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Robert Holyst
Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, PL-01-224 Warsaw, Poland

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Article
Published: 02 August 2021 in Physical Review E
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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. Molecular dynamic simulations of the soft-sphere fluid confirm the existence of the transition in the interacting system. We introduce a stationary state Helmholtz-like function whose minimum determines the stable positions of the internal wall. This transition can be used as a paradigm of transitions in stationary states and the Helmholtz-like function as a paradigm of the thermodynamic description of these states.

ACS Style

Yirui Zhang; Marek Litniewski; Karol Makuch; Paweł J. Żuk; Anna Maciołek; Robert Hołyst. Continuous nonequilibrium transition driven by heat flow. Physical Review E 2021, 104, 024102 .

AMA Style

Yirui Zhang, Marek Litniewski, Karol Makuch, Paweł J. Żuk, Anna Maciołek, Robert Hołyst. Continuous nonequilibrium transition driven by heat flow. Physical Review E. 2021; 104 (2):024102.

Chicago/Turabian Style

Yirui Zhang; Marek Litniewski; Karol Makuch; Paweł J. Żuk; Anna Maciołek; Robert Hołyst. 2021. "Continuous nonequilibrium transition driven by heat flow." Physical Review E 104, no. 2: 024102.

Journal article
Published: 19 June 2021 in Molecules
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The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): K1=3.36±0.43×107M1 and K2=1.90±0.61×105M1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.

ACS Style

Karolina Kucharska; Marta Pilz; Krzysztof Bielec; Tomasz Kalwarczyk; Patrycja Kuźma; Robert Hołyst. Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA. Molecules 2021, 26, 3748 .

AMA Style

Karolina Kucharska, Marta Pilz, Krzysztof Bielec, Tomasz Kalwarczyk, Patrycja Kuźma, Robert Hołyst. Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA. Molecules. 2021; 26 (12):3748.

Chicago/Turabian Style

Karolina Kucharska; Marta Pilz; Krzysztof Bielec; Tomasz Kalwarczyk; Patrycja Kuźma; Robert Hołyst. 2021. "Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA." Molecules 26, no. 12: 3748.

Research article
Published: 12 April 2021 in ACS Applied Polymer Materials
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The effective viscosity in polymer solutions probed by diffusion of nanoparticles depends on their size. It is a well-defined function of the probe size, the radius of gyration, mesh size (correlation length), activation energy, and its parameters. As the nanoparticle’s size exceeds the radius of gyration of polymer coils, the effective viscosity approaches its macroscopic limiting value. Here, we apply the equation for effective viscosity in the macroscopic limit to the following polymer solutions: hydroxypropyl cellulose (HPC) in water, polymethylmethacrylate (PMMA) in toluene, and polyacrylonitrile (PAN) in dimethyl sulfoxide (DMSO). We compare them with previous data for PEG/PEO in water and PDMS in ethyl acetate. We determine polymer parameters from the measurements of the macroscopic viscosity in a wide range of average polymer molecular weights (24–300 kg/mol), temperatures (283–303 K), and concentrations (0.005–1.000 g/cm3). In addition, the polydispersity of polymers is taken into account in the appropriate molecular weight averaging functions. We provide the model applicable for the study of nanoscale probe diffusion in polymer solutions and macroscopic characterization of different polymer materials via rheological measurements.

ACS Style

Airit Agasty; Agnieszka Wisniewska; Tomasz Kalwarczyk; Kaloian Koynov; Robert Holyst. Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis. ACS Applied Polymer Materials 2021, 3, 2813 -2822.

AMA Style

Airit Agasty, Agnieszka Wisniewska, Tomasz Kalwarczyk, Kaloian Koynov, Robert Holyst. Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis. ACS Applied Polymer Materials. 2021; 3 (5):2813-2822.

Chicago/Turabian Style

Airit Agasty; Agnieszka Wisniewska; Tomasz Kalwarczyk; Kaloian Koynov; Robert Holyst. 2021. "Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis." ACS Applied Polymer Materials 3, no. 5: 2813-2822.

Journal article
Published: 01 April 2021 in Scientific Reports
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Hydrophobicity is one of the most critical factors governing the adsorption of molecules and objects, such as virions, on surfaces. Even moderate change of wetting angle of plastic surfaces causes a drastic decrease ranging from 2 to 5 logs of the viruses (e.g., T4 phage) in the suspension due to adsorption on polymer vials' walls. The effect varies immensely in seemingly identical containers but purchased from different vendors. Comparison of glass, polyethylene, polypropylene, and polystyrene containers revealed a threshold in the wetting angle of around 95°: virions adsorb on the surface of more hydrophobic containers, while in more hydrophilic vials, phage suspensions are stable. The polypropylene surface of the Eppendorf-type and Falcon-type can accommodate from around 108 PFU/ml to around 1010 PFU/ml from the suspension. The adsorption onto the container’s wall might result in complete scavenging of virions from the bulk. We developed two methods to overcome this issue. The addition of surfactant Tween20 and/or plasma treatment provides a remedy by modulating surface wettability and inhibiting virions' adsorption. Plastic containers are essential consumables in the daily use of many bio-laboratories. Thus, this is important not only for phage-related research (e.g., the use of phage therapies as an alternative for antibiotics) but also for data comparison and reproducibility in the field of biochemistry and virology.

ACS Style

Łukasz Richter; Karolina Księżarczyk; Karolina Paszkowska; Marta Janczuk-Richter; Joanna Niedziółka-Jönsson; Jacek Gapiński; Marcin Łoś; Robert Hołyst; Jan Paczesny. Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research. Scientific Reports 2021, 11, 1 -12.

AMA Style

Łukasz Richter, Karolina Księżarczyk, Karolina Paszkowska, Marta Janczuk-Richter, Joanna Niedziółka-Jönsson, Jacek Gapiński, Marcin Łoś, Robert Hołyst, Jan Paczesny. Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research. Scientific Reports. 2021; 11 (1):1-12.

Chicago/Turabian Style

Łukasz Richter; Karolina Księżarczyk; Karolina Paszkowska; Marta Janczuk-Richter; Joanna Niedziółka-Jönsson; Jacek Gapiński; Marcin Łoś; Robert Hołyst; Jan Paczesny. 2021. "Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research." Scientific Reports 11, no. 1: 1-12.

Rapid communication
Published: 21 December 2020 in The Journal of Physical Chemistry Letters
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Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure–function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus. Supported by the analysis of electron tomography images, these results advocate the ∼150 nm-wide interchromosomal channels filled with the aqueous diluted protein solution. The nucleus is percolated by these channels to allow various cargos to migrate freely at the nanoscale. We determined the volume of interchromosomal channels in the HeLa cell nucleus to 237 ± 61 fL, which constitutes 34% of the cell nucleus volume. The volume fraction of mobile proteins in channels equals 16% ± 4%, and the concentration is 1 mM.

ACS Style

Grzegorz Bubak; Karina Kwapiszewska; Tomasz Kalwarczyk; Krzysztof Bielec; Tomasz Andryszewski; Michalina Iwan; Szymon Bubak; Robert Hołyst. Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements. The Journal of Physical Chemistry Letters 2020, 12, 294 -301.

AMA Style

Grzegorz Bubak, Karina Kwapiszewska, Tomasz Kalwarczyk, Krzysztof Bielec, Tomasz Andryszewski, Michalina Iwan, Szymon Bubak, Robert Hołyst. Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements. The Journal of Physical Chemistry Letters. 2020; 12 (1):294-301.

Chicago/Turabian Style

Grzegorz Bubak; Karina Kwapiszewska; Tomasz Kalwarczyk; Krzysztof Bielec; Tomasz Andryszewski; Michalina Iwan; Szymon Bubak; Robert Hołyst. 2020. "Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements." The Journal of Physical Chemistry Letters 12, no. 1: 294-301.

Paper
Published: 28 August 2020 in Nanoscale
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We present the study of the nanoprobes' diffusion in the extracellular matrix (ECM) of multicellular spheroids.

ACS Style

Marta Pilz; Karina Kwapiszewska; Tomasz Kalwarczyk; Grzegorz Bubak; Dominika Nowis; Robert Hołyst. Transport of nanoprobes in multicellular spheroids. Nanoscale 2020, 12, 19880 -19887.

AMA Style

Marta Pilz, Karina Kwapiszewska, Tomasz Kalwarczyk, Grzegorz Bubak, Dominika Nowis, Robert Hołyst. Transport of nanoprobes in multicellular spheroids. Nanoscale. 2020; 12 (38):19880-19887.

Chicago/Turabian Style

Marta Pilz; Karina Kwapiszewska; Tomasz Kalwarczyk; Grzegorz Bubak; Dominika Nowis; Robert Hołyst. 2020. "Transport of nanoprobes in multicellular spheroids." Nanoscale 12, no. 38: 19880-19887.

Review
Published: 03 August 2020 in Viruses
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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.

ACS Style

Jan Paczesny; Łukasz Richter; Robert Hołyst. Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review. Viruses 2020, 12, 845 .

AMA Style

Jan Paczesny, Łukasz Richter, Robert Hołyst. Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review. Viruses. 2020; 12 (8):845.

Chicago/Turabian Style

Jan Paczesny; Łukasz Richter; Robert Hołyst. 2020. "Recent Progress in the Detection of Bacteria Using Bacteriophages: A Review." Viruses 12, no. 8: 845.

Research article
Published: 31 July 2020 in The Journal of Physical Chemistry Letters
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Metabolic reactions in living cells are limited by diffusion of reagents in cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in cytosol should be preceded with careful measurements of the physical properties of the cellular interior. 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 nano-probes ranging in diameters from 1nm to 150nm. Irrespective of cell line origin (epithelial-mesenchymal, cancerous-non-cancerous, male-female, young-adult), we obtained similar dependence of the viscosity on size of nanoprobes, with characteristic length-scales of 20±11nm (hydrodynamic radii of major crowders in the cytoplasm) and 4.6±0.7nm (radii of inter-crowder gaps). Moreover, we revealed that cytoplasm behaves as a liquid for length scale smaller than 100nm and as a physical gel for larger length scales.

ACS Style

Karina Kwapiszewska; Krzysztof Szczepański; Tomasz Kalwarczyk; Bernadeta Michalska; Paulina Patalas-Krawczyk; Jędrzej Szymański; Tomasz Andryszewski; Michalina Iwan; Jerzy Duszyński; Robert Hołyst. Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines. The Journal of Physical Chemistry Letters 2020, 11, 6914 -6920.

AMA Style

Karina Kwapiszewska, Krzysztof Szczepański, Tomasz Kalwarczyk, Bernadeta Michalska, Paulina Patalas-Krawczyk, Jędrzej Szymański, Tomasz Andryszewski, Michalina Iwan, Jerzy Duszyński, Robert Hołyst. Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines. The Journal of Physical Chemistry Letters. 2020; 11 (16):6914-6920.

Chicago/Turabian Style

Karina Kwapiszewska; Krzysztof Szczepański; Tomasz Kalwarczyk; Bernadeta Michalska; Paulina Patalas-Krawczyk; Jędrzej Szymański; Tomasz Andryszewski; Michalina Iwan; Jerzy Duszyński; Robert Hołyst. 2020. "Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines." The Journal of Physical Chemistry Letters 11, no. 16: 6914-6920.

Article
Published: 28 July 2020 in Physical Review Letters
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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.

ACS Style

Łukasz Richter; Paweł J. Żuk; Piotr Szymczak; Jan Paczesny; Krzysztof M. Bąk; Tomasz Szymborski; Piotr Garstecki; Howard A. Stone; Robert Hołyst; Carlos Drummond. Ions in an AC Electric Field: Strong Long-Range Repulsion between Oppositely Charged Surfaces. Physical Review Letters 2020, 125, 056001 .

AMA Style

Łukasz Richter, Paweł J. Żuk, Piotr Szymczak, Jan Paczesny, Krzysztof M. Bąk, Tomasz Szymborski, Piotr Garstecki, Howard A. Stone, Robert Hołyst, Carlos Drummond. Ions in an AC Electric Field: Strong Long-Range Repulsion between Oppositely Charged Surfaces. Physical Review Letters. 2020; 125 (5):056001.

Chicago/Turabian Style

Łukasz Richter; Paweł J. Żuk; Piotr Szymczak; Jan Paczesny; Krzysztof M. Bąk; Tomasz Szymborski; Piotr Garstecki; Howard A. Stone; Robert Hołyst; Carlos Drummond. 2020. "Ions in an AC Electric Field: Strong Long-Range Repulsion between Oppositely Charged Surfaces." Physical Review Letters 125, no. 5: 056001.

Paper
Published: 20 July 2020 in The Analyst
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We performed brightness analysis at a single molecular level of doxorubicin, daunorubicin, epirubicin, and idarubicin. The method was sensitive enough to confirm that the binding of drugs to the DNA occurs in two reactions.

ACS Style

Ying Zhou; Krzysztof Bielec; Pakorn Pasitsuparoad; Robert Hołyst. Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA. The Analyst 2020, 145, 1 .

AMA Style

Ying Zhou, Krzysztof Bielec, Pakorn Pasitsuparoad, Robert Hołyst. Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA. The Analyst. 2020; 145 (20):1.

Chicago/Turabian Style

Ying Zhou; Krzysztof Bielec; Pakorn Pasitsuparoad; Robert Hołyst. 2020. "Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA." The Analyst 145, no. 20: 1.

Journal article
Published: 06 July 2020 in Polymer
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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.

ACS Style

Airit Agasty; Agnieszka Wisniewska; Tomasz Kalwarczyk; Kaloian Koynov; Robert Holyst. Scaling equation for viscosity of polydimethylsiloxane in ethyl acetate: From dilute to concentrated solutions. Polymer 2020, 203, 122779 .

AMA Style

Airit Agasty, Agnieszka Wisniewska, Tomasz Kalwarczyk, Kaloian Koynov, Robert Holyst. Scaling equation for viscosity of polydimethylsiloxane in ethyl acetate: From dilute to concentrated solutions. Polymer. 2020; 203 ():122779.

Chicago/Turabian Style

Airit Agasty; Agnieszka Wisniewska; Tomasz Kalwarczyk; Kaloian Koynov; Robert Holyst. 2020. "Scaling equation for viscosity of polydimethylsiloxane in ethyl acetate: From dilute to concentrated solutions." Polymer 203, no. : 122779.

Original contribution
Published: 21 June 2020 in Rheologica Acta
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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 \(G^{\prime }\) 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.

ACS Style

Agnieszka Wiśniewska; Tomasz Kalwarczyk; Jedrzej Szymanski; Katarzyna Kryszczuk; Kinga Matuła; Robert Holyst. Cell extract gels as an example of active matter. Rheologica Acta 2020, 59, 575 -582.

AMA Style

Agnieszka Wiśniewska, Tomasz Kalwarczyk, Jedrzej Szymanski, Katarzyna Kryszczuk, Kinga Matuła, Robert Holyst. Cell extract gels as an example of active matter. Rheologica Acta. 2020; 59 (8):575-582.

Chicago/Turabian Style

Agnieszka Wiśniewska; Tomasz Kalwarczyk; Jedrzej Szymanski; Katarzyna Kryszczuk; Kinga Matuła; Robert Holyst. 2020. "Cell extract gels as an example of active matter." Rheologica Acta 59, no. 8: 575-582.

Research article
Published: 19 June 2020 in ACS Omega
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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.

ACS Style

Keyang Yin; Dandan Lu; Bangping Sun; Tomasz Kalwarczyk; Robert Hołyst; Junying Hao; Hongguang Li; Jingcheng Hao. Photoluminescent, Ferromagnetic, and Hydrophobic Sponges for Oil–Water Separation. ACS Omega 2020, 5, 15077 -15082.

AMA Style

Keyang Yin, Dandan Lu, Bangping Sun, Tomasz Kalwarczyk, Robert Hołyst, Junying Hao, Hongguang Li, Jingcheng Hao. Photoluminescent, Ferromagnetic, and Hydrophobic Sponges for Oil–Water Separation. ACS Omega. 2020; 5 (25):15077-15082.

Chicago/Turabian Style

Keyang Yin; Dandan Lu; Bangping Sun; Tomasz Kalwarczyk; Robert Hołyst; Junying Hao; Hongguang Li; Jingcheng Hao. 2020. "Photoluminescent, Ferromagnetic, and Hydrophobic Sponges for Oil–Water Separation." ACS Omega 5, no. 25: 15077-15082.

Research article
Published: 08 June 2020 in eLife
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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.

ACS Style

Marta Gawrys-Kopczynska; Marek Konop; Klaudia Maksymiuk; Katarzyna Kraszewska; Ladislav Derzsi; Krzysztof Sozanski; Robert Holyst; Marta Pilz; Emilia Samborowska; Leszek Dobrowolski; Kinga Jaworska; Izabella Mogilnicka; Marcin Ufnal. TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats. eLife 2020, 9, 1 .

AMA Style

Marta Gawrys-Kopczynska, Marek Konop, Klaudia Maksymiuk, Katarzyna Kraszewska, Ladislav Derzsi, Krzysztof Sozanski, Robert Holyst, Marta Pilz, Emilia Samborowska, Leszek Dobrowolski, Kinga Jaworska, Izabella Mogilnicka, Marcin Ufnal. TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats. eLife. 2020; 9 ():1.

Chicago/Turabian Style

Marta Gawrys-Kopczynska; Marek Konop; Klaudia Maksymiuk; Katarzyna Kraszewska; Ladislav Derzsi; Krzysztof Sozanski; Robert Holyst; Marta Pilz; Emilia Samborowska; Leszek Dobrowolski; Kinga Jaworska; Izabella Mogilnicka; Marcin Ufnal. 2020. "TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats." eLife 9, no. : 1.

Journal article
Published: 20 May 2020 in Ecotoxicology and Environmental Safety
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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.

ACS Style

Sen Hou; Zhenzhen Jia; Katarzyna Kryszczuk; Da Chen; Lining Wang; Robert Holyst; Xizeng Feng. Joint effect of surfactants and cephalexin on the formation of Escherichia coli filament. Ecotoxicology and Environmental Safety 2020, 199, 110750 .

AMA Style

Sen Hou, Zhenzhen Jia, Katarzyna Kryszczuk, Da Chen, Lining Wang, Robert Holyst, Xizeng Feng. Joint effect of surfactants and cephalexin on the formation of Escherichia coli filament. Ecotoxicology and Environmental Safety. 2020; 199 ():110750.

Chicago/Turabian Style

Sen Hou; Zhenzhen Jia; Katarzyna Kryszczuk; Da Chen; Lining Wang; Robert Holyst; Xizeng Feng. 2020. "Joint effect of surfactants and cephalexin on the formation of Escherichia coli filament." Ecotoxicology and Environmental Safety 199, no. : 110750.

Journal article
Published: 16 May 2020 in Entropy
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We study a quantity T defined as the energy U, stored in non-equilibrium steady states (NESS) over its value in equilibrium U 0 , Δ U = U − U 0 divided by the heat flow J U 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 = U 0 ∗ f ( J U ) . 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.

ACS Style

Yirui Zhang; Konrad Giżyński; Anna Maciołek; Robert Hołyst. Storage of Energy in Constrained Non-Equilibrium Systems. Entropy 2020, 22, 557 .

AMA Style

Yirui Zhang, Konrad Giżyński, Anna Maciołek, Robert Hołyst. Storage of Energy in Constrained Non-Equilibrium Systems. Entropy. 2020; 22 (5):557.

Chicago/Turabian Style

Yirui Zhang; Konrad Giżyński; Anna Maciołek; Robert Hołyst. 2020. "Storage of Energy in Constrained Non-Equilibrium Systems." Entropy 22, no. 5: 557.

Research article
Published: 08 May 2020 in The Journal of Physical Chemistry B
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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 liquids with 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 with 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, opening the door for a wide range of potential applications.

ACS Style

Geping Zhang; Hongxia Zhu; Jingfei Chen; Mengjun Chen; Tomasz Kalwarczyk; Robert Hołyst; Hongguang Li; Jingcheng Hao. Self-Stabilized Giant Aggregates in Water from Room-Temperature Ionic Liquids with an Asymmetric Polar–Apolar–Polar Architecture. The Journal of Physical Chemistry B 2020, 124, 4651 -4660.

AMA Style

Geping Zhang, Hongxia Zhu, Jingfei Chen, Mengjun Chen, Tomasz Kalwarczyk, Robert Hołyst, Hongguang Li, Jingcheng Hao. Self-Stabilized Giant Aggregates in Water from Room-Temperature Ionic Liquids with an Asymmetric Polar–Apolar–Polar Architecture. The Journal of Physical Chemistry B. 2020; 124 (22):4651-4660.

Chicago/Turabian Style

Geping Zhang; Hongxia Zhu; Jingfei Chen; Mengjun Chen; Tomasz Kalwarczyk; Robert Hołyst; Hongguang Li; Jingcheng Hao. 2020. "Self-Stabilized Giant Aggregates in Water from Room-Temperature Ionic Liquids with an Asymmetric Polar–Apolar–Polar Architecture." The Journal of Physical Chemistry B 124, no. 22: 4651-4660.

Preprint content
Published: 19 March 2020
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BackgroundThere is an ongoing debate whether trimethylamine-oxide (TMAO), a molecule present in seafood and a derivate of microbiota metabolism, is beneficial or harmful for the circulatory system. Interestingly, deep-water animals accumulate TMAO that protects proteins such as lactate dehydrogenase (LDH) against high hydrostatic pressure. We hypothesized that TMAO may benefit the circulatory system by protecting cardiac LDH exposed to hydrostatic stress (HS) produced by contracting heart.Methods and ResultsMale, 6-week-old, Sprague-Dawley (SD, n=40) and Spontaneously-Hypertensive-Heart-Failure (SHHF n=18) rats were divided into either Water or TMAO oral treatment. After 56 weeks, half of Water and TMAO SD rats were given isoprenaline (ISO) to produce catecholamine stress. In vitro, LDH with or without TMAO was exposed to HS (changes in pressure 0-250mmHg x 280min−1) and was evaluated using fluorescence correlation spectroscopy. After 58 weeks of the treatment survival was 100% in SD-Water, SD-TMAO, ISO-TMAO and 90% in ISO-Water. In SHHF-Water survival was 66% vs 100% in SHHF-TMAO. In general, TMAO-treated rats showed higher diuresis and natriuresis. In comparison to SHHF-Water, SHHF-TMAO showed significantly lower diastolic arterial blood pressure, plasma NT-proBNP and expression of angiotensinogen and AT1 receptors in the heart. In separate experiments, intravenous TMAO but not vehicle or urea significantly increased diuresis in SD. In vitro, exposure of LDH to HS with or without TMAO did not affect the protein structure.ConclusionsTMAO reduces mortality in SHHF rats that is associated with diuretic, natriuretic and hypotensive effects. HS produced by the contracting heart is neutral for cardiac LDH structure.

ACS Style

Marta Gawrys-Kopczynska; Marek Konop; Klaudia Maksymiuk; Katarzyna Kraszewska; Ladislav Derzsi; Krzysztof Sozański; Robert Holyst; Marta Pilz; Emilia Samborowska; Leszek Dobrowolski; Kinga Jaworska; Izabella Mogilnicka; Marcin Ufnal. TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats. 2020, 1 .

AMA Style

Marta Gawrys-Kopczynska, Marek Konop, Klaudia Maksymiuk, Katarzyna Kraszewska, Ladislav Derzsi, Krzysztof Sozański, Robert Holyst, Marta Pilz, Emilia Samborowska, Leszek Dobrowolski, Kinga Jaworska, Izabella Mogilnicka, Marcin Ufnal. TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats. . 2020; ():1.

Chicago/Turabian Style

Marta Gawrys-Kopczynska; Marek Konop; Klaudia Maksymiuk; Katarzyna Kraszewska; Ladislav Derzsi; Krzysztof Sozański; Robert Holyst; Marta Pilz; Emilia Samborowska; Leszek Dobrowolski; Kinga Jaworska; Izabella Mogilnicka; Marcin Ufnal. 2020. "TMAO, a seafood-derived molecule, produces diuresis and reduces mortality in heart failure rats." , no. : 1.

Journal article
Published: 24 February 2020 in Biosensors and Bioelectronics
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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.

ACS Style

Łukasz Richter; Paweł Albrycht; Monika Księżopolska-Gocalska; Ewa Poboży; Robert Bachliński; Volodymyr Sashuk; Jan Paczesny; Robert Hołyst. Fast and efficient deposition of broad range of analytes on substrates for surface enhanced Raman spectroscopy. Biosensors and Bioelectronics 2020, 156, 112124 .

AMA Style

Łukasz Richter, Paweł Albrycht, Monika Księżopolska-Gocalska, Ewa Poboży, Robert Bachliński, Volodymyr Sashuk, Jan Paczesny, Robert Hołyst. Fast and efficient deposition of broad range of analytes on substrates for surface enhanced Raman spectroscopy. Biosensors and Bioelectronics. 2020; 156 ():112124.

Chicago/Turabian Style

Łukasz Richter; Paweł Albrycht; Monika Księżopolska-Gocalska; Ewa Poboży; Robert Bachliński; Volodymyr Sashuk; Jan Paczesny; Robert Hołyst. 2020. "Fast and efficient deposition of broad range of analytes on substrates for surface enhanced Raman spectroscopy." Biosensors and Bioelectronics 156, no. : 112124.

Journal article
Published: 14 February 2020 in The Journal of Physical Chemistry B
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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.

ACS Style

Krzysztof Bielec; Grzegorz Bubak; Tomasz Kalwarczyk; Robert Holyst. Analysis of Brightness of a Single Fluorophore for Quantitative Characterization of Biochemical Reactions. The Journal of Physical Chemistry B 2020, 124, 1941 -1948.

AMA Style

Krzysztof Bielec, Grzegorz Bubak, Tomasz Kalwarczyk, Robert Holyst. Analysis of Brightness of a Single Fluorophore for Quantitative Characterization of Biochemical Reactions. The Journal of Physical Chemistry B. 2020; 124 (10):1941-1948.

Chicago/Turabian Style

Krzysztof Bielec; Grzegorz Bubak; Tomasz Kalwarczyk; Robert Holyst. 2020. "Analysis of Brightness of a Single Fluorophore for Quantitative Characterization of Biochemical Reactions." The Journal of Physical Chemistry B 124, no. 10: 1941-1948.