The natural selection of metabolism explains curvature in allometric scaling

I simulate the natural selection of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. The simulation model starts with a single ancestor in each clade at the Cretaceous–Palaeogene boundary 65 million years ago. The release of inter‐specific competition by the extinction of dinosaurs make it possible for each clade to diversify into a multitude of species across a wide range of empty niches. The selection of mass in these species depends on the net assimilated energy that depends on 1) the handling of the resources in the different niches, and on 2) mass‐specific metabolism that defines the pace of the handling process. The model is fitted to explain the maximum observed body masses over time and the current inter‐specific allometry for metabolism. The selection of mass‐specific metabolism is found to bend the metabolic allometry over time, even when all species have the same selection on the per‐generation time‐scale of natural selection. This is because the smaller species evolve over a larger number of generations than the larger species. The strongest curvature is in the placental clade, where the estimated rate of exponential increase in mass‐specific metabolism is 9.3 × 10^?9 (95% CI: 7.3 × 10^?9 – 1.1 × 10^?8) on the per‐generation time‐scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar size.     

Effects of divalent cations,temperature, osmotic pressure gradient,and vesicle curvature on phosphatidylserine vesicle fusion

Summary Fusion of phosphatidylserine vesicles induced by divalent cations, temperature and osmotic pressure gradients across the membrane was studied with respect to variations in vesicle size. Vesicle fusion was followed by two different methods: 1) the Tb/DPA fusion assay, whereby the fluorescent intensity upon mixing of the internal aqueous contents of fused lipid vesicles was monitored, and 2) measurement of the changes in turbidity of the vesicle suspension due to vesicle fusion. It was found that the threshold concentration of divalent cations necessary to induce vesicle fusion depended on the size of vesicles; as the diameter of the vesicle increased, the threshold value increased and the extent of fusion became less. For the osmotic pressure-induced vesicle fusion, the larger the diameter of vesicles, the smaller was the osmotic pressure gradient required to induce membrane fusion. Divalent cations, temperature increase and vesicle membrane expansion by osmotic pressure gradient all resulted in increase in surface energy (tension) of the membrane. The degree of membrane fusion correlated with the corresponding surface energy changes of vesicle membranes due to the above fusion-inducing agents. The increase in surface energy of 9.5 dyn/cm from the reference state corresponded to the threshold point of phosphatidylserine membrane fusion. An attempt was made to explain the factors influencing fusion phenomena on the basis of a single unifying theory.     

Mechanism of negative membrane curvature generation by I-BAR domains

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Autotropism, automorphogenesis, and gravity

Segments of organs that have undergone gravitropic curvature later straighten during the course of gravitropism or after the g ‐vector becomes randomized on a clinostat. Little is known about the mechanisms underlying these and perhaps related phenomena which have been described with various overlapping terms such as autotropism, autotropic straightening, automorphosis, automorphogenesis, automorphic curvature, and gravitropic straightening. The types of phenomena that historically have been named by the above terms are reviewed critically with respect to an interaction with gravitropism. We suggest that the term "autotropism" should not be applied to the phenomenon of organ straightening that occurs during the course of gravitropism, since this straightening is part of a complex series of local growth adjustments overall through time, and since this phenomenon is not itself a tropistic response to a directional exogenous stimulus. It is suggested that the term autotropism should be used only for the phenomenon of organ straightening that occurs after the g ‐vector is randomized on a clinostat or withdrawn in the microgravity conditions of spaceflight. Usage of the term automorphogenesis is most appropriate for describing curvatures or orientations that result from morphological relationships such as in nastic curvatures.     

Lipidation of the autophagy proteins LC3 and GABARAP is a membrane-curvature dependent process

The phagophore membrane is highly curved along the rim of the open cup, suggesting that the molecular mechanisms governing its formation and growth could rely on membrane curvature-dependent events. To this end, we recently reported that lipidation of the LC3 protein family is facilitated on highly curved membranes in vitro. We further showed that the conjugating enzyme ATG3 contains an amphipathic helix that is responsible for this membrane curvature dependency, and that the maintenance of this amphipathic structure is essential for ATG3 function in vivo.     

Mechanisms of membrane deformation by lipid-binding domains

Among an increasing number of lipid-binding domains, a group that not only binds to membrane lipids but also changes the shape of the membrane has been found. These domains are characterized by their strong ability to transform globular liposomes as well as flat plasma membranes into elongated membrane tubules both in vitro and in vivo. Biochemical studies on the structures of these proteins have revealed the importance of the amphipathic helix, which potentially intercalates into the lipid bilayer to induce and/or sense membrane curvature. Among such membrane-deforming domains, BAR and F-BAR/EFC domains form crescent-shaped dimers, suggesting a preference for a curved membrane, which is important for curvature sensing. Bioinformatics in combination with structural analyses has been identifying an increasing number of novel families of lipid-binding domains. This review attempts to summarize the evidence obtained by recent studies in order to gain general insights into the roles of membrane-deforming domains in a variety of biological events.     

Geometric and potential driving formation and evolution of biomolecular surfaces

This paper presents new geometrical flow equations for the theoretical modeling of biomolecular surfaces in the context of multiscale implicit solvent models. To account for the local variations near the biomolecular surfaces due to interactions between solvent molecules, and between solvent and solute molecules, we propose potential driven geometric flows, which balance the intrinsic geometric forces that would occur for a surface separating two homogeneous materials with the potential forces induced by the atomic interactions. Stochastic geometric flows are introduced to account for the random fluctuation and dissipation in density and pressure near the solvent–solute interface. Physical properties, such as free energy minimization (area decreasing) and incompressibility (volume preserving), are realized by some of our geometric flow equations. The proposed approach for geometric and potential forces driving the formation and evolution of biological surfaces is illustrated by extensive numerical experiments and compared with established minimal molecular surfaces and molecular surfaces. Local modification of biomolecular surfaces is demonstrated with potential driven geometric flows. High order geometric flows are also considered and tested in the present work for surface generation. Biomolecular surfaces generated by these approaches are typically free of geometric singularities. As the speed of surface generation is crucial to implicit solvent model based molecular dynamics, four numerical algorithms, a semi-implicit scheme, a Crank–Nicolson scheme, and two alternating direction implicit (ADI) schemes, are constructed and tested. Being either stable or conditionally stable but admitting a large critical time step size, these schemes overcome the stability constraint of the earlier forward Euler scheme. Aided with the Thomas algorithm, one of the ADI schemes is found to be very efficient as it balances the speed and accuracy.