Thermodynamics and bioenergetics

The mechanisms of action of mitochondrial targeting agents in cancer: inhibiting oxidative phosphorylation and inducing apoptosis

The tumor microenvironment affects the structure and metabolic function of mitochondria in tumor cells. This process involves changes in metabolic activity, an increase in the amount of reactive oxygen species (ROS) in tumor cells compared to normal cells, the production of more intracellular free radicals, and the activation of oxidative pathways. From a practical perspective, it is advantageous to develop drugs that target mitochondria for the treatment of malignant tumors. Such drugs can enhance the selectivity of treatments for specific cell groups, minimize toxic effects on normal tissues, and improve combinational treatments. Mitochondrial targeting agents typically rely on small molecule medications (such as synthetic small molecules agents, active ingredients of plants, mitochondrial inhibitors or autophagy inhibitors, and others), modified mitochondrial delivery system agents (such as lipophilic cation modification or combining other molecules to form targeted mitochondrial agents), and a few mitochondrial complex inhibitors. This article will review these compounds in three main areas: oxidative phosphorylation (OXPHOS), changes in ROS levels, and endogenous oxidative and apoptotic processes.

Myoglobin regulates fatty acid trafficking and lipid metabolism in mammary epithelial cells

Myoglobin (MB) is known to bind and deliver oxygen in striated muscles at high expression levels. MB is also expressed at much reduced levels in mammary epithelial cells, where the protein´s function is unclear. In this study, we aim to determine whether MB impacts fatty acid trafficking and facilitates aerobic fatty acid ß-oxidation in mammary epithelial cells. We utilized MB-wildtype versus MB-knockout mice and human breast cancer cells to examine the impact of MB and its oxygenation status on fatty acid metabolism in mouse milk and mammary epithelia. MB deficient cells were generated through CRISPR/Cas9 and TALEN approaches and exposed to various oxygen tensions. Fatty acid profiling of milk and cell extracts were performed along with cell labelling and immunocytochemistry. Our findings show that MB expression in mammary epithelial cells promoted fatty acid oxidation while reducing stearyl-CoA desaturase activity for lipogenesis. In cells and milk product, presence of oxygenated MB significantly elevated indices of limited fatty acid ß-oxidation, i.e., the organelle-bound removal of a C2 moiety from long-chain saturated or monounsaturated fatty acids, thus shifting the composition toward more saturated and shorter fatty acid species. Presence of the globin also increased cytoplasmic fatty acid solubility under normoxia and fatty acid deposition to lipid droplets under severe hypoxia. We conclude that MB can function in mammary epithelia as intracellular O2-dependent shuttle of oxidizable fatty acid substrates. MB's impact on limited oxidation of fatty acids could generate inflammatory mediator lipokines, such as 7-hexadecenoate. Thus, the novel functions of MB in breast epithelia described herein range from controlling fatty acid turnover and homeostasis to influencing inflammatory signalling cascade. Future work is needed to analyse to what extent these novel roles of MB also apply to myocytic cell physiology and malignant cell behaviour, respectively.

Empowering roots-Some current aspects of root bioenergetics

Roots of higher plants provide the shoot with nutrients and water. In exchange, they receive photosynthates, which serve both as energy source and building blocks for maintenance and growth. While studies in plant bioenergetics used to focus on photosynthesis, several more recent findings also aroused or renewed interest in energy conversion and allocation in roots. Root building costs were identified as a long-undervalued trait, which turned out to be highly relevant for stress tolerance and nutrient use efficiency. Reduced building costs per root length (e.g., by aerenchyma formation or by increasing the cell size) are beneficial for exploring the soil for nutrient-rich patches, especially in low-input agrosystems. Also, an apparent mismatch was frequently found between the root energy budget in the form of the ATP pool on the one side and the apparent costs on the other side, particularly the costs of membrane transport under stress conditions, e.g., the Na⁺ detoxification costs resulting from Na⁺ sequestration at the plasma membrane. Ion transport across the plasma membrane (and also endomembranes) is coupled to the proton motive force usually believed to be exclusively generated by H⁺ ATPases. Recently, an alternative mechanism, the biochemical pH clamp, was identified which relies on H⁺ formation and binding in the apoplast and the cytosol, respectively, driven by metabolism (so-called active buffering). On this background, several aspects of root bioenergetics are discussed. These are (1) root respiration in soil, with a critical view on calorimetric vs. gas exchange measurements; (2) processes of energy conversion in mitochondria with a special focus on the role of the alternative oxidases, which allow adjusting carbon flow through metabolic pathways to membrane transport processes; and (3) energy allocation, in particular to transport across the plasma membrane forming the interface to soil solution. A concluding remark is dedicated to modeling root bioenergetics for optimizing further breeding strategies. Apparent "energy spoilers" may bestow the plant with a yet unidentified advantage only unfolding their beneficial effect under certain environmental conditions.

Physical and chemical properties of carbon nanotubes in view of mechanistic neuroscience investigations. Some outlook from condensed matter, materials science and physical chemistry

The open border between non-living and living matter, suggested by increasingly emerging fields of nanoscience interfaced to biological systems, requires a detailed knowledge of nanomaterials properties. An account of the wide spectrum of phenomena, belonging to physical chemistry of interfaces, materials science, solid state physics at the nanoscale and bioelectrochemistry, thus is acquainted for a comprehensive application of carbon nanotubes interphased with neuron cells. This review points out a number of conceptual tools to further address the ongoing advances in coupling neuronal networks with (carbon) nanotube meshworks, and to deepen the basic issues that govern a biological cell or tissue interacting with a nanomaterial. Emphasis is given here to the properties and roles of carbon nanotube systems at relevant spatiotemporal scales of individual molecules, junctions and molecular layers, as well as to the point of view of a condensed matter or materials scientist. Carbon nanotube interactions with blood-brain barrier, drug delivery, biocompatibility and functionalization issues are also regarded.

Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches

Studying cell metabolism serves a plethora of objectives such as the enhancement of bioprocess performance, and advancement in the understanding of cell biology, of drug target discovery, and in metabolic therapy. Remarkable successes in these fields emerged from heuristics approaches, for instance, with the introduction of effective strategies for genetic modifications, drug developments and optimization of bioprocess management. However, heuristics approaches have showed significant shortcomings, such as to describe regulation of metabolic pathways and to extrapolate experimental conditions. In the specific case of bioprocess management, such shortcomings limit their capacity to increase product quality, while maintaining desirable productivity and reproducibility levels. For instance, since heuristics approaches are not capable of prediction of the cellular functions under varying experimental conditions, they may lead to sub-optimal processes. Also, such approaches used for bioprocess control often fail in regulating a process under unexpected variations of external conditions. Therefore, methodologies inspired by the systematic mathematical formulation of cell metabolism have been used to address such drawbacks and achieve robust reproducible results. Mathematical modelling approaches are effective for both the characterization of the cell physiology, and the estimation of metabolic pathways utilization, thus allowing to characterize a cell population metabolic behavior. In this article, we present a review on methodology used and promising mathematical modelling approaches, focusing primarily to investigate metabolic events and regulation. Proceeding from a topological representation of the metabolic networks, we first present the metabolic modelling approaches that investigate cell metabolism at steady state, complying to the constraints imposed by mass conservation law and thermodynamics of reactions reversibility. Constraint-based models (CBMs) are reviewed highlighting the set of assumed optimality functions for reaction pathways. We explore models simulating cell growth dynamics, by expanding flux balance models developed at steady state. Then, discussing a change of metabolic modelling paradigm, we describe dynamic kinetic models that are based on the mathematical representation of the mechanistic description of nonlinear enzyme activities. In such approaches metabolic pathway regulations are considered explicitly as a function of the activity of other components of metabolic networks and possibly far from the metabolic steady state. We have also assessed the significance of metabolic model parameterization in kinetic models, summarizing a standard parameter estimation procedure frequently employed in kinetic metabolic modelling literature. Finally, some optimization practices used for the parameter estimation are reviewed.

Thermal Resonance and Cell Behavior

From a thermodynamic point of view, living cell life is no more than a cyclic process. It starts with the newly separated daughter cells and restarts when the next generations grow as free entities. During this cycle, the cell changes its entropy. In cancer, the growth control is damaged. In this paper, we analyze the role of the volume–area ratio in the cell in relation to the heat exchange between cell and its environment in order to point out its effect on cancer growth. The result holds to a possible control of the cancer growth based on the heat exchanged by the cancer toward its environment and the membrane potential variation, with the consequence of controlling the ions fluxes and the related biochemical reactions. This second law approach could represent a starting point for a possible future support for the anticancer therapies, in order to improve their effectiveness for the untreatable cancers.

Statistical Mechanics of Non-Muscle Myosin IIA in Human Bone Marrow-Derived Mesenchymal Stromal Cells Seeded in a Collagen Scaffold: A Thermodynamic Near-Equilibrium Linear System Modified by the Tripeptide Arg-Gly-Asp (RGD)

Mesenchymal stromal cells (MSCs) were obtained from human bone marrow and amplified in cultures supplemented with human platelet lysate. Once semi-confluent, cells were seeded in solid collagen scaffolds that were rapidly colonized by the cells generating a 3D cell scaffold. Here, they acquired a myofibroblast phenotype and when exposed to appropriate chemical stimulus, developed tension and cell shortening, similar to those of striated and smooth muscle cells. Myofibroblasts contained a molecular motor-the non-muscle myosin type IIA (NMMIIA) whose crossbridge (CB) kinetics are dramatically slow compared with striated and smooth muscle myosins. Huxley's equations were used to determine the molecular mechanical properties of NMMIIA. Thank to the great number of NMMIIA molecules, we determined the statistical mechanics (SM) of MSCs, using the grand canonical ensemble which made it possible to calculate various thermodynamic entities such as the chemical affinity, statistical entropy, internal energy, thermodynamic flow, thermodynamic force, and entropy production rate. The linear relationship observed between the thermodynamic force and the thermodynamic flow allowed to establish that MSC-laden in collagen scaffolds were in a near-equilibrium stationary state (affinity ≪ RT), MSCs were also seeded in solid collagen scaffolds functionalized with the tripeptide Arg-Gly-Asp (RGD). This induced major changes in NMMIIA SM particularly by increasing the rate of entropy production. In conclusion, collagen scaffolds laden with MSCs can be viewed as a non-muscle contractile bioengineered tissue operating in a near-equilibrium linear regime, whose SM could be substantially modified by the RGD peptide.

Detecting Endogenous Microbial Metabolism and Differentiating Between Abiotic and Biotic Signals Observed by Bioelectrochemical Systems in Soils

Unambiguous detection of chemical and physical signatures of microbial life on Mars or other solar system bodies requires differentiation between signals produced by biotic and abiotic processes; instruments aimed at generalized in situ extant life detection would therefore increase the science return of a life-detection mission. Here, we investigate Bioelectrochemical Systems (BES) as a technique to measure microbial metabolism (which produces electrical current and redox changes) and distinguish between potential abiotic and biotic responses in environmental samples. Samples from inhabited niches should contain everything necessary to produce current, that is, catalysts (microorganisms) and fuel (nutrients). BES can also probe for inactive organisms in less energetically rich areas by adding a fuel to drive metabolism. A commercial potting soil and a Mars simulant soil were inoculated in the anodic chamber of microbial fuel cells, and current was monitored over time. Addition of a fuel (electron donor) source was tested for metabolic stimulation of endogenous microbes. Redox reactions between Mars simulant soil and the introduced electron donor (lactate) produced false-positive results, emphasizing the importance of careful interpretation of signals obtained. The addition of lactate to both soils resulted in enhanced biologically produced current, allowing stimulation and detection of dormant microbes. Our results demonstrate that BES provide an approach to detect metabolism in samples without prior knowledge of the organisms present, and that thorough electrochemical analyses and experimental design are necessary to determine if signals are biotic.

Membrane Transport of Nonelectrolyte Solutions in Concentration Polarization Conditions: Hr Form of the Kedem–Katchalsky–Peusner Equations

In this paper, the Kedem–Katchalsky equations in matrix form for nonhomogeneous ternary nonelectrolyte solutions were applied for interpretation of transport through the membrane mounted in horizontal plane. Coefficients Hijr, Hijr, and Hdetr=detHr (for nonhomogeneous solutions), Hij and Hdet=detH (for homogeneous solutions) (i, j ∈ {1, 2, 3}, r = A, B), ψij=HijA−HijB/Hij, and ψdet=HdetA−HdetB/Hdet were calculated on the basis of experimentally determined coefficients (Lp, σ1, σ2ω11, ω22, ω21, ω12, ζ1r, and ζ2r) for glucose in aqueous ethanol solutions and two configurations of the membrane system. From the calculations, it results that the values of coefficients H12r, H13r, H22r, H23r, H32r, H33r, and Hdetr depend nonlinearly on solution concentration as well as on a configuration of membrane system. Besides, the values of coefficients H21r, H12, H21, H22, H33r, and Hdet depend linearly on solution concentration. The value of coefficients H13, H23, and H33 do not depend on solution concentration. The coefficients ψ12, ψ13, ψ22 = ψ23, ψ32 = ψ33, and ψdet depend nonlinearly on solution concentration and for C¯1 ≈ 9.24 mol m−3 are equal to zero. For C¯1 < 9.24 mol m−3, the values of coefficients ψ12 and ψ13 are negative and for C¯1 > 9.23 mol m−3, positive. In contrast, the values of coefficients ψ22 = ψ23, ψ32 = ψ33, and ψdet for C¯1 < 9.24 mol m−3 are positive and for C¯1 > 9.24 mol m−3, negative. For ψ = 0, we can observe nonconvective state, in which concentration Rayleigh number reaches the critical value RC = 1691.09, for ψ<0 is convective state with convection directed straight down and for ψ>0 is convective state with convection directed straight up.

A 'Nobel' Look at Metabolism

Metabolism has recently been in the spotlight because of technical advances in metabolite measurement; however, it is not a new topic in the Nobel Prize's history. Emerging evidence suggests that metabolism is more complex than was previously believed. Retrospective analysis of the Nobel Prize-winning metabolic discoveries may inspire future studies.

Two-ion theory of energy coupling in ATP synthesis rectifies a fundamental flaw in the governing equations of the chemiosmotic theory

The vital coupled processes of oxidative phosphorylation and photosynthetic phosphorylation synthesize molecules of adenosine-5'-triphosphate (ATP), the universal biological energy currency, and sustain all life on our planet. The chemiosmotic theory of energy coupling in oxidative and photophosphorylation was proposed by Mitchell >50years ago. It has had a contentious history, with part of the accumulated body of experimental evidence supporting it, and part of it in conflict with the theory. Although the theory was strongly criticized by many prominent scientists, the controversy has never been resolved. Here, the mathematical steps of Mitchell's original derivation leading to the principal equation of the chemiosmotic theory are scrutinized, and a fundamental flaw in them has been identified. Surprisingly, this flaw had not been detected earlier. Discovery of such a defect negates, or at least considerably weakens, the theoretical foundations on which the chemiosmotic theory is based. Ad hoc or simplistic ways to remedy this defect are shown to be scientifically unproductive and sterile. A novel two-ion theory of biological energy coupling salvages the situation by rectifying the fundamental flaw in the chemiosmotic theory, and the governing equations of the new theory have been shown to accurately quantify and predict extensive recent experimental data on ATP synthesis by F₁F_O-ATP synthase without using adjustable parameters. Some major biological implications arising from the new thinking are discussed. The principles of energy transduction and coupling proposed in the new paradigm are shown to be of a very general and universal nature. It is concluded that the timely availability after a 25-year research struggle of Nath's torsional mechanism of energy transduction and ATP synthesis is a rational alternative that has the power to solve the problems arising from the past, and also meet present and future challenges in this important interdisciplinary field of research.

Linear irreversible thermodynamics and Onsager reciprocity for information-driven engines

In the recent progress in nonequilibrium thermodynamics, information has been recognized as a kind of thermodynamic resource that can drive thermodynamic current without any direct energy injection. In this paper, we establish the framework of linear irreversible thermodynamics for a broad class of autonomous information processing. In particular, we prove that the Onsager reciprocity holds true with information: The linear response matrix is well-defined and is shown symmetric with both of the information affinity and the conventional thermodynamic affinity. As an application, we derive a universal bound for the efficiency at maximum power for information-driven engines in the linear regime. Our result reveals the fundamental role of information flow in linear irreversible thermodynamics.

The thermodynamic efficiency of ATP synthesis in oxidative phosphorylation

As the chief energy source of eukaryotic cells, it is important to determine the thermodynamic efficiency of ATP synthesis in oxidative phosphorylation (OX PHOS). Previous estimates of the thermodynamic efficiency of this vital process have ranged from Lehninger's original back-of-the-envelope calculation of 38% to the often quoted value of 55-60% in current textbooks of biochemistry, to high values of 90% from recent information theoretic considerations, and reports of realizations of close to ideal 100% efficiencies by single molecule experiments. Hence this problem has been reinvestigated from first principles. The overall thermodynamic efficiency of ATP synthesis in the mitochondrial energy transduction OX PHOS process has been found to lie between 40 and 41% from four different approaches based on a) estimation using structural and biochemical data, b) fundamental nonequilibrium thermodynamic analysis, c) novel insights arising from Nath's torsional mechanism of energy transduction and ATP synthesis, and d) the overall balance of cellular energetics. The torsional mechanism also offers an explanation for the observation of a thermodynamic efficiency approaching 100% in some experiments. Applications of the unique, molecular machine mode of functioning of F₁F_O-ATP synthase involving direct inter-conversion of chemical and mechanical energies in the design and fabrication of novel, man-made mechanochemical devices have been envisaged, and some new ways to exorcise Maxwell's demon have been proposed. It is hoped that analysis of the fundamental problem of energy transduction in OX PHOS from a fresh perspective will catalyze new avenues of research in this interdisciplinary field.

Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions

Thermodynamics is an important driving factor for chemical processes and for life. Earlier work has shown that each cancer has its own molecular signaling network that supports its life cycle and that different cancers have different thermodynamic entropies characterizing their signaling networks. The respective thermodynamic entropies correlate with 5-year survival for each cancer. We now show that by overlaying mRNA transcription data from a specific tumor type onto a human protein-protein interaction network, we can derive the Gibbs free energy for the specific cancer. The Gibbs free energy correlates with 5-year survival (Pearson correlation of -0.7181, p value of 0.0294). Using an expression relating entropy and Gibbs free energy to enthalpy, we derive an empirical relation for cancer network enthalpy. Combining this with previously published results, we now show a complete set of extensive thermodynamic properties and cancer type with 5-year survival.

The Balance of Fluid and Osmotic Pressures across Active Biological Membranes with Application to the Corneal Endothelium

The movement of fluid and solutes across biological membranes facilitates the transport of nutrients for living organisms and maintains the fluid and osmotic pressures in biological systems. Understanding the pressure balances across membranes is crucial for studying fluid and electrolyte homeostasis in living systems, and is an area of active research. In this study, a set of enhanced Kedem-Katchalsky (KK) equations is proposed to describe fluxes of water and solutes across biological membranes, and is applied to analyze the relationship between fluid and osmotic pressures, accounting for active transport mechanisms that propel substances against their concentration gradients and for fixed charges that alter ionic distributions in separated environments. The equilibrium analysis demonstrates that the proposed theory recovers the Donnan osmotic pressure and can predict the correct fluid pressure difference across membranes, a result which cannot be achieved by existing KK theories due to the neglect of fixed charges. The steady-state analysis on active membranes suggests a new pressure mechanism which balances the fluid pressure together with the osmotic pressure. The source of this pressure arises from active ionic fluxes and from interactions between solvent and solutes in membrane transport. We apply the proposed theory to study the transendothelial fluid pressure in the in vivo cornea, which is a crucial factor maintaining the hydration and transparency of the tissue. The results show the importance of the proposed pressure mechanism in mediating stromal fluid pressure and provide a new interpretation of the pressure modulation mechanism in the in vivo cornea.

Bioengineering thermodynamics of biological cells

BACKGROUND

Cells are open complex thermodynamic systems. They can be also regarded as complex engines that execute a series of chemical reactions. Energy transformations, thermo-electro-chemical processes and transports phenomena can occur across the cells membranes. Moreover, cells can also actively modify their behaviours in relation to changes in their environment.

METHODS

Different thermo-electro-biochemical behaviours occur between health and disease states. But, all the living systems waste heat, which is no more than the result of their internal irreversibility. This heat is dissipated into the environment. But, this wasted heat represent also a sort of information, which outflows from the cell toward its environment, completely accessible to any observer.

RESULTS

The analysis of irreversibility related to this wasted heat can represent a new approach to study the behaviour of the cells themselves and to control their behaviours. So, this approach allows us to consider the living systems as black boxes and analyze only the inflows and outflows and their changes in relation to the modification of the environment. Therefore, information on the systems can be obtained by analyzing the changes in the cell heat wasted in relation to external perturbations.

CONCLUSIONS

The bioengineering thermodynamics bases are summarized and used to analyse possible controls of the calls behaviours based on the control of the ions fluxes across the cells membranes.

Statistical Mechanics of the Human Placenta: A Stationary State of a Near-Equilibrium System in a Linear Regime

All near-equilibrium systems under linear regime evolve to stationary states in which there is constant entropy production rate. In an open chemical system that exchanges matter and energy with the exterior, we can identify both the energy and entropy flows associated with the exchange of matter and energy. This can be achieved by applying statistical mechanics (SM), which links the microscopic properties of a system to its bulk properties. In the case of contractile tissues such as human placenta, Huxley's equations offer a phenomenological formalism for applying SM. SM was investigated in human placental stem villi (PSV) (n = 40). PSV were stimulated by means of KCl exposure (n = 20) and tetanic electrical stimulation (n = 20). This made it possible to determine statistical entropy (S), internal energy (E), affinity (A), thermodynamic force (A / T) (T: temperature), thermodynamic flow (v) and entropy production rate (A / T x v). We found that PSV operated near equilibrium, i.e., A ≺≺ 2500 J/mol and in a stationary linear regime, i.e., (A / T) varied linearly with v. As v was dramatically low, entropy production rate which quantified irreversibility of chemical processes appeared to be the lowest ever observed in any contractile system.

Rewriting the epigenetic code for tumor resensitization: a review

In cancer chemotherapy, one axiom, which has practically solidified into dogma, is that acquired resistance to antitumor agents or regimens, nearly inevitable in all patients with metastatic disease, remains unalterable and irreversible, rendering therapeutic rechallenge futile. However, the introduction of epigenetic therapies, including histone deacetylase inhibitors (HDACis) and DNA methyltransferase inhibitors (DNMTIs), provides oncologists, like computer programmers, with new techniques to “overwrite” the modifiable software pattern of gene expression in tumors and challenge the “one and done” treatment prescription. Taking the epigenetic code-as-software analogy a step further, if chemoresistance is the product of multiple nongenetic alterations, which develop and accumulate over time in response to treatment, then the possibility to hack or tweak the operating system and fall back on a “system restore” or “undo” feature, like the arrow icon in the Windows XP toolbar, reconfiguring the tumor to its baseline nonresistant state, holds tremendous promise for turning advanced, metastatic cancer from a fatal disease into a chronic, livable condition. This review aims 1) to explore the potential mechanisms by which a group of small molecule agents including HDACis (entinostat and vorinostat), DNMTIs (decitabine and 5-azacytidine), and redox modulators (RRx-001) may reprogram the tumor microenvironment from a refractory to a nonrefractory state, 2) highlight some recent findings, and 3) discuss whether the current “once burned forever spurned” paradigm in the treatment of metastatic disease should be revised to promote active resensitization attempts with formerly failed chemotherapies.

A thermo-physical analysis of the proton pump vacuolar-ATPase: the constructal approach

Pumping protons across a membrane was a critical step at the origin of life on earth, and it is still performed in all living organisms, including in human cells. Proton pumping is paramount to keep normal cells alive, e.g. for lysosomal digestion and for preparing peptides for immune recognition, but it goes awry in cancer cells. They acidify their microenvironment hence membrane voltage is lowered, which in turn induces cell proliferation, a hallmark of cancer. Proton pumping is achieved by means of rotary motors, namely vacuolar ATPases (V-ATPase), which are present at many of the multiple cellular interfaces. Therefore, we undertook an examination of the thermodynamic properties of V-ATPases. The principal result is that the V-ATPase-mediated control of the cell membrane potential and the related and consequent environmental pH can potentially represent a valuable support strategy for anticancer therapies. A constructal theory approach is used as a new viewpoint to study how V-ATPase can be modulated for therapeutic purposes. In particular, V-ATPase can be regulated by using external fields, such as electromagnetic fields, and a theoretical approach has been introduced to quantify the appropriate field strength and frequency for this new adjuvant therapeutic strategy.

Success and failure of colloidal approaches in adhesion of microorganisms to surfaces

Biofilms are communities of cells attached to surfaces, their contributions to biological process may be either a benefit or a threat depending on the microorganism involved and on the type of substrate and environment. Biofilm formation is a complex series of steps; due to the size of microorganisms, the initial phase of biofilm formation, the bacterial adhesion to the surface, has been studied and modeled using theories developed in colloidal science. In this review the application of approaches such as Derjaguin, Landau, Verwey, Overbeek (DLVO) theory and its extended version (xDLVO), to bacterial adhesion is described along with the suitability and applicability of such approaches to the investigation of the interface phenomena regulating cells adhesion. A further refinement of the xDLVO theory encompassing the brush model is also discussed. Finally, the evidences of phenomena neglected in colloidal approaches, such as surface heterogeneity and fluid flow, likely to be the source of failure are defined.

Different chemical reaction times between normal and solid cancer cells

Entropy generation approach has been developed in order to use it for the analysis of complex systems with particular regards to biological systems in order to evaluate their stationary states. The entropy generation is related to the transport processes related to energy flows. Moreover, cancer can be described as an open complex dynamic and self-organizing system. Using the entropy generation approach it is possible to point out different chemical reaction time between normal and solid cancer cells.

From cycling between coupled reactions to the cross-bridge cycle: mechanical power output as an integral part of energy metabolism

ATP delivery and its usage are achieved by cycling of respective intermediates through interconnected coupled reactions. At steady state, cycling between coupled reactions always occurs at zero resistance of the whole cycle without dissipation of free energy. The cross-bridge cycle can also be described by a system of coupled reactions: one energising reaction, which energises myosin heads by coupled ATP splitting, and one de-energising reaction, which transduces free energy from myosin heads to coupled actin movement. The whole cycle of myosin heads via cross-bridge formation and dissociation proceeds at zero resistance. Dissipation of free energy from coupled reactions occurs whenever the input potential overcomes the counteracting output potential. In addition, dissipation is produced by uncoupling. This is brought about by a load dependent shortening of the cross-bridge stroke to zero, which allows isometric force generation without mechanical power output. The occurrence of maximal efficiency is caused by uncoupling. Under coupled conditions, Hill’s equation (velocity as a function of load) is fulfilled. In addition, force and shortening velocity both depend on [Ca²⁺]. Muscular fatigue is triggered when ATP consumption overcomes ATP delivery. As a result, the substrate of the cycle, [MgATP²⁻], is reduced. This leads to a switch off of cycling and ATP consumption, so that a recovery of [ATP] is possible. In this way a potentially harmful, persistent low energy state of the cell can be avoided.

Comparative statistical mechanics of myosin molecular motors in rat heart, diaphragm and tracheal smooth muscle

PURPOSE

Statistical mechanics establishes a link between microscopic properties of matter and its bulk properties. A. Huxley's equations (1957) [1] provide the necessary phenomenological formalism to use statistical mechanics.

METHODS

We compared statistical mechanics in rat diaphragm in tetanus (tet; n=10) and twitch (tw; n=12) modes, in heart in twitch mode (n=20), and in tracheal smooth muscle in tetanus mode (TSM; n=10). This powerful tool makes it possible to determine: (i) statistical entropy (S) which is related to the dispersal of energy and represents a measure of the degree of disorder in muscular system; (ii) thermodynamic force A/T (chemical affinity A and temperature T); (iii) thermodynamic flow (υ); (iv) entropy production rate (A/T×υ), which quantifies irreversible chemical processes generated by myosin crossbridge (CB) molecular motors.

RESULTS

All muscles studied operated near equilibrium, i.e., A<<2500J/mol and in a stationary linear regime, i.e., A/T varied linearly with υ. The heart operated farther from equilibrium than both diaphragm (tet and tw) and TSM, as attested by its high entropy production rate. S was of the same order of magnitude in heart and TSM but lower in diaphragm (tet and tw).

CONCLUSION

CB kinetics derived from A. Huxley's equations conferred a characteristic profile in terms of statistical mechanics on each muscle type. All studied muscles differed in terms of statistical entropy, chemical affinity, and entropy production rate. Stimulation mode (tet and tw) modulated CB kinetics and statistical mechanics. All muscle types operated near equilibrium and in a stationary linear regime.

Energetics of glucose metabolism: a phenomenological approach to metabolic network modeling

A new formalism to describe metabolic fluxes as well as membrane transport processes was developed. The new flux equations are comparable to other phenomenological laws. Michaelis-Menten like expressions, as well as flux equations of nonequilibrium thermodynamics, can be regarded as special cases of these new equations. For metabolic network modeling, variable conductances and driving forces are required to enable pathway control and to allow a rapid response to perturbations. When applied to oxidative phosphorylation, results of simulations show that whole oxidative phosphorylation cannot be described as a two-flux-system according to nonequilibrium thermodynamics, although all coupled reactions per se fulfill the equations of this theory. Simulations show that activation of ATP-coupled load reactions plus glucose oxidation is brought about by an increase of only two different conductances: a [Ca²⁺] dependent increase of cytosolic load conductances, and an increase of phosphofructokinase conductance by [AMP], which in turn becomes increased through [ADP] generation by those load reactions. In ventricular myocytes, this feedback mechanism is sufficient to increase cellular power output and O₂ consumption several fold, without any appreciable impairment of energetic parameters. Glucose oxidation proceeds near maximal power output, since transformed input and output conductances are nearly equal, yielding an efficiency of about 0.5. This conductance matching is fulfilled also by glucose oxidation of β-cells. But, as a price for the metabolic mechanism of glucose recognition, β-cells have only a limited capability to increase their power output.

Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

Background

Geobacter sulfurreducens is a member of the Geobacter species, which are capable of oxidation of organic waste coupled to the reduction of heavy metals and electrode with applications in bioremediation and bioenergy generation. While the metabolism of this organism has been studied through the development of a stoichiometry based genome-scale metabolic model, the associated regulatory network has not yet been well studied. In this manuscript, we report on the implementation of a thermodynamics based metabolic flux model for Geobacter sulfurreducens. We use this updated model to identify reactions that are subject to regulatory control in the metabolic network of G. sulfurreducens using thermodynamic variability analysis.

Findings

As a first step, we have validated the regulatory sites and bottleneck reactions predicted by the thermodynamic flux analysis in E. coli by evaluating the expression ranges of the corresponding genes. We then identified ten reactions in the metabolic network of G. sulfurreducens that are predicted to be candidates for regulation. We then compared the free energy ranges for these reactions with the corresponding gene expression fold changes under conditions of different environmental and genetic perturbations and show that the model predictions of regulation are consistent with data. In addition, we also identify reactions that operate close to equilibrium and show that the experimentally determined exchange coefficient (a measure of reversibility) is significant for these reactions.

Conclusions

Application of the thermodynamic constraints resulted in identification of potential bottleneck reactions not only from the central metabolism but also from the nucleotide and amino acid subsystems, thereby showing the highly coupled nature of the thermodynamic constraints. In addition, thermodynamic variability analysis serves as a valuable tool in estimating the ranges of Δ_rG' of every reaction in the model leading to the prediction of regulatory sites in the metabolic network, thereby characterizing the regulatory network in both a model organism such as E. coli as well as a non model organism such as G. sulfurreducens.

Thermodynamics of organisms in the context of dynamic energy budget theory

We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.

Statistical mechanics of myosin molecular motors in skeletal muscles

Statistical mechanics provides the link between microscopic properties of matter and its bulk properties. The grand canonical ensemble formalism was applied to contracting rat skeletal muscles, the soleus (SOL, n = 30) and the extensor digitalis longus (EDL, n = 30). Huxley's equations were used to calculate force (pi) per single crossbridge (CB), probabilities of six steps of the CB cycle, and peak muscle efficiency (Eff(max)). SOL and EDL were shown to be in near-equilibrium (CB cycle affinity 2.5 kJ/mol) and stationary state (linearity between CB cycle affinity and myosin ATPase rate). The molecular partition function (z) was higher in EDL (1.126+/-0.005) than in SOL (1.050+/-0.003). Both pi and Eff(max) were lower in EDL (8.3+/-0.1 pN and 38.1+/-0.2%, respectively) than in SOL (9.2+/-0.1 pN and 42.3+/-0.2%, respectively). The most populated step of the CB cycle was the last detached state (D3) (probability P(D3): 0.890+/-0.004 in EDL and 0.953+/-0.002 in SOL). In each muscle group, both pi and Eff(max) linearly decreased with z and statistical entropy and increased with P(D3). We concluded that statistical mechanics and Huxley's formalism provided a powerful combination for establishing an analytical link between chemomechanical properties of CBs, molecular partition function and statistical entropy.

Local dissipation and coupling properties of cellular oscillators: a case study on calcium oscillations

Synchronised signal transduction between cells is crucial, since it assures fast and immutable information processing, which is vital for flawless functioning of living organisms. The question arises how to recognise the ability of a cell to be easily coupled with other cells. In the present paper, we investigate the system properties that determine best coupling abilities and assure the most efficient signal transduction between cells. A case study is done for intercellular calcium oscillations. For a particular diffusion-like coupled system of cellular oscillators, we determined the minimal gap-junctional permeability that is necessary for synchronisation of initially asynchronous oscillators. Our results show that dissipation is a crucial system property that determines the coupling ability of cellular oscillators. We found that low dissipation assures synchronisation of coupled cells already at very low gap-junctional permeability, whereas highly dissipative oscillators require much higher gap-junctional permeability in order to synchronise. The results are discussed in the sense of their biological importance for systems where the synchronous responses of cells were recognised to be indispensable for appropriate physiological functioning of the tissue.

Kemp elimination in membrane mimetic reaction media: probing catalytic properties of catanionic vesicles formed from double-tailed amphiphiles

The rate-determining deprotonation of 5-nitrobenzisoxazole (Kemp elimination) by hydroxide is efficiently catalyzed by vesicles formed from dimethyldioctadecylammonium chloride (C(18)()C(18)()(+)()). Gradual addition of sodium didecyl phosphate (C(10)()C(10)()(-)()) leads to the formation of catanionic vesicles, which were characterized by cryo-electron microscopy, and their main phase transition temperatures (DSC) and zeta-potentials. Increasing percentages of C(10)()C(10)()(-)() in the vesicular bilayers decrease the catalysis of the Kemp elimination. A detailed kinetic analysis, supported by consideration of substrate binding site polarities and counterion binding percentages, suggest that the catalytic effects of C(18)()C(18)()(+)()/C(10)()C(10)()(-)() catanionic vesicles are primarily determined by the binding of catalytically active hydroxide ions to the vesicular surface area. The formation of neutral microdomains between 10 and 30 mol % of C(10)()C(10)()(-)() in the bilayer, as revealed by DSC, is not apparent from the catalytic effects found for these vesicles. Interestingly, the catalytic effects observed for 50 mol % C(10)()C(10)()(-)() in the catanionic vesicles indicate an asymmetric distribution of C(18)()C(18)()(+)() and C(10)()C(10)()(-)() over the bilayer leaflets. The overall kinetic results illustrate the highly complex mix of factors which determines catalytic effects on reactions occurring in biological cell membranes.