Evolutionary cell biology: Functional insight from “Endless forms most beautiful”

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking

Effect of mutual coupling on torque production in switched reluctance motors

In many cases, the normal operation of switched reluctance machines requires excitation of two or more phases simultaneously. When multiple phases are conducting simultaneously, the flux paths from each phase will overlap, which may lead to localized saturation. In such cases, the flux linkage must be considered a function not just of the current in the test winding but of all excited windings. The degree of mutual coupling between phases influences the per-phase magnetization curves and torque characteristics. In machines with even phase numbers, the degree of mutual coupling between phases varies due to discontinuities in the phase polarity arrangement. From nonlinear finite element simulations, it is possible to compare the i - loop diagrams under single-phase and multiphase excitations, and hence the torque produced. The mutual flux linkage from each phase can be calculated separately for each rotor position using the frozen permeability method, to further analyze the mutual coupling effects. For a given excitation current profile, the torque can be maximized by careful arrangement of the phase polarities

Mixing in density- and viscosity-stratified flows

The lock-exchange problem is used extensively to study the flow dynamics of density-driven flows, such as gravity currents, and as a canonical problem to mixing in stratified flows. Opposite halves of a domain are filled with two fluids of different densities and held in place by a lock-gate. Upon release, the density difference drives the flow causing the fluids to slosh back and forth. In many scenarios, density stratification will also impose a viscosity stratification (e.g., if there are suspended sediments or the two fluids are distinct). However, numerical models often neglect variable viscosity. This paper characterizes the effect of both density and viscosity stratification in the lock-exchange configuration. The governing Navier-Stokes equations are solved using direct numerical simulation. Three regimes are identified in terms of the viscosity ratio μ 2 / μ 1 = (1 + γ) between the dense and less dense fluids: when γ ≪ 1, the flow dynamics are similar to the equal-viscosity case; for intermediate values (γ ∼ 1), viscosity inhibits interface-scale mixing leading to a global reduction in mixing and enhanced transfer between potential and kinetic energy. Increasing the excess viscosity ratio further (γ ≫ 1) results in significant viscous dissipation. Although many gravity or turbidity current models assume constant viscosity, our results demonstrate that viscosity stratification can only be neglected when γ ≪ 1. The initial turbidity current composition could enhance its ability to become self-sustaining or accelerating at intermediate excess viscosity ratios. Currents with initially high excess viscosity ratio may be unable to dilute and propagate long distances because of the decreased mixing rates and increased dissipation

Pulse propagation in gravity currents

Real world gravity current flows rarely exist as a single discrete event, but are instead made up of multiple surges. This paper examines the propagation of surges as pulses in gravity currents. Using theoretical shallow-water modeling, we analyze the structure of pulsed flows created by the sequential release of two lock-boxes. The first release creates a gravity current, while the second creates a pulse that eventually propagates to the head of the first current. Two parameters determine the flow structure: the densimetric Froude number at the head of the current, Fr, and a dimensionless time between releases, tre. The shallow-water model enables the flow behavior to be mapped in (Fr, tre) space. Pulse speed depends on three critical characteristic curves: two that derive from the first release and correspond to a wavelike disturbance which reflects between the head of the current and the back of the lock-box and a third that originates from the second release and represents the region of the flow affected by the finite supply of source material. Pulses have non-negative acceleration until they intersect the third characteristic, after which they decelerate. Variations in pulse speed affect energy transfer and dissipation. Critically for lahars, landslides, and avalanches, pulsed flows may change from erosional to depositional, further affecting their dynamics. Gravity current hazard prediction models for such surge-prone flows may underpredict risk if they neglect internal flow dynamics

Hydrodynamic studies of floating structures: Comparison of wave-structure interaction modelling

Current panel methods for wave-structure interactions employ the potential flow theory, which provide fast, reliable and relatively accurate predictions for the marine structures, and now some open source packages, NEMOH and HAMS, are available. In this research, the relative utility and performance of NEMOH and HAMS is compared with the well-known, state-of-art software, WAMIT. To bring focus to these comparisons, this research is based on three different floating structures: the truncated cylinder; the truncated cylinder with heave plate; and a novel multi-axis TALOS wave energy converter. To make the comparison more useful, this research investigates the incomplete and overlapped panels for the simple cylinder, to examine whether the respective code can handle these and still provide a meaningful solution. The comparisons may help us to understand whether the incomplete and/or overlapped panels can be used for simplifying the numerical modelling of those very complicated marine structures. From the comparisons, it can be seen the open source software, NEMOH and HAMS, both could produce very good results for the simple single marine structure, but also exhibit different capacities in dealing with more complicated marine structures. Specifically, HAMS could handle the thin structures and the overlapped panels effectively as WAMIT

Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids

Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms

Inadequacy of fluvial energetics for describing gravity current autosuspension

Gravity currents, such as sediment-laden turbidity currents, are ubiquitous natural flows that are driven by a density difference. Turbidity currents have provided vital motivation to advance understanding of this class of flows because their enigmatic long run-out and driving mechanisms are not properly understood. Extant models assume that material transport by gravity currents is dynamically similar to fluvial flows. Here, empirical research from different types of particle-driven gravity currents is integrated with our experimental data, to show that material transport is fundamentally different from fluvial systems. Contrary to current theory, buoyancy production is shown to have a non-linear dependence on available flow power, indicating an underestimation of the total kinetic energy lost from the mean flow. A revised energy budget directly implies that the mixing efficiency of gravity currents is enhanced

Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage-Specific Application but Conserved Trends.

Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage

Bone marrow injection stimulates hepatic ductular reactions in the absence of injury via macrophage-mediated TWEAK signaling

Tissue progenitor cells are an attractive target for regenerative therapy. In various organs, bone marrow cell (BMC) therapy has shown promising preliminary results, but to date no definite mechanism has been demonstrated to account for the observed benefit in organ regeneration. Tissue injury and regeneration is invariably accompanied by macrophage infiltration, but their influence upon the progenitor cells is incompletely understood, and direct signaling pathways may be obscured by the multiple roles of macrophages during organ injury. We therefore examined a model without injury; a single i.v. injection of unfractionated BMCs in healthy mice. This induced ductular reactions (DRs) in healthy mice. We demonstrate that macrophages within the unfractionated BMCs are responsible for the production of DRs, engrafting in the recipient liver and localizing to the DRs. Engrafted macrophages produce the cytokine TWEAK (TNF-like weak inducer of apoptosis) in situ. We go on to show that recombinant TWEAK activates DRs and that BMC mediated DRs are TWEAK dependent. DRs are accompanied by liver growth, occur in the absence of liver tissue injury and hepatic progenitor cells can be isolated from the livers of mice with DRs. Overall these results reveal a hitherto undescribed mechanism linking macrophage infiltration to DRs in the liver and highlight a rationale for macrophage derived cell therapy in regenerative medicine