Xist ribonucleoproteins promote female sex-biased autoimmunity.

Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.

Müller Glial Cell-Dependent Regeneration of the Retina in Zebrafish and Mice.

Sight is one of our most precious senses. People fear losing their sight more than any other disability. Thus, restoring sight to the blind is an important goal of vision scientists. Proregenerative species, such as zebrafish, provide a system for studying endogenous mechanisms underlying retina regeneration. Nonregenerative species, such as mice, provide a system for testing strategies for stimulating retina regeneration. Key to retina regeneration in zebrafish and mice is the Müller glial cell, a malleable cell type that is amenable to a variety of regenerative strategies. Here, we review cellular and molecular mechanisms used by zebrafish to regenerate a retina, as well as the application of these mechanisms, and other strategies to stimulate retina regeneration in mice. Although our focus is on Müller glia (MG), niche components and their impact on MG reprogramming are also discussed.

Live-cell imaging reveals kinetic determinants of quality control triggered by ribosome stalling.

Translation of problematic mRNA sequences induces ribosome stalling, triggering quality-control events, including ribosome rescue and nascent polypeptide degradation. To define the timing and regulation of these processes, we developed a SunTag-based reporter to monitor translation of a problematic sequence (poly[A]) in real time on single mRNAs. Although poly(A)-containing mRNAs undergo continuous translation over the timescale of minutes to hours, ribosome load is increased by ∼3-fold compared to a control, reflecting long queues of ribosomes extending far upstream of the stall. We monitor the resolution of these queues in real time and find that ribosome rescue is very slow compared to both elongation and termination. Modulation of pause strength, collision frequency, and the collision sensor ZNF598 reveals how the dynamics of ribosome collisions and their recognition facilitate selective targeting for quality control. Our results establish that slow clearance of stalled ribosomes allows cells to distinguish between transient and deleterious stalls.

Capillary oxygen regulates demand-supply coupling by triggering connexin40-mediated conduction: Rethinking the metabolic hypothesis.

Coupling red blood cell (RBC) supply to O2 demand is an intricate process requiring O2 sensing, generation of a stimulus, and signal transduction that alters upstream arteriolar tone. Although actively debated, this process has been theorized to be induced by hypoxia and to involve activation of endothelial inwardly rectifying K+ channels (KIR) 2.1 by elevated extracellular K+ to trigger conducted hyperpolarization via connexin40 (Cx40) gap junctions to upstream resistors. This concept was tested in resting healthy skeletal muscle of Cx40-/- and endothelial KIR2.1-/- mice using state-of-the-art live animal imaging where the local tissue O2 environment was manipulated using a custom gas chamber. Second-by-second capillary RBC flow responses were recorded as O2 was altered. A stepwise drop in PO2 at the muscle surface increased RBC supply in capillaries of control animals while elevated O2 elicited the opposite response; capillaries were confirmed to express Cx40. The RBC flow responses were rapid and tightly coupled to O2; computer simulations did not support hypoxia as a driving factor. In contrast, RBC flow responses were significantly diminished in Cx40-/- mice. Endothelial KIR2.1-/- mice, on the other hand, reacted normally to O2 changes, even when the O2 challenge was targeted to a smaller area of tissue with fewer capillaries. Conclusively, microvascular O2 responses depend on coordinated electrical signaling via Cx40 gap junctions, and endothelial KIR2.1 channels do not initiate the event. These findings reconceptualize the paradigm of blood flow regulation in skeletal muscle and how O2 triggers this process in capillaries independent of extracellular K+.

Geometric phase predicts locomotion performance in undulating living systems across scales.

Self-propelling organisms locomote via generation of patterns of self-deformation. Despite the diversity of body plans, internal actuation schemes and environments in limbless vertebrates and invertebrates, such organisms often use similar traveling waves of axial body bending for movement. Delineating how self-deformation parameters lead to locomotor performance (e.g. speed, energy, turning capabilities) remains challenging. We show that a geometric framework, replacing laborious calculation with a diagrammatic scheme, is well-suited to discovery and comparison of effective patterns of wave dynamics in diverse living systems. We focus on a regime of undulatory locomotion, that of highly damped environments, which is applicable not only to small organisms in viscous fluids, but also larger animals in frictional fluids (sand) and on frictional ground. We find that the traveling wave dynamics used by mm-scale nematode worms and cm-scale desert dwelling snakes and lizards can be described by time series of weights associated with two principal modes. The approximately circular closed path trajectories of mode weights in a self-deformation space enclose near-maximal surface integral (geometric phase) for organisms spanning two decades in body length. We hypothesize that such trajectories are targets of control (which we refer to as "serpenoid templates"). Further, the geometric approach reveals how seemingly complex behaviors such as turning in worms and sidewinding snakes can be described as modulations of templates. Thus, the use of differential geometry in the locomotion of living systems generates a common description of locomotion across taxa and provides hypotheses for neuromechanical control schemes at lower levels of organization.

Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors.

Aberrant translation initiation at non-AUG start codons is associated with multiple cancers and neurodegenerative diseases. Nevertheless, how non-AUG translation may be regulated differently from canonical translation is poorly understood. Here, we used start codon-specific reporters and ribosome profiling to characterize how translation from non-AUG start codons responds to protein synthesis inhibitors in human cells. These analyses surprisingly revealed that translation of multiple non-AUG-encoded reporters and the endogenous GUG-encoded DAP5 (eIF4G2/p97) mRNA is resistant to cycloheximide (CHX), a translation inhibitor that severely slows but does not completely abrogate elongation. Our data suggest that slowly elongating ribosomes can lead to queuing/stacking of scanning preinitiation complexes (PICs), preferentially enhancing recognition of weak non-AUG start codons. Consistent with this model, limiting PIC formation or scanning sensitizes non-AUG translation to CHX. We further found that non-AUG translation is resistant to other inhibitors that target ribosomes within the coding sequence but not those targeting newly initiated ribosomes. Together, these data indicate that ribosome queuing enables mRNAs with poor initiation context-namely, those with non-AUG start codons-to be resistant to pharmacological translation inhibitors at concentrations that robustly inhibit global translation.

Mechanistic framework for reduced-order models in soft materials: Application to three-dimensional granular intrusion.

Soft materials often display complex behaviors that transition through apparent solid- and fluid-like regimes. While a growing number of microscale simulation methods exist for these materials, reduced-order models that encapsulate the macroscale physics are often desired to predict how external bodies interact with soft media. Such an approach could provide direct insights in diverse situations from impact and penetration problems to locomotion over natural terrains. This work proposes a systematic program to develop three-dimensional (3D) reduced-order models for soft materials from a fundamental basis using continuum symmetries and rheological principles. In particular, we derive a reduced-order, 3D resistive force theory (3D-RFT), which is capable of accurately and quickly predicting the resistive stress distribution on arbitrary-shaped bodies intruding through granular media. Aided by a continuum description of the granular medium, a comprehensive set of spatial symmetry constraints, and a limited amount of reference data, we develop a self-consistent and accurate 3D-RFT. We verify the model capabilities in a wide range of cases and show that it can be quickly recalibrated to different media and intruder surface types. The premises leading to 3D-RFT anticipate application to other soft materials with strongly hyperlocalized intrusion behavior.

Self-propulsion via slipping: Frictional swimming in multilegged locomotors.

Locomotion is typically studied either in continuous media where bodies and legs experience forces generated by the flowing medium or on solid substrates dominated by friction. In the former, centralized whole-body coordination is believed to facilitate appropriate slipping through the medium for propulsion. In the latter, slip is often assumed minimal and thus avoided via decentralized control schemes. We find in laboratory experiments that terrestrial locomotion of a meter-scale multisegmented/legged robophysical model resembles undulatory fluid swimming. Experiments varying waves of leg stepping and body bending reveal how these parameters result in effective terrestrial locomotion despite seemingly ineffective isotropic frictional contacts. Dissipation dominates over inertial effects in this macroscopic-scaled regime, resulting in essentially geometric locomotion on land akin to microscopic-scale swimming in fluids. Theoretical analysis demonstrates that the high-dimensional multisegmented/legged dynamics can be simplified to a centralized low-dimensional model, which reveals an effective resistive force theory with an acquired viscous drag anisotropy. We extend our low-dimensional, geometric analysis to illustrate how body undulation can aid performance in non-flat obstacle-rich terrains and also use the scheme to quantitatively model how body undulation affects performance of biological centipede locomotion (the desert centipede Scolopendra polymorpha) moving at relatively high speeds (∼0.5 body lengths/sec). Our results could facilitate control of multilegged robots in complex terradynamic scenarios.

Coordinating tiny limbs and long bodies: Geometric mechanics of lizard terrestrial swimming.

Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body-limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards (Brachymeles and Lerista) and laboratory studies of fully limbed lizards (Uma scoparia and Sceloporus olivaceus) and a snake (Chionactis occipitalis) reveal that body-wave dynamics can be described by a combination of standing and traveling waves; the ratio of the amplitudes of these components is inversely related to the degree of limb reduction and body elongation. The geometric theory (which replaces laborious calculation with diagrams) helps explain our observations, predicting that the advantage of traveling-wave body undulations (compared with a standing wave) emerges when the dominant thrust-generation mechanism arises from the body rather than the limbs and reveals that such soil-dwelling lizards propel via "terrestrial swimming" like sand-swimming lizards and snakes. We test our hypothesis by inducing the use of traveling waves in stereotyped lizards via modulating the ground-penetration resistance. Study of a limbed/undulatory robophysical model demonstrates that a traveling wave is beneficial when propulsion is generated by body-environment interaction. Our models could be valuable in understanding functional constraints on the evolutionary processes of elongation and limb reduction as well as advancing robot designs.

Vegf signaling between Müller glia and vascular endothelial cells is regulated by immune cells and stimulates retina regeneration.

In the zebrafish retina, Müller glia (MG) can regenerate retinal neurons lost to injury or disease. Even though zebrafish MG share structure and function with those of mammals, only in zebrafish do MG function as retinal stem cells. Previous studies suggest dying neurons, microglia/macrophage, and T cells contribute to MG's regenerative response [White et al., Proc. Natl. Acad. Sci. U.S.A. 114, E3719 (2017); Hui et al., Dev. Cell 43, 659 (2017)]. Although MG end-feet abut vascular endothelial (VE) cells to form the blood-retina barrier, a role for VE cells in retina regeneration has not been explored. Here, we report that MG-derived Vegfaa and Pgfa engage Flt1 and Kdrl receptors on VE cells to regulate MG gene expression, Notch signaling, proliferation, and neuronal regeneration. Remarkably, vegfaa and pgfa expression is regulated by microglia/macrophages, while Notch signaling in MG is regulated by a Vegf-dll4 signaling system in VE cells. Thus, our studies link microglia/macrophage, MG, and VE cells in a multicomponent signaling pathway that controls MG reprogramming and proliferation.

Field-mediated locomotor dynamics on highly deformable surfaces.

Studies of active matter-systems consisting of individuals or ensembles of internally driven and damped locomotors-are of interest to physicists studying nonequilibrium dynamics, biologists interested in individuals and swarm locomotion, and engineers designing robot controllers. While principles governing active systems on hard ground or within fluids are well studied, another class of systems exists at deformable interfaces. Such environments can display mixes of fluid-like and elastic features, leading to locomotor dynamics that are strongly influenced by the geometry of the surface, which, in itself, can be a dynamical entity. To gain insight into principles by which locomotors are influenced via a deformation field alone (and can influence other locomotors), we study robot locomotion on an elastic membrane, which we propose as a model of active systems on highly deformable interfaces. As our active agent, we use a differential driven wheeled robotic vehicle which drives straight on flat homogeneous surfaces, but reorients in response to environmental curvature. We monitor the curvature field-mediated dynamics of a single vehicle interacting with a fixed deformation as well as multiple vehicles interacting with each other via local deformations. Single vehicles display precessing orbits in centrally deformed environments, while multiple vehicles influence each other by local deformation fields. The active nature of the system facilitates a differential geometry-inspired mathematical mapping from the vehicle dynamics to those of test particles in a fictitious "spacetime," allowing further understanding of the dynamics and how to control agent interactions to facilitate or avoid multivehicle membrane-induced cohesion.

Robotic swimming in curved space via geometric phase.

Locomotion by shape changes or gas expulsion is assumed to require environmental interaction, due to conservation of momentum. However, as first noted in [J. Wisdom, Science 299, 1865-1869 (2003)] and later in [E. Guéron, Sci. Am. 301, 38-45 (2009)] and [J. Avron, O. Kenneth, New J. Phys, 8, 68 (2006)], the noncommutativity of translations permits translation without momentum exchange in either gravitationally curved spacetime or the curved surfaces encountered by locomotors in real-world environments. To realize this idea which remained unvalidated in experiments for almost 20 y, we show that a precision robophysical apparatus consisting of motors driven on curved tracks (and thereby confined to a spherical surface without a solid substrate) can self-propel without environmental momentum exchange. It produces shape changes comparable to the environment's inverse curvatures and generates movement of [Formula: see text] cm per gait. While this simple geometric effect predominates over short time, eventually the dissipative (frictional) and conservative forces, ubiquitous in real systems, couple to it to generate an emergent dynamics in which the swimming motion produces a force that is counter-balanced against residual gravitational forces. In this way, the robot both swims forward without momentum and becomes fixed in place with a finite momentum that can be released by ceasing the swimming motion. We envision that our work will be of use in a broad variety of contexts, such as active matter in curved space and robots navigating real-world environments with curved surfaces.

Robots as models of evolving systems.

Experimental robobiological physics can bring insights into biological evolution. We present a development of hybrid analog/digital autonomous robots with mutable diploid dominant/recessive 6-byte genomes. The robots are capable of death, rebirth, and breeding. We map the quasi-steady-state surviving local density of the robots onto a multidimensional abstract "survival landscape." We show that robot death in complex, self-adaptive stress landscapes proceeds by a general lowering of the robotic genetic diversity, and that stochastically changing landscapes are the most difficult to survive.

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression.

OBJECTIVES: Systemic Lupus Erythematosus is a complex autoimmune disease that leads to significant worsening of quality of life and mortality. Flares appear unpredictably during the disease course and therapies used are often only partially effective. These challenges are mainly due to the molecular heterogeneity of the disease, and in this context, personalized medicine-based approaches offer major promise. With this work we intended to advance in that direction by developing MyPROSLE, an omic-based analytical workflow for measuring the molecular portrait of individual patients to support clinicians in their therapeutic decisions. METHODS: Immunological gene-modules were used to represent the transcriptome of the patients. A dysregulation score for each gene-module was calculated at the patient level based on averaged z-scores. Almost 6100 Lupus and 750 healthy samples were used to analyze the association among dysregulation scores, clinical manifestations, prognosis, flare and remission events and response to Tabalumab. Machine learning-based classification models were built to predict around 100 different clinical parameters based on personalized dysregulation scores. RESULTS: MyPROSLE allows to molecularly summarize patients in 206 gene-modules, clustered into nine main lupus signatures. The combination of these modules revealed highly differentiated pathological mechanisms. We found that the dysregulation of certain gene-modules is strongly associated with specific clinical manifestations, the occurrence of relapses or the presence of long-term remission and drug response. Therefore, MyPROSLE may be used to accurately predict these clinical outcomes. CONCLUSIONS: MyPROSLE (https://myprosle.genyo.es) allows molecular characterization of individual Lupus patients and it extracts key molecular information to support more precise therapeutic decisions.

Colloidal robotics.

Robots have components that work together to accomplish a task. Colloids are particles, usually less than 100 µm, that are small enough that they do not settle out of solution. Colloidal robots are particles capable of functions such as sensing, computation, communication, locomotion and energy management that are all controlled by the particle itself. Their design and synthesis is an emerging area of interdisciplinary research drawing from materials science, colloid science, self-assembly, robophysics and control theory. Many colloidal robot systems approach synthetic versions of biological cells in autonomy and may find ultimate utility in bringing these specialized functions to previously inaccessible locations. This Perspective examines the emerging literature and highlights certain design principles and strategies towards the realization of colloidal robots.

Laser Doppler Fluximetry in Cutaneous Vasculature: Methods for Data Analyses.

INTRODUCTION: Acquisition of a deeper understanding of microvascular function across physiological and pathological conditions can be complicated by poor accessibility of the vascular networks and the necessary sophistication or intrusiveness of the equipment needed to acquire meaningful data. Laser Doppler fluximetry (LDF) provides a mechanism wherein investigators can readily acquire large amounts of data with minor inconvenience for the subject. However, beyond fairly basic analyses of erythrocyte perfusion (fluximetry) data within the cutaneous microcirculation (i.e., perfusion at rest and following imposed challenges), a deeper understanding of microvascular perfusion requires a more sophisticated approach that can be challenging for many investigators. METHODS: This manuscript provides investigators with clear guidance for data acquisition from human subjects for full analysis of fluximetry data, including levels of perfusion, single- and multiscale Lempel-Ziv complexity (LZC) and sample entropy (SampEn), and wavelet-based analyses for the major physiological components of the signal. Representative data and responses are presented from a recruited cohort of healthy volunteers, and computer codes for full data analysis (MATLAB) are provided to facilitate efforts by interested investigators. CONCLUSION: It is anticipated that these materials can reduce the challenge to investigators integrating these approaches into their research programs and facilitate translational research in cardiovascular science.

Probing Hydrodynamic Fluctuation-Induced Forces with an Oscillating Robot.

We study the dynamics of an oscillating, free-floating robot that generates radially expanding gravity-capillary waves at a fluid surface. In open water, the device does not self-propel; near a rigid boundary, it can be attracted or repelled. Visualization of the wave field dynamics reveals that when near a boundary, a complex interference of generated and reflected waves induces a wave amplitude fluctuation asymmetry. Attraction increases as wave frequency increases or robot-boundary separation decreases. Theory on confined gravity-capillary wave radiation dynamics developed by Hocking in the 1980s captures the observed parameter dependence due to these "Hocking fields." The flexibility of the robophysical system allows detailed characterization and analysis of locally generated nonequilibrium fluctuation-induced forces [M. Kardar and R. Golestanian, Rev. Mod. Phys. 71, 1233 (1999)RMPHAT0034-686110.1103/RevModPhys.71.1233].

Collective dynamics in entangled worm and robot blobs.

Living systems at all scales aggregate in large numbers for a variety of functions including mating, predation, and survival. The majority of such systems consist of unconnected individuals that collectively flock, school, or swarm. However, some aggregations involve physically entangled individuals, which can confer emergent mechanofunctional material properties to the collective. Here, we study in laboratory experiments and rationalize in theoretical and robophysical models the dynamics of physically entangled and motile self-assemblies of 1-cm-long California blackworms (Lumbriculus variegatus, Annelida: Clitellata: Lumbriculidae). Thousands of individual worms form braids with their long, slender, and flexible bodies to make a three-dimensional, soft, and shape-shifting "blob." The blob behaves as a living material capable of mitigating damage and assault from environmental stresses through dynamic shape transformations, including minimizing surface area for survival against desiccation and enabling transport (negative thermotaxis) from hazardous environments (like heat). We specifically focus on the locomotion of the blob to understand how an amorphous entangled ball of worms can break symmetry to move across a substrate. We hypothesize that the collective blob displays rudimentary differentiation of function across itself, which when combined with entanglement dynamics facilitates directed persistent blob locomotion. To test this, we develop a robophysical model of the worm blobs, which displays emergent locomotion in the collective without sophisticated control or programming of any individual robot. The emergent dynamics of the living functional blob and robophysical model can inform the design of additional classes of adaptive mechanofunctional living materials and emergent robotics.

Functional consequences of convergently evolved microscopic skin features on snake locomotion.

The small structures that decorate biological surfaces can significantly affect behavior, yet the diversity of animal-environment interactions essential for survival makes ascribing functions to structures challenging. Microscopic skin textures may be particularly important for snakes and other limbless locomotors, where substrate interactions are mediated solely through body contact. While previous studies have characterized ventral surface features of some snake species, the functional consequences of these textures are not fully understood. Here, we perform a comparative study, combining atomic force microscopy measurements with mathematical modeling to generate predictions that link microscopic textures to locomotor performance. We discover an evolutionary convergence in the ventral skin structures of a few sidewinding specialist vipers that inhabit sandy deserts-an isotropic texture that is distinct from the head-to-tail-oriented, micrometer-sized spikes observed on a phylogenetically broad sampling of nonsidewinding vipers and other snakes from diverse habitats and wide geographic range. A mathematical model that relates structural directionality to frictional anisotropy reveals that isotropy enhances movement during sidewinding, whereas anisotropy improves movement during slithering via lateral undulation of the body. Our results highlight how an integrated approach can provide quantitative predictions for structure-function relationships and insights into behavioral and evolutionary adaptations in biological systems.

Mechanism and function of root circumnutation.

Early root growth is critical for plant establishment and survival. We have identified a molecular pathway required for helical root tip movement known as circumnutation. Here, we report a multiscale investigation of the regulation and function of this phenomenon. We identify key cell signaling events comprising interaction of the ethylene, cytokinin, and auxin hormone signaling pathways. We identify the gene Oryza sativa histidine kinase-1 (HK1) as well as the auxin influx carrier gene OsAUX1 as essential regulators of this process in rice. Robophysical modeling and growth challenge experiments indicate circumnutation is critical for seedling establishment in rocky soil, consistent with the long-standing hypothesis that root circumnutation facilitates growth past obstacles. Thus, the integration of robotics, physics, and biology has elucidated the functional importance of root circumnutation and uncovered the molecular mechanisms underlying its regulation.