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Search results for: POLYMERASE CHAIN REACTION THERMOANAEROBACTER TENGCONGENSIS
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Recombinant !ermostable AP Exonuclease from Thermoanaerobacter tengcongensis: Cloning, Expression, Purification, Properties and PCR Application
PublicationApurinic/apyrimidinic (AP) sites in DNA are considered to be highly mutagenic and must be corrected to preserve genetic integrity, especially at high temperatures. !e gene encoding a homologue of AP exonuclease was cloned from the thermophilic anaerobic bacterium Thermoanaerobacter tengcongensis and transformed into Escherichia coli. The protein product showed high identity (80%) to human Ape1 nuclease, whereas to E. coli exonuclease...
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A simple modification to improve the accuracy of methylation-sensitive restriction enzyme quantitative polymerase chain reaction
PublicationDNA digestion with endonucleases sensitive to CpG methylation such as HpaII followed by polymerase chain reaction (PCR) quantitation is commonly used in molecular studies as a simple and inexpensive solution for assessment of region-specific DNA methylation. We observed that the results of such analyses were highly overestimated if mock-digested samples were applied as the reference.We determined DNA methylation levels in several...
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Detection of Blastocystis hominis in unpreserved stool specimens byusing polymerase chain reaction
PublicationBlastocystis hominis jest pasożytem występującym na całym świecie. Patogenność tego pasożyta nie jest jeszcze w pełni udowodniona, aczkolwiek opisanych jest wiele przypadków, sugerujących, że B. hominis może wywoływać objawy żołądkowo-jelitowe. Wykrywanie tego pasożyta opiera się na bezpośredniej obserwacji mikroskopowej rozmazów i zagęszczonych próbek kału lub rozmazów utrwalonych, jednakże w pewnych przypadkach nie jest to możliwe.Celem...
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublicationWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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The suitability of DNA extracted from formalin-fixed, paraffin-embedded tissues for double differential polymerase chain reaction analysis
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Detection ofHelicobacterspecies in liver and stomach tissues of patients with chronic liver diseases using polymerase chain reaction-denaturing gradient gel electrophoresis and immunohistochemistry
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Detection of Helicobacter rodentium-like DNA in the liver tissue of patients with chronic liver diseases by polymerase chain reaction–denaturing gradient gel electrophoresis and DNA sequence analysis
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Synthesis of oxathiolone fused chalkones bearing O-aminoalkyl side chain. Comparison of stability of isomeric benzoxathiolones under alkylation reaction conditions
PublicationIzomeryczne oksatiolonowe sprzężone chalkony zawierające O-alkilowe łańcuchy boczne otrzymano w wyniku kondensacji odpowiednich benzoksatiolonów z podstawionymi benzaldehydami. Wyjściowe benzoksatiolony otrzymano w wyniku alkilowania odpowiednich fenoli chlorkami aninoalkilowymi, jednakże reakcja była często komplikowana w wyniku otwarcia pierścienia oksatiolonowego poprzez grupę aminową. Określono aktywność cytotoksyczną i przeciwdrobnoustrojową...
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Techniki biologii molekularnej w analityce produktów mięsnych
PublicationW pracy przedstawiono możliwości wykorzystania reakcji PCR (Polymerase Chain Reaction) do identyfikacji patogennych drobnoustrojów a także do badania składu surowcowego w mięsnych produktach żywnościowych.
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublicationDNA polymerase is an enzyme which plays crucial role in replication and DNA repair. It found application in PCR (polymerase chain reaction) where catalyses process of in vitro DNA synthesis. To meet the demands posed by mod- ern diagnostic, molecular biology or genetic engineering it is necessary to improve DNA polymerases to obtain new or better features useful in these fields. So far implemented modifications in majority are...
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PCR-ELISA: inexpensive alternative to quantitative PCR
PublicationPCR-ELISA (polymerase chain reaction-enzyme linked immunosorbent assay), a combination of PCR and ELISA methods, has been used since late 1980s. The technique is based on specially labelled DNA fragments which are captured by specific DNA sequences and detected by antibodies. The whole procedure of PCR-ELISA is divided into three steps: DNA extraction, PCR reaction and detection by ELISA. The method has been found as very specific...
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5-Bromo-2′-deoxycytidine—a potential DNA photosensitizer
PublicationA double-stranded oligonucleotide, 80 base pairs in length, was multiply labeled with 5-bromo-2′-deoxycytidine (BrdC) using polymerase chain reaction (PCR). The modified oligonucleotide was irradiated with 300 nm photons and its damage was assayed by employing DHPLC, LC-MS and denaturing polyacrylamide gel electrophoresis (PAGE). Two types of damage were demonstrated, namely, single strand breaks (SSBs) and intrastrand cross-links...
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PCR-RFLP assays for species-specific identification of fungi belonging to Scopulariopsis and related genera
PublicationFungi of the Scopulariopsis genus, commonly found in the environment, are opportunistic pathogens that can cause various types of human infections. So far, no efficient molecular method has been developed for species differentiation among Scopulariopsis and related genera. In order to advance this field, we have evaluated performance of polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assays, based...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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Phylogenetic trees of genus Oncidium Sw. based on analysis of DNA sequences
Open Research DataGenus Oncidium Sw. is widely regarded as a polyphiletic, and the taxonomic boundaries between him and such genera as Odontoglossum Kunth. or Miltonia Lindley remain blurred. The goal of the study was to determine the phylogenetic relationships within the genus Oncidium s.lato based on the DNA sequences analysis. The correlation between molecular data...
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A simple modification of PCR thermal profile applied to evade persisting contamination
PublicationThe polymerase chain reaction (PCR), one of the most commonly applied methods of diagnostics and molecular biology has a frustrating downside known as the false positive signal or contamination. Several solutions to avoid and to eliminate PCR contaminations have been worked out to date but the implementation of these solutions to laboratory practice may be laborious and time consuming. A simple approach to circumvent the problem...
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Acclimation of denitrifying activated sludge to a single vs. complex external carbon source during a start-up of sequencing batch reactors treating ammonium-rich anaerobic sludge digester liquors
PublicationIn this study, denitrification of ammonium- reach anaerobic sludge digester liquor was investigated during start-up periods of two laboratory- scale ‘‘fill-and-draw’’ reactors. One reactor was fed with a single carbon source (ethanol), whereas the other reactor was fed with a complex carbon source (fusel oil). During two acclimation experiments, the structure of microbial community involved in denitrification was analyzed using...
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Identification and cloning of C. albicans SC5314 genes encoding L-methionine biosynthetic pathway enzymes.
Open Research DataEnzymes of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p), O-acetylhomoserine sulfhydrylase (Met15p) and cystathionine-γ-synthase (Str2p) could be exploited as molecular targets for antifungal chemotherapy. The goal of the study was to identify and clone genes encoding mentioned above enzymes. MET2, MET15 and STR2 genes...
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Resistance of Escherichia coli and Enterococcus spp. to selected antimicrobial agents present in municipal
PublicationIn this study, the susceptibility to erythromycin (E) and to trimethoprim/sulfamethoxazole (SXT) among isolates of Enterococcus spp. and Escherichia coli was tested, respectively. Both fecal indicators were detected and isolated from raw(RW) and treated wastewater (TW) as well as from samples of activated sludge (AS) collected in a local wastewater treatment plant (WWTP). Biodiversity of bacterial community in AS was also monitored...
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The New LM-PCR/Shifter Method for the Genotyping of Microorganisms Based on the Use of a Class IIS Restriction Enzyme and Ligation Mediated PCR
PublicationThis study details and examines a novel Ligation-Mediated - Polymerase Chain Reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4 base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s)...
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Clinical studies of detecting COVID-19 from exhaled breath with electronic nose
PublicationThe COVID‑19 pandemic has attracted numerous research studies because of its impact on society and the economy. The pandemic has led to progress in the development of diagnostic methods, utilizing the polymerase chain reaction (PCR) as the gold standard for coronavirus SARS‑CoV‑2 detection. Numerous tests can be used at home within 15 min or so but of with lower accuracy than PCR. There is still a need for point‑of‑care tests available...
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An investigation on the role of GMA grafting degree on the efficiency of PET/PP-g-GMA reactive blending: morphology and mechanical properties
PublicationGlycidyl methacrylate (GMA) has been grafted on polypropylene (PP) with the aid of styrene (St) comonomer, by changing dicumyl peroxide initiator content, GMA level, and St concentration. The performance of the resulting PP-g-GMA reactive material towards static and dynamic mechanical properties of poly (ethylene terephthalate) (PET) was monitored in terms of grafting reaction variables and compatibilizer content. Fourier transform...
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Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor
PublicationRolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line...
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Effect of hydroxylated soybean oil and bio-based propanediol on the structure and thermal properties of synthesized bio-polyurethanes
PublicationThe aim of this work was to obtain bio-polyurethanes using synthetic compounds and bio-components, i.e. bio-glycols. Bio-polyurethanes were prepared by means of the prepolymer method. Prepolymers were synthesized from 4,4′-diphenylmethane diisocyanate (MDI) and a polyol mixture containing 75% by weight of commercial polyether and 25% by weight of hydroxylated soybean oils (H2 or H3), the latter being obtained in the reaction with...
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Loop-mediated isothermal amplification (LAMP) as a diagnostic tool in detection of infectious diseases
PublicationLoop-mediated isothermal amplification (LAMP) is a gene amplification method which amplifies DNA with high specificity and efficiency under isothermal conditions. Because of its rapidity and simplicity, it is a valuable diagnostic tool in the early detection and identification of infectious diseases. LAMP method is based on the use of a set of four to six specially designed primers spanning six to eight distinct sequences on the...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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New Approaches for Escherichia coli Genotyping
PublicationEasy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing...
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B-GALACTOSIDASE ARTHROBACTER SP. 32cB - OBTAINING THE GENE SEQUENCE, CONSTRUCTION OF THE EXPRESSION SYSTEM, BIOSYNTHESIS AND BIOCHEMICAL CHARACTERIZATION OF THE ENZYME
PublicationINTRODUCTION: β-Galactosidase is an enzyme which catalyzes the hydrolysis of O glycosidic bond in β-galactosides. Another activity of β galactosidase is a transglycosylation activity. The main industrial use of this protein is the hydrolysis of lactose in milk in a cooling conditions. Synthesis of galactooligosaccharides, which are mostly used as a prebiotics added to some foods or available as dietary supplements, is only one...
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Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods
PublicationApart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus,...
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Synthesis, structure and properties of poly(ether-urethane)s synthesized using a tri-functional oxypropylated glycerol as a polyol
PublicationThe main aim of this work was to obtain poly(ether-urethane)s using tri-functional polyoxyalkylene polyol (Rokopol G1000), which introducing the chemical cross-links into the structure of polyurethanes. Poly(ether-urethane)s were prepared using two-step method, called prepolymer method, which involves in the first step the reaction of 4,4'-diphenylmethane diisocyanate (MDI) and tri-functional polypropylene glycol glycerol triether...
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Solid-State Modification of Poly(butylene terephthalate) with a Bio-Based Fatty Acid Dimer Diol Furnishing Copolyesters with Unique Morphologies
PublicationCopolyesters based on poly(butylene terephthalate) (PBT) and a bio-based fatty acid dimer diol (FADD) were prepared by solid-state modification (SSM). The chemical incorporation of the FADD into the backbone of the PBT was proven using various techniques. It was clear that the incorporation rate was diffusion-limited rather than reaction-limited. From quantitative 13C NMR a nonrandom chemical microstructure was obtained at all...
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Emulsifi ers from renewable materials: an eco-friendly synthesis and properties
PublicationThe focus of this study was the preparation of novel bio based polyglycerol emulsifiers characterized by a one pot synthesis, thus by modified properties with respect to interfacial activity and effectiveness as emulsion stabilizers. The final products of the esterification process, carried out in the presence of carboxylates were used directly as emulsifiers (without purification or fractionation). Polyglycerol emulsifiers obtained...
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Catena-Poly[[(tetrahydrofuran-[kappa]O)lithium(I)]-bis([mu]-trimethylsilanolato-[kappa]2O:O)-gallium(III)-bis([mu]-trimethylsilanolato-[kappa]2O:O)-[(tetrahydrofuran-[kappa]O)lithium(I)]-[mu]-bromido]
PublicationThe title chain polymer compound, [GaLi2Br(C3H9OSi)4(C4H8O)2]n, was obtained in the reaction of GaBr3 with Me3SiOLi in toluene/tetrahydrofuran. The GaIII atom, located on a twofold rotation axis, is coordinated by four trimethylsilanolate ligands and has a distorted tetrahedral geometry. The LiI atom is four coordinated by one bridging Br atom located on an inversion centre, two trimethylsilanolate ligands and one tetrahydrofurane...
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Synthesis, structure and properties of poly(ester-urethane)s obtained using bio-based and petrochemical1,3-propanediol and 1,4-butanediol
PublicationIn this paper, the poly(ester-urethane)s obtained using petrochemical and bio-based chain extenders were prepared and characterized. The influence of glycols’ origin on the chemical structure, mechanical and thermal properties of the prepared polyurethanes was studied. The materials were synthesised by prepolymer method. The first step involved the reaction of α,ω-dihydroxy(ethylene-butylene adipate (POLIOS 55/20) with 4,4’-diphenylmethane...
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Effect of modified soybeen oil amount on rheological characteriza-tion of polyurethane pre-polymers
PublicationPolyurethanes (Pu’s) are the polymeric materials which have got urethane groups in the structure. The properties of Pu’s depend both on the method of preparation and monomers used. Polyurethanes are produced by two methods known as one step or two step method called as “pre-polymers method”, especially for the case of segmented polyurethanes (SPU’s). These materials are thermoplastic block copolymers of the (AB)n type consisting...
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Synteza, struktura chemiczna i właściwości bezizocyjanianowych poliuretanów otrzymywanych z wykorzystaniem CO2 oraz surowców pochodzenia naturalnego.
PublicationZ uwagi na wciąż rosnącą świadomość proekologiczną, politykę zrównoważonego rozwoju, a także nurt zielonej chemii wiodącym trendem w przemyśle tworzyw sztucznych jest poszukiwanie alternatywnych metod otrzymywania materiałów polimerowych. Komercyjnie poliuretany otrzymywane są w wyniku reakcji poliaddycji di- lub poliizocyjanianów z poliolami i małocząsteczkowymi przedłużaczami łańcucha. Z uwagi na niekorzystne właściwości diizocyjanianów,...
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Application of surface active amino acid ionic liquids as phase-transfer catalyst
PublicationFive structurally related morpholinium derived ionic liquids containing N-acetyl-glycinate anion were synthesized and their thermal stability, surface properties and activity as phase transfer catalysts investigated. The thermal properties were studied by differential scanning calorimetry, while the adsorption at the air/water interface and micellization behavior was analyzed by surface tension measurements, conductometry and isothermal...
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Bioactive quaternary ammonium ionic liquids.
PublicationAn ionic liquid (IL) is an organic compound that contains at least one ionic bond. It consists of an organic cation and an organic or inorganic anion. It is an organic salt having a melting point below 100C. A very interesting group of IL are those with a long chain quaternary ammonium cation. They are formed by direct synthesis or by an anion-exchange reaction in quaternary ammonium halides. Popular and cheap precursors for the...
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Copper(I) halide cluster-based coordination polymers modulated by chiral ditopic dithiodianthranilide ligands: synthesis, crystal structure and photoluminescence
PublicationReaction of copper(I) halides with chiral dithiodianthranilidesmdtaandbdtaafforded polymeric complexeswhere polynuclear CuX clusters were linked together by ditopic bridging ligands into 1D chains or 2D layerstructures. In the case of racemic ligands double stranded chain polymers were formed where the Cu4X4(X = I or Br) cores are connected by enantiomeric pairs of the ditopic ligands. In contrast, a homochiralmdtaligand created...
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Dual functionality of amphiphilic 1-alkyl-3-methylimidazolium hydrogen sulfate ionic liquids: surfactants with catalytic function
PublicationA series of amphiphilic 1-alkyl-3-methylimidazolium hydrogen sulfate ionic liquids were synthesized. Acidic hydrogen sulfate ionic liquids with the alkyl chains C6–C14 are characterized by good surface properties. Their surface properties (adsorption and micellization parameters, degree of ionization of micelles, Krafft temperatures and thermodynamic parameters) were determined. Synthesized ionic liquids were applied as a co-catalyst...
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Studies on Aminoanthraquinone-Modified Glassy Carbon Electrode: Synthesis and Electrochemical Performance toward Oxygen Reduction
PublicationIn this paper, 9,10-anthraquinone (AQ) derivative-modified glassy carbon (GC) electrodes were studied towards the electrochemical reduction of oxygen in aqueous and non-aqueous solutions. The reaction of 1-chloro-9,10-anthraquinone with aliphatic diamines was applied for the synthesis of amino-9,10-anthraquinone derivatives. The obtained AQ derivatives were grafted onto the surface of glassy carbon electrodes by electropolymerisation...
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Studies on Aminoanthraquinone-Modified Glassy Carbon Electrode: Synthesis and Electrochemical Performance toward Oxygen Reduction
PublicationIn this paper, 9,10-anthraquinone (AQ) derivative-modified glassy carbon (GC) electrodes werestudied towards the electrochemical reduction of oxygen in aqueous and non-aqueous solutions. The reaction of 1-chloro-9,10-anthraquinone with aliphatic diamines was applied for the synthesis of amino-9,10-anthraquinone derivatives. The obtained AQ derivatives were grafted onto the surface of glassy carbon electrodes by electropolymerisation...
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Structure, morphology and mechanical behaviour of novel bio-based polyurethane composites with microcrystalline cellulose
PublicationThe aim of this work was to obtain bio-based polyurethane composites using biocomponents such as, bio-glycol, modified natural oil-based polyol, and microcrystalline cellulose (MCC). The prepolymer method was used to prepare the bio-based polyurethane matrix. Prepolymer synthesised from 4,4’-diphenylmethane diisocyanate (MDI) and a polyol mixture containing 75% wt. commercial polyether and 25% wt. hydroxylated soybean oils (H3)...
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Reclaimed rubber in-situ grafted with soybean oil as a novel green reactive plasticizer in SBR/silica compounds
PublicationPolymer recycling and biodegradable polymeric materials are two major routes towards the sustainable development of polymer materials which contributes to the management of waste. In this regard, an eco-friendly approach is presented wherein high reclaiming degree of ground tire rubber (GTR) was achieved by low-temperature oxidation under swollen action of soybean oil. In-situ reclaimed GTR with soybean oil was cured into reactive...
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The ILs-assisted electrochemical synthesis of TiO2 nanotubes: The effect of ionic liquids on morphology and photoactivity
PublicationFacile and environmentally benign one-step titanium anodization method for TiO2 nanotubes (NTs) formation in a presence of ionic liquids (ILs) was proposed. Influence of the IL structure and its content in ethylene glycol electrolyte on morphology, surface properties and photoactivity of the TiO2 NTs was investigated. Possible interactions between IL and TiO2 NTs as well as the mechanism of NTs formation during anodic oxidation...
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Synthesis, structure and properties of novel poly(hydroxyurethane)s obtained by non-isocyanate route
PublicationNon-isocyanate polyurethanes (NIPUs) can be synthesized by polyaddition of five-membered bis(cyclic carbonate)s and primary diamines. NIPUs are an alternative for the commonly used (in the form of foams, elastomers, coatings or fibers) in the industry polyurethanes obtained using toxic and moisture sensitive diisocyanates, polyols and low-molecular weight chain extenders. The main aim of this work was to synthesize non-isocyanate...
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ALIS-FLP: amplified ligation selected fragment-length polymorphism method for microbial genotyping
PublicationA DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs in that only one specific restriction enzyme (TspRI) is used. The cohesive ends of the DNA fragments are ligated with two types of oligonucleotide....