Search results for: ODORANT BINDING PROTEINS
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Chromogenic amides of pyridine-2,6-dicarboxylic acid as anion receptors
PublicationThe synthesis of simple, chromogenic pyridine-2,6-dicarboxylic acid amides, derivates of isomeric nitroanilines and aminonitrophenols, and their ion binding properties are described. The ligands' response to ionic species was examined by naked eye and was studied with the use of UV-Vis spectroscopy in DMSO and its mixture with water. The effect of the localisation and the type of the substituents in aromatic rings were discussed....
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Effects of artificial lighting on bioactivity of sweet red pepper (Capsicum annuum L.)
PublicationRecent studies have shown that artificial light effectively promotes the growth and development of red peppers when light spectra, intensities and duration are controlled. Cited reports deal mostly with studies involving with the growth stages of pepper. Changes in the biochemical status of plants were not studied. Therefore, this study focuses on the changes in the content of some bioactive compounds (polyphenols, flavonoids,...
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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublicationProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Design, synthesis, and biological evaluation of tetrahydroquinolinones and tetrahydroquinolines with anticancer activity
PublicationColorectal cancer (CRC) is the most commonly diagnosed cancer in Europe and the United States and the second leading cause of cancer related mortality. A therapeutic strategy used for the treatment of CRC involves targeting the intracellular levels of reactive oxygen species (ROS). In this study, we synthesized a series of novel tetrahydroquinolinones and assessed their ability to inhibit CRC growth and proliferation by evoking...
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Low-power microwave-induced fabrication of functionalised few-layer black phosphorus electrodes: A novel route towards Haemophilus Influenzae pathogen biosensing devices
PublicationIn this paper, various passivation schemes were applied at few-layer black phosphorus (FLBP) to achieve covalent functionalisation with 4-azidobenzoic acid, improving its electrochemical response intended for analytical and biosensing applications. The thermal and microwave assisted modification procedures in toluene and dime-thylformamide resulted in high reversibility of reactions on functionalised FLBP using a ferricyanide/ferrocya-nide...
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A new human IgG avidity test, using mixtures of recombinant antigens (rROP1, rSAG2, rGRA6), for the diagnosis of difficult-to-identify phases of toxoplasmosis
PublicationThe preliminary diagnostic utility of two mixtures of Toxoplasma gondii recombinant antigens (rROP1+rSAG2 and rROP1+rGRA6) in IgG ELISA and IgG avidity test has been evaluated. A total of 173 serum samples from patients with toxoplasmosis and seronegative people were examined. The sensitivity of IgG ELISA for rROP1+rSAG2 and rROP1+rGRA6 was 91.1% and 76.7%, respectively, while the reactivity for sera from patients where acute toxoplasmosis...
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Genetic and pharmacologic proteasome augmentation ameliorates Alzheimer’s-like pathology in mouse and fly APP overexpression models
PublicationThe proteasome has key roles in neuronal proteostasis, including the removal of misfolded and oxidized proteins, presynaptic protein turnover, and synaptic efficacy and plasticity. Proteasome dysfunction is a prominent feature of Alzheimer’s disease (AD). We show that prevention of proteasome dysfunction by genetic manipulation delays mortality, cell death, and cognitive deficits in fly and cell culture AD models. We developed...
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Studies on applicability of new solid-phase microextraction fibers for the selective extraction and determination of short - chain monocarboksylic acids
PublicationShort-chain monocarobxylic acids, sometimes referred to as volatile fatty acids (VFA), are a group of low molecular weight alkyl monocarboxylic acids that are widely distributed within the environment. These molecules contain any from 2 to 8 carbon atoms and originate from the anaerobic biodegradation of organic matter such as carbohydrates, proteins, and fats. These compounds are commonly found in the effluents from animal farming,...
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...
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Możliwości zastosowań, potencjalne źródła oraz ewolucja technologiczna sposobu otrzymywania trehalozy ze szczególnym uwzględnieniem enzymu syntazy trehalozy [EC 5.4.99.16]
PublicationJedna z wiodących gałęzi współczesnej biotechnologii opiera się na produkcji białek – przede wszystkim enzymów. Są one powszechnie wykorzystywane: od przemysłu chemicznego poprzez przemysł spożywczy aż po medycynę i życie codzienne (czy ktoś wyobraża sobie w dzisiejszych czasach proszek do prania „bez enzymu”). Przed rozwojem nowoczesnych metod biologii molekularnej i inżynierii genetycznej pozyskiwano interesujące substancje z...
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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Towards the Application of Structure-Property Relationship Modeling in Materials Science: Predicting the Seebeck Coefficient for Ionic Liquid/Redox Couple Systems
PublicationThis work focuses on determining the influence of both ionic liquid (IL) type and redox couple concentration on Seebeck coefficient values of such a system. The quantitative structure property relationship (QSPR) and read-across techniques are proposed as methods to identify structural features of ILs (mixed with LiI/I2 redox couple), which have the most influence on the Seebeck coefficient (Se) values of the system. ILs consisting...
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Evaluation of Three Peptide Immobilization Techniques on a QCM Surface Related to Acetaldehyde Responses in the Gas Phase
PublicationThe quartz-crystal microbalance is a sensitive and universal tool for measuring concentrations of various gases in the air. Biochemical functionalization of the QCM electrode allows a label-free detection of specific molecular interactions with high sensitivity and specificity. In addition, it enables a real-time determination of its kinetic rates and affinity constants. This makes QCM a versatile bioanalytical screening tool for...
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Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid
PublicationOne of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat’s efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanoparticle’s solubility and electrical properties is the use of a stabilizing component...
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Designing efficient A-D-A1-D-A type fullerene free acceptor molecules with enhanced power conversion efficiency for solar cell applications
PublicationThe achievement of highly efficient power conversion efficiency (PCE) is a big concern for non-fullerene organic solar cells (NF-OSCs) because PCE can depend on numerous variables. Here, new five novel acceptor molecules without fullerenes were developed and investigated using DFT (density functional theory) and TD-DFT (time dependent-density functional theory). Compared to the recently synthesized molecule (PZ-dIDTC6), the developed...
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Low-energy positron scattering from gas-phase benzene
PublicationIn this paper we are presenting calculations of the elastic cross section of positrons with gas-phase benzene for the energy range from 0.25 eV to 9.0 eV. The calculations are done with the molecular R-matrix method for positron-scattering from poly-atomic molecules using a scaling factor to scale the electron-positron interaction. The scaling factor influences the position of the poles of the R-matrix. We adjust the scaling factor...
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Białka prokariotycznego systemu MMR: rola oraz interakcje
PublicationUszkodzenia komórkowego DNA w postaci błędnie sparowanych lub niesparowanych zasad azotowych są wynikiem niewłaściwie zachodzących procesów metabolizmu DNA, takich jak replikacja, rekombinacja oraz naprawa DNA. Utrwalenie tego rodzaju zmian prowadzi do powstania mutacji. System MMR (ang. DNA mismatch repair) usuwa te uszkodzenia przyczyniając się do zwiększenia wierności replikacji DNA oraz utrzymania stabilności genomu komórki....
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-MAG1S
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-MIC1S
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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On the Correlation of Lignocellulosic Filler Composition with the Performance Properties of Poly(ε-Caprolactone) Based Biocomposites
PublicationIn this work, three types of agricultural waste: olive stones (OS), date seed (DS) and wheat bran (WB) were applied as potential lignocellulosic fillers in poly(ε-caprolactone) (PCL) based biocomposites. Differences in composites’ performance were related to the higher content of proteins, noted for WB comparing to other fillers applied, which enhanced plasticization of PCL matrix. The mechanical properties of biocomposites were...
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Genetic and pharmacologic proteasome augmentation ameliorates Alzheimer’s-like pathology in mouse and fly APP overexpression models
PublicationThe proteasome has key roles in neuronal proteostasis, including the removal of misfolded and oxidized proteins, presynaptic protein turnover, and synaptic efficacy and plasticity. Proteasome dysfunction is a prominent feature of Alzheimer’s disease (AD). We show that prevention of proteasome dysfunction by genetic manipulation delays mortality, cell death, and cognitive deficits in fly and cell culture AD models. We developed...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Coffee silverskin as a potential bio-based antioxidant for polymer materials: Brief review
PublicationCoffee silverskin is one of the by-products generated by the coffee industry. Although it is not the most burdensome one, because it stands only for ~4.2 wt % of coffee, it seems like an auspicious raw material for industrial processes. Coffee silverskin is characterized by a relatively low moisture content of ~5–7%, so it often does not require quite energy-consuming drying processes. The chemical composition of coffee silverskin,...
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Chemical composition of shells from red (Strongylocentrotus franciscanum) and green (Strongylocentrotus droeba-chiensis) sea urchin
PublicationThe shells from red and green sea urchins accounted for 47.9 and 40.7% of their body weights, respectively. The red and green sea urchin shells contained 91.08 and 90.77% minerals and 4.06 and 4.99% proteins, respectively. The shells did not contain any chitin. Sea urchin shells had a relatively large amount of naphthoquinone pigments, 121 mg per 100 g in red and 163 mg per 100 g in green species. The small quantities of glucosamine...
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Chemistry of human breast milk – a comprehensive review of the composition and role of milk metabolites in child development
PublicationEarly nutrition has an enormous influence on a child's physiological function, immune system maturation and cognitive development. Human breast milk (HBM) is recognized as the gold standard for human infant nutrition. Accordingly to WHO report breastfeeding is consider as an unequalled way of providing ideal food to the infant, which is required for his healthy growth and development. HBM contains various macronutrients (carbohydrates,...
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Chitosan-based electrospun nanofibers for encapsulating food bioactive ingredients: A review
PublicationToday, society has been more aware of healthy food products and related items containing bioactive compounds, which potentially contribute to human health. Unfortunately, the long-term stability and bioactivity of biologically active compounds against environmental factors compromise their target and effective action. In this way, lab-designed vehicles, such as nanoparticles and nanofibers, provide enough properties for their preservation...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Synthesis of bicoumarin thiophosphate derivatives as steroid sulfatase inhibitors
PublicationBased on the frameworks of 7-hydroxy-2,3-dihydro-1H-cyclopenta[c]chromen-4-one, 3-hydroxy- 7,8,9,10-tetrahydro-6H-benzo[c]chromen-6-one and 3-hydroxy-8,9,10,11-tetrahydro-7H-cyclohepta[c] chromen-6-one, a series of bicoumarin thiophosphate analogs have been synthesized and biologically evaluated. Additionally, their binding modes have been modeled using docking techniques. The inhibitory properties of the synthesized compounds...
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New uranium(vi) and isothiouronium complexes: synthesis, crystal structure, spectroscopic characterization and a DFT study
PublicationThe crystal structures of S,S′-2,5-dimethylbenzene-1,4-diylbis(methylisothiouronium) diacetate (1_ac), S,S′-2,5-dimethylbenzene-1,4-diylbis(methylisothiouronium) dichloride (1_Cl), 1_U complex, S,S′-naphthalene-1,4-diylbis(methylisothiouronium) dichloride (2_Cl), and 2_U complex were determined for the first time. The supramolecular structures of the compounds obtained are mainly based on hydrogen bonding and ionic interactions...
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Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: The example of dibenzazepine derivatives
PublicationIt is widely believed that the hydrophobic effect governs the binding of guest molecules to cyclodextrins (CDs). However, it is also known that high hydrophobicity of guest molecules does not always translate to the formation of stable inclusion complexes with CDs. Indeed, a plethora of other factors can play a role in the efficiency of guest–CD interactions, rendering structure-based prediction of the complexation efficiency with...
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Quantum and carbon dots conjugated molecularly imprinted polymers as advanced nanomaterials for selective recognition of analytes in environmental, food and biomedical applications
PublicationSamples with complex matrix analyzed during explanation of pathogenesis of various diseases and food or environmental monitoring request advanced analytical and instrumental devices. Among the materials used for described purposes, quantum (QDs) or carbon dots (CDs) layered by molecularly imprinted polymer (MIP) shells have gained widespread attention. Unique optical and physicochemical properties of QDs/CDs together with high...
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Microwave-assisted synthesis of zinc derivatives of potato starch
PublicationZincatated potato starch was prepared in a solid-state, microwave-assisted reaction using generated in situ sodium tetrahydroxozincate [Na2Zn(OH)4]. For comparison, zincatation of starch was also carriedout on convectional heating. Depending on the irradiation conditions, the products of either mono- or crosslinking esterification were formed. Higher power applied at shorter exposition offered products ofmonoesterification, and...
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Study of Icosahedral Clusters in Close-packed Simple Liquids
PublicationThe local structure of liquid copper was determined using Steinhardt order parameters, with particular attention paid to icosahedral clusters. The positions of atoms were obtained from three sets of molecular dynamics simulations, with the forces obtained from: the Sutton-Chen (SC) potential, the Naval Research Laboratory total energy tight-binding (NRL-TB) method and the divide-and-conquer learn-on-the-fly (DCLOTF) method, respectively....
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Bioactive compounds and the antioxidant capacity in new kiwi fruit cultivars
PublicationThe aim of this investigation was to find the best among seven different kiwi fruit cultivars (‘Hayward’, ‘Daheung’, ‘Haenam’, ‘Bidan’, ‘Hort16A’, ‘Hwamei’ and ‘SKK12’) for human consumption and to classify them as groups. Therefore, the contents of bioactive compounds and the level of antioxidant capacities of these cultivars were determined in four different extracts and compared. It was found that the contents of the bioactive...
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Synthesis and steroid sulfatase inhibitory activities of N-phosphorylated 3-(4-aminophenyl)-coumarin-7-O-sulfamates
PublicationIn the present work, we report convenient methods for the synthesis and biological evaluation of N-phosphorylated derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as potential steroid sulfatase (STS) inhibitors. Their binding modes were modeled using docking techniques. The inhibitory effects of the synthesized compounds were tested on STS isolated from human placenta. All of the newly synthesised coumarin derivatives were...
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Influence of S-Oxidation on Cytotoxic Activity of Oxathiole-Fused Chalcones
PublicationSynthesis, in vitro cytotoxic activity, and interaction with tubulin of oxidized, isomeric 1-(5-alkoxybenzo[d] [1,3]oxathiol-6-yl)-3-phenylprop-2-en-1-ones and 1-(6- alkoxybenzo[d][1,3]oxathiol-5-yl)-3-phenylprop-2-en-1- ones are described. Most of the compounds demonstrated cytotoxic activity at submicromolar concentrations. It was found that oxidation of sulfur atom of the oxathiole-fused chalcones strongly influenced activity...
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Synthesis and steroid sulfatase inhibitory activities of N-alkanoyl tyramine phosphates and thiophosphates
PublicationA series of phosphate and thiophosphate analogs based on the frameworks of N-alkanoyl tyramines have been synthesized and biologically evaluated. Their binding modes have been modeled using docking techniques. The inhibitory effects of the synthesized compounds were tested on STS isolated from the human placenta as well as the MCF-7, MDA-MB-231 and SkBr3 cancer cell lines. Most of the new STS inhibitors possessed potent activity...
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A magnetic imprinted polymer nano-adsorbent with embedded quantum dots and mesoporous carbon for the microextraction of triazine herbicides
PublicationA magnetic molecularly imprinted polymer (MMIP) adsorbent incorporating amino-functionalized magnetite nanoparticles, nitrogen-doped graphene quantum dots and mesoporous carbon (MIP@MPC@NGQDs@ Fe3O4–NH2) was fabricated to extract triazine herbicides from fruit juice. The embedded magnetite nanoparticles simplified the isolation of the adsorbent from the sample solution. The N-GQDs and MPC enhanced adsorption by affinity binding...
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Aggregation of imidazoacridinones - spectroscopic and microcalorimetric approach
PublicationImidazoacridinones (IA) belong to a group of polycyclic heteroaromatic antitumor compounds. IA create the aggregated form in water solution. Self-association of substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules....
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Biopolymer based nanomaterials in drug delivery systems: A review
PublicationDrug delivery systems (DDS) are used to achieve a higher therapeutic effects of a pharmaceutical drug or natural compound in a specific diseased site with minimal toxicological effect and these systems consists of liposomes, microspheres, gels, prodrugs and many. Nanotechnology is a rapidly developing multi-disciplinary science that ensures the fabrication of the polymers to nanometer scale for various medical applications. Uses...
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Application of safirinium N-hydroxysuccinimide esters to derivatization of peptides for high-resolution mass spectrometry, tandem mass spectrometry, and fluorescent labeling of bacterial cells
PublicationMass spectrometry methods are commonly used in the identification of peptides and biomarkers. Due to a relatively low abundance of proteins in biological samples, there is a need for the development of novel derivatization methods that would improve MS detection limits. Hence, novel fluorescent N-hydroxysuccinimide esters of dihydro-[1,2,4]triazolo[4,3-a]pyridin-2-ium carboxylates (Safirinium P dyes) have been synthesized. The...
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Application of human bile salts for in vitro digestion models
PublicationIn this study, experimental in vitro models simulating the environment of the human gastrointestinal tract were used to assess the impact of physiological surfactants, such as bile salts, on the kinetics of digestion. Bile salts are biosurfactants synthesised in the liver and secreted together with bile into the small intestine. There are many reports on the role of bile salts in lipolysis, but the knowledge of their influence...
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Suppressors of lapC mutation identify new regulators of LpxC, which mediates the first committed step in lipopolysaccharide biosynthesis
PublicationGram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Geometric analogue of holographic reduced representation
PublicationHolographic reduced representations (HRRs) are distributed representations of cognitive structuresbased on superpositions of convolution-bound n-tuples. Restricting HRRs to n-tuples consisting of 1,one reinterprets the variable binding as a representation of the additive group of binary n-tupleswith addition modulo 2. Since convolutions are not defined for vectors, the HRRs cannot be directlyassociated with geometric structures....
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Novel chalcone-derived pyrazoles as potential therapeutic agents for the treatment of non-small cell lung cancer
PublicationLung cancer is considered to account for approximately one-fifth of all malignant tumor-related deaths worldwide and is therefore one of the most lethal malignancies. Pyrazole scaffold possesses a wide range of biological and pharmacological activities, which play important roles in medicinal chemistry. The present study reports the synthesis and in vitro biological characterization of nine pyrazoles derived from chalcones as potential...