Housekeeping Heat Research Articles

Proteome analysis of an aggressive and a hypoaggressive isolates of Fusarium oxysporum f. sp albedinis showing several differently expressed-proteins related to the aggressiveness

Fusarium oxysporum f. sp albedinis (Foa) attacks date palm and causes severe yield losses. Here, we provide the first proteome for two isolates of Foa, Mrabet (MRB), aggressive, and Ahardane (AHR), hypoaggressive. While the cultural parameters didn't correlate with aggressiveness, β-1,3-glucanase and β-1,4-mannanase were higher in MRB. Moreover, 99 proteins were at least two-fold up-regulated in MRB compared to AHR. A subset of these proteins involved in amino acid metabolism and in protein biosynthesis were almost absent in AHR. Other overexpressed proteins in MRB are housekeeping enzymes or heat shock proteins or involved in defense mechanisms or in chitin biosynthesis.

Martingale Structure for General Thermodynamic Functionals of Diffusion Processes Under Second-Order Averaging

Novel hidden thermodynamic structures have recently been uncovered during the investigation of nonequilibrium thermodynamics for multiscale stochastic processes. Here we reveal the martingale structure for a general thermodynamic functional of inhomogeneous singularly perturbed diffusion processes under second-order averaging, where a general thermodynamic functional is defined as the logarithmic Radon–Nykodim derivative between the laws of the original process and a comparable process (forward case) or its time reversal (backward case). In the forward case, we prove that the regular and anomalous parts of a thermodynamic functional are orthogonal martingales. In the backward case, while the regular part may not be a martingale, we prove that the anomalous part is still a martingale. With the aid of the martingale structure, we prove the integral fluctuation theorem satisfied by the regular and anomalous parts of a general thermodynamic functional. Further extensions and applications to stochastic thermodynamics are also discussed, including the martingale structure and fluctuation theorems for the regular and anomalous parts of entropy production and housekeeping heat in the absence or presence of odd variables.

Non-equilibrium steady-states of memoryless quantum collision models

We investigate the steady state properties arising from the open system dynamics described by a memoryless (Markovian) quantum collision model, corresponding to a master equation in the ultra-strong coupling regime. By carefully assessing the work cost of switching on and off the system-environment interaction, we show that only a coupling Hamiltonian in the energy-preserving form drives the system to thermal equilibrium, while any other interaction leads to non-equilibrium steady states that are supported by steady-state currents. These currents provide a neat exemplification of the housekeeping work and heat. Furthermore, we characterize the specific form of system-environment interaction that drives the system to a steady-state exhibiting coherence in the energy eigenbasis, thus, giving rise to families of states that are non-passive.

The role of fluctuations in determining cellular network thermodynamics.

The steady state distributions of phenotypic responses within an isogenic population of cells result from both deterministic and stochastic characteristics of biochemical networks. A biochemical network can be characterized by a multidimensional potential landscape based on the distribution of responses and a diffusion matrix of the correlated dynamic fluctuations between N-numbers of intracellular network variables. In this work, we develop a thermodynamic description of biological networks at the level of microscopic interactions between network variables. The Boltzmann H-function defines the rate of free energy dissipation of a network system and provides a framework for determining the heat associated with the nonequilibrium steady state and its network components. The magnitudes of the landscape gradients and the dynamic correlated fluctuations of network variables are experimentally accessible. We describe the use of Fokker-Planck dynamics to calculate housekeeping heat from the experimental data by a method that we refer to as Thermo-FP. The method provides insight into the composition of the network and the relative thermodynamic contributions from network components. We surmise that these thermodynamic quantities allow determination of the relative importance of network components to overall network control. We conjecture that there is an upper limit to the rate of dissipative heat produced by a biological system that is associated with system size or modularity, and we show that the dissipative heat has a lower bound.

Martingale theory for housekeeping heat

The housekeeping heat is the energy exchanged between a system and its environment in a nonequilibrium process that results from the violation of detailed balance. We describe fluctuations of the housekeeping heat in mesoscopic systems using the theory of martingales, a mathematical framework widely used in probability theory and finance. We show that the exponentiated housekeeping heat (in units of kBT, with kB the Boltzmann constant and T the temperature) of a Markovian nonequilibrium process under arbitrary time-dependent driving is a martingale process. From this result, we derive universal equalities and inequalities for the statistics of stopping times and suprema of the housekeeping heat. We test our results with numerical simulations of a system driven out of equilibrium and described by Langevin dynamics.

Decomposition of the entropy production rate and nonequilibrium thermodynamics of switching diffusion processes.

A switching diffusion process (SDP) is a widely used stochastic model in physics and biology, especially for molecular motors that exhibit a discrete internal chemical kinetics as well as a continuous external mechanical motion. The nonequilibrium thermodynamics of switching diffusion processes has not been extensively studied yet. In the present paper, we propose the decomposition of the entropy production rate in one-dimensional SDPs, based on the flux decomposition. However, similar decompositions of the housekeeping heat dissipation rate and free energy dissipation rate cannot guarantee the non-negativity of each decomposed component. Hence, we modify this decomposition with the flow of exponential relative information under steady-state fluxes, resulting in another decomposition with all non-negative components. Furthermore, we also provide the nonequilibrium thermodynamics of one-dimensional SDPs under the perspectives of coarse -graining and exchange of information between the chemical kinetics and mechanical motion, resulting in several other decompositions of entropy production rate. Finally, we generalize all the results to high-dimensional SDPs with a more general mathematical treatment.

Decomposition of the entropy production rate and nonequilibrium thermodynamics of switching diffusion processes

A switching diffusion process (SDP) is a widely used stochastic model in physics and biology, especially for molecular motors that exhibit a discrete internal chemical kinetics as well as a continuous external mechanical motion. The nonequilibrium thermodynamics of switching diffusion processes has not been extensively studied yet. In the present paper, we propose the decomposition of the entropy production rate in one-dimensional SDPs, based on the flux decomposition. However, similar decompositions of the housekeeping heat dissipation rate and free energy dissipation rate cannot guarantee the non-negativity of each decomposed component. Hence, we modify this decomposition with the flow of exponential relative information under steady-state fluxes, resulting in another decomposition with all non-negative components. Furthermore, we also provide the nonequilibrium thermodynamics of one-dimensional SDPs under the perspectives of coarse -graining and exchange of information between the chemical kinetics and mechanical motion, resulting in several other decompositions of entropy production rate. Finally, we generalize all the results to high-dimensional SDPs with a more general mathematical treatment.

Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage–Guldberg’s law of mass action

Macroscopic entropy production rate σ(tot) in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation rate and a house-keeping heat dissipation rate: σ(tot)=σ(fd)+σ(hk); σ(fd)=-dA/dt, where A is a generalized free energy function. This yields a novel nonequilibrium free energy balance equation dA/dt=-σ(tot)+σ(hk), which is on a par with celebrated entropy balance equation dS/dt=σ(tot)+η(ex) where η(ex) is the rate of entropy exchange with the environment. For kinetic systems with complex balance, σ(fd) and σ(hk) are the macroscopic limits of stochastic free energy dissipation rate and house-keeping heat dissipation rate, which are both nonnegative, in the Delbrück–Gillespie description of the stochastic chemical kinetics. A full kinetic and thermodynamic theory of chemical reaction systems that transcends mesoscopic and macroscopic levels emerges.

Fluctuation theorems for excess and housekeeping heat for underdamped Langevin systems

We present a simple derivation of the integral fluctuation theorems for excess housekeeping heat for an underdamped Langevin system, without using the concept of dual dynamics. In conformity with the earlier results, we find that the fluctuation theorem for housekeeping heat holds when the steady state distributions are symmetric in velocity, whereas there is no such requirement for the excess heat. We first prove the integral fluctuation theorem for the excess heat, and then show that it naturally leads to the integral fluctuation theorem for housekeeping heat. We also derive the modified detailed fluctuation theorems for the excess and housekeeping heats.

Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems

Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further reference to the intrinsic degree of freedom within each Markov state. It includes an extended free-energy balance and a second law which are valid for driven stochastic dynamics with an ideal external regenerating system. Our result suggests new ingredients for a generalized thermodynamics of self-organization in driven systems.

A decomposition of irreversible diffusion processes without detailed balance

As a generalization of deterministic, nonlinear conservative dynamical systems, a notion of canonical conservative dynamics with respect to a positive, differentiable stationary density ρ(x) is introduced: \documentclass[12pt]{minimal}\begin{document}$\dot{x}=j(x)$\end{document}ẋ=j(x) in which ∇·(ρ(x)j(x)) = 0. Such systems have a conserved “generalized free energy function” F[u] = ∫u(x, t)ln (u(x, t)/ρ(x))dx in phase space with a density flow u(x, t) satisfying ∂ut = −∇·(ju). Any general stochastic diffusion process without detailed balance, in terms of its Fokker-Planck equation, can be decomposed into a reversible diffusion process with detailed balance and a canonical conservative dynamics. This decomposition can be rigorously established in a function space with inner product defined as ⟨ϕ, ψ⟩ = ∫ρ−1(x)ϕ(x)ψ(x)dx. Furthermore, a law for balancing F[u] can be obtained: The non-positive dF[u(x, t)]/dt = Ein(t) − ep(t) where the “source” Ein(t) ⩾ 0 and the “sink” ep(t) ⩾ 0 are known as house-keeping heat and entropy production, respectively. A reversible diffusion has Ein(t) = 0. For a linear (Ornstein-Uhlenbeck) diffusion process, our decomposition is equivalent to the previous approaches developed by Graham and Ao, as well as the theory of large deviations. In terms of two different formulations of time reversal for a same stochastic process, the meanings of dissipative and conservative stationary dynamics are discussed.

Nonequilibrium Thermodynamics of Stochastic Systems with Odd and Even Variables

The total entropy production of stochastic systems can be divided into three quantities. The first corresponds to the excess heat, while the second two comprise the housekeeping heat. We denote these two components the transient and generalized housekeeping heat and we obtain an integral fluctuation theorem for the latter, valid for all Markovian stochastic dynamics. A previously reported formalism is obtained when the stationary probability distribution is symmetric for all variables that are odd under time reversal, which restricts consideration of directional variables such as velocity.

Physical origins of entropy production, free energy dissipation, and their mathematical representations

A unifying mathematical theory of nonequilibrium thermodynamics of stochastic systems in terms of master equations is presented. As generalizations of isothermal entropy and free energy, two functions of state play central roles: the Gibbs entropy S and the relative entropy F , which are related via the stationary distribution of the stochastic dynamics. S satisfies the fundamental entropy balance equation dS/dt = e p - h d/T with entropy production rate e p ≥ 0 and heat dissipation rate h d, while dF/dt = -f d ≤ 0. For closed systems that satisfy detailed balance: Te p(t)=f d(t). For open systems, one has Te p(t) = f d(t)+Q hk(t), where the housekeeping heat, Q hk ≥ 0, was first introduced in the phenomenological nonequilibrium steady-state thermodynamics put forward by Oono and Paniconi. Q hk represents the irreversible work done by the surrounding to the system that is kept away from reaching equilibrium. Hence, entropy production e p consists of free energy dissipation associated with spontaneous relaxation (i.e., self-organization), f d, and active energy pumping that sustains the open system Q hk. The amount of excess heat involved in the relaxation Q ex = h d - Q hk = f d -T(dS/dt). Two kinds of irreversibility, and the meaning of the arrow of time, emerge. Quasistationary processes, adiabaticity, and maximum principle for entropy are also generalized to nonequilibrium settings.

Dynamics of Arabidopsis thaliana soluble proteome in response to different nutrient culture conditions

In an effort to determine the best extraction procedure compatible with the high-reproducible 2-DE, different methods of soluble protein extraction from Arabidopsis cell culture suspensions grown in Gamborg B5 medium were tested. A reference 2-DE map was established for this soluble extract revealing 1184 spots. The most abundant protein spots were excised, trypsin-digested, and mass spectra obtained via MALDI-TOF and/or LC coupled to ESI-MS. Three hundred and thirty one proteins were identified and their functions were defined based on sequence comparisons and classified in different protein families. In order to analyze the impact of culture medium on the Arabidopsis proteome, we performed the 2-DE map from Arabidopsis cell suspensions cultured in another growth medium Murashige and Skoog (M-S) and 327 major spots were identified. Using PDQuest imaging analysis, significant increases in the amount of several housekeeping enzymes, stress/defense proteins, and heat shock proteins were found in M-S medium. Modified expression of certain proteins and detection of new isoforms involved in nitrate assimilation, nitrogen, and sulfur metabolism were also observed in the M-S medium. This study provides the first 2-DE maps of the soluble proteome of Arabidopsis cell suspensions. The comparative analysis of the Arabidopsis proteome in respect to different nutrient supplies shows that the culture medium may significantly influence the expression pattern of major soluble proteins in Arabidopsis cells. This work also constitutes an important step for further proteomic analysis concerning cell responses to abiotic or biotic stresses.

Integral fluctuation theorem for the housekeeping heat

The housekeeping heat $Q\hk$ is the dissipated heat necessary to maintain the violation of detailed balance in nonequilibrium steady states. By analyzing the evolution of its probability distribution, we prove an integral fluctuation theorem $\mean{\exp[-\beta Q\hk]}=1$ valid for arbitrary driven transitions between steady states. We discuss Gaussian limiting cases and the difference between the new theorem and both the Hatano-Sasa and the Jarzynski relation.

&cestflwr; Introducing Professor Lutz Nover, Plant Stress Section Editor

Dear Colleagues, Most of this issue of Cell Stress & Chaperones is devoted to papers that mine the Arabidopsis genomic database for new members of stress response gene families (for a brief review, see Martienssen and McCombie 2001). The results are frequently compared with those in other organisms, for which entire genomic databases are available. This issue is thus an appropriate vehicle for introducing Professor Lutz Nover as founding editor of our new section, “Plant Stress.” Since 1993, Lutz has been Professor of Molecular Cell Biology at the Biocenter of Goethe University in Frankfurt, Germany. He is presently Head of the Department of Molecular Cell Biology in the Botanical Institute at the Biocenter. He studied biology at Martin Luther University in Halle in the former East Germany. His PhD thesis was on alkaloid biosynthesis and its developmental control in Penicillium. Lutz began working on plant heat stress responses in 1978 while searching for inducible gene expression in tomato cell cultures. Working together, he and Klaus-Dieter Scharf observed that the induction of heat stress protein (Hsp) synthesis was connected with rapid dephosphorylation of ribosomal protein S6 (Scharf and Nover 1982). The pronounced molecular association of the prominent small Hsps in plants after heat stress led to the discovery of the heat stress granules. These are giant cytosolic multichaperone complexes that function as storage sites for housekeeping messenger ribonucleoproteins and heat stress transcription factor HsfA2 (Nover et al 1983, 1989; Scharf et al 1998; Kirschner et al 2000). During 1989 and 1990, the cloning and sequencing of the first plant heat stress transcription factors were accomplished, facilitated by a visit from K.-D. Scharf as a guest scientist in D. Baltimore's lab at the Whitehead Institute (Scharf et al 1990). Some plant Hsfs were found to be heat stress proteins in their own right. Tomato Hsfs were characterized in the following years with respect to their activator functions (Treuter et al 1993). Aromatic, hydrophobic, acidic amino acid motifs were defined as central elements of transcription-activating proteins in general (Doring et al 2000), and control of nuclear import and export of plant Hsfs was studied (Heerklotz et al 2001). In addition to the publications on the original studies described above, Lutz found time to write the first and most comprehensive compilation and critical analysis of the cellular stress response literature (Nover 1991). In the same year, he edited a second monograph that brought together reviews of the effects of heat stress on development in a range of organisms (Hightower and Nover 1991). These monographs demonstrated his versatility and broad range of thinking, which are excellent attributes for an editor. Cell Stress & Chaperones is already the beneficiary of Professor Nover's considerable editorial skills, and the present issue, for which Nover and Jan Miernyk were monitoring editors, offers ample evidence of this (Nover and Miernyk 2001). I would also like to thank Jan for suggesting the theme of this issue. To date, there have been only a few green papers in our journal. Professor Nover et al (1996) contributed a review on plant Hsfs. A second paper was contributed on chloroplast small Hsps (Harndahl et al 1999) and a third on a chloroplast transit peptide (Ivey and Bruce 2000). Thus, we have been open to publishing plant papers since the beginning of the journal, and we would like to encourage our colleagues in the plant stress response field to send their manuscripts to Cell Stress & Chaperones. We hope that the establishment of a dedicated section on plant stress, the appointment of a world renowned colleague in plant stress responses as section editor, and the publication of this issue on Arabidopsis will show our continuing commitment to intellectual cross-pollination in the stress response field.