Quantitative analysis of the viscoelastic properties of thin regions of fibroblasts using atomic force microscopy

Viscoelasticity of the leading edge, i.e., the lamellipodium, of a cell is the key property for a deeper understanding of the active extension of a cell's leading edge. The fact that the lamellipodium of a cell is very thin (<1000 nm) imparts special challenges for accurate measurements of its viscoelastic behavior. It requires addressing strong substrate effects and comparatively high stresses (>1 kPa) on thin samples. We present the method for an atomic force microscopy-based microrheology that allows us to fully quantify the viscoelastic constants (elastic storage modulus, viscous loss modulus, and the Poisson ratio) of thin areas of a cell (<1000 nm) as well as those of thick areas. We account for substrate effects by applying two different models-a model for well-adhered regions (Chen model) and a model for nonadhered regions (Tu model). This method also provides detailed information about the adhered regions of a cell. The very thin regions relatively near the edge of NIH 3T3 fibroblasts can be identified by the Chen model as strongly adherent with an elastic strength of approximately 1.6 +/- 0.2 kPa and with an experimentally determined Poisson ratio of approximately 0.4 to 0.5. Further from the edge of these cells, the adherence decreases, and the Tu model is effective in evaluating its elastic strength ( approximately 0.6 +/- 0.1 kPa). Thus, our AFM-based microrheology allows us to correlate two key parameters of cell motility by relating elastic strength and the Poisson ratio to the adhesive state of a cell. This frequency-dependent measurement allows for the decomposition of the elastic modulus into loss and storage modulus. Applying this decomposition and Tu's and Chen's finite depth models allow us to obtain viscoelastic signatures in a frequency range from 50 to 300 Hz, showing a rubber plateau-like behavior.     

Diversity and population structure of a near-shore marine-sediment viral community

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.     

Regulation of platelet production: the normal response to perturbation and cyclical platelet disease

An age-structured model for the regulation of platelet production is developed, and compared with both normal and pathological platelet production. We consider the role of thrombopoietin (TPO) in this process, how TPO affects the transition between megakaryocytes of various ploidy classes, and their individual contributions to platelet production. After the estimation of the relevant parameters of the model from both in vivo and in vitro data, we use the model to numerically reproduce the normal human response to a bolus injection of TPO. We further show that our model reproduces the dynamic characteristics of autoimmune cyclical thromobocytopenia if the rate of platelet destruction in the circulation is elevated to more than twice the normal value.     

Interaction of spatial diffusion and delays in models of genetic control by repression

A class of models based on the Jacob and Monod theory of genetic repression for control of biosynthetic pathways in cells is considered. Both spatial diffusion and time delays are taken into account. A method is developed for representing the effects of spatial diffusion as distributed delay terms. This method is applied to two specific models and the interaction between the diffusion and the delays is treated in detail. The destabilization of the steadystate and the bifurcation of oscillatory solutions are studied as functions of the diffusivities and the delays. The limits of very small and very large diffusivities are analyzed and comparisons with well-mixed compartment models are made.On leave from North Carolina State University