An integrated proteomics analysis of bone tissues in response to mechanical stimulation

Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. However, it is still poorly understood how genes and proteins in bone cells are orchestrated to respond to mechanical stimulations. In this research, we applied integrated proteomics, statistical, and network biology techniques to study proteome-level changes to bone tissue cells in response to two different conditions, normal loading and fatigue loading. We harvested ulna midshafts and isolated proteins from the control, loaded, and fatigue loaded Rats. Using a label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) experimental proteomics technique, we derived a comprehensive list of 1,058 proteins that are differentially expressed among normal loading, fatigue loading, and controls. By carefully developing protein selection filters and statistical models, we were able to identify 42 proteins representing 21 Rat genes that were significantly associated with bone cells' response to quantitative changes between normal loading and fatigue loading conditions. We further applied network biology techniques by building a fatigue loading activated protein-protein interaction subnetwork involving 9 of the human-homolog counterpart of the 21 rat genes in a large connected network component. Our study shows that the combination of decreased anti-apoptotic factor, Raf1, and increased pro-apoptotic factor, PDCD8, results in significant increase in the number of apoptotic osteocytes following fatigue loading. We believe controlling osteoblast differentiation/proliferation and osteocyte apoptosis could be promising directions for developing future therapeutic solutions for related bone diseases

Estimation of mutation rates in cultured mammalian cells

The factors that affect reliable estimations of mutation rates ([mu]) in cultured mammalian somatic cell populations by fluctuation analysis are studied experimentally and statistically. We analyze the differential effect of the final cell population size in each culture (Nt) and the number of parallel cultures (C) on the variation in the rate estimates () inferred from the P0 method. The analysis can be made after the derivation of the variance of , which is a measure of variation of for a given combination of Nt and C in a number of repeat experiments. The variance of is inversely proportional to C and to the square of Nt. Nt determines the probability of occurrence of mutation in a cell culture. By influencing the size of P0, Nt also determines whether a rate estimate is obtainable from the experiment. Since Po is estimated from the fraction of cultures containing no mutation in a set of C cultures, C becomes a determining factor for the accuracy of . The rate estimated from is biased, but the bias is in general 2 orders of magnitude smaller than . By the selection of an appropriate combination of Nt and C for the experiment, this bias can be reduced even further.Based on the notion of comparing two proportions, we propose a test statistic and have applied it to experimental results for a test of equality of mutation rates in different cell lines. This development places the comparison of mutation rates on a statistical basis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25103/1/0000535.pd

A deterministic approach for the estimation of mutation rates in cultured mammalian cells

Unequal growth rates between mutant and wild-type cells in a large population constitute a problem for the estimation of mutation rate. Over a period of cell growth, a selective advantage of one cell type over the other might lead to considerable error in the estimation of mutation rate if equal growth rates are assumed. In this study, we propose a formula and apply it to the estimation of spontaneous mutation rate in a growing population of Chinese hamster V79 cells in which ouabain-resistant mutant cells exhibit a slower growth rate than the wild-type cells. The formula is a generalization of that previously presented by Armitage (1953), and this is the first attempt to apply the deterministic approach for mutation rate estimation to cultured mammalian cells. The value of the estimated rate is compred with that derived from a parallel experiment using the fluctuation test of Luria and Delbruck (1943). The limitations and advantages of taking the deterministic approach to mutation rate estimation in mammalian cell systems are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25744/1/0000304.pd

Effects of acceleration on the collision of particles in the rotating black hole spacetime

We study the collision of two geodesic particles in the accelerating and rotating black hole spacetime and probe the effects of the acceleration of black hole on the center-of-mass energy of the colliding particles and on the high-velocity collision belts. We find that the dependence of the center-of-mass energy on the acceleration in the near event-horizon collision is different from that in the near acceleration-horizon case. Moreover, the presence of the acceleration changes the shape and position of the high-velocity collision belts. Our results show that the acceleration of black holes brings richer physics for the collision of particles.Comment: 7 pages, 2 figures, The corrected version accepted for publication in EPJ

Phantom scalar emission in the Kerr black hole spacetime

We study the absorption probability and Hawking radiation spectra of a phantom scalar field in the Kerr black hole spacetime. We find that the presence of the negative kinetic energy terms modifies the standard results in the greybody factor, super-radiance and Hawking radiation. Comparing with the usual scalar particle, the phantom scalar emission is enhanced in the black hole spacetime.Comment: 11 pages, 6 figures, a revised version accepted for publication in CQ

Density pertubation of unparticle dark matter in the flat Universe

The unparticle has been suggested as a candidate of dark matter. We investigated the growth rate of the density perturbation for the unparticle dark matter in the flat Universe. First, we consider the model in which unparticle is the sole dark matter and find that the growth factor can be approximated well by $f=(1+3\omega_u)\Omega^{\gamma}_u$, where $\omega_u$ is the equation of state of unparticle. Our results show that the presence of $\omega_u$ modifies the behavior of the growth factor $f$. For the second model where unparticle co-exists with cold dark matter, the growth factor has a new approximation $f=(1+3\omega_u)\Omega^{\gamma}_u+\alpha \Omega_m$ and $\alpha$ is a function of $\omega_u$. Thus the growth factor of unparticle is quite different from that of usual dark matter. These information can help us know more about unparticle and the early evolution of the Universe.Comment: 6pages, 4 figures, accepted for publication in Eur. Phys. J.

Holographic Superconductors with Power-Maxwell field

With the Sturm-Liouville analytical and numerical methods, we investigate the behaviors of the holographic superconductors by introducing a complex charged scalar field coupled with a Power-Maxwell field in the background of $d$-dimensional Schwarzschild AdS black hole. We note that the Power-Maxwell field takes the special asymptotical solution near boundary which is different from all known cases. We find that the larger power parameter $q$ for the Power-Maxwell field makes it harder for the scalar hair to be condensated. We also find that, for different $q$, the critical exponent of the system is still 1/2, which seems to be an universal property for various nonlinear electrodynamics if the scalar field takes the form of this paper.Comment: 14 pages, 1 figure, and 2 table

The torsion cosmology in Kaluza-Klein theory

We have studied the torsion cosmology model in Kaluza-Klein theory. We considered two simple models in which the torsion vectors are $A_{\mu}=(\alpha,0,0,0)$ and $A_{\mu}=a(t)^2(0,\beta,\beta,\beta)$, respectively. For the first model, the accelerating expansion of the Universe can be not explained without dark energy which is similar to that in the standard cosmology. But for the second model, we find that without dark energy the effect of torsion can give rise to the accelerating expansion of the universe and the alleviation of the well-known age problem of the three old objects for appropriated value of the model parameter $\beta$. These outstanding features of the second torsion cosmology model have been supported by the Type Ia supernovae (SNIa) data.Comment: 12 pages, 2 figures. Accepted for publication in JCA

Dirac quasinormal modes of the Reissner-Nordstr\"om de Sitter black hole

The quasinormal modes of the Reissner-Nordstr\"om de Sitter black hole for the massless Dirac fields are studied using the P\"oshl-Teller potential approximation. We find that the magnitude of the imaginary part of the quasinormal frequencies decreases as the cosmological constant or the orbital angular momentum increases, but it increases as the charge or the overtone number increases. An interesting feature is that the imaginary part is almost linearly related to the real part as the cosmological constant changes for fixed charge, and the linearity becomes better as the orbital angular momentum increases. We also prove exactly that the Dirac quasinormal frequencies are the same for opposite chirality.Comment: 10 pages, 6 figures, Phys. Rev. D in pres

Analytical study on holographic superconductors with backreactions

We employ the variational method for the Sturm-Liouville eigenvalue problem to analytically investigate the properties of the holographic superconductors. We find that the analytic method is still powerful when the backreaction is turned on. Reducing step size in the iterative procedure, we observe that the consistency of results between the analytic and numerical computations can be further improved. The obtained analytic result can be used to back up the numerical computations in the holographic superconductor in the fully backreacted spacetime.Comment: 10 pages, accepted by JHE