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Search results for: LIGAND/DNA INTERACTIONS
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Wiązanie się do DNA oraz jego międzyłańcuchowe sieciowanie DNA przez tria-zoloakrydony i aktynomycynę D.**2003, 125 s. 35 rys. 10 tab. bibliogr. 202 poz. maszyn. Rozprawa doktorska /03.07.2003/ P. Gdań. Wydz. Chem. Promotor: prof. dr hab. inż. J. Konopa.
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Differential Response of MDA-MB-231 and MCF-7 Breast Cancer Cells to In Vitro Inhibition with CTLA-4 and PD-1 through Cancer-Immune Cells Modified Interactions
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Effect of new bisacridines IKE16, IKE18 and IE10 on the yeast topoisomerase II relaxation activity
Open Research DataThe datasets contain the results of new bisacridines IKE16, IKE18 and IE10 inhibition activity against yeast topoisomerase II. DNA topoisomerases (Topo) are enzymes that catalyze changes in the spatial structure of DNA and play an important role in replication, transcription and recombination. Beyond their normal functions, DNA topo are significant...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Application of potential theory in calculating wave-induced vertical forces on horizontal cylinders near a plane boundary
PublicationHydrodynamiczne obciażenia wywołane falowaniem morskim działajace na poziomo ułożoną przy dnie rurę, rozpatrywane są w ujęciu dyfrakcyjnym przy założeniu istnienia funkcji potencjału. Potencjał zdefiniowano jako superpozycję potencjału fali inicjującej oraz potencjału perturbacji spowodowanej istnieniem obiektu przy dnie. Wyniki rozwiązań teoretycznych porównano z wynikami doswiadczeń przeprowadzonych w Wielkim Kanale falowym w...
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Concurrent DNA Copy-Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients
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Down-regulation of DNA topoisomerase IIalpha leads to prolonged cell cycle transit in G2 and early M phases and increased survival to microtubule-interacting agents
PublicationInhibitory polimeryzacji mikrotubul wykazują preferencyjną toksyczność wobec komórek mitotycznych. W ramach tego projektu badaliśmy czy oporność komórek ludzkich białaczek na inhibitor mikrotubul, winkrystynę, prowadzi do zmian w regulacji progresji cyklu komórkowego. Nasze wyniki wskazują, że oporności na winkrystynę towarzyszą zmiany w długości fazy G2 i M w nieobecności i obecności inhibitora wrzeciona mitotycznego, nokodazolu....
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Supramolecular structures formed by 2-aminopyridine derivatives. Part I. Hydrogenbonding networks via N-H...N interactions and the conformational polymorphism of N,N´-bis(2-piridyl)aryldiamines
PublicationOtrzymano serię N,N´-bis(2-pirydylo)arylodiamin w postaci monokryształów. Zgodnie z oczekiwaniami, powstawały dwie odmiany polimorficzne. Forma EE z układem wiązań R22(8) figuruje jako jednowymiarowe taśmy. Stwierdzono, że ugrupowanie 2-aminopirydylowe stanowi synton supramolekularny za pomocą którego można projektować struktury w ciele stałym. Właściwości tego syntonu były badane z wykorzystaniem metod dyfrakcyjnych oraz spektroskopii...
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Jan Biernat prof. dr hab. inż.
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Gene expression, DNA damage and other stress markers in Sinapis alba L. exposed to heavy metals with special reference to sewage sludge application on contaminated sites
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The relationship between 8-oxo-7,8-dihydro-2′-deoxyguanosine level and extent of cytosine methylation in leukocytes DNA of healthy subjects and in patients with colon adenomas and carcinomas
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Cu(II) complexes with peptides from FomA protein containing -His-Xaa-Yaa-Zaa-His and -His-His-motifs. ROS generation and DNA degradation
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Anion binding by p-aminoazobenzene-derived aromatic amides: spectroscopic and electrochemical studies
PublicationThe synthesis and complexing properties of p-aminoazobenzene-derived mono-, bis-, and trisamides were described. Ligands 3 and 4 bind anions, including fluorides, chlorides, bromides, acetates, benzoates, dihydrogen phosphates, hydrogen sulfates, and p-toluenesulfonates, in chloroform forming 1 : 1 complexes. The highest value of stability constant was evaluated for the 4-F− complex (log K = 5.63 ± 0.21). On the basis of 1H NMR,...
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Opinia na temat wpływu projektowanego mostu przez Wisłę w Kiezmarku na kształtowanie hydrodynamiki przepływu wód, powstanie lokalnych rozmyć dna, powstanie zjawisk lodowych i ruch rumowiska w rejonie podpór nurtowych
PublicationZgodnie z tytułem opracowania, celem pracy jest wykonanie przekrojowych obliczeń hydraulicznych i hydrologicznych sprawdzających wpływ umieszczenia w korycie głównym Wisły podpór nurtowych nr 10 i 11 realizowanego w Kiezmarku mostu drogowego w dwóch wariantach projektowych. W ramach opracowania zrealizowano następujący zakres prac. 1) Zebranie, selekcja i analiza niezbędnych danych hydrologicznych i hydrometrycznych na badanym...
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Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors
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Do not die, become senescent: a new type of cellular resistance induced by topoisomerase II inhibitors in tumor cells with functional p53
PublicationJednym z efektów wywoływanych przez związki przeciwnowotworowe w komórkach nowotworowych jest trwałe zahamowanie wzrostu, związane z pojawieniem się markerów procesu starzenia komórkowego. Proponuje się, że może to być nowy sposób na zahamowanie postępu choroby nowotworowej. W naszych badaniach wykazujemy, że zahamowanie wzrostu indukowane przez związki z grupy inhibitorów topoizomerazy II w komórkach raka płuc A549 jest związane...
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Józef Kur prof. dr hab.
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The good, the bad, and the ugly: space use and intraguild interactions among three opportunistic predators—cat (Felis catus), dog (Canis lupus familiaris), and red fox (Vulpes vulpes)—under human pressure
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Genotoxicity of selected pharmaceuticals, their binary mixtures, and varying environmental conditions – study with human adenocarcinoma cancer HT29 cell line
PublicationPharmaceutical residues are present in the environment in mixtures and their adverse effects may also result from interactions that occur between compounds. Studies presented in this work focus on genotoxicity of pharmaceuticals from different therapeutic groups in mixtures and in individual solutions impacted with different environmental conditions assessed using comet assay (alkaline approach). Binary mixtures of pharmaceuticals...
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Ion recognition properties of new pyridine-2,6-dicarboxamide bearing propeller-like pendant residues: multi-spectroscopic approach
PublicationThe synthesis and ion binding properties of new amide derived from propeller-like tris(2-pyridyl)amine and 2,6-pyridinedicarboxylic acid chloride were described. Amide binds divalent metal cations: copper(II), nickel(II), zinc(II), and lead(II) in acetonitrile. In acetonitrile:water mixture (9:1 v/v) amide interacts only with copper(II) and nickel(II) cations forming complexes of 1:1 stoichiometry. It was found that the introduction...
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Electron ionization and low energy electron attachment to molecules of biological interest
PublicationEthylenediaminetetraacetic acid (EDTA) and 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) were investigated by electron impact ionization and low energy electron attachment. Both compounds are components of biological buffers and often are used as DNA stabilizers in irradiation studies. hus it is of a great importance to understand their potential interactions with radiation. Our results revealed that at least one of them, EDTA, may...
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Electron ionization and low energy electron attachment to molecules of biological interest
PublicationEthylenediaminetetraacetic acid (EDTA) and 2-amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) were investigated by electron impact ionization and low energy electron attachment. Both compounds are components of biological buffers and often are used as DNA stabilizers in irradiation studies. hus it is of a great importance to understand their potential interactions with radiation. Our results revealed that at least one of them, EDTA, may...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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DNA methylation pattern is altered in childhood T-cell acute lymphoblastic leukemia patients as compared with normal thymic subsets: insights into CpG island methylator phenotype in T-ALL
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
PublicationTwo analytical procedures are proposed where HILIC and RPLC techniques are coupled with tandem mass spectrometry detection for rapid determination of trace amounts of nicotine in zero-level liquids for electronic cigarettes. Samples are prepared on the basis of the approach “dilute & shoot” which makes this important step quick and not complicated. The chromatographic separation was carried out on a Zorbax XDB column (RPLC method)...
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Combined spline wavelet decomposition for 3d seafloor imaging from multibeam sonar echoes
PublicationThe paper proposes combined spline-wavelet approach to the raw echoes seaflor imaging from Multibeam Sonar System (MBSS) records. Wavelet representation is closely related to image representation, due to its unique approximations properties. Splines have the best approximation properties among all known wavelets of a given order, so they are best suited for approximating of smooth seafloor surface. Additionaly, wavelet bases have...
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D-loop sequences retrieved from Canis lupus familiaris mitochondrial genome
Open Research DataCanine mitochondrial genome is built of 16727 bp. Non-coding control region (mtCR), called also D-loop, begins with 15458 nucleotide and ends with 16727 nucleotide. The length of this fragment is 1270 bp (Kim et al., 1998). D-loop region is responsible for replication and transcription of mitochondrial DNA. Mutations that occur within it may cause irregularity...
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Synthesis, physicochemical and theoretical studies on new rhodium and ruthenium dimers. Relationship between structure and cytotoxic activity
PublicationTwo dimeric compounds of the general formulae (Et3NH)2[Rh2(μ2-L)4Cl2] (1) (where L = thiophene-2-carboxylate) and [((η6-p-cymene)Ru)2(μ-Cl)3]PF6 (2) have been synthesized using a new method. The unique anionic complex 1 (space group P bca) has octahedral coordination in which the equatorial positions are occupied by the oxygen atoms of four thiophene-2-carboxylates in a paddle wheel fashion. In complex 2 (space group ), each Ru(II)...
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Tadeusz Stolarski prof. dr hab. inż.
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Anion–cation interactions in a series of salts with substituted Hphen, Hbpy and H2bpy cations and [W(CN)8]4− anion: polymer with “super-short” N–H⋯N hydrogen bridges containing exclusively anions and H+
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Association between plasma proteome profiles analysed by mass spectrometry, a lymphocyte-based DNA-break repair assay and radiotherapy-induced acute mucosal reaction in head and neck cancer patients
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Evaluation and cellular responses of modulators of TRF1/TRF2 protein’s function as potential anticancer drugs interfering with telomeric shelterin’s function
PublicationA number of proteins that interact with telomeres have been identified in human cells, indicating the high plasticity of human nucleoprotein complex organization. The most important complex is the "shelterin" complex, which consists of six proteins: TRF1, TRF2, TIN2, POT1, TPP1. The TRF1 and TRF2 directly bind to telomeric double-stranded DNA and the TIN2 protein. The TIN2 protein also binds to the TPP1 protein, stabilizing the...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Piotr Skurski prof. dr hab.
PeoplePiotr Stanisław Skurski (ur. 25 sierpnia 1969 w Gdańsku) – polski chemik specjalizujący się w chemii kwantowej i fizycznej, profesor nauk chemicznych, profesor zwyczajny Wydziału Chemii Uniwersytetu Gdańskiego, kierownik Katedry Chemii Teoretycznej i Pracowni Chemii Kwantowej na tym wydziale, a także Professor of Chemistry w Henry Eyring Center for Theoretical Chemistry na Uniwersytecie Utah w Stanach Zjednoczonych. W latach 2011-2016 członek...
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Marek Moszyński dr hab. inż.
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Opposite pressure impact on electron-phonon coupling in Eu2+ and Ce3+ doped AlN
Open Research DataThis data analyzes the influence of pressure on electron–lattice interactions in the 5d excited states of Ce3+ and Eu2+ in the AlN host based on pressure-dependent photoluminescence and photoluminescence excitation spectra. High-pressure measurements on AlN samples doped with Eu2+ and Ce3+ ions reveal that the Stokes shift increases with pressure for...
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Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
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Probing the Magnetic Anisotropy of Co(II) Complexes Featuring Redox-Active Ligands
PublicationCoordination complexes that possess large magnetic anisotropy (otherwise known as zero-field splitting, ZFS) have possible applications in the field of magnetic materials, including single molecule magnets (SMMs). Previous studies have explored the role of coordination number and geometry in controlling the magnetic anisotropy and SMM behavior of high-spin (S = 3/2) Co(II) complexes. Building upon these efforts, the present work...
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Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2′-deoxycytidine level in cultured cancerous cell lines
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Accurate, Direct, and High-Throughput Analyses of a Broad Spectrum of Endogenously Generated DNA Base Modifications with Isotope-Dilution Two-Dimensional Ultraperformance Liquid Chromatography with Tandem Mass Spectrometry: Possible Clinical Implication
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Genes Involved in the Processes of Cell Proliferation, Migration, Adhesion, and Tissue Development as New Potential Markers of Porcine Granulosa Cellular Processes In Vitro: A Microarray Approach
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“Bone Development” Is an Ontology Group Upregulated in Porcine Oocytes Before In Vitro Maturation: A Microarray Approach
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“Cell Migration” Is the Ontology Group Differentially Expressed in Porcine Oocytes Before and After In Vitro Maturation: A Microarray Approach
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Polyp of stomach and duodenum - Male, 72 - Tissue image [7110729594541341]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Recent Advances in Polymer Nanocomposites: Unveiling the Frontier of Shape Memory and Self-Healing Properties—A Comprehensive Review
PublicationShape memory and self-healing polymer nanocomposites have attracted considerable attention due to their modifiable properties and promising applications. The incorporation of nanomaterials (polypyrrole, carboxyl methyl cellulose, carbon nanotubes, titania nanotubes, graphene, graphene oxide, mesoporous silica) into these polymers has significantly enhanced their performance, opening up new avenues for diverse applications. The...
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Copper(I) iodide ribbons coordinated with thiourea derivatives
PublicationTwo products of the reactions of CuI with 1-benzoyl-3-(4-bromophenyl)thiourea and with 1-benzoyl-3-(2-iodophenyl)thiourea have been obtained and characterized, namely poly[[[1-benzoyl-3-(4-bromophenyl)thiourea-κS]-µ3-iodidocopper(I)] acetone hemisolvate], {[CuI(C₁₄H₁₁BrN₂OS)]‧0.5C₃H₆O}ₙ, and poly-[µ₄-iodido-µ₃-iodido-[N-(benzo[d]thiazol-2-yl)benzamide-κN]dicopper(I)], [Cu₂I₂(C₁₄H₁₀N₂OS)]ₙ. Their structures, determined by single-crystal...
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Sequences of internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2 of psychrotolerant pigment-producing yeast-like fungi
Open Research DataDNA encoding ITS1-5.8S-ITS2 fragments of psychrotolerant pigment-producing yeast-like fungi named Red, Pink and Black were PCR amplified using ITS1 5' TCCGTAGGTGAACCTGCGG 3' and ITS4 5’ TCCTCCGCTTATTGATATGC 3’ primers and sequenced by Sanger method using the same primers.
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...