Order from Chaos:  Observing Hormesis at the Proteome Level

Abstract

We report on an observed regularity in the overall response of cell proteome under influence of different doses of a peroxisome proliferator. Our analysis for the first time demonstrates presence of hormesis at the cellular level. It is shown that despite the fact that the response of individual proteins remains unpredictable, the perturbation of proteome as a whole (measured as the average departure of protein abundances from the corresponding values of the control group) shows regularity: It initially decreases, reaches a minimum, and then increases as the concentration of the used proliferator continue to increase. The work is based on the available data of Anderson at al. on the effects of peroxisome proliferator LY171883 on protein abundances in mouse liver when administrated at different concentrations.

Study of proteome maps using partial ordering

“…The limiting case of completely negligible role of the off-diagonal matrix elements correspond to transforming the problem of characterization of proteomics maps to that of characterization of cellular proteome, because the role of the x, y) coordinates has been eliminated. That the analysis of proteome map and proteome, though related, is distinct is well illustrated by a paper of Randić and Estrada (2005), who examined the reported variations of protein abundances as concentration of particular peroxisome proliferator was changes over two orders of magnitude. Thus, by ignoring the (x, y) coordinates they were able to detect a nonlinear dose response at the cellular level, the phenomenon that has been known previously to holds for an organism (animal, plant) as a whole (Calabrese and Baldwin, 2003).…”

Milestones in graphical bioinformatics

“…Using their data, Randić and Estrada [16] selected 99 protein spots for which they measured the difference of the abundance of individual proteins from the abundance in the control group. Figure 19 In this analysis no information on x, y coordinates were used, and thus the analysis pertains to cell proteome, and not to proteomics maps.…”

“…This continues the code: 0 0 0 0 0 0 0 0 0 1 1. Returning to vertex 8, we first go to vertex 16, because the edge (8,16) has not yet been visited, rather than returning to vertex 7, because edge (8, 7) has already been visited. Edges that have not yet obtained label 0 have precedent over edges that already have binary assignment 0.…”

“…Edges that have not yet obtained label 0 have precedent over edges that already have binary assignment 0. Our code thus continues with 0 for edge (8,16), then 1 for edge (16,8) …”

Elucidating the Mechanism(s) of Hormesis at the Cellular Level: The Universal Cell Response

“…heat stress) on ageing is an example [23][24][25][26][27][28] . Such stimuli, indeed a number of external stressors, have quite non-specific effects on protein glycation and oxidation and perhaps on the proteome as a whole [28,29] . To explicate such cases in terms of specific molecular processes would seem otiose.…”