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Wyniki wyszukiwania dla: LIGAND/DNA INTERACTIONS
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Influence of G2 arrest on the cytotoxicity of DNA topoisomerase inhibitorstoward human carcinoma cells with different p53 status
PublikacjaRola bloku G2 w efekcie cytotoksycznym inhibitorów DNA topoizomeraz w stosunku do ludzkich komórek rakowych różniących się funkcjonalnością białka p53.
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublikacjaWe 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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Decisional-DNA-Based Digital Twin Implementation Architecture for Virtual Engineering Objects
PublikacjaDigital twin (DT) is an enabling technology that integrates cyber and physical spaces. It is well-fitted for manufacturing setup since it can support digitalized assets and data analytics for product and process control. Conventional manufacturing setups are still widely used all around the world for the fabrication of large-scale production. This article proposes a general DT implementation architecture for engineering objects/artifacts...
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Effects of Salvia officinalis and Thymus vulgaris on oxidant-induced DNA damage and antioxidant status in HepG2 cells
PublikacjaSalvia officinalis (SO) and Thymus vulgaris (TV) are medicinal plants well known for their curative powers. However, the molecular mechanisms responsible for these abilities of sage and thyme have not been fully understood yet. In this study we investigated the composition and the quantitative estimation of plant extracts, the protective effects of plant extracts against hydrogen peroxide- and 2,3-dimethoxy-1,4 naphthoquinone-induced...
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Reactions of (Ph)tBuP-P(SiMe3)Li·3THF with [(PNP)TiCl2] and [MeNacNacTiCl2·THF]. Synthesis of first PNP titanium(IV) complex with phosphanylphosphinidene ligand [(PNP)Ti(Cl){η2-P-P(Ph)tBu}]
PublikacjaLithium derivative of diphosphane (Ph)tBuP-P(SiMe3)Li (1) was isolated for the first time and investigated in reactions with β-diketiminate (MeNacnac− = [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2C6H3) and PNP-pincer (PNP = N[2-PiPr2-4-methylphenyl]2) Ti(III) complexes. The β-diketiminate titanium(III) complex containing phosphanylphosphido ligand [MeNacNacTi(Cl){η2-P(SiMe3)-P(Ph)tBu}] (2) was prepared in reaction of [MeNacNacTiCl2·THF]...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublikacjaThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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Structure and hyperfine interactions in Bi1−xNdxFeO3 solid solutions prepared by solid-state sintering
PublikacjaThe series of polycrystalline ceramic powders, Bi1xNdxFeO3 (x = 0.11) was successfully synthesized by mixed oxide method followed by pressureless sintering. X-ray diffraction and Mössbauer spectroscopy were used as complementary methods to study structure and hyperfine interactions of the samples. It was found that with an increase of Nd content, within the range of x = 0.20.3 a structural phase transition from rhombohedral to...
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Unwinding Au+···Au+ Bonded Filaments in Ligand-Supported Gold(I) Polymer under Pressure
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An investigation on the chemistry of the R2P=P ligand: reactions of a phosphanylphosphinidene complex of tungsten(VI) with electrophilic reagents
PublikacjaThe nucleophilic properties of the title compound [(2,6-i-Pr2C6H3N)2(Cl)W(η2-t-Bu2PvP)]Li·3DME (1) were investigated in reactions with selected electrophilic reagents such as MeI, M(CO)5THF (M = Cr, Mo, W), AlCl3, and GaCl3. Methylation of 1 by MeI yields phosphanylphosphido complexes [(2,6-i-Pr2C6H3N)2W(X)(1,2-η-t-Bu2PvP–CH3)] (X = Cl, I) (2-Cl/2-I) with the formation of a new P–C bond. Moreover, 1 reacts with electrophilic compounds...
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Smart Embedded Systems with Decisional DNA Knowledge Representation
PublikacjaEmbedded systems have been in use since the 1970s. For most of their history embedded systems were seen simply as small computers designed to accomplish one or a few dedicated functions; and they were usually working under limited resources i.e. limited computing power, limited memories, and limited energy sources. As such, embedded systems have not drawn much attention from researchers, especially from those in the artificial...
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Pursuing Listeners’ Perceptual Response in Audio-Visual Interactions - Headphones vs Loudspeakers: A Case Study
PublikacjaThis study investigates listeners’ perceptual responses in audio-visual interactions concerning binaural spatial audio. Audio stimuli are coupled with or without visual cues to the listeners. The subjective test participants are tasked to indicate the direction of the incoming sound while listening to the audio stimulus via loudspeakers or headphones with the head-related transfer function (HRTF) plugin. First, the methodology...
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Experience Based Decisional DNA (DDNA) to Support Sustainable Product Design
PublikacjaThis paper presents the idea of providing engineering design knowledge to designers working on sustainable product design and development process. The new product development process often requires significant amount of design knowledge which can be saved and recalled by designers during the design process. This knowledge is very important for successful sustainable product development as it can include material selection, product...
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Algorytm budowy reprezentacji przedziałowej grafu jako heurystyka dla problemu mapowania DNA
PublikacjaW pracy dokonano analizy przydatności algorytmu Corneil'a budowy reprezentacji przedziałowej grafu jako heurystyki dla problemu tworzenia map fizycznych DNA. Prezentowana analiza dotyczy dwóch osobno rozpatrywanych przypadków, w których do danych wzorcowych wprowadzamy odpowiednio błędy negatywne (reprezentujące niedobór informacji) oraz błędy pozytywne (reprezentujące fałszywe informacje). Rozpatrywany algorytm zachowuje się znacznie...
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Numerical calculations of behaviour of ship double-bottom structure during grounding
PublikacjaIdeą projektu CORET jest dodanie do obecnej konstrukcji dna podwójnego statku specjalnych powłok polimerowo-betonowych w celu zwiększenia odporności na rozszczelnienie podczas kolizji, czy wejścia na mieliznę. Aby poprawnie zaprojektować te bariery ochronne konieczne jest przeprowadzenie symulacji numerycznej. Tworzenie modelu numerycznego konstrukcji podczas kolizji jest bardzo złożone i wymaga wykonania symulacji pomocniczych...
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Anticancer and antimicrobial properties of novel η6-p-cymene ruthenium(ii) complexes containing a N,S-type ligand, their structural and theoretical characterization
PublikacjaRuthenium(II) complexes are lately of great scientific interest due to their chemotherapeutic potential asanticancer and antimicrobial agents. Here we present the synthesis of new pyrazole carbothioamidederivatives and their four arene–ruthenium complexes. The title compounds were characterized with theapplication of IR, NMR, mass spectrometry, elemental analysis and X-ray diffraction. Additionally, for newcomplexes DFT calculations...
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublikacjaTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Topochemical, Single‐Crystal‐to‐Single‐Crystal [2+2] Photocycloadditions Driven by Chalcogen‐Bonding Interactions
PublikacjaThe face-to-face association of (E)-1,2-di(4-pyridyl)ethylene (bpen) molecules into rectangular motifs stabilized for the first time by chalcogen bonding (ChB) interactions is shown to provide photoreactive systems leading to cyclobutane formation through single-crystal-to-single-crystal [2+2] photodimerizations. The chelating chalcogen bond donors are based on original aromatic, ortho-substituted bis(selenocyanato)benzene derivatives...
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The exposure to UV filters: Prevalence, effects, possible molecular mechanisms of action and interactions within mixtures
PublikacjaSubstances that can absorb sunlight and harmful UV radiation such as organic UV filters are widely used in cosmetics and other personal care products. Since humans use a wide variety of chemicals for multiple purposes it is common for UV filters to co-occur with other substances either in human originating specimens or in the environment. There is increasing interest in understanding such co-occurrence in form of potential synergy, antagonist,...
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Double-Blind Reputation vs. Intelligent Fake VIP Attacks in Cloud-Assisted Interactions
PublikacjaWe consider a generic model of Client-Server interactions in the presence of Sender and Relay, conceptual agents acting on behalf of Client and Server, respectively, and modeling cloud service providers in the envisaged "QoS as a Service paradigm". Client generates objects which Sender tags with demanded QoS level, whereas Relay assigns the QoS level to be provided at Server. To verify an object's right to a QoS level, Relay detects...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublikacjaWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Experimental and theoretical investigation of conformational states and noncovalent interactions in crystalline sulfonamides with a methoxyphenyl moiety
PublikacjaFour sulfonamide derivatives with a methoxyphenyl moiety, namely N-{4-[(2-methoxyphenyl)sulfamoyl] phenyl}acetamide (1a), N-{4-[(3-methoxyphenyl)sulfamoyl]phenyl}acetamide (1b), 4-amino-N-(2- methoxyphenyl)benzenesulfonamide (2a) and 4-amino-N-(3-methoxyphenyl)benzenesulfonamide (2b), have been synthesized and characterized physiochemically by CHNS, MS, FT-IR, 1H NMR, 13C NMR, PXRD and TG methods. Crystal structures were determined...
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Termodynamika oddziaływań i przejść strukturalnych DNA w układach wodnych na podstawie symulacji metodą dynamiki molekularnej
PublikacjaKwas deoksyrybonukleinowy jest jednym z najistotniejszych elementów każdej żywej komórki ze względu na rolę głównego nośnika informacji genetycznej. Posiada on instrukcje potrzebne do wzrostu, budowy, funkcjonowania oraz namnażania się wielu żywych organizmów, w tym także wirusów. Okazuje się, że w zależności od warunków środowiskowych, DNA może przyjmować wiele różnych struktur drugorzędowych, z których większość stanowi formy...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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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
PublikacjaG-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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Studies on the solid-liquid equilibria and intermolecular interactions Urea binary mixtures with Sulfanilamide and Sulfacetamide
PublikacjaThe binary phase diagrams of Sulfanilamide-Urea (SN-U) and Sulfacetamide-Urea (SC-U) were measured using differential scanning calorimetry technique (DSC). Both examined mixtures were found to form simple binary eutectics. The limited miscibility in the solid state observed by DSC, proving inability of co-crystallization in new multi-molecular form, was also confirmed using PXRD and FTIR-ATR measurements of solid dispersions...
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Manifestation of Intermolecular Interactions in the IR Spectra of 2- and 4-Methylmethcathinones Hydrochlorides: DFT Study and Hirshfeld Surfaces Analysis
PublikacjaThis paper reports a Hirshfeld surfaces analysis of crystalline 2- and 4-methylmethcathinone (2-MMC and 4-MMC) hydrochlorides to analyze NH∙Cl and CH∙∙∙Cl intermolecular interactions and approve the formation of the NН2+–Cl– salt fragment in both 2-MMC∙HCl and 4-MMC∙HCl crystals. Two isomeric dimers were separated from the corresponding crystal packing to model IR spectra of the crystalline 2-MMC∙HCl...
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Manufacturing collective intelligence by the means of Decisional DNA and virtual engineering objects, process and factory
PublikacjaEngineering collective intelligence is paramount in current industrial times. This research proposes and presents case studies for collective knowledge structures required in the industry field. Knowledge structures such as Set of Experience and Decisional DNA are extended into more advanced knowledge structures for manufacturing processes. These structures are called Virtual Engineering Object, Virtual Engineering Process and...
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UV-induced electron transfer between triethylamine and 5-bromo-2′-deoxyuridine. A puzzle concerning the photochemical debromination of labeled DNA
Publikacja5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding...
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Determination of Odour Interactions in Gaseous Mixtures Using Electronic Nose Methods with Artificial Neural Networks
PublikacjaThis paper presents application of an electronic nose prototype comprised of eight sensors, five TGS-type sensors, two electrochemical sensors and one PID-type sensor, to identify odour interaction phenomenon in two-, three-, four- and five-component odorous mixtures. Typical chemical compounds, such as toluene, acetone, triethylamine, α-pinene and n-butanol, present near municipal landfills and sewage treatment plants were subjected...
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Comparison of immune response in sheep immunized with DNA vaccine encoding Toxoplasma gondii GRA7 antigen in different adjuvant formulations
PublikacjaPraca przedstawia badania dotyczące odpowiedzi immunologicznej owiec immunizowanych plazmidowym DNA kodującym antygen granul GRA7 Toxoplasma gondii w trzech różnych formulacjach adjuvanta. Sześćdziesiąt owiec było szczepionych domięśniowo z DNa plazmidów. Dwanaście otrzymało liposomową formę plazmidu pVAXIgGRA7, 12 formulację z Emulsigen P plazmidu pVAXIgGRA7 1 12 formulację z Emulsigen D plazmidu pVAXIgGRA7. Wszystkie zwierzęta...
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Modulation of immune response to Toxoplasma gondii in sheep by immunization with a DNA vaccine encoding ROP1 antigen as a fusion protein with ovine CD154
PublikacjaNiniejszy artykuł prezentuje porównanie skuteczności działania w immunizacji owiec dwóch antytoksoplazmozowych szczepionek DNA: kodującej białko ROP1 Toxoplasma gondii oraz kodującej w/w antygen i owczą cząsteczkę CD154 lokalizowaną na powierzchni aktywowanych komórek T. Otrzymane wyniki badań pokazały, iż domięśniowe podanie szczepionki DNA zawierającej gen kodujący ROP1 i CD154 znacząco wzmacnia odpowiedź immunologiczną szczepionych...
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Transport of Particles in Intestinal Mucus under Simulated Infant and Adult Physiological Conditions: Impact of Mucus Structure and Extracellular DNA
PublikacjaThe final boundary between digested food and the cells that take up nutrients in the small intestine is a protective layer of mucus. In this work, the microstructural organization and permeability of the intestinal mucus have been determined under conditions simulating those of infant and adult human small intestines. As a model, we used the mucus from the proximal (jejunal) small intestines of piglets and adult pigs. Confocal...
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Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA): Past, Present and Future
PublikacjaThis article reviews research work on set of experience knowledge structure (SOEKS)-decisional DNA (DDNA) done in the past, ongoing, and planned for the future. Firstly, the concept of the knowledge representation technique of SOEKS-DDNA is discussed, and then an attempt is made to organize the past research related with it in chronological order. This work focuses on the review on SOEKS-DDNA, its application in different domains,...
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Reactivity study of a β-diketiminate titanium(III) complex with a phosphanylphosphido ligand towards chlorophosphanes. A new method of synthesis of β-diketiminate titanium(IV) complexes with versatile phosphanylphosphinidenes
PublikacjaThe reactivity of ab-diketiminate titanium(III) complex with a phosphanylphosphido ligand, [MeNacNacTi(Cl){g2-P(SiMe3)-PtBu2}] (1)(MeNacNac= [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2Ph), was investigatedtowards selected chlorophosphanes, such astBu2PCl,iPr2PCl, Cy2PCl, (Cy)tBuPCl, (Me)tBuPCl, (Ph)tBuPCl, Ph2PCl, (iPr2N)tBuPCl and (Et2N)2PCl. The reactions withtBu2PCl and Ph2PCl lead mainly to theearlier described complex [MeNacNacTi(Cl){g2-P-PtBu2}]...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublikacjaWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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The impact of interactions between polyphenolic antioxidants on the redox-related chemical and biological properties of their mixtures – the extension of food synergy concept.
PublikacjaThe results of studies indicate that chemopreventive efficiency of isolated phytochemicals is lower than that of polyphenol-rich foods. This discrepancy has been ascribed to the food synergy concept that assumes additive or even synergistic influence of different food ingredients on human health. The results presented in the dissertation made it possible to propose an alternative and innovative explanation of these observations. The...
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Defining the Genetic Basis of Plant–Endophytic Bacteria Interactions
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Model equations for interactions of hydrated species in transmembrane transport
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Lipid-protein interactions in membranes: a molecular modelling study
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Influence of local electron interactions on phonon spectrum in iron
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Septic safe interactions with smart glasses in health care
PublikacjaIn this paper, septic safe methods of interaction with smart glasses, due to the health care environment applications consideration, are presented. The main focus is on capabilities of an optical, proximity-based gesture sensor and eye-tracker input systems. The design of both interfaces is being adapted to the open smart glasses platform that is being developed under the eGlasses project. Preliminary results obtained from the...
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Interactions of Chromium Ions with Starch Granules in an Aqueous Environment
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Conformational changes of peptidoglycan fragments during their interactions with vancomycin
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Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities.
PublikacjaCelem pracy było scharakteryzowanie odziaływania związku C-1305 z DNA w porównaniu do innych inhibitorów topoizomerazy II. Badania pokazują, że C-1305 odziaływuje preferencyjnie z parami CG, interkaluje do DNA i zaburza sąsiednie otoczenie w bardzo charakterystyczny sposób, który nie został zaobserwowany u pozostałych 22 badanych związków.
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One-tube cell lysis and DNA extraction procedure for PCR based detection of Mycobacterium ulcerans in aquatic insects, molluscs and fish.
PublikacjaMycobacterium ulcerans jest bakterią wywołującą choroby skóry u ludzi i zwierząt. W trakcie prowadzonych badań opracowano prostą w wykonaniu metodę ekstrakcji DNA Mycobacterium ulcerans z próbek środowiskowych oraz klinicznych. Opracowana metoda izolacji DNA może być przydatna w badaniu źródeł infekcji oraz dróg szerzenia się Mycobacterium ulcerans.
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DNA structure and integrity checkpoints in the cell cycle and their role in drug targeting and resistance of tumor cells to anticancer treatment
PublikacjaW artykule dokonaliśmy przeglądu literatury dotyczącej różnych typów uszkodzeń DNA indukowanych przez różne czynniki terapeutyczne w komórkach nowotworowych. Omówiliśmy także w jaki sposób aktywują różne typy punktów kontrolnych w cyklu komórkowym i w jaki sposób punkty te są regulowane przez inne szlaki sygnalizacji wewnątrzkomórkowej takie jak szlaki naprawy uszkodzeń DNA, stresu komórkowego i śmierci-przeżycia. W szczególności...
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Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems
PublikacjaBiological systems are complex and the problem of their description lies in mutual interactions between their components. This paper is focused on model experiment-based studies which can reduce these difficulties. The ternary aqueous N-methylacetamide (NMA)–Na2HPO4 system has been studied by means of the FTIR spectroscopy. A novel difference spectra method aimed to extract the spectral contribution of water affected simultaneously...
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublikacjaSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...