Search results for: amino acids biosynthesis
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp.,recognizes novel asymmetric sequence 5´-ACGGA(N11/9)-3
PublicationA novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5′-ACGGA-3′ and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found...
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A new Thermus sp. class-IIS enzyme subfamily: isolation of a ''twin'' endo nuclease TspDTI with a novel specificity 5´-ATGAA(N11/9)-3´, related to TspGWI, Taqll and Tth111II. 5´-ATGAA(N11/9)-3´, spokrewnionej z TspGWI, TaqII i Tth111II.
PublicationOdkryto i scharakteryzowano nową subrodzinę enzymów klasy IIS z Thermus sp.
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublicationDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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Comparative Analysis of Metabolic Variations, Antioxidant Profiles and Antimicrobial Activity of Salvia hispanica (Chia) Seed, Sprout, Leaf, Flower, Root and Herb Extracts
PublicationThe purpose of this study was to evaluate the phytochemical profiles of the seeds, sprouts, leaves, flowers, roots and herb of Salvia hispanica and to demonstrate their significant contribution to antioxidant and antimicrobial activities. Applied methods were: HPLC-DAD coupled with post-column derivatization with ABTS reagent, untargeted metabolomics performed by LC-Q-Orbitrap HRMS, and two-fold micro-dilution broth method, which...
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A new 1-nitro-9-aminoacridine derivative targeting yeast topoisomerase II able to overcome fluconazole-resistance
PublicationFungal resistance remains a significant threat and a leading cause of death worldwide. Thus, overcoming microbial infections have again become a serious clinical problem. Although acridine derivatives are widely analyzed as anticancer agents, only a few reports have demonstrated their antifungal activity. In an effort to develop biologically active antifungals, twelve novel C-857 (9-(2′ -hydroxyethylamino)-1-nitroacridine) and...
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Direct amination of boron-doped diamond by plasma polymerized allylamine film
PublicationA novel microwave pulsed-plasma based method for the modification of the hydrogen-terminated polycrystalline boron-doped diamond (BDD) with a thin film of polymerized allylamine (PPAAm) is reported. A modified BDD surface is resistant to hydrolysis and delamination and is characterized by a high density of positively charged amino groups. Pulsed microwave plasma was applied to improve the degree of cross-linking and bonding of...
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An LC-MS/MS Method for a Comprehensive Determination of Metabolites of BTEX Anaerobic Degradation in Bacterial Cultures and Groundwater
PublicationBTEX (benzene, toluene, ethylbenzene, and the different xylene isomers), known for carcinogenic and neurotoxic effects, are common environmental contaminants. The first step for the development of the bioremediation technologies is the detection of intense microbial degradation in contaminated waters in the quest for the most active bacterial strains. This requires the multispecies analysis for BTEX metabolites which are considered...
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Nowe monomery pochodzenia roślinnego w syntezie termoplastycznych elastomerów poliuretanowych
PublicationJak dotychczas w syntezie termoplastycznych elastomerów poliuretanowych (TPU) są powszechnie wykorzystywane surowce pochodzenia petrochemicznego. Sytuacja jednak zmienia się dynamicznie i w wielu gospodarkach świata widoczne są już trendy, polegające na coraz większym wykorzystaniu substancji pochodzenia roślinnego w produkcji surowców, np. glikoli, izocyjanianów czy polioli, jako zamienników analogów syntetycznych. Praca obejmuje...
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Meldrum’s acid assisted formation of tetrahydroquinolin‑2‑one derivatives a short synthetic pathway to the biologically useful scaffold
PublicationA new method for the preparation of tetrahydroquinolin-2-one derivatives is presented. This approach involves a two-step reaction between enaminones and acylating agents, immediately followed by electrophilic cyclization, all within a single synthesis procedure, eliminating the need to isolate intermediates. The entire process is facilitated by the use of acyl Meldrum’s acids which not only shortens the preparation time of the...
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Novel 1,2,3-Triazole Derivatives as Mimics of Steroidal System—Synthesis, Crystal Structures Determination, Hirshfeld Surfaces Analysis and Molecular Docking
PublicationHerein, we present the synthesis and crystal structures determination of five 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives containing halogen atoms, 6a–e, which may be used as an excellent mimic of steroids in the drug development process. Good quality crystals obtained for all of the synthesized compounds allowed the analysis of their molecular structures. Subsequently, the determined crystal structures were used to calculate...
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Marcin Włoch dr inż.
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Synthesis, structural and spectroscopic properties of asymmetric schiff bases derived from 2,3-diaminopyridine
PublicationTwo Schiff base derivatives, 4-(2-amino-3-pyridyliminomethyl)phenol (I) and 3-(2-amino-3- pyridyliminomethyl)nitrobenzene (II ), were synthesised and characterised by spectroscopy. The structure of I was determined by single crystal X-ray diffraction studies. The asymmetric Schiff base derived from 2,3-diaminopyridine selectively recognise transition and heavy metal cations, and some anion. Ligands I and II form stable complexes...
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Design, Synthesis, and Enzymatic Evaluation of Novel ZnO Quantum Dot-Based Assay for Detection of Proteinase 3 Activity
PublicationHerein, the synthesis and application of functionalized quantum dot-based protease probes is described. Such probes are composed of nontoxic ZnO nanocrystals decorated by amino groups followed by linker and labeled peptide attachment. Spherical NH2-terminated ZnO quantum dots (QDs) with the average size ranging from 4 to 8 nm and strong emission centered at 530 nm were prepared using the sol−gel method. The fluorescence of ZnO...
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Synthesis and polymerisation techniques of molecularly imprinted polymers
PublicationMolecularly Imprinted Polymers (MIPs) are materials that has been processed using the molecular imprinting technique which permit to obtain well-defined three-dimensional cavities, with affinity to a template molecule, in the polymer matrix. Technology involves three strategies, i.e., covalent, non-covalent and semi-covalent approach, but the most popular is non-covalent approach. The most important components for the synthesis...
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Partial characterization of three Korean white lotus cultivars
PublicationThe nutritional and bioactive values of Korean white lotus cultivars (Muan, Chungyang, and Garam)extracted with methanol, water, and acetone solvents were evaluated by the contents of their bioactive compounds and antioxidant activity determined by ABTS, CUPRAC, FRAP, DPPH, and β-carotene-linoleic acid assays. HPLC, fluorometry, and FTIR spectroscopy were employed for evaluation of polyphenols and fatty acids. All lotus cultivar...
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Carboxylation Enhances Fragmentation of Furan upon Resonant Electron Attachment
PublicationWe report a dissociative electron attachment study to 2-furoic acid (C5H4O3) isolated in a gas phase, which is a model molecule consisting of a carboxylic group and a furan ring. Dissociation of furan by low energy electrons is accessible only via electronic excited Feshbach resonances at energies of incident electrons above 5 eV. On the other hand, carboxylic acids are well- known to dissociate via attachment of electrons at subexcitation energies....
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A New Approach to Chemical Recycling of Polyamide 6.6 and Synthesis of Polyurethanes with Recovered Intermediates
PublicationA new efficient method for the chemical decomposition of polyamide 6.6 by the glycolysis and amino-glycolysis processes was proposed. The glycolysis was conducted using the mass excess of ethylene glycol (EG) as a decomposing agent in the presence of a catalyst. Also, a mixture of EG and triethylenetetramine was used as another decomposing agent in the amino- glycolysis process. The described process of decomposition did not...
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Antifungal Activity of Homoaconitate and Homoisocitrate Analogs
PublicationThirteen structural analogs of two initial intermediates of the L-alpha-aminoadipate pathway of L-lysine biosynthesis in fungi have been designed and synthesized, including fluoro- and epoxy-derivatives of homoaconitate and homoisocitrate. Some of the obtainedcompounds exhibited at milimolar range moderate enzyme inhibitory properties against homoaconitase and/or homoisocitrate dehydrogenase of Candida albicans. The structural...
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Sposób wytwarzania kwasu 4-amino
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublicationINTRODUCTION. β-Galactosidase [EC 3.2.1.23] is an enzyme that catalyzes the hydrolysis of O-glycosidic linkages in galactosides. It is commercially used in dairy industry for the production of milk with reduced lactose content. Potentially, the best method for lactose removal under cooling conditions should be carried out with a cold-adapted enzyme. AIM. The aim of this study was to determine the taxonomic affiliation of the isolate...
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The Use of Artificial Neural Networks and Decision Trees to Predict the Degree of Odor Nuisance of Post-Digestion Sludge in the Sewage Treatment Plant Process
PublicationThis paper presents the application of artificial neural networks and decision trees for the prediction of odor properties of post-fermentation sludge from a biological-mechanical wastewater treatment plant. The input parameters were concentrations of popular compounds present in the sludge, such as toluene, p-xylene, and p-cresol, and process parameters including the concentration of volatile fatty acids, pH, and alkalinity in...
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Convenient and efficient synthesis of functionalized unsymmetrical Z-alkenyl disulfanes
PublicationWe developed a simple and efficient method for the synthesis of functionalized unsymmetrical Z-alkenyl disulfanes under mild conditions in moderate to good yields. The designed method is based on the reaction of Z-alkenyl thiotosylates with thiols in the presence of base. The developed method allows the preparation of unsymmetrical Z-alkenyl disulfanes bearing additional hydroxy, carboxy, or amino functionalities.
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Convenient and Efficient Synthesis of Functionalized 2-Sulfenylindoles
PublicationA simple, efficient, and practical sulfenylation at the C2 position of N-tosylindoles under mild conditions was developed. The designed transformation is based on the reaction of N-tosylindoles with BuLi and S-alkyl, and S-aryl phosphorodithioates or thiotosylates to produce 2-sulfenylindoles in moderate to high yields. The presence of additional hydroxy, carboxy, or amino functionalities did not disturb the formation of products
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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Preparation, composition and properties of fish silage produced with post-coagulation sludge
PublicationPost-coagulation sludge was added to fish fydrolyzates (silage). Silage was prepared using whole sprats. Technology of the process has been modified and sulphuric acid was replaced with phosphoric acid. The objective was to evaleuate the quality of produced silage during storage, particulary the changes of peroxide value and amount of free acids in silage fat.
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GC Chromatograms for isomerization of alpha-pinene
Open Research DataData contain results of the catalytic tests for the isomerization of alpha-pinene for the Ti3C2Tx MXenes produced via acidic etching aluminum from MAX Phase (Ti3C2-Al-Ti3C2-Al-Ti3C2) using different etching agents, HF/HCl and HF/H2SO4 with different weight ratios (1:3, 1:4, and 1:5). The samples were labeled as MXene HF/HCl X:Y and MXene HF/H2SO4 X:Y,...
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Review on Current Status of Echinocandins Use
PublicationFungal infections are rising all over the world every year. There are only five medical compound classes for treatment: triazoles, echinocandins, polyenes, flucytosine and allylamine. Currently, echinocandins are the most important compounds, because of their wide activity spectrum and much lower sides effects that may occur during therapy with other drugs. Echinocandins are secondary metabolites of fungi, which can inhibit the...
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Molecular modelling of transition state analogue inhibitors of glucosamine-6-P synthase and glucose-6-P isomerase.
PublicationStruktura kompleksu 2-amino-2-deoksy-D-glucitolo-6-P (ADGP) z centrum aktywnym syntazy GlcN-6-P z E. coli została wykorzystAna jako punkt wyjścia do modelowania molekularnego analogów ADGP. Używając programu GROMOS96 wygenerowano konformacje analogów o najniższych energiach wewnętrznych, które następnie ''dokowano'' w centrum aktywnym enzymu. Dokonano syntezy wybranych związków i określono parametry kinetyczne i termodynamiczne...
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Determination of bromhexine and its metabolites in equine serum samples by liquid chromatography – Tandem mass spectrometry: Applicability to the elimination study after single oral dose
PublicationBromhexine (BH), expectorant used in the treatment of respiratory disorders associated with viscid or excessive mucus, is not permitted for use in the competing horse by many authorities in horseracing and Olympic disciplines. Metabolic studies are of the great importance in anti-doping field because they allow for updating the selection of the most appropriate markers for prohibited substances, such as metabolites present at higher...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Convenient and efficient synthesis of functionalized unsymmetrical alkynyl sulfides
PublicationWe developed a simple and efficient method for the synthesis of functionalized unsymmetrical alkynyl sulfides under mild conditions in good yields. The designed method is based on the reaction of 5,5-dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-disulfanyl derivatives with lithium acetylides. The developed method allows the preparation of unsymmetrical alkynyl sulfides bearing additional hydroxyl, carboxyl, or amino functionalities.
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Determination of SCFAs in water using GC-FID. Selection of the separation system
PublicationIn the present study, an analytical procedure was developed for the determination of short-chain fatty acids (SCFAs) in landfill leachate and municipal wastewater employing injection of aqueous samples to gas chromatograph with flame ionization detector (GC-FID). Chromatographic conditions such as a separation system, injection volume, oven temperature program were investigated and selected. With two columns, one with a polar (polyethylene...
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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublicationMany polyphenols bind proteins, therefore our research was focused on the potential of protein binding to polyphenols of investigated fruits and their health-related effects. The contents of polyphenols and related antioxidant activities of traditional, citrus and exotic fruits were compared. The presence of polyphenols (flavonoids and phenolic acids) in the investigated samples and their interaction with human serum albumin (HSA)...
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TGA data of MXenes catalysts
Open Research DataData contain results from TGA measurement of the Ti3C2Tx MXenes produced via acidic etching aluminum from MAX Phase (Ti3C2-Al-Ti3C2-Al-Ti3C2) using different etching agents, HF/HCl and HF/H2SO4 with different weight ratios (1:3, 1:4, and 1:5). The samples were labeled as MXene HF/HCl X:Y and MXene HF/H2SO4 X:Y, where X:Y means the acids weight ratios. ...
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Adsorption and desorption of N2 measurement of MXenes catalysts
Open Research DataData contain results from adsorption and desorption of N2 measurement of the Ti3C2Tx MXenes produced via acidic etching aluminum from MAX Phase (Ti3C2-Al-Ti3C2-Al-Ti3C2) using different etching agents, HF/HCl and HF/H2SO4 with different weight ratios (1:3, 1:4, and 1:5). The samples were labeled as MXene HF/HCl X:Y and MXene HF/H2SO4 X:Y, where X:Y...
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Exploring the cocrystallization potential of urea and benzamide
PublicationThe cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis...
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Chapter 4. Electricity generation from glucose microbial fuel cell
PublicationThe microbial fuel cell was constructed to generate electricity with simultaneous digestion of a glucose fuel by a bacterial biofilm. The decomposition of glucose resulted in releasing of electrons to an anode and to production of some by-products, e.g. metane or organic acids. It was found that maximum electric power density strongly depended on the proton transport through the proton exchange membrane seperating the anolyte and...
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Novel binary mixtures of alkanolamine based deep eutectic solvents with water - thermodynamic calculation and correlation of crucial physicochemical properties
PublicationThis paper demonstrates the assessment of physicochemical and thermodynamic properties of aqueous solutions of novel deep eutectic solvent (DES) built of tetrabutylammonium chloride and 3-amino-1-propanol or tetrabutylammonium bromide and 3-amino-1-propanol or 2-(methylamino)ethanol or 2-(butylamino)ethanol. Densities, speeds of sound, refractive indices, and viscosities for both pure and aqueous mixtures of DES were investigated...
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Novel Binary Mixtures of Alkanolamine Based Deep Eutectic Solvents with Water—Thermodynamic Calculation and Correlation of Crucial Physicochemical Properties
PublicationThis paper demonstrates the assessment of physicochemical and thermodynamic properties of aqueous solutions of novel deep eutectic solvent (DES) built of tetrabutylammonium chloride and 3-amino-1-propanol or tetrabutylammonium bromide and 3-amino-1-propanol or 2-(methylamino)ethanol or 2-(butylamino)ethanol. Densities, speeds of sound, refractive indices, and viscosities for both pure and aqueous mixtures of DES were investigated...
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Synthesis and Fluorescent Properties of 6-(4-Biphenylyl)-3,9-dihydro-9-oxo-5H-imidazo[1,2-A]purine Analogues of Acyclovir and Ganciclovir
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SYNTHESIS AND FLUORESCENT PROPERTIES OF THE TRICYCLIC ANALOGUES OF ACYCLOVIR LINKED WITH NITROGEN HETBROCYCLIC UNITS
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Increased plasma concentration of 4-pyridone-3-carboxamide-1-ß-D-ribonucleoside (4PYR) in lung cancer. Preliminary studies
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Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
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DDQ-mediated synthesis of functionalized unsymmetrical disulfanes
PublicationWe developed a simple and efficient method for the synthesis of functionalized unsymmetrical disulfanes under mild conditions in good yields. The designed method is based on the reaction of bis(5,5- dimethyl-2-thioxo-1,3,2-dioxaphosphorinan-2-yl)disulfane with thiols in the presence of 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ). The developedmethod allows the preparation of unsymmetrical disulfanes bearing additional hydroxy, carboxy,...
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XRD patterns of MXenes catalysts
Open Research DataData contain results from XRD measurements of the Ti3C2Tx MXenes produced via acidic etching aluminum from MAX Phase (Ti3C2-Al-Ti3C2-Al-Ti3C2) using different etching agents, HF/HCl and HF/H2SO4 with different weight ratios (1:3, 1:4, and 1:5). The samples were labeled as MXene HF/HCl X:Y and MXene HF/H2SO4 X:Y, where X:Y means the acids weight ratios....
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Raman spectra of MXenes catalysts
Open Research DataData contain results from Raman spectroscopy of the Ti3C2Tx MXenes produced via acidic etching aluminum from MAX Phase (Ti3C2-Al-Ti3C2-Al-Ti3C2) using different etching agents, HF/HCl and HF/H2SO4 with different weight ratios (1:3, 1:4, and 1:5). The samples were labeled as MXene HF/HCl X:Y and MXene HF/H2SO4 X:Y, where X:Y means the acids weight ratios. ...