuron in a dense forest of other labeled cells requires a high magnification objective with a large numerical aperture that, consequently, can image only a small field of view. Calcium imaging has traditionally been performed on animals that are stationary from anesthetization or immobilization to avoid imaging artifacts induced by animal motion. As a result, calcium imaging studies have historically focused on small brain regions in immobile animals that exhibit little or no behavior (6).No previous neurophysiological study has attained whole-brain imaging with cellular resolution in a...

Cells typically maintain characteristic shapes, but the mechanisms of self-organization for robust morphological maintenance remain unclear in most systems. Precise regulation of rod-like shape in Escherichia coli cells requires the MreB actin-like cytoskeleton, but the mechanism by which MreB maintains rod-like shape is unknown. Here, we use time-lapse and 3D imaging coupled with computational analysis to map the growth, geometry, and cytoskeletal organization of single bacterial cells at subcellular resolution. Our results demonstrate that feedback between cell geometry and MreB localization maintains rod-like cell shape by targeting cell wall growth to regions of negative cell wall curvature. Pulsechase labeling indicates that growth is heterogeneous and correlates spatially and temporally with MreB localization, whereas MreB inhibition results in more homogeneous growth, including growth in polar regions previously thought to be inert. Biophysical simulations establish that curvature feedback on the localization of cell wall growth is an effective mechanism for cell straightening and suggest that surface deformations caused by cell wall insertion could direct circumferential motion of MreB. Our work shows that MreB orchestrates persistent, heterogeneous growth at the subcellular scale, enabling robust, uniform growth at the cellular scale without requiring global organization.bacterial cytoskeleton | biophysical modeling | morphogenesis H ow cells maintain stable and defined morphologies is a fundamental question in all branches of life. Building cellularscale structures with the correct spatial architecture and mechanical properties requires that nanometer-scale proteins have the ability to detect and alter cell shape across multiple length scales. In walled organisms such as plants (1-5), fungi (6), and bacteria (7-10), morphogenesis is often achieved through an interplay between the cytoskeleton and cell wall synthesis. A central challenge in bacterial physiology is to understand the feedback between cell shape and the coordination of wall growth by the cytoskeleton.The cell wall plays a critical mechanical role in balancing turgor stress in virtually all bacteria and is both necessary and sufficient to define cell shape (11). The bacterial cell wall is a mesh-like network of sugar strands cross-linked by peptides (11,12). In rod-shaped Escherichia coli cells, cell wall growth occurs along the cylindrical body. Biophysical modeling has suggested that a random pattern of insertion cannot preserve cell shape (13), indicating that spatial coordination of the growth machinery is necessary for cell shape maintenance. Several lines of evidence demonstrate that the actin homolog MreB (14, 15) plays a major role in this coordination in most rod-shaped bacteria. The small molecule A22 depolymerizes MreB and causes a gradual transition from a rod-like to a spherical shape (15)(16)(17). This observation suggests that the disruption of MreB changes the patterning of new material insertion, although the nature of this...

The rod shape of most bacteria requires the actin homolog, MreB. Whereas MreB was initially thought to statically define rod shape, recent studies found that MreB dynamically rotates around the cell circumference dependent on cell wall synthesis. However, the mechanism by which cytoplasmic MreB is linked to extracytoplasmic cell wall synthesis and the function of this linkage for morphogenesis has remained unclear. Here we demonstrate that the transmembrane protein RodZ mediates MreB rotation by directly or indirectly coupling MreB to cell wall synthesis enzymes. Furthermore, we map the RodZ domains that link MreB to cell wall synthesis and identify mreB mutants that suppress the shape defect of ΔrodZ without restoring rotation, uncoupling rotation from rod-like growth. Surprisingly, MreB rotation is dispensable for rodlike shape determination under standard laboratory conditions but is required for the robustness of rod shape and growth under conditions of cell wall stress.bacterial cytoskeleton | bacterial cell shape | cell growth | cytoskeleton dynamics | robust rod shape B acterial cell shape is structurally determined by a rigid peptidoglycan (PG) cell wall built outside of the cytoplasmic membrane by a series of cell wall assembly enzymes (1). In many rod-shaped species these enzymes are coordinated by the actinlike protein, MreB, though the mechanism coupling this cytoplasmic protein to the extracellular cell wall enzymes and the specific functions executed by MreB have remained largely mysterious. Polymeric MreB is necessary to maintain rod-shaped cells, as inhibition of MreB polymerization or deletion of mreB cause cells to lose their rod shape. Initially, MreB was thought to form long helical structures that statically define rod shape (2, 3). Later, improved fluorescent fusion proteins and imaging methods revealed that MreB forms short polymers that dynamically rotate around the cell circumference (4-7).This circumferential rotation requires cell wall synthesis and is conserved across both Gram-negative and Gram-positive species (5-7), leading multiple groups to conclude that rotation promotes rod-shape formation. However, experimentally testing this hypothesis has proven difficult because all previous attempts to disrupt rotation have either led to cell death or massive cell shape changes, making it impossible to isolate the specific function of MreB rotation (5, 6). Furthermore, it remained difficult to explain the mechanistic link between cell wall growth and MreB rotation because of their separation in space by the cytoplasmic membrane. Here, we address both the coupling of MreB to cell wall synthesis and the function of MreB rotation. Results and DiscussionRodZ Rotates Similarly to MreB. We initially set out to identify proteins necessary for MreB rotation. In Escherichia coli, multiple proteins have been suggested to interact with MreB, including the penicillin binding protein (PBP) cell wall synthesis enzymes and RodZ, an integral membrane protein that directly binds MreB (8-11). PBP2 inhibitor...

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 156 neurons for the duration of an 8 minute recording and consistently found more neurons more quickly than manual or semi-automated approaches.

Bacteria have remarkably robust cell shape control mechanisms. For example, cell diameter only varies by a few percent across a given population. The bacterial actin homolog, MreB, is necessary for establishment and maintenance of rod shape although the detailed properties of MreB that are important for shape control remained unknown. In this study, we perturb MreB in two ways: by treating cells with the polymerization-inhibiting drug A22 and by creating point mutants in mreB. These perturbations modify the steady-state diameter of cells over a wide range, from 790 5 30 nm to 1700 5 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 three-dimensional images of MreB and cell shape. Our results indicate that the helical pitch angle of MreB inversely correlates with the cell diameter of Escherichia coli. Other correlations between MreB and cell diameter 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 organizes the cell wall growth machinery to produce a chiral cell wall structure and dictate cell diameter.

Summary Pathogenic Vibrio cholerae remains a major human health concern. V. cholerae has a characteristic curved rod morphology, with a longer outer face and a shorter inner face. Previously, the mechanism and function of this curvature were unknown. Here we identify and characterize CrvA, the first curvature determinant in V. cholerae. CrvA self-assembles into filaments at the inner face of cell curvature. Unlike traditional cytoskeletons, CrvA localizes to the periplasm, and thus could be considered a periskeletal element. To quantify how curvature forms, we developed QuASAR (Quantitative Analysis of Sacculus Architecture Remodeling), which measures subcellular peptidoglycan dynamics. QuASAR reveals that CrvA asymmetrically patterns peptidoglycan insertion rather than removal, causing more material insertion into the outer face than the inner face. Furthermore, crvA is quorum regulated and CrvA-dependent curvature increases at high cell density. Finally, we demonstrate that CrvA promotes motility in hydrogels and confers an advantage in host colonization and pathogenesis.

A bacteria's shape plays a large role in determining its mechanism of motility, energy requirements, and ability to avoid predation. Although it is a major factor in cell fitness, little is known about how cell shape is determined or maintained. These problems are made worse by a lack of accurate methods to measure cell shape in vivo, as current methods do not account for blurring artifacts introduced by the microscope. Here, we introduce a method using 2D active surfaces and forward convolution with a measured point spread function to measure the 3D shape of different strains of E. coli from fluorescent images. Using this technique, we are also able to measure the distribution of fluorescent molecules, such as polymers, on the cell surface. This quantification of the surface geometry and fluorescence distribution allow for a more precise measure of 3D cell shape and is a useful tool for measuring protein localization and the mechanisms of bacterial shape control.

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