Dissecting flux balances to measure energetic costs in cell biology: techniques and challenges

Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic costs. The most direct experimental measurements of these costs involve modulating the activity of cellular processes and determining the resulting changes in energetic fluxes. In this review, we present a flux balance framework to aid in the design and interpretation of such experiments, and discuss the challenges associated with measuring the relevant metabolic fluxes. We then describe selected techniques that enable measurement of these fluxes. Finally, we review prior experimental and theoretical work that has employed techniques from biochemistry and nonequilibrium physics to determine the energetic costs of cellular processes.Comment: 27 pages, 3 figure

A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes

Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overlapping genes. We show that the appearance of positive selection is caused by assuming that selection operates independently on each gene in an overlapping pair, thereby ignoring the unique evolutionary constraints on overlapping coding regions. Our method uses an exact evolutionary model, thereby voiding the need for approximation or intensive computation. We test the method by simulating the evolution of overlapping genes of different types as well as under diverse evolutionary scenarios. Our results indicate that the independent estimation approach leads to the false appearance of positive selection even though the gene is in reality subject to negative selection. Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases

Nutrition and oral health in sport:Time for action

Our recent BJSM editorial stressed that it is ‘time for action’ regarding sports nutrition oral health1. Oral health is poor in elite athletes and is consistently associated with performance impacts as we have shown across studies involving more than 800 athletes2-4. This situation exists despite poor oral health being preventable with well evidenced effective, low-cost strategies5. Since solutions are readily available why does this situation persist and what can be done to benefit athlete performance and health

Cationic liposome–microtubule complexes: Pathways to the formation of two-state lipid–protein nanotubes with open or closed ends

Intermolecular interactions between charged membranes and biological polyelectrolytes, tuned by physical parameters, which include the membrane charge density and bending rigidity, the membrane spontaneous curvature, the biopolymer curvature, and the overall charge of the complex, lead to distinct structures and morphologies. The self-assembly of cationic liposome–microtubule (MT) complexes was studied, using synchrotron x-ray scattering and electron microscopy. Vesicles were found to either adsorb onto MTs, forming a “beads on a rod” structure, or undergo a wetting transition and coating the MT. Tubulin oligomers then coat the external lipid layer, forming a tunable lipid–protein nanotube. The beads on a rod structure is a kinetically trapped state. The energy barrier between the states depends on the membrane bending rigidity and charge density. By controlling the cationic lipid/tubulin stoichiometry it is possible to switch between two states of nanotubes with either open ends or closed ends with lipid caps, a process that forms the basis for controlled chemical and drug encapsulation and release

Advanced tissue engineering scaffold design for regeneration of the complex hierarchical periodontal structure

Aim: This study investigated the competence of an osteoinductive biphasic scaffold to simultaneously regenerate alveolar bone, periodontal ligament and cementum. Materials and Methods: A biphasic scaffold was built by attaching a fused deposition modeled bone compartment to a melt electrospun periodontal compartment. The bone compartment was coated with a calcium phosphate layer for increasing osteoinductivity, seeded with osteoblasts and cultured in vitro for 6 weeks. The resulting constructs were then complemented with the placement of PDL cell sheets on the periodontal compartment, attached to a dentin block and subcutaneously implanted into rats for 8 weeks. Scanning electron microscopy, x-ray diffraction, alkaline phosphatase and DNA content quantification, confocal laser microscopy, micro computerized tomography and histological analysis were employed to evaluate the scaffold’s performance. Results: The in vitro study showed that alkaline phosphatase activity was significantly increased in the CaP coated samples and they also displayed enhanced mineralization. In the in vivo study, significantly more bone formation was observed in the coated scaffolds. Histological analysis revealed that the large pore size of the periodontal compartment permitted vascularization of the cell sheets, and periodontal attachment was achieved at the dentin interface. Conclusions: This work demonstrates that the combination of cell sheet technology together with an osteoinductive biphasic scaffold could be utilized to address the limitations of current periodontal regeneration techniques.The authors report no conflicts of interest related to this study. This study was supported by the NHMRC, the Australian Research Council and the Australian Dental Research Foundation. This study was additionally supported by Pedro Costa's PhD grant from the Portuguese Foundation for Science and Technology (SFRH/BD/62452/2009)