Living systems are open systems, where the laws of nonequilibrium thermodynamics play the important role. Therefore, studying living systems from a nonequilibrium thermodynamic aspect is interesting and useful. In this review, we briefly introduce th...
Xylanases have a broad range of applications in agro-industrial processes. In this study, we report on the discovery and characterization of a new thermotolerant GH10 xylanase from Bacillus safensis, designated as BsXyn10. The xylanase gene (bsxyn10)...
13 November 2024
Methicillin-resistant Staphylococcus aureus (MRSA) is associated with the acquisition of nosocomial infections, community-acquired infections, and infections related to livestock animals. In the pursuit of molecular targets in the development process...
Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to convert sp...
A general theory explaining how electromagnetic waves affect cells and biological systems has not been completely accepted yet; nevertheless, extremely low-frequency electromagnetic fields (ELF-EMFs) can interfere with and modify several molecular ce...
This study focuses on biochemical pathways of complex biochemical formation, taking into account various thermodynamic parameters that change as the complexity and molecular weight of complex molecules increase. We conducted a study of the co-directi...
Modelling is a tool used to decipher the biochemical mechanisms involved in transcriptional control. Experimental evidence in genetics is usually supported by theoretical models in order to evaluate the effects of all the possible interactions that c...
Living systems waste heat in their environment. This is the measurable effect of the irreversibility of the biophysical and biochemical processes fundamental to their life. Non-equilibrium thermodynamics allows us to analyse the ion fluxes through th...
There is a remarkable wealth of thermodynamic information in freely accessible databases, the LSER database being a classical example. The LSER, or Abraham solvation parameter model, is a very successful predictive tool in a variety of applications i...
Quinone/hydroquinone couples play a crucial role in a variety of biochemical processes and chemical syntheses. Extending from our previous work, a practical dataset including the thermodynamic driving forces of 12 chemical processes for 118 quinone/h...
We review a coherent mesoscopic presentation of thermodynamics and fluctuations far from and near equilibrium, applicable to chemical reactions, energy transfer and transport processes, and electrochemical systems. Both uniform and spatially dependen...
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we...
Inulinases are enzymes involved in the hydrolysis of inulin, which can be used in the food industry to produce high-fructose syrups and fructo-oligosaccharides. For this purpose, different Aspergillus strains and substrates were tested for inulinase...
A cell signaling system is in a non-equilibrium state, and it includes multistep biochemical signaling cascades (BSCs), which involve phosphorylation of signaling molecules, such as mitogen-activated protein kinase (MAPK) pathways. In this study, the...
Ion flux through membrane channels is passively driven by the electrochemical potential differences across the cell membrane. Nonequilibrium thermodynamics has been successful in explaining transport mechanisms, including the ion transport phenomenon...
In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting...
The synthetic properties of the Thiamine diphosphate (ThDP)-dependent pyruvate dehydrogenase E1 subunit from Escherichia coli (EcPDH E1) was assessed for carboligation reactions with aliphatic ketoacids. Due to its role in metabolism, EcPDH E1 was pr...
Thermodynamics studies the transformations of energy occurring in open systems. Living systems, with particular reference to cells, are complex systems in which energy transformations occur. Thermo-electro-chemical processes and transports occur acro...
The seed represents a critical stage in the life cycle of flowering plants. It corresponds to a dry structure carrying the plant embryo in dormant or quiescent state. Orthodox seeds possess a very low water content, preventing biochemical reactions,...
Chitin is an effective sorbent which can be used in environmental monitoring, beyond obvious applications in withholding metal-containing pollutants from wastewater- or nuclear fuel reprocessing flows, since background levels in (purified) chitin are...
Darwinian fitness describes the capacity of an organism to appropriate resources from the environment and to convert these resources into net-offspring production. Studies of competition between related types indicate that fitness is analytically des...
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...
In this paper we review various information-theoretic characterizations of the approach to equilibrium in biological systems. The replicator equation, evolutionary game theory, Markov processes and chemical reaction networks all describe the dynamics...
Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular re...
For many years, we have devoted our research to the study of the thermodynamic properties of hydrophobic hydration processes in water, and we have proposed the Ergodic Algorithmic Model (EAM) for maintaining the thermodynamic properties of any hydrop...
Bacteriophage endolysins degrade the bacterial peptidoglycan and are considered enzymatic alternatives to small-molecule antibiotics. In particular, the multimeric streptococcal endolysin PlyC has appealing antibacterial properties. However, a compre...
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of...
The intra-annual heat exchange process has a considerable influence on the energy circulation, material metabolism, and ecological succession of lakes. The input and output of heat in an ice-covered lake provide the basic dynamic force driving change...
Temperature influences the life of many organisms in various ways. A great number of organisms live under conditions where their ability to adapt to changes in temperature can be vital and largely determines their fitness. Understanding the mechanism...
Biomolecular condensates are crucial compartments within cells, relying on their material properties for function. They form and persist through weak, transient interactions, often undetectable by classical biochemical approaches. Hence, microscopy-b...
DNA-dependent DNA and RNA polymerases are important modulators of biological functions such as replication, transcription, recombination, or repair. In this work performed in cell-free media, we studied the ability of selected DNA polymerases to over...
Hydrogels have become indispensable in biomedical research and regenerative therapies due to their high water content, tissue-like mechanics, and tunable biochemical properties. However, their behavior under altered gravitational conditions—par...
Temperature is a crucial regulator of the rate and direction of biochemical reactions and cell processes. The recent data indicating the presence of local thermal gradients associated with the sites of high-rate thermogenesis, on the one hand, demons...
Markov chain perturbation theory is a rapidly developing subfield of the theory of stochastic processes. This review outlines emerging applications of this theory in the analysis of stochastic models of chemical reactions, with a particular focus on...
Selective inhibition of CYP17A1 17,20-lyase is critical for treating hyperandrogenic disorders without the cortisol-depleting side effects of non-selective drugs like abiraterone. We evaluated tanshinones from Salvia miltiorrhiza as potential selecti...
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectot...
Wastewater discharge into aquatic systems has become a severe threat to the ecosystem. Herein, Direct Red 28 (DR28) dye removal from an aqueous solution was executed with the application of date fruit seed biochar (DFSB). Fourier transform infrared s...
The present work investigates a two-stage process scheme for cheese whey valorization through energy recovery in different forms by means of bio-electrochemical systems. The first stage consisted of an integrated bio-electrochemical process for H2 an...
Since Coronavirus disease 2019 (COVID-19) still presents a considerable threat, it is beneficial to provide therapeutic supplements against it. In this respect, glycoprotein lactoferrin (LF) and lactoferricin (LFC), a natural bioactive peptide yielde...
Biomass and other carbonaceous materials can be gasified to produce syngas with high concentrations of CO and H2. Feedstock materials include wood, dedicated energy crops, grain wastes, manufacturing or municipal wastes, natural gas, petroleum and ch...
Small interfering RNA (siRNA) is the most important tool for the manipulation of mRNA expression and needs protection from intracellular nucleases when delivered into the cell. In this work, we examined the effects of siRNA modification with the phos...
MTHFR deficiency still deserves an investigation to associate the phenotype to protein structure variations. To this aim, considering the MTHFR wild type protein structure, with a catalytic and a regulatory domain and taking advantage of state-of-the...
In our recent studies, we have developed a thermodynamic biochemical model able to select the resonant frequency of an extremely low frequency electromagnetic field (ELF-EMF) specifically affecting different types of cancer, and we have demonstrated...
Alzheimer’s disease (AD) is characterized by amyloid-beta (Aβ) plaque accumulation and neurodegeneration. This study identified gyrophoric acid, a lichen-derived phenolic metabolite, as a dual-action Aβ42 inhibitor preventing aggregat...
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the re...
Determining the postmortem interval remains one of the most persistent and fragmented challenges in forensic science. Conventional approaches—thermal, biochemical, molecular, or entomological—capture only isolated fragments of a single ph...
The interactions of ligands with nucleic acids are central to numerous reactions in the biological cell. How such reactions are affected by harsh environmental conditions such as low temperatures, high pressures, and high concentrations of destructiv...
Temperature is an important parameter in bioprocesses, influencing the structure and functionality of almost every biomolecule, as well as affecting metabolic reaction rates. In industrial biotechnology, the temperature is usually tightly controlled...
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on avail...
The design and development of scaffolds play a crucial role in tissue engineering. In this regard, the study aims to establish the influence of porosity on the morpho-structural, physical–chemical, and biochemical characteristics of the polylac...
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