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Wyniki wyszukiwania dla: ligand/dna interactions
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Empirical investigation on labour market interactions in an enlarged Europe
PublikacjaThis paper proposes an empirical assessment of economic interactions between the labour markets ofthe integrating EU over the period of time 1995-2005. Drawing on recently made available industrystatistics, we provide a sector level study (13 tradable sectors, including manufacturing and services),analysing the contemporary evolution of domestic and trade partners' employment levels. Given theintensification of trade relations...
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Framework for Product Innovation Using SOEKS and Decisional DNA
PublikacjaProduct innovation always requires a foundation based on both knowledge and experience. The production and innovation process of products is very similar to the evolution process of humans. The genetic information of humans is stored in genes, chromosomes and DNA. Similarly, the information about the products can be stored in a system having virtual genes, chromosomes and decisional DNA. The present paper proposes a framework for...
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Intramolecular interactions in crystals of tris(2,6-diisopropylphenoxy)silanethiol and its sodium salts
PublikacjaHydrolytically stable tris(2,6-diisopropylphenoxy)silanethiol has been obtained and reacted with sodium. Solid state interactions within and between the molecules of tris(2,6-diisopropylphenoxy)silanethiol including S-H---π-interactions between the S-H unit and the π-system of the arene have been analyzed. The interactions are documented by X-ray diffraction and FT-IR spectroscopy.
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Application of decisional DNA in web data mining
PublikacjaPrzedstawiono pilotową koncepcję i aplikację integracji reprezentacji wiedzy opartej na decyzyjnym DNA oraz systemów pozyskiwania wiedzy i danych z Internetu. Wskazano na zalety proponowanej integracji oraz przedstawiono kierunki przyszłych badań w tym zakresie.
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Adding Intelligence to Cars Using the Neural Knowledge DNA
PublikacjaIn this paper we propose a Neural Knowledge DNA based framework that is capable of learning from the car’s daily operation. The Neural Knowledge DNA is a novel knowledge representation and reasoning approach designed to support discovering, storing, reusing, improving, and sharing knowledge among machines and computing devices. We examine our framework for drivers' classification based on their driving behaviour. The experimental...
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Reactions of lithiated diphosphanes R2P-P(SiMe3)LiTHF (R = tBu, iPr) with [(PNP)TiCl2]. Two different coordination types of phosphanylphosphido ligand to the metal center.
Publikacja[(PNP)TiCl2] (PNP = N[2-PiPr2-4-methylphenyl]2) reacts with one equivalent of lithium derivative of diphosphane R2P-P(SiMe3)LinTHF (R = tBu, iPr) in toluene and forms the first complex with g1-coordination [(PNP)Ti(Cl){g1-P(SiMe3)-PtBu2}] (1) and complex with g2-coordination [(PNP)Ti(Cl){g2-P(SiMe3)-PiPr2}] (2) of phosphanylphosphido ligands to the titanium center. The similar reaction with two equivalents of tBu2P-P(SiMe3)LinTHF...
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Decisional DNA based embedded systems: a new perspective
PublikacjaOmówiono nowe kierunki i perspektywy badań w zakresie systemów podporządkowanych opartych na decyzyjnym DNA.
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Decisional DNA digitral TV: concept and initial experiments
PublikacjaPrzedstawiono pierwsze wyniki eksperymentalnej integracji telewizji cyfrowej z decyzyjnym DNA reprezentujacym wiedze o odbiorcy programow.
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Molecular Insights into the Interactions Between Human Serum Albumin and Phospholipid Membranes
PublikacjaIn this study, molecular dynamics simulations were employed to analyze interactions between phospholipid membranes and human serum albumin (HSA) in the presence of mono- and divalent cations. Two types of membranes, composed of dipalmitoyl phosphatidylcholine (DPPC) and dipalmitoyl phosphatidylethanolamine (DPPE), were utilized. The results revealed that both systems exhibited high stability. The DPPE complexes displayed a greater...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublikacjaFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Set of Experience and Decisional DNA: Experience-Based Knowledge Structures
PublikacjaThis chapter presents a description of Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA), argumentation for a knowledge representation, composition, configuration and metrics. SOEKS is a combination of filtered and amalgamated information obtained from formal decision events. It facilitates effective explicit representation of decisional experience taken from different technologies. SOEKS comprises variables,...
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Wybrane metody badania poziomu metylacji DNA w komórkach eukariotycznych
PublikacjaMetylacja regionów promotorowych jest jednym z głównych mechanizmów regulacji transkrypcji genów u eukariota. W komórkach ssaczych metylacja DNA zachodzi głównie na reszcie cytozyny występującej w dinukleotydach CpG i jest katalizowana przez metylotransferazy DNA (DNMT1, DNMT3A i DNMT3B) (Turek Plewa, Jagodziński 2005). Mapowanie 5 metylocytozyny w DNA genomowym jest jednym z narzędzi do badania wpływu metylacji na tkankowo-specyficzną...
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublikacjaPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublikacjaInteractions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide...
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublikacjaDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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Chalcogen bonding interactions in a series of aromatic selenocyanates
PublikacjaSelenium atoms in aromatic selenocyanates are characterized by the occurrence of two σ-holes, a stronger one in the prolongation of the NC–Se bond and a weaker one in the prolongation of the Ar–Se bond. The crystal structures of several bis(selenocyanato) derivatives, prepared by a method originally developed for ortho bis-substituted derivatives, illustrate very well this difference, with a short NC–Se⋯NC ChB interaction organizing...
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Interplay of hydrogen bonding and aryl-perfluoroaryl interactions in construction of supramolecular aggregates
PublikacjaThe stacking between aryl and perfluoroaryl units is an important class of the aromatic – aromatic interactions that has attracted rapidly growing interest in recent years. Continuing interest of our group in this subject it had been prepared three new complexes of pentafluorobenzoic acid with benzyl alcohol, 4-methylbenzyl alcohol and 4-tert-butylbenzyl alcohol and in the next step investigated their self-assembly modes by...
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Examining Government-Citizen Interactions on Twitter using Visual and Sentiment Analysis
PublikacjaThe goal of this paper is to propose a methodology comprising a range of visualization techniques to analyze the interactions between government and citizens on the issues of public concern taking place on Twitter, mainly through the official government or ministry accounts. The methodology addresses: 1) the level of government activity in different countries and sectors; 2) the topics that are addressed through such activities;...
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Intermolecular Hydrogen Bonding Directed by Aryl–Perfluoroaryl π–π Stacking Interactions
PublikacjaThe crystal structures of five compounds capable of forming self-complementary hydrogen bonds but crystallizing as catemers or creating more complex crystal structures were compared with their complexes prepared by cocrystallization with perfluoroaryl compounds. The results of X-ray diffraction revealed that in all the cases the π–π stacking interactions caused reorganization of hydrogen bonds and induced creation of the expected...
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Analysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
PublikacjaAnalysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
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Analysis of odor interactions in ternary gas mixtures using electronic nose
PublikacjaIn recent years there has been a noticeable increase in interest in the use of electronic noses in analytical chemistry. These devices perform a holistic analysis of the gas mixtures composition, without the separation and identification of its individual components. For this reason e-noses are increasingly replacing the conventional olfactometers, due to the significantly shorter analysis time and possible automation. In the work...
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Applying Decisional DNA to Internet of Things: The Concept and Initial Case Study
PublikacjaIn this article, we present a novel approach utilizing Decisional DNA to help the Internet of Things capture decisional events and reuse them for decision making in future operations. The Decisional DNA is a domain-independent, standard and flexible knowledge representation structure that allows its domains to acquire, store, and share experiential knowledge and formal decision events in an explicit way. We apply this approach...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublikacjaThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublikacjaAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Radiosensitization of DNA in presence of Pt(II)-based compounds
PublikacjaX-ray irradiation of plasmid DNA in presence of platinum (II)-based compounds was carried out in order to assess the radiosensitization capabilities of these drugs. In present investigations pBR322 plasmid DNA was used to monitor the effectiveness of chosen compounds in inducing strand breaks. Samples were incubated in the presence of potential radiosensitisers: platinum (II) bromide and cis-diamminedibromoplatinum (II). The results...
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Decisional DNA, reflexive ontologies, and security: developing decisional trust
PublikacjaOmowiono model osiagania zaufania decyzjnego opartego na decyzyjnym DNA, refleksyjnych ontologiach oraz na bezpieczenstwie technologicznym.
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Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex
PublikacjaZa pomocą metod chemi obliczeniowej badano właściwości molekularne kompleksu telomerowego białka TEBP z Oxytricha nova w kompleksie trójskkładnikowym z DNA o sekwencji telomerowej. Wyliczone wartości energii kompleksowania wskazują specyficznie na jedną z dróg tworzenia kompleksu, gdzie wpierw podjednostka alfa łaczy się z DNA a następnie podjednostka beta dołącza się do takiego dwuskładnikowego kompleksu. Policzone rozkłady molekularnego...
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Ligand Design by Ionomers. ESR of MoV in Perfluorinated Ionomer Supports
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Group 11 complexes with a phosphanylphosphaalkene ligand: preparation and stability study
PublikacjaThe reactivities of two selected phosphanylphosphaalkenes, Ph2C=P-PtBu2 (1a) and (p-MeO-Ph)2C=P-PtBu2 (1b), toward CuCl, AgCl and (tht)AuCl (tht = tetrahydrothiophene) were investigated. As a result, new phosphanylphosphaalkene dimeric and monomeric complexes were formed (Cu and Ag dimeric and Au monomeric). All obtained products were air and moisture stable and light insensitive.
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Sulfurization of phosphanylphosphinidene ligand: Access to phosphinothioyltrithiophosphonato platinum(II) complexes
PublikacjaThe reactivity of phosphanylphosphinidene Pt(0) complexes [DppePt(η2-P–PtBu2)] (1) and [(pTol3P)2Pt(η2-P–PtBu2)] (2) toward sulfur was studied. Reactions of 1 and 2 with an excess of sulfur led to the formation of the first transition metal complexes 3 and 4 with phosphinothioyltrithiophosphonato ligands with the formula [tBu2P(=S)–P(=S)S2]2-. In contrast to previous reports on the phosphanylphosphinidene moiety sulfurization,...
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LemPhos – New P-Chiral Phospholene Core Based Ligand
PublikacjaSynthesis and modifications of new chiral phospholene-based scaffolds are described. The construction of base molecules was accomplished via McCormack synthesis. Separation of single P-epimers was accomplished with column chromatography on silica gel.
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Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation
PublikacjaHypoxia—a hallmark of solid tumors—makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet...
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How water mediates the long-range interactions between remote protein molecules
PublikacjaThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublikacjaA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Isolation and structure of a covalent cross-link adduct between mitomycin C and DNA
PublikacjaA DNA cross-link adduct of the antitumor agent mitomycin C (MC) to DNA has been isolated and characterized; the results provide direct proof for bifunctional alkylation of DNA by MC. Exposure of MC to Micrococcus luteus DNA under reductive conditions and subsequent nuclease digestion yielded adducts formed between MC and deoxyguanosine residues. In addition to the two known monoadducts, a bisadduct was obtained. Reductive MC activation...
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Obrazy akustyczne dna morskiego w wybranych akwenach Bałtyku
PublikacjaMetody akustyczne obserwacji obszarów podwodnych mórz i oceanów stosowane są od początku XX wieku. Początkowo były to echosondy nawigacyjne najczęściej składające się z pojedynczych przetworników. Następnie zaczęto stosować sonary do wykrywania obiektów stanowiących przeszkody nawigacyjne pod woda, które miały głównie zastosowanie w marynarce wojennej. W drugiej połowie XX wieku rozpoczęto konstruowanie urządzeń akustycznych, których...
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Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublikacjaIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...
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Gaining knowledge through experience: developing decisional DNA applications in robotics
PublikacjaOmówiono nowatorskie podejscie do zastosowania wiedzy opartej na doświadczeniu i budowie decyzyjnego DNA w obszarach związanych z robotyką.In this article, we explore an approach that integrates Decisional DNA, a domain-independent, flexible, and standard knowledge representation structure, with robots in order to test the usability and suitability of this novel knowledge representation structure. Core issues in using this Decisional...
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Modyfikacje polimeraz DNA jako rozwiązania problemów w reakcjach PCR
PublikacjaReakcja PCR już od wielu lat jest podstawowym narzędziem stosowanym w biotechnologii molekularnej. Nadal napotykamy jednak liczne problemy podczas jej przeprowadzania związane z trudnymi matrycami, obecnością inhibitorów itp. Optymalizacja reakcji PCR jest więc niezbędna w celu poprawy wyników. Jednym z rozwiązań tych problemów może być modyfikowanie polimeraz DNA. W powyższym artykule opisano problemy i rozwiązania zależne polimerazy...
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The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions
PublikacjaExperiments were carried out to determine the dependence of the physical form of supercoiled DNA films on the initial temperature of the substrate. Such films are often used in irradiation experiments involving low energy particles, like electrons or photons. In order to obtain absolute values for cross sections for such experiments, the spatial distribution of the sample in the film has to be well estimated. These investigations...
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Development of novel optoelectronic sensory structures utilising colour centres in nanodiamonds and their interactions with analytes
PublikacjaThe goal of this dissertation was to develop and assess surface modifications of fluorescent nanodiamonds (NDs) for optical sensing. Three modification routes were tested, each aimed at a different application. Modification with poly-L-lysine (pLys) was verified for optical sensing of pH via an interrelationship between electrically negative (NV¯) and neutral (NV0) nitrogen-vacancy centres. Immobilisation of Ochratoxin A (OTA),...
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublikacjaNumerous antitumor and carcinogenic compounds are able to modify DNA by forming covalent bonds with its constituents, while some anticarcinogenic compounds are known to prevent such a modification. All these processes are of vital biological import_ance, though deeper inside into factors influencing formation of DNA adducts is difficult due to the low level of their occurrence. 32P-Postlabelling approach ensures very sensitive...
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Radio- and photosensitization of DNA with compounds containing platinum and bromine atoms
Publikacja. Irradiations of plasmid DNA by both X-rays and UV light in the presence and absence of compounds containing platinum and bromine atoms were performed in order to asses the sensitization potential of these compounds. Plasmid DNA pBR322 was incubated with platinum (II) bromide, hydrogen hexabromoplatinate (IV), hydrogen hexahydroxyplatinate (IV) and sodium hexahydroxyplatinate (IV). Incubation was followed by X-ray or UV irradiations....
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Interactions of dissolved dsDNA with intercalating drug by anodic voltammetry and spectroscopy. Influence of pH
PublikacjaOddziaływanie związku przeciwnowotworowego C-1305 z DNA było badane przy pomocy impulsowej voltametrii różnicowej oraz spektroskopii UV/Vis. Triazoloakrydon C-1305 oddziałuje z DNA na dwóch drogach: przez interkalacje pomiedzy pary zasad oraz przez wiązanie sie w małym rowku helisy. W fizjologicznym pH (7,4) stałe wiązania wynoszą: K1=3,36E+5 i K2=0,18E+5 [1/M] a wielkość miejsca wiązania: n1=2,5 i n2=4,0, odpowiednio dla pierwszego...
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Toward Intelligent Vehicle Intrusion Detection Using the Neural Knowledge DNA
PublikacjaIn this paper, we propose a novel intrusion detection approach using past driving experience and the neural knowledge DNA for in-vehicle information system security. The neural knowledge DNA is a novel knowledge representation method designed to support discovering, storing, reusing, improving, and sharing knowledge among machines and computing systems. We examine our approach for classifying malicious vehicle control commands...
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Smart innovation process enhancement using SOEKS and decisional DNA
PublikacjaProduct innovation always requires a foundation based on both knowledge and experience. The production and innovation process of products is very similar to the evolution process of humans. The genetic information of humans is stored in genes, chromosomes and DNA. Similarly, the information about the products can be stored in a system having virtual genes, chromosomes and decisional DNA (DDNA). The present paper proposes...
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A proposal for knowledge sharing in the e-Decisional community using Decisional DNA
PublikacjaZaproponowano model platformy wspomagającej wymianę wiedzy w społeczeństwie decyzyjnym opartym na decyzyjnym DNA.
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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The interaction of antitumor 1-nitroacridines with DNA in cell-free systems
PublikacjaUzyskano nowe pochodne 1-nitro i 3-nitroakrydyny wykazujące zdolność do specyficznego cięcia DNA w miejscach bezzasadowych. Z użyciem oligonukleotydu z indukowanym miejscem bezzasadowym potwierdzono taką aktywność u obu otrzymanych pochodnych.