The model of T4 phage, Lambda phage and Escherichia coli is often used in research on virus-host interactions. This paper reports for the first time the thermodynamic driving force of biosynthesis, catabolism and metabolism for the three organisms, on the M9 medium. Moreover, the influence of activities of nutrients and metabolic products is analyzed. All three organisms were found to have very similar Gibbs energies of metabolism. Moreover, since they share the same catabolism, their Gibbs energies of catabolism are identical. However, Gibbs energies of biosynthesis differ. The calculated thermodynamic properties have been used to explain the coexistence of both bacteria and phages in a dynamic equilibrium in natural ecosystems.

To understand microbial growth with mathematical models has a long tradition that dates back to the pioneering work of Jacques Monod in the 1940s. Growth laws are simple mathematical expressions that aim at describing growth rates of microbes as functions of external parameters, in particular nutrient concentrations. These laws are now widely applied to construct, e.g., dynamic ecosystem models. However, to explain the growth laws from underlying (first) principles is extremely challenging. In the second half of the 20th century, numerous experimental approaches aimed at precisely measuring heat production during microbial growth to determine the entropy balance in a growing cell and to quantify the exported entropy. This has led to the development of thermodynamic theories of microbial growth, which have generated fundamental understanding and identified principle limitations of the growth process. Whereas these approaches considered a growing microbe as a black box, modern theories heavily rely on genomic resources to describe and model genome-scale networks to explain microbial growth. Interestingly, however, thermodynamic constraints are often included in modern modelling approaches only in a rather superficial fashion, and it appears that recent modelling approaches and classical theories are disconnected fields. In order to stimulate a closer interaction between these fields, we here review various theoretical approaches that aim at describing microbial growth based on thermodynamic principles. We start with classical black-box models of cellular growth, and continue with genome-scale modelling approaches that include thermodynamics, before we place these models in the context of fundamental considerations based on non-equilibrium statistical mechanics. We conclude by identifying conceptual overlaps between the fields and suggest how the various types of theories and models can be integrated. We outline how concepts from one approach may help to inform or constrain another, and we demonstrate how genome-scale models can be used to infer classical black-box parameters, which are experimentally accessible in growth experiments. Such integration will allow understanding to what extent microbes can be viewed as thermodynamic machines, and how close they operate to theoretical optima.

Cognitive functions are based on neuronal plasticity, which is provided by various mechanisms involving numerous bioactive molecules, the most important of which are endocannabinoids (eCBs). Over the past three decades, a lot of data have been accumulated on the involvement of eCBs in the mechanisms of memory and other cognitive functions. These functions are impaired in neurodegenerative diseases such as Alzheimer's disease (AD) and temporal lobe epilepsy (TLE). The main pathological feature of neurons in AD and TLE is increased excitability; therefore, an activation of the endocannabinoid system, which controls cellular excitation, may be a promising approach in their therapy. The available information about the effect of (endo)cannabinoids on cognitive functions is contradictory, which may depend on the drugs used, their dose, and the experimental conditions. There is an extensive literature indicating a protective effect of cannabinoids in the treatment of neurodegenerative diseases in humans and in animal models of cognitive deficits. This review, focusing on the recent researches, is devoted to the analysis of the effects of endocannabinoid system activation on cognitive functions in norm and in the brain with neurodegeneration that occurs in AD and TLE diseases. Possible reasons for inconsistencies in the available data are discussed.

Different hypotheses of carcinogenesis have been proposed based on local genetic factors and physiologic mechanisms. It is assumed that changes of the metric invariants of a biologic system (BS) determine general mechanisms of cancer development. Numerous data demonstrate an existence of three invariant feedback patterns of BS: negative feedback (NFB), positive feedback (PFB) and reciprocal links (RL). These base patterns represent basis elements of a Lie algebra sl(2,R) and imaginary part of coquaternion. Considering coquaternion as a model of a functional core of a BS, conditions of the system can be identified with the points of three families of hypersurfaces in R42: hyperboloids of one sheet, hyperboloids of two sheets and double-cones. Corresponding quadratic form relates negative and positive entropy contributions of base elements to the energy level of the system, so that anabolic states of the system will correspond to the points of a hyperboloid of one sheet, while catabolic conditions to the points of a hyperboloid of two sheets. Equilibrium states will lie in a double cone. Hypothetically anabolic and catabolic states dominate intermittently oscillating around the equilibrium. Deterioration of base elements increases positive entropy and causes domination of catabolic states which is the main metabolic determinant of cancer. Corresponding trajectory of a malfunctioning system will have a tendency to remain inside the double cone.

Different hypotheses of carcinogenesis have been proposed based on local genetic factors and physiologic mechanisms. It is assumed that changes of the metric invariants of a biologic system (BS) determine general mechanisms of cancer development. Numerous data demonstrate an existence of three invariant feedback patterns of BS: negative feedback (NFB), positive feedback (PFB) and reciprocal links (RL). These base patterns represent basis elements of a Lie algebra and imaginary part of coquaternion. Considering coquaternion as a model of a functional core of a BS, conditions of the system can be identified with the points of three families of hypersurfaces in R⁴₂: hyperboloids of one sheet, hyperboloids of two sheets and double-cones. Corresponding quadratic form relates negative and positive entropy contributions of base elements to the energy level of the system, so that anabolic states of the system will correspond to the points of a hyperboloid of one sheet, while catabolic conditions to the points of a hyperboloid of two sheets. Equilibrium states will lie in a double cone. Hypothetically anabolic and catabolic states dominate intermittently oscillating around the equilibrium. Deterioration of base elements increases positive entropy and causes domination of catabolic states which is the main metabolic determinant of cancer. Corresponding trajectory of a malfunctioning system will have a tendency to remain inside the double cone.

The heat and matter transfer during glucose catabolism in living systems and their relation with entropy production are a challenging subject of the classical thermodynamics applied to biology. In this respect, an analogy between mechanics and thermodynamics has been performed via the definition of the entropy density acceleration expressed by the time derivative of the rate of entropy density and related to heat and matter transfer in minimum living systems. Cells are regarded as open thermodynamic systems that exchange heat and matter resulting from irreversible processes with the intercellular environment. Prigogine’s minimum energy dissipation principle is reformulated using the notion of entropy density acceleration applied to glucose catabolism. It is shown that, for out-of-equilibrium states, the calculated entropy density acceleration is finite and negative and approaches as a function of time a zero value at global thermodynamic equilibrium for heat and matter transfer independently of the cell type and the metabolic pathway. These results could be important for a deeper understanding of entropy generation and its correlation with heat transfer in cell biology with special regard to glucose catabolism representing the prototype of irreversible reactions and a crucial metabolic pathway in stem cells and cancer stem cells.

Extensive genome structure variation, such as copy number variations (CNVs) and presence/absence variations, is the basis for the remarkable maize genetic diversity; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication of the maize 9-lipoxygenase gene, ZmLOX5, leads to increased resistance of maize to herbivory by fall armyworms (FAW). Previously, we showed that ZmLOX5-derived oxylipins are required for defense against chewing insect herbivores and identified several inbred lines, including Yu796, that contained duplicated CNVs of ZmLOX5, referred to as Yu796-2×LOX5. To test whether introgression of the Yu796-2×LOX5 locus into the herbivore-susceptible B73 background that contains a single ZmLOX5 gene is a feasible approach to increase resistance, we generated a series of near-isogenic lines that contained either 2, 1 or 0 copies of the Yu796-2×LOX5 locus in the B73 background by six back crosses (BC6). Droplet digital PCR (ddPCR) confirmed the successful introgression of the Yu796-2×LOX5 locus in B73. The resulting B73-2×LOX5 inbred line displayed increased resistance against FAW associated with increased expression of ZmLOX5, increased wound-induced production of its primary oxylipin product, the α-ketol, 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (9,10-KODA), and the downstream defense hormones regulated by this molecule, 12-oxo-phytodienoic acid (12-OPDA) and abscisic acid (ABA). Surprisingly, wound-induced JA-Ile production was not increased in B73-2×LOX5, resulting from the increased JA catabolism. Furthermore, B73-2×LOX5 displayed enhanced drought tolerance likely due to increased ABA and 12-OPDA content. Taken together, this study revealed that the duplicated CNV of ZmLOX5 quantitively contributes to maize antiherbivore defense and presents proof-of-concept evidence that the introgression of naturally occurring duplicated CNVs of a defensive gene into the productive, but susceptible, crop varieties is a feasible breeding approach for enhancing plant resistance to herbivory and tolerance to abiotic stress.