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Search results for: LIGAND/DNA INTERACTIONS
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Regulation of the switch from early to late bacteriophage λ DNA replication
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Diagnosis of Brain Tumors Through Global Specific DNA Methylation Analysis
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Molecular Diagnostics of Brain Tumours by Measuring the 5-Methylcytosine Level in Their DNA
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P04.06 Temozolomide influence on global DNA methylation in glioblastoma cell lines
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Effects of Base π-Stacking on Damage to DNA by Low-Energy Electrons
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Representing and Managing Experiential Knowledge with Decisional DNA and its Drimos® Extension
PublicationThe Semantic Web concept is proposing a future concept of the WorldWideWeb (WWW) where both humans and man-made systems are able to interconnect and exchange knowledge. One of the challenges of Semantic Web is smart and trusted accommodation of knowledge in artificial systems so it can be unified, enhanced, reused, shared, communicated and distributed with added aptitude. Our research represents an important component of addressing...
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Direct cloning of heavy metal resistance genes from metagenomic DNA
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Trójwymiarowe obrazowanie dna morskiego ze szczególnym uwzględnieniem wód płytkich
PublicationW ostatnim dziesięcioleciu nabrały znaczenia obserwacje szerokokątne (ang. swath scan) przy pomocy sonarów bocznych i sonarów wielowiązkowych. Wynikiem pomiarów dokonywanych przy pomocy sonarów wielowiązkowych jest jednak duża liczba danych geoprzestrzennych o precyzyjnie określonej referencji geograficznej, charakteryzujących się zróżnicowaną dynamiką i posiadających zróżnicowaną rozdzielczość. Stwarza to problemy w procesie...
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Discriminating macromolecular interactions based on an impedimetric fingerprint supported by multivariate data analysis for rapid and label-free Escherichia coli recognition in human urine
PublicationThis manuscript presents a novel approach to address the challenges of electrode fouling and highly complex electrode nanoarchitecture, which are primary concerns for biosensors operating in real environments. The proposed approach utilizes multiparametric impedance discriminant analysis (MIDA) to obtain a fingerprint of the macromolecular interactions on flat glassy carbon surfaces, achieved through self-organized, drop-cast,...
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Capping ligand initiated CuInS2 quantum dots decoration on, ZnIn2S4 microspheres surface under different alkalinity levels resulting in different hydrogen evolution performance
PublicationSurface distribution of quantum dots (QDs) at the semiconductor matrix caused by synthesis condition (e.g. pH of solution during coupling) could lead to different photocatalytic activity. Thus, achieving an optimal covering of semiconductor matrix by QDs has been challenging. Herein, the influence of the alkalinity level of aqueous decoration medium for the coupling of mercaptoundecanoic acid (MUA) capped CuInS2 quantum dots (CIS)...
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DNA Computing and Molecular Programming (International Meeting on DNA Computing and Molecular Programming)
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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The description of non-linear interactions of wave and non-wave modes in a non-adiabatic plasma flow
PublicationThe method of derivation of non-linear equations for interacting modes is explained and applied to a plasma's flow affected by a magnetic field. It is based on the linear projecting of the total perturbation field into specific variations of variables in individual modes of a flow. The method may be applied in many examples of fluid flows with different mechanisms of non-adiabaticity. It is of special importance in complex flows...
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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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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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Multi-layer graphene oxide alone and in a composite with nanosilica: Preparation and interactions with polar and nonpolar adsorbates
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Interactions between components of SrTi0.98 Nb0.02O3-δ-YSZ and SrTi0.98 Nb0.02O3-δ -CeO2 composites
PublicationComposites consisting of SrTiO3-based perovskite and either yttria-stabilized zirconia or ceria were investigated. The mechanical compatibility and possible inter-diffusion between phases were characterized by scanning electron microscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy. A gradual disappearance of Ce-containing phases with an increase in the temperature of reduction in hydrogen was noticed. Moreover,...
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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Supramolecular Assemblies of Hydrogen Bonded Carboxylic Acid Dimers Mediated by Phenyl-Pentafluorophenyl Stacking Interactions.
PublicationKwas pentafluorobenzoesowy tworzy heterodimery z kwasami benzoesowym i 2,4,6-trimetylobenzoesowym w wyniku oddziaływań typu pi-pi reszt fenylowych i pentafluorofenylowych. Otrzymane kokryształy wymienionych kwasów z 1,4-bisarylobutadiynami zawierały homodimery tworzone przez cząsteczki kwasów, pomiędzy którymi znajdowały się cząsteczki diarylodiacetylenów.
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Air bubble and oil droplet interactions in centrifugal fields during air-sparged hydrocyclone flotation
PublicationWzajemne oddziaływania pęcherzyka powietrza i kropli oleju w polu siły odśrodkowej były rozpatrywane w odniesieniu do warunków procesowych obecnych podczas flotacji za pomocą hydrocyklonu. Efektywności zetknięcia się kropli oleju z pęcherzykami powietrza zostały zidentyfikowane jako znacząco mniejsze w porównaniu do efektywności zetknięcia się cząstek minerałów. Wyznaczono czasy zderzenia i styku ślizgowego. Chociaż przyczepność...
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Application of an extended DLVO theory for the calculation of the interactions between emulsified oil droplets in alcohol solutions
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Metal–metal interactions in bent cyano-bridged trinuclear octacyanomolybdate(IV)–platinum(IV) complexes
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Proton-Electron Hole Interactions in Sr(Ti,Fe)O3−δ Mixed-Conducting Perovskites
PublicationOxides in which total electrical conductivity is determined by the partial conductivities of three types of charge carriers i.e. holes/ electrons, oxygen ions, and protons are key components of well-functioning proton ceramic fuel cells. Apart from electrochemical properties also easily modified microstructure is an important feature of the electrodes. In the paper, a group of SrTi1−xFexO3−δ (STF, x = 0.2–0.8) perovskites prepared...
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Application of the Harmonic Balance Method for Spatial Harmonic Interactions Analysis in Axial Flux PM Generators
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Assessing the Interactions of Statins with Human Adenylate Kinase Isoenzyme 1: Fluorescence and Enzyme Kinetic Studies
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Human–environment interactions in medieval Poland: a perspective from the analysis of faunal stable isotope ratios
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GTR/Thermoplastics Blends: How Do Interfacial Interactions Govern Processing and Physico-Mechanical Properties?
PublicationIn this work, GTR/thermoplastics blends (in ratio 50/50 and 75/25 wt.%) were prepared by melt-compounding in an internal mixer. During research, trans-polyoctenamer rubber (TOR), ethylene-vinyl acetate copolymer (EVA), ethylene-octene copolymer (EOC), and linear low-density polyethylene (LLDPE), were used in their thermoplastic phase. Microstructure and processing-performance property interrelationships of the studied materials...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers
PublicationAromatic heptaene macrolides (AHMs) belong to the group of polyene macrolide antifungal antibiotics. Members of this group were the first to be used in the treatment of systemic fungal infections. Amphotericin B (AmB), a non-aromatic representative of heptaene macrolides, is of significant clinical importance in the treatment of internal mycoses. It includes the all-trans heptaene chromophore, whereas the native AHMs contain two...
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Interactions of amphotericin B derivative of low toxicity with biological membrane components - the Langmuir monolayer approach
PublicationMetodą monowarstw Langmuira zbadano naturę oddziaływań nowej pochodnej antybiotyku przeciwgrzybowego amfoterycyny B o niskiej toksyczności, tj. estru metylowego N-metylo-N-D-fruktopiranozyloamfoterycyny B (MF-AME)z komponentami błon biologicznych: ergosterolem, występującym w komórkach grzybowych i cholesterolem występującym w komórkach zwierzęcych oraz z modelowym fosfolipidem DPPC i na tej podstawie stwierdzono, że zróżnicowanie...
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Charge distribution and magnetic interactions in PrBa2Cu3O7 with substitutional defects and oxygen disorder: the ab initio approach
PublicationW artykule zaprezentowano rezultaty kwantowomechanicznych obliczeń ''ab initio: struktury elektronowej układu PrBa2Cu3O7 zawierającego defekty substytucyjne (Pr_Ba) w podsieci barowo-tlenowej oraz wykazującego zaburzoną stechiometrię tlenową (O5). Badane defekty są odpowiedzialne za redystrybucję ładunku w układzie. Defekty Pr_Ba generują silnie zlokalizowane momenty magnetyczne, które oddziałują głównie na płaszczyzny miedziowo-tlenowe.
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Convivium-Exchanges and Interactions in the Arts of Medieval Europe Byzantium and the Mediterranean
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Evidence of Ligand Elasticity Occurring in Temperature-, Light-, and Pressure-Induced Spin Crossover in 1D Coordination Polymers [Fe(3ditz)3]X2(X = ClO4-, BF4-)
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CERVIX UTERI, Exocervix - Female, 46 - Cell image [4140730008823071]
Open Research DataThis is the histopathological image of CERVIX UTERI cell 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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Wpływ dodatku kwasu deoksyrybonukleinowego (DNA) na właściwości mechaniczne żeli żelatynowych
PublicationKwasy nukleinowe cieszą się coraz większym zainteresowaniem pod względem zastosowania ich w przemyśle farmaceutycznym, kosmetycznym oraz żywnościowym. Określono wpływ dodatku długo- i krótkołańcuchowych kwasów nukleinowych na właściwości mechaniczne żeli żelatynowych. Badania wykazały występowanie specyficznych interakcji pomiędzy żelatyną a kwasami nukleinowymi oraz pozwoliły na ocenę wpływu tych oddziaływań na twardość, kohezyjność,...
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Altered levels of circulating nuclear and mitochondrial DNA in patients with Papillary Thyroid Cancer
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Diet is Not Responsible for the Presence of Several Oxidatively Damaged DNA Lesions in Mouse Urine
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Selenium Supplementation Reduced Oxidative DNA Damage in Adnexectomized BRCA1 Mutations Carriers
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Comparison of Oxidative Stress/DNA Damage in Semen and Blood of Fertile and Infertile Men
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Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms
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Confirmative electric DNA array-based test for food poisoning Bacillus cereus
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Theoretical Study of Damage to DNA by 0.2−1.5 eV Electrons Attached to Cytosine
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Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
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Bonding in Phosphanylphosphinidene Complexes of Transition Metals and their Correlation with Structures, 31 P NMR Spectra, and Reactivities
PublicationTheoretical studies of the bonding interactions and most important properties are carried out for isolable phosphanylphosphinidene complexes of transition metals. Three main types of phosphanylphosphinidene complexes are distinguished, based on the way in which the phosphanylphosphinidene ligand bonds to the metal center: (i) side-on complexes of platinum, where the R2Pβ–Pα ligand mimics structural features of free singlet phosphanylphosphinidenes...
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Long-term changes in the Leucobryo-Pinetum community: interactions between the tree-stand, understorey and moss layer
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Synthesis, characterization, and interactions of single-walled carbon nanotubes modified with doxorubicin with Langmuir–Blodgett biomimetic membranes
PublicationThe synthesis, characterization, and the influence of single-walled carbon nanotubes (SWCNTs) modified with an anticancer drug doxorubicin (DOx) on the properties of model biological membrane as well as the comparison of the two modes of modification has been presented. The drug was covalently attached to the nanotubes either preferentially on the sides or at the ends of the nanotubes by the formation of hydrazone bond. The efficiency...
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Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its N-methylated derivatives
PublicationZbadano hydratację glicyny i jej metylowych pochodnych: N-metyloglicyny (NMG), N,N-dimetyloglicyny (DMG) i N,N,N-trimetyloglicyny (TMG) przy wykorzystaniu spektroskopii FTIR, z zastosowaniem cząsteczki HDO jako sondy molekularnej. Ilościowa wersja metody widm różnicowych pozwoliła na wyizolowanie widma wody zaburzonej przez substancję rozpuszczoną. Wyniki widmowe zostały skonfrontowane z obliczeniami teoretycznymi w ramach teorii...
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The influence of electron-electron and electron-phonon interactions on electron charge orderings in quasi-one-dimensional systems
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