Search

Barbara Dymek,1,2 Piotr Sklepkiewicz,1 Michal Mlacki,1 Nazan Cemre Güner,1 Patrycja Nejman-Gryz,3 Katarzyna Drzewicka,1 Natalia Przysucha,3 Aleksandra Rymaszewska,1 Magdalena Paplinska-Goryca,3 Agnieszka Zagozdzon,1 Małgorzata Proboszcz,3 Łukasz Krzemiński,1 Jan H von der Thüsen,4 Katarzyna Górska,3 Karolina Dzwonek,1 Zbigniew Zasłona,1 Pawel Dobrzanski,1 Rafał Krenke3 1Molecure SA, Warsaw, 02-089, Poland; 2Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, 02-097, Poland; 3Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, 02-097, Poland; 4Department of Pathology, Erasmus Medical Center, Rotterdam, 3015 GD, the NetherlandsCorrespondence: Barbara Dymek, Żwirki i Wigury 101, Warsaw, 02-089, Poland, Tel +48 22 552 67 24, Email b.dymek@molecure.comIntroduction: Sarcoidosis is a systemic disease of unknown etiology characterized by granuloma formation in the affected tissues. The pathologically activated macrophages are causatively implicated in disease pathogenesis and play important role in granuloma formation. Chitotriosidase (CHIT1), macrophage-derived protein, is upregulated in sarcoidosis and its levels correlate with disease severity implicating CHIT1 in pathology.Methods: CHIT1 was evaluated in serum and bronchial mucosa and mediastinal lymph nodes specimens from sarcoidosis patients. The therapeutic efficacy of OATD-01 was assessed ex vivo on human bronchoalveolar lavage fluid (BALF) macrophages and in vivo in the murine models of granulomatous inflammation.Results: CHIT1 activity was significantly upregulated in serum from sarcoidosis patients. CHIT1 expression was restricted to granulomas and localized in macrophages. Ex vivo OATD-01 inhibited pro-inflammatory mediators’ production (CCL4, IL-15) by lung macrophages. In the acute model of granulomatous inflammation in mice, OATD-01 showed anti-inflammatory effects reducing the percentage of neutrophils and CCL4 concentration in BALF. In the chronic model, inhibition of CHIT1 led to a decrease in the number of organized lung granulomas and the expression of sarcoidosis-associated genes.Conclusion: In summary, CHIT1 activity was increased in sarcoidosis patients and OATD-01, a first-in-class CHIT1 inhibitor, demonstrated efficacy in murine models of granulomatous inflammation providing a proof-of-concept for its clinical evaluation in sarcoidosis.Keywords: chitinase, OATD-01, granuloma, macrophages, interstitial lung disease

Metal detoxification is essential for bacteria’s survival in adverse environments and their pathogenesis in hosts. Understanding the underlying mechanisms is crucial for devising antibacterial treatments. In the Gram-negative bacterium Escherichia coli , membrane-bound sensor CusS and its response regulator CusR together regulate the transcription of the cus operon that plays important roles in cells’ resistance to copper/silver, and they belong to the two-component systems (TCSs) that are ubiquitous across various organisms and regulate diverse cellular functions. In vitro protein reconstitution and associated biochemical/physical studies have provided significant insights into the functions and mechanisms of CusS–CusR and related TCSs. Such studies are challenging regarding multidomain membrane proteins like CusS and also lack the physiological environment, particularly the native spatial context of proteins inside a cell. Here, we use stroboscopic single-molecule imaging and tracking to probe the dynamic behaviors of both CusS and CusR in live cells, in combination with protein- or residue-specific genetic manipulations. We find that copper stress leads to a cellular protein concentration increase and a concurrent mobilization of CusS out of clustered states in the membrane. We show that the mobilized CusS has significant interactions with CusR for signal transduction and that CusS’s affinity toward CusR switches on upon sensing copper at the interfacial metal-binding sites in CusS’s periplasmic sensor domains, prior to ATP binding and autophosphorylation at CusS’s cytoplasmic kinase domain(s). The observed CusS mobilization upon stimulation and its surprisingly early interaction with CusR likely ensure an efficient signal transduction by providing proper conformation and avoiding futile cross talks.

The article compares the classic Fenton reagent (Fe2+/H2O2) with its modification with zero-valent iron (ZVI/H2O2) to remove azo dye Acid Red 27 from aqueous solutions at a concentration of 100 mg/L. For both methods, the most favorable parameter values ​​were determined at which visual discoloration of the solutions tested was obtained (for Fe2+/H2O2:pH 3.5, H2O2=60 mg/L, Fe2+/H2O2=0.3, t=15 min, and for ZVI/H2O2: pH 3, H2O2=40 mg/L, ZVI=80 mg/L, t=15 min). Under these conditions, the COD value was reduced by 71.5% and 69.2% for the classic Fenton and its modification, respectively. A reduction in toxicity was also obtained for Vibrio fischeri bacteria to below 25% by using the Microtox test. ZVI digestion at acidic pH for 10 minutes allowed to shorten the reaction time by about four times - from 15 to 4 minutes. BET analysis showed that the specific surface area increases with the digestion time, which significantly accelerates the reaction. The visual discoloration of aqueous solutions was obtained, and the final COD values ​​were very small, ranging from 49-53 mg O2/L. According to the Vibrio fischeri toxicity classification test for water samples, all solutions of dyes tested can be considered as non-toxic (toxicity value

Aim of this paper is to present the properties of carbon preforms for the production of biomorphic composites. Carbon samples were obtained through pyrolysis of paulownia wood, replicating the microstructure of the cellulosic precursor. Many characterization methods such as Raman Spectroscopy, light microscopy, hardness tests and pore size analyzer detection were used to investigate the microstructure of the product as well as the pore size of carbon samples. Obtained results showed that the parts of early or late wood template play an important role in the pore size, specific surface area and pore volume of the product. This review aims to be a comprehensive description of the development of carbon chars: from wood templates and their microstructure to potential applications of biomorphic materials.

In this framework, an investigation of biomorphous composite materials was performed. The application of a natural reinforcement allows to obtain biomorphous composite materials. Pine wood samples were subjected to the pyrolysis process in order to obtain carbon char. The samples were subjected to Atomic Layer Deposition and the sol-gel coating process in order to obtain a titanium oxide and titanium carbide coating, respectively. Ti-gel carbon char samples were subjected to ceramisation. Pure carbon char coated with TiO and TiC was infiltrated with an Al alloy. The investigations of the obtained composite materials were performed using light microscopy, transmission and scanning electron microscopy for microstructure determination. Raman spectroscopy and X-ray analysis were performed, along with hardness and tribological tests. Crystallites were detected after infiltration of the porous samples with an Al alloy, which were up to several microns in size, depending on the selected coating. As a result of the investigation on coating samples, a significantly smaller presence of Al carbides was found. An increase of hardness and wear resistance of biomorphous composite materials containing the carbides phase was confirmed. The TiO2coating prevents the occurrence of a reaction during the infiltration process and the formation of Al carbides.

The aim of submitted paper is to present influence of manufacturing parameters on optical properties and surface morphology of composite materials with a polymer matrix reinforced by TiO 2 and SiO 2 and Bi 2 O 3 nanoparticles. The novelty proposed by the authors is the use of TiO 2 and SiO 2 and Bi 2 O 3 nanoparticles simultaneously in polymeric matrix. This allows using the combined effect of nanoparticles to a result composite material. The thin films of composite material were prepared by using spin-coating method with various spinning rates from solutions of different concentration of nanoparticles. In order to prepare the spinning solution polymer, Poly(methyl methacrylate) (PMMA) was used as a matrix. The reinforcing phase was the mixture of the nanoparticles of SiO 2 , TiO 2 and B 2 O 3 . In order to identify the surface morphology of using thin films and arrangement of the reinforcing phase Atomic Force Microscope (AFM) and Scanning Electron Microscope (SEM) were used. In order to study the optical properties of the obtained thin films, the thin films of composites was subjected to an ellipsometry analysis. The measurements of absorbance of the obtained materials, from which the value of the band gap width was specified, were carried out using the UV/VIS spectroscopy. The optical properties of obtain composite thin films depend not only on the individual components used, but also on the morphology and the interfacial characteristics. Controlling the participation of three kinds of nanoparticles of different sizes and optical parameters allows to obtaining the most optimal optical properties of nanocomposites and also controlling the deposition parameters allows to obtaining the most optimal surface morphology of nanocomposites.

The aim of the research was to create thin, nanofibrous composite mats with a polyvinylpyrrolidone (PVP) matrix, with the reinforcing phase in the form of silicon oxide (SiO 2 ) nanoparticles. SiO 2 nanopowder was obtained using the zol-gel method with a mixture of tetraethyl orthosilicate (TEOS, Si (OC2H5)), hydrochloric acid (HCl), ethanol (C3H5OH) and distilled water. The produced colloidal suspension was subjected to a drying process and a calcination process at 550 °C, resulting in an amorphous silica nanopowder with an average particle diameter of 20 nm. The morphology and structure of the manufactured SiO 2 nanoparticles was tested using transmission electron microscopy (TEM) and X-ray diffraction analysis (XRD). Then, using the electrospinning method with a 15% (weight) solution of PVP in ethanol and a 15% solution of PVP/EtOH containing the produced nanoparticles equivalent to 5% of the mass concentration relative to the polymer matrix, polymer PVP nanofibres and PVP/SiO 2 composite nanofibres/SiO 2 nanoparticles were produced. The morphology and chemical composition of the produced polymer and composite nanofibres were tested using a scanning electron microscope (SEM) with an energy dispersive spectrometer (EDS). The analysis of the impact of the reinforcing phase on the absorption of electromagnetic radiation was conducted on the basis of UV–vis spectra, based on which the rated values of band gaps of the produced thin fibrous mats were assessed.

Physical forces have long been recognized for their effects on the growth, morphology, locomotion, and survival of eukaryotic organisms1. Recently, mechanical forces have been shown to regulate processes in bacteria, including cell division2, motility3, virulence4, biofilm initiation5,6, and cell shape7,8, although it remains unclear how mechanical forces in the cell envelope lead to changes in molecular processes. In Gram-negative bacteria, multicomponent protein complexes that form rigid links across the cell envelope directly experience physical forces and mechanical stresses applied to the cell. Here we manipulate tensile and shear mechanical stress in the bacterial cell envelope and use single-molecule tracking to show that shear (but not tensile) stress within the cell envelope promotes disassembly of the tripartite efflux complex CusCBA, a system used by E. coli to resist copper and silver toxicity, thereby making bacteria more susceptible to metal toxicity. These findings provide the first demonstration that mechanical forces, such as those generated during colony overcrowding or bacterial motility through submicron pores, can inhibit the contact and function of multicomponent complexes in bacteria. As multicomponent, trans-envelope efflux complexes in bacteria are involved in many processes including antibiotic resistance9, cell division10, and translocation of outer membrane components11, our findings suggest that the mechanical environment may regulate multiple processes required for bacterial growth and survival.

The aim of the study was the production of thin composite nanofibrous mats PAN/TiO2 nanoparticles using the electrospinning method from solution of PAN/TiO2/DMF. TiO2 nanoparticles were obtained using sol-gel method. To prepare sol mixture, organic alkoxides precursor of titanium isopropoxide and water solution were used. Calcination of TiO-gel and following milling were carried out to obtain nanoparticles of TiO2 rutile phase. In order to analyze the structure of the obtained particles, we used X-ray diffraction analysis (XRD) and energy dispersive spectrometer (EDS). Analysis of the morphology and chemical composition of the resulting composite nanofibers were carried out using a scanning electron microscope (SEM) with EDS. The analysis of the optical properties and the energy band structure prepared nanoparticles and thin composite nanofibrous mats were determined by spectral analysis of the absorbance as a function of the energy of radiation obtained using a UV–Vis spectrophotometer.

In bacteria, trigger factor (TF) is the molecular chaperone that interacts with the ribosome to assist the folding of nascent polypeptides. Studies in vitro have provided insights into the function and mechanism of TF. Much is to be elucidated, however, about how TF functions in vivo. Here, we use single-molecule tracking, in combination with genetic manipulations, to study the dynamics and function of TF in living E. coli cells. We find that TF, besides interacting with the 70S ribosome, may also bind to ribosomal subunits and form TF-polypeptide complexes that may include DnaK/DnaJ proteins. The TF-70S ribosome interactions are highly dynamic inside cells, with an average residence time of ∼0.2 s. Our results confirm that the signal recognition particle weakens TF's interaction with the 70S ribosome, and further identify that this weakening mainly results from a change in TF's binding to the 70S ribosome, rather than its unbinding. Moreover, using photoconvertible bimolecular fluorescence complementation, we selectively probe TF2 dimers in the cell and show that TF2 does not bind to the 70S ribosome but is involved in the post-translational interactions with polypeptides. These findings contribute to the fundamental understanding of molecular chaperones in assisting protein folding in living cells.

The investigations presented in this paper describe surface treatment performed on samples of heat-treated cast magnesium and aluminium alloy. The structure and chemical composition as well as the functional and mechanical properties of the obtained gradient/monolithic films were analysed by high resolution transmission electron microscopy and scanning electron microscopy, Raman spectroscopy, the ball-on-disk tribotester and scratch testing. Moreover, investigation of the electrochemical corrosion behaviour of the samples was carried out by means of potentiodynamic polarisation curves in 1-M NaCl solution. The coatings produced by chemical vapour deposition did not reveal any delamination or defects and they adhere closely to the substrate. The coating thickness was in a range of up to 2.5 microns. Investigations using Raman spectra of the DLC films confirmed a multiphase character of the diamond-like carbon layer, revealing the sp2 and sp3 electron hybridisation responsible for both the hardness and the friction coefficient. The best wear resistance test results were obtained for the magnesium alloy substrate - AZ61, for which the measured value of the friction path length was equal to 630 m.

Heme-copper oxidases (HCOs) are key enzymes in prokaryotes and eukaryotes for energy production during aerobic respiration. They catalyze the reduction of the terminal electron acceptor, oxygen, and utilize the Gibbs free energy to transport protons across a membrane to generate a proton (ΔpH) and electrochemical gradient termed proton motive force (PMF), which provides the driving force for the adenosine triphosphate (ATP) synthesis. Excessive PMF is known to limit the turnover of HCOs, but the molecular mechanism of this regulatory feedback remains relatively unexplored. Here we present a single-enzyme study that reveals that cytochrome bo₃ from Escherichia coli, an HCO closely homologous to Complex IV in human mitochondria, can enter a rare, long-lifetime leak state during which proton flow is reversed. The probability of entering the leak state is increased at higher ΔpH. By rapidly dissipating the PMF, we propose that this leak state may enable cytochrome bo₃, and possibly other HCOs, to maintain a suitable ΔpH under extreme redox conditions.

Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein’s displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria.

Ascorbate levels and redox states, as well as the activities of the enzymes of ascorbate metabolism, were analyzed in roots of tomato seedlings during the culture on a medium supplemented with auxin and compared to the control cultured on an auxin-free medium. Biochemical parameters were determined separately in the distal part of the root where the inhibitory effect of auxin on root elongation growth is observed and in the proximal half on the organ which reacts to auxin treatment with increased lateral root proliferation. ASC peroxidase activity was found to be stimulated by auxin treatment in the lateral-root forming part of the root. This effect was not observed in the distal part of the organ. On the other hand, ASC oxidase activity was raised by auxin exclusively in the distal part of the root. An inhibitory effect of auxin supplementation to the medium on ASC—reducing enzymes was observed. The dehydroascorbate reductase activity was found to be inhibited by auxin only in the proximal part, while the activity of monodehydroascorbate reductase in both, the proximal and distal parts of the root. Ascorbate content increased in roots during culture irrespective of the presence of auxin. However, auxin treatment resulted in higher DHA levels and more significant participation of DHA in the total ascorbate pool when compared to the control grown on the auxin-free medium. Similar to auxin, adding DHA to the culture medium stimulated lateral root formation and inhibited primary root elongation. In contrast to DHA, ASC treatment affected significantly neither lateral root formation nor primary root growth and partly reversed the stimulatory effect of IAA on root formation and the inhibitory effect on root elongation. These results suggest that auxin induced changes in ascorbate metabolism may be involved in developmental reactions in tomato roots.

Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle., Binding and unbinding of transcription regulators at operator sites regulates gene expression. By single-molecule tracking of metal-sensing regulators, here the authors show that the unbinding kinetics depends on regulator concentration and chromosome condensation, and varies with their metal-binding states.

Mechanisms for cellular uptake of nanoparticles have important implications for nanoparticulate drug delivery and toxicity. We have explored the mechanism of uptake of amorphous silica nanoparticles of 14 nm diameter, which agglomerate in culture medium to hydrodynamic diameters around 500 nm. In HT29, HaCat and A549 cells, cytotoxicity was observed at nanoparticle concentrations ≥ 1 μg/ml, but DNA damage was evident at 0.1 μg/ml and above. Transmission electron microscopy (TEM) combined with energy-dispersive X-ray spectroscopy confirmed entry of the silica particles into A549 cells exposed to 10 μg/ml of nanoparticles. The particles were observed in the cytoplasm but not within membrane bound vesicles or in the nucleus. TEM of cells exposed to nanoparticles at 4°C for 30 minutes showed particles enter cells when activity is low, suggesting a passive mode of entry. Plasma lipid membrane models identified physical interactions between the membrane and the silica NPs. Quartz crystal microbalance experiments on tethered bilayer lipid membrane systems show that the nanoparticles strongly bind to lipid membranes, forming an adherent monolayer on the membrane. Leakage assays on large unilamellar vesicles (400 nm diameter) indicate that binding of the silica NPs transiently disrupts the vesicles which rapidly self-seal. We suggest that an adhesive interaction between silica nanoparticles and lipid membranes could cause passive cellular uptake of the particles.

Recently, studies have been reported in which fluorescently labeled redox proteins have been studied with a combination of spectroscopy and electrochemistry. In order to understand the effect of the dye on the protein-electrode interaction, voltammetry and surface analysis have been performed on protein films of dye-labeled and unlabeled forms of a cysteine-surface variant (L93C) and the wild type (wt) of the copper containing nitrite reductase (NiR) from Alcaligenes faecalis S6. The protein has been adsorbed onto gold electrodes modified with self-assembled monolayers (SAMs) made up of 6-mercaptohexanol (6-OH) and mixtures of various octanethiols. Electrochemical and surface-analytical techniques were utilized to explore the influence of the SAM composition on wt and L93C NiR enzyme activity and the orientation of the enzyme molecules with respect to the electrode/SAM. The unlabeled L93C NiR enzyme is only electroactive on mixed SAMs composed of positive 8-aminooctanethiol (8-NH(2)) and 8-mercaptooctanol (8-OH). No enzymatic activity is observed on SAMs consisting of pure 6-OH, 8-OH, or pure 8-NH(2). Modification of L93C NiR with the ATTO 565 dye resulted in enzymatic activity on SAMs of 6-OH, but not on SAMs of 8-OH. Quartz crystal microbalance with dissipation measurements show that well-ordered and rigid protein films (single orientation of the protein) are formed when NiR is electroactive. By contrast, electrode-NiR combinations for which no electrochemical activity is observed still have NiR adsorbed on the surfaces, but a less-structured and water-rich film is formed. For the unlabeled L93C NiR, bilayer formation is observed, suggesting that the Cys93 residue is orientated away from the surface and able to form disulfide bridges to a second layer of L93C NiR. The results indicate that interfacial electron transfer is only possible if the negatively charged surface patch surrounding the electron-entry site of NiR is directed toward the electrode. This can be achieved either by introducing positive charges in the SAM or, when the SAM does not carry a charge, by labeling the enzyme with an ATTO 565 dye, which has some hydrophobic character, close to the electron entry site of the NiR.

A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Förster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (≥520 μM), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer.