Splenic monocytes mediate inflammatory response and exacerbate myocardial ischemia/reperfusion injury in a mitochondrial cell-free DNA-TLR9-NLRP3-dependent fashion.

The spleen contributes importantly to myocardial ischemia/reperfusion (MI/R) injury. Nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) recruits inflammasomes, initiating inflammatory responses and mediating tissue injury. We hypothesize that myocardial cell-free DNA (cfDNA) activates the splenic NLRP3 inflammasome during early reperfusion, increases systemic inflammatory response, and exacerbates myocardial infarct. Mice were subjected to 40 min of ischemia followed by 0, 1, 5, or 15 min, or 24 h of reperfusion. Splenic leukocyte adoptive transfer was performed by injecting isolated splenocytes to mice with splenectomy performed prior to left coronary artery occlusion. CY-09 (4 mg/kg) was administered 5 min before reperfusion. During post-ischemic reperfusion, splenic protein levels of NLRP3, cleaved caspase-1, and interleukin-1ß (IL-1ß) were significantly elevated and peaked (2.1 ± 0.2-, 3.4 ± 0.4-, and 3.2 ± 0.2-fold increase respectively, p < 0.05) within 5 min of reperfusion. In myocardial tissue, NLRP3 was not upregulated until 24 h after reperfusion. Suppression by CY09, a specific NLRP3 inflammasome inhibitor, or deficiency of NLRP3 significantly reduced myocardial infarct size (17.3% ± 4.2% and 33.2% ± 1.8% decrease respectively, p < 0.01). Adoptive transfer of NLRP3-/- splenocytes to WT mice significantly decreased infarct size compared to transfer of WT splenocytes (19.1% ± 2.8% decrease, p < 0.0001). NLRP3 was mainly activated at 5 min after reperfusion in CD11b+ and LY6G- splenocytes, which significantly increased during reperfusion (24.8% ± 0.7% vs.14.3% ± 0.6%, p < 0.0001). The circulating cfDNA level significantly increased in patients undergoing cardiopulmonary bypass (CPB) (43.3 ± 5.3 ng/mL, compared to pre-CPB 23.8 ± 3.5 ng/mL, p < 0.01). Mitochondrial cfDNA (mt-cfDNA) contributed to NLRP3 activation in macrophages (2.1 ± 0.2-fold increase, p < 0.01), which was inhibited by a Toll-like receptor 9(TLR9) inhibitor. The NLRP3 inflammasome in splenic monocytes is activated and mediates the inflammatory response shortly after reperfusion onset, exacerbating MI/R injury in mt-cfDNA/TLR9-dependent fashion. The schema reveals splenic NLRP3 mediates the inflammatory response in macrophages and exacerbates MI/R in a mitochondrial cfDNA/ TLR9-dependent fashion.

Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular ciliate Stentor.

Evolution of multicellularity from early unicellular ancestors is arguably one of the most important transitions since the origin of life1,2. Multicellularity is often associated with higher nutrient uptake3, better defense against predation, cell specialization and better division of labor4. While many single-celled organisms exhibit both solitary and colonial existence3,5,6, the organizing principles governing the transition and the benefits endowed are less clear. Using the suspension-feeding unicellular protist Stentor coeruleus, we show that hydrodynamic coupling between proximal neighbors results in faster feeding flows that depend on the separation between individuals. Moreover, we find that the accrued benefits in feeding current enhancement are typically asymmetric- individuals with slower solitary currents gain more from partnering than those with faster currents. We find that colony-formation is ephemeral in Stentor and individuals in colonies are highly dynamic unlike other colony-forming organisms like Volvox carteri 3. Our results demonstrate benefits endowed by the colonial organization in a simple unicellular organism and can potentially provide fundamental insights into the selective forces favoring early evolution of multicellular organization.

Spontaneous phase coordination and fluid pumping in model ciliary carpets.

Ciliated tissues, such as in the mammalian lungs, brains, and reproductive tracts, are specialized to pump fluid. They generate flows by the collective activity of hundreds of thousands of individual cilia that beat in a striking metachronal wave pattern. Despite progress in analyzing cilia coordination, a general theory that links coordination and fluid pumping in the limit of large arrays of cilia remains lacking. Here, we conduct in silico experiments with thousands of hydrodynamically interacting cilia, and we develop a continuum theory in the limit of infinitely many independently beating cilia by combining tools from active matter and classical Stokes flow. We find, in both simulations and theory, that isotropic and synchronized ciliary states are unstable. Traveling waves emerge regardless of initial conditions, but the characteristics of the wave and net flows depend on cilia and tissue properties. That is, metachronal phase coordination is a stable global attractor in large ciliary carpets, even under finite perturbations to cilia and tissue properties. These results support the notion that functional specificity of ciliated tissues is interlaced with the tissue architecture and cilia beat kinematics and open up the prospect of establishing structure to function maps from cilium-level beat to tissue-level coordination and fluid pumping.

Intracellular coupling modulates biflagellar synchrony.

Beating flagella exhibit a variety of synchronization modes. This synchrony has long been attributed to hydrodynamic coupling between the flagella. However, recent work with flagellated algae indicates that a mechanism internal to the cell, through the contractile fibres connecting the flagella basal bodies, must be at play to actively modulate flagellar synchrony. Exactly how basal coupling mediates flagellar coordination remains unclear. Here, we examine the role of basal coupling in the synchronization of the model biflagellate Chlamydomonas reinhardtii using a series of mathematical models of decreasing levels of complexity. We report that basal coupling is sufficient to achieve inphase, antiphase and bistable synchrony, even in the absence of hydrodynamic coupling and flagellar compliance. These modes can be reached by modulating the activity level of the individual flagella or the strength of the basal coupling. We observe a slip mode when allowing for differential flagellar activity, just as in experiments with live cells. We introduce a dimensionless ratio of flagellar activity to basal coupling that is predictive of the mode of synchrony. This ratio allows us to query biological parameters which are not yet directly measurable experimentally. Our work shows a concrete route for cells to actively control the synchronization of their flagella.

Instability-driven oscillations of elastic microfilaments.

Cilia and flagella are highly conserved slender organelles that exhibit a variety of rhythmic beating patterns from non-planar cone-like motions to planar wave-like deformations. Although their internal structure, composed of a microtubule-based axoneme driven by dynein motors, is known, the mechanism responsible for these beating patterns remains elusive. Existing theories suggest that the dynein activity is dynamically regulated, via a geometric feedback from the cilium's mechanical deformation to the dynein force. An alternative, open-loop mechanism based on a 'flutter' instability was recently proven to lead to planar oscillations of elastic filaments under follower forces. Here, we show that an elastic filament in viscous fluid, clamped at one end and acted on by an external distribution of compressive axial forces, exhibits a Hopf bifurcation that leads to non-planar spinning of the buckled filament at a locked curvature. We also show the existence of a second bifurcation, at larger force values, that induces a transition from non-planar spinning to planar wave-like oscillations. We elucidate the nature of these instabilities using a combination of nonlinear numerical analysis, linear stability theory and low-order bead-spring models. Our results show that, away from the transition thresholds, these beating patterns are robust to perturbations in the distribution of axial forces and in the filament configuration. These findings support the theory that an open-loop, instability-driven mechanism could explain both the sustained oscillations and the wide variety of periodic beating patterns observed in cilia and flagella.

Motile cilia create fluid-mechanical microhabitats for the active recruitment of the host microbiome.

We show that mucociliary membranes of animal epithelia can create fluid-mechanical microenvironments for the active recruitment of the specific microbiome of the host. In terrestrial vertebrates, these tissues are typically colonized by complex consortia and are inaccessible to observation. Such tissues can be directly examined in aquatic animals, providing valuable opportunities for the analysis of mucociliary activity in relation to bacteria recruitment. Using the squid-vibrio model system, we provide a characterization of the initial engagement of microbial symbionts along ciliated tissues. Specifically, we developed an empirical and theoretical framework to conduct a census of ciliated cell types, create structural maps, and resolve the spatiotemporal flow dynamics. Our multiscale analyses revealed two distinct, highly organized populations of cilia on the host tissues. An array of long cilia ([Formula: see text]25 [Formula: see text]m) with metachronal beat creates a flow that focuses bacteria-sized particles, at the exclusion of larger particles, into sheltered zones; there, a field of randomly beating short cilia ([Formula: see text]10 [Formula: see text]m) mixes the local fluid environment, which contains host biochemical signals known to prime symbionts for colonization. This cilia-mediated process represents a previously unrecognized mechanism for symbiont recruitment. Each mucociliary surface that recruits a microbiome such as the case described here is likely to have system-specific features. However, all mucociliary surfaces are subject to the same physical and biological constraints that are imposed by the fluid environment and the evolutionary conserved structure of cilia. As such, our study promises to provide insight into universal mechanisms that drive the recruitment of symbiotic partners.

Evaluating efficiency and robustness in cilia design.

Motile cilia are used by many eukaryotic cells to transport flow. Cilia-driven flows are important to many physiological functions, yet a deep understanding of the interplay between the mechanical structure of cilia and their physiological functions in healthy and diseased conditions remains elusive. To develop such an understanding, one needs a quantitative framework to assess cilia performance and robustness when subject to perturbations in the cilia apparatus. Here we link cilia design (beating patterns) to function (flow transport) in the context of experimentally and theoretically derived cilia models. We particularly examine the optimality and robustness of cilia design. Optimality refers to efficiency of flow transport, while robustness is defined as low sensitivity to variations in the design parameters. We find that suboptimal designs can be more robust than optimal ones. That is, designing for the most efficient cilium does not guarantee robustness. These findings have significant implications on the understanding of cilia design in artificial and biological systems.

Inferring the temporal order of cancer gene mutations in individual tumor samples.

The temporal order of cancer gene mutations in tumors is essential for understanding and treating the disease. Existing methods are unable to infer the order of mutations that are identified at the same time in individual tumor samples, leaving the heterogeneity of the order unknown. Here, we show that through a complex network-based approach, which is based on the newly defined statistic -carcinogenesis information conductivity (CIC), the temporal order in individual samples can be effectively inferred. The results suggest that tumor-suppressor genes might more frequently initiate the order of mutations than oncogenes, and every type of cancer might have its own unique order of mutations. The initial mutations appear to be dedicated to acquiring the function of evading apoptosis, and some order constraints might reflect potential regularities. Our approach is completely data-driven without any parameter settings and can be expected to become more effective as more data will become available.

An activation force-based affinity measure for analyzing complex networks.

Affinity measure is a key factor that determines the quality of the analysis of a complex network. Here, we introduce a type of statistics, activation forces, to weight the links of a complex network and thereby develop a desired affinity measure. We show that the approach is superior in facilitating the analysis through experiments on a large-scale word network and a protein-protein interaction (PPI) network consisting of ∼5,000 human proteins. The experiment on the word network verifies that the measured word affinities are highly consistent with human knowledge. Further, the experiment on the PPI network verifies the measure and presents a general method for the identification of functionally similar proteins based on PPIs. Most strikingly, we find an affinity network that compactly connects the cancer-associated proteins to each other, which may reveal novel information for cancer study; this includes likely protein interactions and key proteins in cancer-related signal transduction pathways.