Search results for: ODORANT-BINDING PROTEINS
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Chemical analysis of the Au-Ag nanoaloys
Open Research DataThe nanostructures of AuAg nanoalloys were prepared by sequential sputtering of gold and silver thin films. Single layer thickness was usually 2.8 nm were deosted by magnetron sputtering method in a Ar plasma. As deposited layers were annealed in Ar atmosphere at 550 degress for 15 minutes. For XPS measurements five samples were selected: pure gold...
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XPS study of the YST ceramics
Open Research DataYttrium-doped strontium titanate was prepared via conventional solid-state reaction method from Y2O3 (Sigma Aldrich, 99,9%), TiO2 (Sigma Aldrich, 99%) and SrCO3 (Sigma Aldrich,98%). For comparision, two other techniques were used for synthesis: Pechini and wet methods. Both kind of samples were measured, after and before reduction process (in a hydrogen)....
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The bile salt content of human bile impacts on simulated intestinal proteolysis of β-lactoglobulin
PublicationThe gastrointestinal hydrolysis of food proteins has been portrayed in scientific literature to predominantly depend on the activity and specificity of proteolytic enzymes. Human bile has not been considered to facilitate proteolysis in the small intestine, but rather to assist in intestinal lipolysis. However, human bile can potentially influence proteins that are largely resistant to gastric digestion, and which are mainly hydrolysed...
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Antibody Cross-Reactivity in Serodiagnosis of Lyme Disease
PublicationLyme disease is a tick-borne disease caused by spirochetes belonging to the Borrelia burgdorferi sensu lato complex. The disease is characterized by a varied course; therefore, the basis for diagnosis is laboratory methods. Currently, a two-tiered serological test is recommended, using an ELISA as a screening test and a Western blot as a confirmatory test. This approach was introduced due to the relatively high number of false-positive...
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A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
PublicationTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures...
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Modeling of the internal combustion engine cooling system
PublicationThe article concerns computer modelling of processes in cooling systems of internal combustion engines. Modelling objectives and existing commercial programs are presented. It also describes Author’s own method of binding graphs used to describe phenomena in the cooling system of a spark ignition engine. The own model has been verified by tests on the engine dynamometer. An example of using a commercial program for experimental...
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The database of localization and expression of classical aquaporins (AQPs) in the male reproductive system in cattle
Open Research DataThe data present research results being part of the OPUS-22 project entitled “In search of new markers of male fertility in cattle. Aquaporins expression in the reproductive organs and sperm of the bulls (Bos taurus)” financed by the National Science Center in Poland (grant no. 2021/43/B/NZ9/00204). The aim of this part of the project was (i) to determine...
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Poly-L-Lysine-modified boron-doped diamond electrodes for the amperometric detection of nucleic acid bases
PublicationBoron-doped diamond (BDD) is a very promising supporting material used in the construction of biosensors for molecular recognition. The direct immobilization of structurally-organized huge molecules, such as poly-L-Lysine (PLL) provides the possibility of determining organic molecules, e.g. nucleic acid bases (e.g. adenine, guanine) or peptides and proteins. This paper describes the direct method for chemical and electrochemical...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Photoresponsive, amide-based derivative of embonic acid for anion recognition
PublicationThe synthesis and ion-binding properties of amide-based derivative of embonic acid andp-aminoazobenzenewere described. The new compound was characterized by X-ray structural analysis and spectroscopic methods.Ligand interacts in acetonitrile with Y-shaped anions (benzoates and acetates) and dihydrogen phosphatesforming complexes of 1:1 stoichiometry. In more polar DMSO the complexes stoichiometry changes to 2:1(L:anion). Light-inducedtranstocisisomerization...
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Enzyme Conjugation - A Promising Tool for Bio-catalytic and Biotransformation Applications – A Review
PublicationEnzymes have revolutionized conventional industrial catalysts as more efficient, eco-friendly, and sustainable substitutes that can be used in different biotechnological processes, food, and pharmaceutical industries. Yet, the enzymes from nature are engineered to make them adapt and enhance their durability in the industrial environment. One promising approach involves the combined use of multiple enzymes that catalyze highly...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublicationThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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A New Expression System Based on Psychrotolerant Debaryomyces macquariensis Yeast and Its Application to the Production of Cold-Active β-D-Galactosidase from Paracoccus sp. 32d
PublicationYeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant species. A eukaryotic expression system working at low temperatures could be particularly useful for the production of thermolabile proteins and proteins that tend to form insoluble aggregates. For this purpose, an expression system based on an Antarctic psychrotolerant...
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Similarities and differences in d6 low-spin ruthenium, rhodium and iridium half-sandwich complexes: synthesis, structure, cytotoxicity and interaction with biological targets
PublicationIn this paper, we discussed the similarities and diferences in d6 low-spin half-sandwich ruthenium, rhodium and iridium complexes containing 2,2′-biimidazole (H2biim). Three new complexes, {[RuCl(H2biim)(η6 -p-cymene)]PF6}2·H2O (1), [(η5 - Cp)RhCl(H2biim)]PF6 (2), and [(η5 -Cp)IrCl(H2biim)]PF6 (3), were fully characterized by CHN, X-ray difraction analysis, UV–Vis, FTIR, and 1 H, 13C and 15N NMR spectroscopies. The complexes exhibit...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublicationThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Direct injection liquid chromatography-mass spectrometry (DI-LC-MS) analysis for rapid lipidomic profiling of extracellular vesicles
PublicationExtracellular vesicles (EVs) are small, spherical particles produced by eukaryotic and prokaryotic cells, surrounded by a bilayer membrane and carrying various bioactive molecules, such as proteins, surface receptors, membrane and soluble proteins, lipids, and nucleic acids. EVs are of substantial interest because of their important roles in cell communication, epigenetic regulation and possible application in disease diagnosis...
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Factors Affecting the Rheological Properties of Foods
PublicationIn this chapter, engineering aspects concerning real body mechanics and the impact of respective food ingredients on said properties are presented together. Food is a complex matrix and each of macro and micro ingredients plays its role in the formation of rheologic properties, and minor changes in the basic ingredient structure may affect the change of these properties significantly. Basic analytic techniques are presented for...
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Anion recognition by n,n'-diarylalkanediamides
PublicationThe preparation of N,N'-diarylalkanediamides from respective aliphatic dicarboxylic acidesand 4-nitroaniline via microwave-promoted reactions is presented. The most positive effect of microwave irradiation was observed for N,N'-bis(4-nitrophenyl)butanediamide. Anion binding studies on the obtained diamides were carried out in DMSO and acetonitrile using UV-vis and 1H NMR spectroscopy. A mechanism for selective fluoride recognition...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Fluoroaromatic substituents attached to carbon nanotubes help to increase oxygen concentration on biocathode in biosensors and biofuel cells
PublicationBased on the known ability of perfluorodecalin/perfluorohydrocarbons to enhance oxygen solubility we modified oxygen sensitive biocathode by adding perfluorinated components to the catholite. This procedure improved the efficiency of the oxygen sensitive cathodes. Glassy carbon electrodes covered with single-wall carbon nanotubes (SWCNTs) with covalently bonded perfluoroaromatic groups were shown to be more sensitive to oxygen,...
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Comparative assessment of two extraction procedures for determination of bioactive compounds in some berries used for daily food consumption
PublicationTwo extractions with methanol and water were used to determine the antioxidant and binding properties of some berries as a supplement to food. Fluorometry, FTIR spectra and radical scavenging assays were used for characterisation of bioactive compounds (polyphenols, flavonoids, flavanols and tannins) and the levels of their antioxidant activities (AAs). The contents of bioactive compounds and AAs in water and methanol polyphenol...
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties
PublicationAminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5′-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting...
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Reduction of the strontium titanate doped by Ytrium ceramics observed by X-ray photoemission spectroscopy method
Open Research DataYtrium-doped strontium titanate (YSTF) ceramics materials were manufactured by three various methods: 1) standard solid-state reaction method from Y2O3 (Sigma Aldrich, 99,9%), TiO2 (Sigma Aldrich, 99%) and SrCO3 (Sigma Aldrich,98%), 2) Pechini method, 3) wet method.
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In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions
PublicationCysteine cathepsins constitute the largest cathepsin family, with 11 proteases in human that are present primarily within acidic endosomal and lysosomal compartments. They are involved in the turnover of intracellular and extracellular proteins. They are synthesized as inactive procathepsins that are converted to mature active forms. Cathepsins play important roles in physiological and pathological processes and, therefore, receive...
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Early Stages of RNA-Mediated Conversion of Human Prions
PublicationPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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Bodybuilders and high-level meat consumers’ behavior towards rabbit, beef, chicken, turkey, and lamb meat: A comparative review
PublicationIn bodybuilders’ diets, protein plays a crucial role in supporting muscle growth and repairing damaged muscle tissue. These individuals meet their protein needs by combining dietary sources with supplements. Animal-based proteins are often preferred over plant-based proteins because they are believed to better support muscle protein synthesis. This review explores the meat consumption patterns of bodybuilders and high-level meat...
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Impact of high-pressure processing on the bioactive compounds of milk - A comprehensive review
PublicationHigh-pressure processing (HPP) is a promising alternative to thermal pasteurization. Recent studies highlighted the effectivity of HPP (400–600 MPa and exposure times of 1–5 min) in reducing pathogenic microflora for up to 5 logs. Analysis of modern scientific sources has shown that pressure affects the main components of milk including fat globules, lactose, casein micelles. The behavior of whey proteins under HPP is very important...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Cloning, expression, and biochemical characterization of a coldactive GDSL-esterase of a Pseudomonas sp. S9 isolated from Spitsbergen island soil
PublicationAn estS9 gene, encoding an esterase of the psychrotolerant bacterium Pseudomonas sp. S9 was cloned and sequenced. The deduced sequence revealed a protein of 636 amino acid residues with a molecular mass of 69 kDa.Further amino acid sequence analysis revealed that the EstS9 enzyme contained a G-D-S-L motif centered at a catalytic serine, an N-terminal catalytic domain and a C-terminal autotransporter domain. Two recombinant E. coli...
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The development of an indirect ELISA for the detection of goose parvovirus antibodies using specific VP3 subunits as the coating antigen
PublicationIn Poland, the leader in goose production in Europe, goose parovirus infection, or Derzsy’s disease (DD), must be reported to the veterinary administration due to the serious economic and epizootic threat to waterfowl production. Prophylactic treatment for DD includes attenuated live or inactivated vaccines. Moreover, the control of DD includes the monitoring of maternal derived antibody (MDA) levels in the offspring and antibody...
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CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
PublicationOverexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Antioxidant activities and bioactive components in some berries
PublicationThe objective of this study was to evaluate the antioxidant and binding effects of gooseberry, a less-stud-ied berry, and to compare with blueberry and cranberry in the model of interaction with human serum albumin (HSA). The relationship between the scavenging properties of dietary polyphenols of the selected berries and their affinities for HSA were investigated by fluorescence anal- ysis. In order to perform the extraction and...
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Immunization with an anti-idiotypic antibody against the broadly lipopolysaccharide-reactive antibody WN1 222-5 induces Escherichia coli R3-core-type specific antibodies in rabbits
PublicationThe mouse monoclonal antibody (mAb) WN1 222-5 recognizes a carbohydrate epitope in the inner core region of LPS that is shared by all strains of Escherichia coli and Salmonella enterica and is able to neutralize their endotoxic activity in vitro and in vivo. Immunization of mice with mAb WN1 222-5 yielded several anti-idiotypic mAbs one of which (mAb S81-19) competitively inhibited binding of mAb WN1 222-5 to E. coli and Salmonella...
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Genotoxic properties of glucosinolates and isothiocyanates present in Brassica vegetables
PublicationThe bioactive phytochemicals found in Brassica vegetables, in this number glucosinolates (GLS), as well as products of their degradation such as isothiocyanates (ITC) and indoles, are regarded as the most promising chemopreventive compounds. These secondary metabolites display stron antibiological activity and constitute defence system preventing the development of agrophages attacking Brassica plants. Such properties suggest...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Comparative Study of the Mechanical Behaviour of Bitumen- and Cement-Dominated Mixtures with Reclaimed Asphalt
PublicationThe bitumen emulsion-based recycling is a commonly used maintenance treatment in the rehabilitation of low-and medium-volume roads in Europe. Nevertheless, the wide range of climatic conditions across the continent resulted in the variety of mixture concepts and the requirements being adopted for various local conditions. In this regard, the most commonly used parameter to distinguish between the main mixture concepts is bitumen...
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Lower rim substituted p-tert-butyl-calix[4]arene. Part 17. synthesis, extractive and ionophoric properties of p-tert-butylcalix[4]arene appended with hydroxamix acid moieties
PublicationThe synthesis and characterization of four p-tert-butylcalix[4]arene-hydroxamic acidc are reported. The dependence of the metal ion binding, assessed by liquid extraction of the metal nitrates from water into dichloromethane in individual and competitive experiments, on the ligand structure, is presented. The results showed that those ligands could be successfully used in separation process of trnasition and heavy metals often...
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Dissociation pathways of protonated water clusters
PublicationRelative abundances of positively ionized water clusters formed in a low-pressure electrical discharge as function of reduced electric field were obtained by using drift cell and quadrupole mass spectrometer. It was noticed that some clusters say with n=4 were more abundant than others, at comparable drift conditions. Dissociation energies have been derived from equilibrium conditions for relative clusters abundances. The Hartree-Fock...
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Iron(III)-selective materials based on a catechol-bearing amide for optical sensing
PublicationThe synthesis and ion-binding properties of a new amide L derived from 3,4-dihydroxybenzoic acid are described. Due to the presence of a catechol unit, the compound interacts selectively with iron(III) in organic solvent (dimethyl sulfoxide, DMSO) to produce a color change from pale yellow to green. The incorporation of the ligand L into polymeric matrices or its encapsulation into surfactant-based spheres enables analyte detection...
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Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging
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