The activity of indigo carmine against bacteriophages: an edible antiphage agent.

Bacteriophage infections in bacterial cultures pose a significant challenge to industrial bioprocesses, necessitating the development of innovative antiphage solutions. This study explores the antiphage potential of indigo carmine (IC), a common FDA-approved food additive. IC demonstrated selective inactivation of DNA phages (P001, T4, T1, T7, λ) with the EC values ranging from 0.

Measurement of large ribosomal subunit size in cytoplasm and nucleus of living human cells.

Ribosomes are the most essential macromolecules in cells, as they serve as production lines for every single protein. Here, we address the demand to study ribosomes in living human cells by applying time-resolved microscopy. We show that oxazole yellow iodide (YO-PRO-1 dye) intercalates tRNA and rRNA with a determined equilibrium constant of 3.

Starvation induces diffusion hindrance at the nanoscale in mammalian cells.

Prolonged starvation leads to acute stress, inducing a state of cellular dormancy with reduced energy consumption. Our research reveals that nutrient deprivation halts the movement of large ribosomal subunits, trapping them in a gel-like structure within the cytoplasm of surviving cells. This effect is due to water efflux from cells, causing a decrease in cell volume to half the original volume.

Quantitative analysis of transferrin uptake into living cells at single-molecule level.

Endocytosis, apart from providing a mechanism for cells to take up nutrients, is the principal route of entry for many nanomedicines. The evaluation of therapeutic delivery efficiency without providing quantitative parameters, like the number of molecules entering the cell and the time of their entry, is very limited. Despite advances in single-molecule methods for in-cell quantitative measurements, they have not become widely used in the study of endocytosis.

Direction of Spontaneous Processes in Non-Equilibrium Systems with Movable/Permeable Internal Walls.

We consider three different systems in a heat flow: an ideal gas, a van der Waals gas, and a binary mixture of ideal gases. We divide each system internally into two subsystems by a movable wall. We show that the direction of the motion of the wall, after release, under constant boundary conditions, is determined by the same inequality as in equilibrium thermodynamics dU-đQ≤0.

Rotational and translational diffusion of biomolecules in complex liquids and HeLa cells.

Diffusive motion accompanies many physical and biological processes. The Stokes-Sutherland-Einstein relation for the translational diffusion coefficient, , agrees with experiments done in simple fluids but fails for complex fluids. Moreover, the interdependence between and rotational diffusion coefficient, , also deviates in complex fluids from the classical relation of / = 4/3 known in simple fluids.

Living Cell as a Self-Synchronized Chemical Reactor.

Thermal fluctuations power all processes inside living cells. Therefore, these processes are inherently random. However, myriad multistep chemical reactions act in concerto inside a cell, finally leading to this chemical reactor's self-replication.

Analytical Form of the Fluorescence Correlation Spectroscopy Autocorrelation Function in Chemically Reactive Systems.

Fluorescence correlation spectroscopy (FCS) applied to chemically reactive systems provides information about chemical reaction equilibrium constants and diffusion coefficients of reactants. These physical quantities are determined from the FCS-measured autocorrelation function, (), as a function of time, . In most of the studied cases, the analytical form of () is well-known for reactions that are much faster than the diffusion time of reactants across the focal volume probed by FCS or when they are much slower than the diffusion time.

Parameters of State in the Global Thermodynamics of Binary Ideal Gas Mixtures in a Stationary Heat Flow.

In this paper, we formulate the first law of global thermodynamics for stationary states of the binary ideal gas mixture subjected to heat flow. We map the non-uniform system onto the uniform one and show that the internal energy U(S*,V,N1,N2,f1*,f2*) is the function of the following parameters of state: a non-equilibrium entropy S*, volume , number of particles of the first component, N1, number of particles of the second component N2 and the renormalized degrees of freedom. The parameters f1*,f2*, N1,N2 satisfy the relation (N1/(N1+N2))f1*/f1+(N2/(N1+N2))f2*/f2=1 (f1 and f2 are the degrees of freedom for each component respectively).

Fundamental Relation for the Ideal Gas in the Gravitational Field and Heat Flow.

We formulate the first law of global thermodynamics for stationary states of the ideal gas in the gravitational field subjected to heat flow. We map the non-uniform system (described by profiles of the density and temperature) onto the uniform one and show that the total internal energy U(S*,V,N,L,M*) is the function of the following parameters of state: the non-equilibrium entropy S*, volume , number of particles, , height of the column along the gravitational force, and renormalized mass of a particle M*. Each parameter corresponds to a different way of energy exchange with the environment.

Steady-state thermodynamics of a system with heat and mass flow coupling.

Equilibrium thermodynamics describes the energy exchange of a body with its environment. Here, we describe the global energy exchange of an ideal gas in the Coutte flow in a thermodynamic-like manner. We derive a fundamental relation between internal energy as a function of parameters of state.

Fundamental Relation for Gas of Interacting Particles in a Heat Flow.

There is a long-standing question of whether it is possible to extend the formalism of equilibrium thermodynamics to the case of nonequilibrium systems in steady-states. We have made such an extension for an ideal gas in a heat flow. Here, we investigated whether such a description exists for the system with interactions: the van der Waals gas in a heat flow.

Comment on "Fluorimetric sensing of ATP in water by an imidazolium hydrazone based sensor" by S. Farshbaf and P. Anzenbacher Jr., , 2019, , 1770.

In the paper, "Fluorimetric sensing of ATP in water by an imidazolium hydrazone based sensor," Farshbaf and Anzenbacher presented the application of bisantrene as a fluorescent ATP sensor in organic-inorganic mixtures of solvents. Encouraged by the results presented in the parent study, we aimed to apply this strategy for physiologically relevant water-based buffers and - preferably - intracellular application. Here we present the results of our investigations and point to the limitations of bisantrene applications as the ATP sensor.

Heteroaggregation of virions and microplastics reduces the number of active bacteriophages in aqueous environments.

The objective of this study is to explore the effects of microplastics on the viability of the bacteriophages in an aqueous environment. Bacteriophages (phages), that is, viruses of bacteria, are essential in homeostasis. It is estimated that phages cause up to 40% of the death of all bacteria daily.

Cellular Uptake of Bevacizumab in Cervical and Breast Cancer Cells Revealed by Single-Molecule Spectroscopy.

Bevacizumab is a biological drug that is now extensively studied in clinics against various types of cancer. Although bevacizumab's action is preferably extracellular, there are reports suggesting its internalization into cancer cells, consequently decreasing its therapeutic potential. Here we are solving this issue by applying fluorescence correlation spectroscopy in living cells.

Thermodynamics of stationary states of the ideal gas in a heat flow.

There is a long-standing question as to whether and to what extent it is possible to describe nonequilibrium systems in stationary states in terms of global thermodynamic functions. The positive answers have been obtained only for isothermal systems or systems with small temperature differences. We formulate thermodynamics of the stationary states of the ideal gas subjected to heat flow in the form of the zeroth, first, and second law.

Effective screening of Coulomb repulsions in water accelerates reactions of like-charged compounds by orders of magnitude.

The reaction kinetics between like-charged compounds in water is extremely slow due to Coulomb repulsions. Here, we demonstrate that by screening these interactions and, in consequence, increasing the local concentration of reactants, we boost the reactions by many orders of magnitude. The reaction between negatively charged Coenzyme A molecules accelerates ~5 million-fold using cationic micelles.

Entanglement of polymer chains in hypertonic medium enhances the delivery of DNA and other biomacromolecules into cells.

Hypothesis: Most experimental procedures applied in modern biology involve cargo delivering into cells. One of the ways to cargo introduction is osmotic-mediated intracellular vesicle swelling. However, its widespread use was hindered due to cargo size (<10 nm) and cell-type-related restrictions.

Transient dynamics in the outflow of energy from a system in a nonequilibrium stationary state.

We investigate the thermal relaxation of an ideal gas from a nonequilibrium stationary state. The gas is enclosed between two walls, which initially have different temperatures. After making one of the walls adiabatic, the system returns to equilibrium.

Ion Complexation Explains Orders of Magnitude Changes in the Equilibrium Constant of Biochemical Reactions in Buffers Crowded by Nonionic Compounds.

The equilibrium constant () of biochemical complex formation in aqueous buffers with high concentration (>20 wt %) of nonionic compounds can vary by orders of magnitude in comparison with the in a pure buffer. The precise molecular mechanisms of these profound changes are not known. Herein, we show up to a 1000-fold decrease of the value of DNA hybridization (at nM concentration) in standard molecular crowder systems such as PEG, dextrans, Ficoll, and glycerol.

Internal energy in compressible Poiseuille flow.

We analyze a compressible Poiseuille flow of ideal gas in a plane channel. We provide the form of internal energy U for a nonequilibrium stationary state that includes viscous dissipation and pressure work. We demonstrate that U depends strongly on the ratio Δp/p_{0}, where Δp is the pressure difference between inlet and outlet and p_{0} is the outlet's pressure.

Quantitative analysis of biochemical processes in living cells at a single-molecule level: a case of olaparib-PARP1 (DNA repair protein) interactions.

Quantitative description of biochemical processes inside living cells and at single-molecule levels remains a challenge at the forefront of modern instrumentation and spectroscopy. This paper demonstrates such single-cell, single-molecule analyses performed to study the mechanism of action of olaparib - an up-to-date, FDA-approved drug for germline-BRCA mutated metastatic breast cancer. We characterized complexes formed with PARPi-FL - fluorescent analog of olaparib and in cancer cells using the advanced fluorescent-based method: Fluorescence Correlation Spectroscopy (FCS) combined with a length-scale dependent cytoplasmic/nucleoplasmic viscosity model.

Continuous nonequilibrium transition driven by heat flow.

We discovered an out-of-equilibrium transition in the ideal gas between two walls, divided by an inner, adiabatic, movable wall. The system is driven out-of-equilibrium by supplying energy directly into the volume of the gas. At critical heat flux we have found a continuous transition to the state with a low-density, hot gas on one side of the movable wall and a dense, cold gas on the other side.