Kinetic-structural analysis of neuronal growth cone veil motility.

Neuronal growth cone advance was investigated by correlative light and electron microscopy carried out on chick dorsal root ganglion cells. Advance was analyzed in terms of the two principal organelles responsible for protrusive motility in the growth cone - namely, veils and filopodia. Veils alternated between rapid phases of protrusion and retraction. Electron microscopy revealed characteristic structural differences between the phases. Our results provide a significant advance in three respects: first, protruding veils are comprised of a densely branched network of actin filaments that is lamellipodial in appearance and includes the Arp2/3 complex. On the basis of this structural and biomarker evidence, we infer that the dendritic nucleation and/or array-treadmilling mechanism of protrusive motility is conserved in veil protrusion of growth cones as in the motility of fibroblasts; second, retracting veils lack dendritic organization but contain a sparse network of long filaments; and third, growth cone filopodia have the capacity to nucleate dendritic networks along their length, a property consistent with veil formation seen at the light microscopic level but not previously understood in supramolecular terms. These elements of veil and filopodial organization, when taken together, provide a conceptual framework for understanding the structural basis of growth cone advance.

Simulating cellular dynamics through a coupled transcription, translation, metabolic model.

In order to predict cell behavior in response to changes in its surroundings or to modifications of its genetic code, the dynamics of a cell are modeled using equations of metabolism, transport, transcription and translation implemented in the Karyote software. Our methodology accounts for the organelles of eukaryotes and the specialized zones in prokaryotes by dividing the volume of the cell into discrete compartments. Each compartment exchanges mass with others either through membrane transport or with a time delay effect associated with molecular migration. Metabolic and macromolecular reactions take place in user-specified compartments. Coupling among processes are accounted for and multiple scale techniques allow for the computation of processes that occur on a wide range of time scales. Our model is implemented to simulate the evolution of concentrations for a user-specifiable set of molecules and reactions that participate in cellular activity. The underlying equations integrate metabolic, transcription and translation reaction networks and provide a framework for simulating whole cells given a user-specified set of reactions. A rate equation formulation is used to simulate transcription from an input DNA sequence while the resulting mRNA is used via ribosome-mediated polymerization kinetics to accomplish translation. Feedback associated with the creation of species necessary for metabolism by the mRNA and protein synthesis modifies the rates of production of factors (e.g. nucleotides and amino acids) that affect the dynamics of transcription and translation. The concentrations of predicted proteins are compared with time series or steady state experiments. The expression and sequence of the predicted proteins are compared with experimental data via the construction of synthetic tryptic digests and associated mass spectra. We present the mathematical model showing the coupling of transcription, translation and metabolism in Karyote and illustrate some of its unique characteristics.