Transport of nanoprobes in multicellular spheroids

M. Pilz, K. Kwapiszewska, T. Kalwarczyk, G. Bubak, D. Nowis and R. Hołyst

Nanoscale, 2020, 12, 19880-19887

The efficient delivery of drugs to cells depends on their diffusion through the extracellular matrix (ECM) of tissues. Here we present a study on the diffusion of nanoprobes of radius from 1 nm to over 100 nm in the ECM of spheroids of three cell types (HeLa, MCF-7 and fibroblasts). We quantified the nanoparticle transport in the spheroids’ proliferating zone. We determined the size-dependent viscosity of the ECM. We revealed that nanoobjects up to 10 nm in radius exhibited unobstructed diffusion in the ECM, regardless of the spheroid type. The presented length-scale dependent viscosity profiles for spheroids pave the way for advanced modelling of drug administration through tissues.

Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines

K. Kwapiszewska , K. Szczepański, T. Kalwarczyk, B. Michalska, P. Patalas-Krawczyk, J. Szymański, T. Andryszewski, M. Iwan, J. Duszyński and R. Hołyst

J. Phys. Chem. Lett. 2020, 11, 16, 6914–6920

Metabolic reactions in living cells are limited by diffusion of reagents in the cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in the cytosol should be preceded by careful measurements of the physical properties of the cellular interior. The cytoplasm is a complex, crowded fluid characterized by effective viscosity dependent on its structure at a nanoscopic length scale. In this work, we present and validate the model describing the cytoplasmic nanoviscosity, based on measurements in seven human cell lines, for nanoprobes ranging in diameters from 1 to 150 nm. Irrespective of cell line origin (epithelial–mesenchymal, cancerous–noncancerous, male–female, young–adult), we obtained a similar dependence of the viscosity on the size of the nanoprobes, with characteristic length-scales of 20 ± 11 nm (hydrodynamic radii of major crowders in the cytoplasm) and 4.6 ± 0.7 nm (radii of intercrowder gaps). Moreover, we revealed that the cytoplasm behaves as a liquid for length scales smaller than 100 nm and as a physical gel for larger length scales.

Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review

J. Paczesny, Ł. Richter and R. Hołyst

Viruses, 2020, 12(8), 845

Bacteria will likely become our most significant enemies of the 21st century, as we are approaching a post-antibiotic era. Bacteriophages, viruses that infect bacteria, allow us to fight infections caused by drug-resistant bacteria and create specific, cheap, and stable sensors for bacteria detection. Here, we summarize the recent developments in the field of phage-based methods for bacteria detection. We focus on works published after mid-2017. We underline the need for further advancements, especially related to lowering the detection (below 1 CFU/mL; CFU stands for colony forming units) and shortening the time of analysis (below one hour). From the application point of view, portable, cheap, and fast devices are needed, even at the expense of sensitivity.

Photoluminescent, Ferromagnetic, and Hydrophobic Sponges for Oil–Water Separation

K. Yin, D. Lu, B. Sun, T. Kalwarczyk, R. Hołyst, J. Hao, H. Li and J.Hao

ACS Omega, 2020, 5, 25, 15077–15082

To find a facile way to produce a hydrophobic sponge that can effectively absorb oils is urgent to resolve the environmental pollution and ecological disaster caused by oil spillage. Here, alkylated carbon dots (C dots) were prepared from pyrolysis of a mixture of dodecylamine and citric acid followed by purification through silica gel column chromatography. Polyurethane sponge was modified by alkylated C dots by a simple dip-coating method, which endows the photoluminescent and hydrophobic sponge with good absorption capacities for various oils and nonpolar organic solvents with high recyclability. The water contact angle of the modified sponge can reach 138.8°. Interestingly, the sponge enables visual absorption under UV irradiation in the dark, which has not been achieved by other carbon-based adsorbents. The sponge was further made ferromagnetic by introducing alkylated Fe3O4 nanoparticles into its structure, which allowed controllable oil–water separation.

Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA

Y. Zhou, K. Bielec, P. Pasitsuparoad and R. Hołyst

Analyst, 2020, 145, 6600-6606

Anthracyclines are one of the most studied anticancer drugs approved for medical treatment. The equilibrium constant (K) of the reaction between these drugs with DNA in both in vitro and in vivo experiments lacks consensus. The K values vary from 104 up to 108 M−1, which suggest a 1000-fold error in determining the effective concentration needed to form the drug–DNA complex. Until 2014, only one study by García [J. Phys. Chem. B, 2014, 118, 1288–1295] showed that the binding of anthracycline representative doxorubicin occurs in two reactions. We support this result by brightness analysis at a single molecular level for the four most common anthracyclines: doxorubicin, daunorubicin, epirubicin, and idarubicin.

Ions in an AC Electric Field: Strong Long-Range Repulsion between Oppositely Charged Surfaces

Ł. Richter, P. J. Żuk, P. Szymczak, J. Paczesny, K. M. Bąk, T. Szymborski, P. Garstecki, H. A. Stone, R. Hołyst and C. Drummond

Phys. Rev. Lett., 2020, 125, 056001

Two oppositely charged surfaces separated by a dielectric medium attract each other. In contrast we observe a strong repulsion between two plates of a capacitor that is filled with an aqueous electrolyte upon application of an alternating potential difference between the plates. This long-range force increases with the ratio of diffusion coefficients of the ions in the medium and reaches a steady state after a few minutes, which is much larger than the millisecond timescale of diffusion across the narrow gap. The repulsive force, an order of magnitude stronger than the electrostatic attraction observed in the same setup in air, results from the increase in osmotic pressure as a consequence of the field-induced excess of cations and anions due to lateral transport from adjacent reservoirs.

Scaling equation for viscosity of polydimethylsiloxane in ethyl acetate: From dilute to concentrated solutions

A. Agasty, A. Wisniewska, T. Kalwarczyk, K. Koynov and R. Holyst

Polymer Volume, 2020, 203, 122779

Rheology of polymer solutions suffers from lack of universal model of viscosity applicable across wide range of concentrations. Here we build such a model on the basis of measured viscosity of polydimethylosiloxane (PDMS) in ethyl acetate in a wide range of polymer concentrations: from dilute up to highly concentrated solutions. The relationship between viscosity and different polymer parameters in solution such as coil size, correlation length ξ, monomer–solvent and monomer–monomer interaction parameter were established experimentally as a function of concentrations [from 0.001g∕cm3 to 8.000g∕cm3], temperature [in a range 283–303K] and molecular masses [9–139kg∕mol]. Entanglement onset at the crossover from dilute to semi-dilute solution as well as the solvent–monomer contact reduction at the crossover from semi-dilute to concentrated regime are captured by the model. This model is in accordance with the Eyring rate theory for activated processes.

TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats

M. Gawrys-Kopczynska, M. Konop, K. Maksymiuk, K. Kraszewska, L. Derzsi, K. Sozanski, R. Holyst, M. Pilz and E. Samborowska

ELIFE 2020, 9

Trimethylamine-oxide (TMAO) is present in seafood which is considered to be beneficial for health. Deep-water animals accumulate TMAO to protect proteins, such as lactate dehydrogenase (LDH), against hydrostatic pressure stress (HPS). We hypothesized that TMAO exerts beneficial effects on the circulatory system and protects cardiac LDH exposed to HPS produced by the contracting heart. Male, Sprague-Dawley and Spontaneously-Hypertensive-Heart-Failure (SHHF) rats were treated orally with either water (control) or TMAO. In vitro, LDH with or without TMAO was exposed to HPS and was evaluated using fluorescence correlation spectroscopy. TMAO-treated rats showed higher diuresis and natriuresis, lower arterial pressure and plasma NT-proBNP. Survival in SHHF-control was 66% vs 100% in SHHF-TMAO. In vitro, exposure of LDH to HPS with or without TMAO did not affect protein structure. In conclusion, TMAO reduced mortality in SHHF, which was associated with diuretic, natriuretic and hypotensive effects. HPS and TMAO did not affect LDH protein structure.

Joint effect of surfactants and cephalexin on the formation of Escherichia coli filament

S. Hou, Z. Jia, K. Kryszczuk, D. Chen, L. Wang, R. Hołyst and X. Feng

Ecotoxicology and Environmental Safety, 2020, 199, 110750

Both antibiotics and surfactants commonly exist in natural environment and have generated great concerns due to their biological influence on the ecosystem. A major concern lies in the capacity of antibiotics to induce bacterial filaments formation, which has potential health risks. However, their joint effect is not clear so far. Here, we studied the joint effect of cephalexin (Cex), a typical antibiotic, and differently charged surfactants on the formation of E. coli filaments. Three kinds of surfactants characterized by different charges were used: cationic surfactant (CTAB), anionic surfactant (SDS) and nonionic surfactant (Tween). Data showed that Cex alone caused the formation of E. coli filaments, elongating their maximum profile from ca. 2 μm (a single E. coli cell) to tens of micrometers (an E. coli filament). A joint use of surfactants with Cex could produce even longer E. coli filaments, elongating the maximum length of the bacteria to larger than 100 μm. The capacity order of different surfactants under their optimum concentrations to produce elongated E. coli filaments was Tween > SDS > CTAB. The E. coli filaments were characterized with a normal DNA distribution and a good cell membrane integrity. We measured the stiffness of bacterial cell wall by atomic force microscopy and correlated the elongation capacity of the E. coli filaments to the stiffness of cell wall. Zeta potential measurement indicated that inserting into or being bound to the cell surface in a large quantity was tested not to be the major way that surfactants interacted with bacteria

Cell extract gels as an example of active matter

A. Wisniewska, T. Kalwarczyk, J. Szymanski, K. Kryszczuk, K. Matula and R. Holyst

Rheologica Acta 2020, 59, 575–582

Cell lysates (cellular extracts) constitute a perfect imitation of the intracellular environment that can provide insight into cellular response to external stimuli. However, most of the presented results are performed for diluted lysates that do not reflect the actual properties of a crowded cellular environment. Here, we report for the first time the measurement of the viscosity and shear storage modulus of highly concentrated Escherichia coli (E. coli) lysates with and without adenosine triphosphate (ATP). By cleavage of DNA content, we showed the value of shear storage modulus GG′ decreases by 19–31% in comparison to control samples. The addition of molecules that provides energy (ATP) allowed to rebuild the structure of the lysate by reversibly increasing viscous properties over elastic ones. When the energy delivered in the form of ATP is consumed by the unliving bacterial lysate, the system returns to its initial state.

Self-Stabilized Giant Aggregates in Water from Room-Temperature Ionic Liquids with an Asymmetric Polar–Apolar–Polar Architecture

G. Zhang, H. Zhu, J. Chen, M. Chen, T. Kalwarczyk, R. Hołyst, H. Li and J. Hao

J. Phys. Chem. B 2020, 124, 22, 4651–4660

We report the assembly of four imidazolium bromides, each of which bears a naphthyl on one side of the imidazolium cation and a branched alkyl chain on the other. This design creates a new type of amphiphilic ionic liquid with an apolar–polar–apolar structure and a low melting point (mp, <−20 °C), which has not been achieved by reported counterparts bearing linear alkyl chains. In solvent-free states, microphase segregation occurs where polar and apolar domains arrange bicontinuously as proved by molecular dynamics (MD) simulations. When dispersed in water, self-stabilized giant aggregates formed with ultrahigh colloidal stability (up to years). MD simulations provide clues of discrete bicontinuous phases within the giant aggregates. These newly discovered self-assemblies provide a heterogeneous reservoir that can accommodate guest molecules including the highly apolar fullerene C60, paving the way for a wide range of potential applications.

Storage of Energy in Constrained Non-Equilibrium Systems

Y. Zhang, K. Giżyński, A. Maciołek and R. Hołyst

Entropy 2020, 22(5), 557

We study a quantity T defined as the energy U, stored in non-equilibrium steady states (NESS) over its value in equilibrium U0 , ΔU=UU0 divided by the heat flow JU going out of the system. A recent study suggests that T is minimized in steady states (Phys.Rev.E.99, 042118 (2019)). We evaluate this hypothesis using an ideal gas system with three methods of energy delivery: from a uniformly distributed energy source, from an external heat flow through the surface, and from an external matter flow. By introducing internal constraints into the system, we determine T with and without constraints and find that T is the smallest for unconstrained NESS. We find that the form of the internal energy in the studied NESS follows U=U0f(JU) . In this context, we discuss natural variables for NESS, define the embedded energy (an analog of Helmholtz free energy for NESS), and provide its interpretation.

Fast and efficient deposition of broad range of analytes on substrates for surface enhanced Raman spectroscopy

Ł. Richter, P. Albrycht, M. Księżopolska-Gocalska, E. Poboży, R. Bachliński, V. Sashuk, J. Paczesny and R. Hołyst

Biosensors and Bioelectronics, 2020, 156, 112124

The majority of analytical chemistry methods requires presence of target molecules directly at a sensing surface. Diffusion of analyte from the bulk towards the sensing layer is random and might be extremely lengthy, especially in case of low concentration of molecules to be detected. Thus, even the most sensitive transducer and the most selective sensing layer are limited by the efficiency of deposition of molecules on sensing surfaces. However, rapid development of new sensing technologies is rarely accompanied by new protocols for analyte deposition. To bridge this gap, we propose a method for fast and efficient deposition of variety of molecules (e.g. proteins, dyes, drugs, biomarkers, amino acids) based on application of the alternating electric field. We show the dependence between frequency of the applied electric field, the intensity of the surface enhanced Raman spectroscopy (SERS) signal and the mobility of the studied analyte. Such correlation allows for a priori selection of parameters for any desired compound without additional optimization. Thanks to the application of the electric field, we improve SERS technique by decrease of time of deposition from 20 h to 5 min, and, at the same time, reduction of the required sample volume from 2 ml to 50 μl. Our method might be paired with number of analytical methods, as it allows for deposition of molecules on any conductive surface, or a conductive surface covered with dielectric layer.

Analysis of Brightness of a Single Fluorophore for Quantitative Characterization of Biochemical Reactions

K. Bielec, G. Bubak, T. Kalwarczyk and R. Hołyst

J. Phys. Chem. B 2020, 124, 10, 1941–1948

Intrinsic molecular brightness (MB) is a number of emitted photons per second per molecule. When a substrate labeled by a fluorophore and a second unlabeled substrate form a complex in solution, the MB of the fluorophore changes. Here we use this change to determine the equilibrium constant (K) for the formation of the complex at pM concentrations. To illustrate this method, we used a reaction of DNA hybridization, where only one of the strands was fluorescently labeled. We determined K at the substrate concentrations from 80 pM to 30 nM. We validated this method against Förster resonance energy transfer (FRET). This method is much simpler than FRET as it requires only one fluorophore in the complex with a very small (a f̃ew percent) change in MB.

Energy storage in steady states under cyclic local energy input

Y. Zhang, R. Hołyst and A. Maciołek

Phys. Rev. E, 2020, 101, 012127

We study periodic steady states of a lattice system under external cyclic energy supply using simulation. We consider different protocols for cyclic energy supply and examine the energy storage. Under the same energy flux, we found that the stored energy depends on the details of the supply, period, and amplitude of the supply. Further, we introduce an adiabatic wall as an internal constraint into the lattice and examine the stored energy with respect to different positions of the internal constrain. We found that the stored energy for constrained systems is larger than its unconstrained counterpart. We also observe that the system stores more energy through large and rare energy delivery, comparing to small and frequent delivery.

(+48) 22 343-31-23

Kasprzaka 44/52, 01-224 Warsaw, Poland