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Search results for: LIGAND/DNA INTERACTIONS
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies
PublicationOsmolytes, the small organic molecules accumulated in cells under environmental stress, can modulate the stability of biopolymers such as proteins and DNA. In spite of many years of research, there is no established molecular mechanism of the influence of osmolytes on DNA structure. Here, we used two model osmolytes that denature (urea) or stabilize (trimethylglycine, TMG) proteins to study their effect on DNA in aqueous solutions...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Towards neural knowledge DNA
PublicationIn this paper, we propose the Neural Knowledge DNA, a framework that tailors the ideas underlying the success of neural networks to the scope of knowledge representation. Knowledge representation is a fundamental field that dedicates to representing information about the world in a form that computer systems can utilize to solve complex tasks. The proposed Neural Knowledge DNA is designed to support discovering, storing, reusing,...
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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublicationZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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Ocena wpływu pokarmowych kwasów nukleinowych i ich komponentów na replikacyjną i naprawczą syntezę DNA w modelach komórek ludzkiego układu pokarmowego
PublicationKwasy nukleinowe, do których należą DNA i RNA, są podstawowymi elementami każdej komórki niezbędnymi do prawidłowego funkcjonowania organizmu. Pomimo, że cząsteczki te stanowią również nieodłączne składniki produktów żywnościowych spożywanych przez człowieka, to badania na temat ich zawartości w żywności oraz wartości odżywczej są ograniczone. Wyniki uzyskane w niniejszej pracy doktorskiej pokazały istotne różnice w ilości, wielkości...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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Viability of decisional DNA in robotics
PublicationThe Decisional DNA is an artificial intelligence system that uses prior experiences to shape future decisions. Decisional DNA is written in the Set Of Experience Knowledge Structure (SOEKS) and is capable of capturing and reusing a broad range of data. Decisional DNA has been implemented in several fields including Alzheimer’s diagnosis, geothermal energy and smart TV. Decisional DNA is well suited to use in robotics due to the...
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Modified DNA polymerases for PCR troubleshooting
PublicationPCR has become an essential tool in biological science. However, researchers often encounter problems with difficult targets, inhibitors accompanying the samples, or PCR trouble related to DNA polymerase. Therefore, PCR optimization is necessary to obtain better results. One solution is using modified DNA polymerases with desirable properties for the experiments. In this article, PCR troubleshooting, depending on the DNA polymerase...
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublicationDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Adding Interpretability to Neural Knowledge DNA
PublicationThis paper proposes a novel approach that adds the interpretability to Neural Knowledge DNA (NK-DNA) via generating a decision tree. The NK-DNA is a promising knowledge representation approach for acquiring, storing, sharing, and reusing knowledge among machines and computing systems. We introduce the decision tree-based generative method for knowledge extraction and representation to make the NK-DNA more explainable. We examine...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Individual Resources and Intercultural Interactions
PublicationThe work environment in multinational corporations (MNCs) is specific and demanding including intercultural interactions with co-workers and clients and using a foreign language. Some individual resources can help in dealing with these circumstances. Individual resources refer to personal dispositions, competencies and prior experiences. With regard to previous studies, a caravan of personal resources, namely Psychological Capital...
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Intercultural interactions at multinational corporations' workplace: Grounded theory.
Publicationenvironments is a new challenge for employees and managers. The aim of the paper is to analyze the social interactions in multicultural environments of multinational corporations (MNCs) as well as to propose a model of intercultural social interactions in MNCs’ specifi c context. Design/methodology/approach: The grounded theory approach was applied to create a model of intercultural interactions in MNCs. The data was obtained during...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Dual inhibition of PI3K/Akt signaling and the DNA damage checkpoint in p53-deficient cells with strong survival signaling: implications for cancer therapy
PublicationOporność komórek nowotworowych na leki uszkadzjące DNA związana jest ściśle ze zdolnością do utrzymywania blok z fazie G2 cyklu komórkowego. Blok ten regulowany jest przez mechanizmy punktu kontrolnego G2/M oraz szlaki przeżycia komórkowego. W pracy badaliśmy rolę szlaku kinazy PI3K/Akt w funkcjonowaniu punktu kontrolnego cyklu komórkowego i wpływ na przeżycie komórek traktowanych lekiem przeciwnowotworowym - cisplatyną. Nasze...
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Regulacja topologii DNA przez topoizomerazę typu II, czyli jak struktura DNA wpływa na funkcjonowanie genów
PublicationW wielu ważnych procesach jakie zachodzą w komórce zmienia się topologia DNA i struktura chromatyny. Enzym, topoizomeraza typu II, jest jednym z ważnych czynników, który reguluje zmiany topologiczne i strukturalne w jądrze, przez co ma bezpośredni lub pośredni wpływ na takie procesy jak uporządkowanie struktury chromatyny poprzez wiązanie pętli chromatyny do szkieletu jądrowego, transkrypcję i replikację DNA, reperację uszkodzeń...
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Discovering interactions between applications with log analysis
PublicationApplication logs record the behavior of a system during its runtime and their analysis can provide useful information. In this article, we propose a method of automated log analysis to discover interactions taking place between applications in an enterprise. We believe that such an automated approach can greatly support enterprise architects in building an up-to-date view of a governed system in a modern, fast-paced development...
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The development of Decisional DNA digital TV
PublicationZaproponowano koncepcje opartej na wiedzy i doswiadczeniu telewizji cyfrowej z wbudowanym decyzyjnym DNA.
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Gentiana asclepiadea exerts antioxidant activity and enhances DNA repair of hydrogen peroxide- and silver nanoparticles-induced DNA damage
PublicationExposure to high levels of different environmental pollutants is known to be associated with induction of DNA damage in humans. Thus DNA repair is of great importance in preventing mutations and contributes crucially to the prevention of cancer. In our study we have focused on quantitative analysis of Gentiana asclepiadea aqueous or methanolic extracts obtained from flower and haulm, their antioxidant potency in ABTS post-column...
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Synthesis, crystal structure and cytotoxic activity of ruthenium(II) piano-stool complex with N,N-chelating ligand
PublicationA mononuclear compound of the general formula [(η6-p-cymene)RuIICl(2,2′-PyBIm)]PF6 has been synthesized from a bidentate N,N-donor ligand, viz. 2,-(2′-pyridyl)benzimidazole (2,2′-PyBIm) and the corresponding chloro-complex [(η6-p-cymene)Ru(μ-Cl)Cl]2 (precursor). The isolated coordination compound was characterized by IR, UV–vis and 1H, 13C NMR spectroscopies. The single crystal X-ray analysis of the complex reveals that the asymmetric...
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Decisional DNA applied to digital TV
PublicationPrzedstawiono nowoczesną koncepcje integracji decyzyjnego DNA z telewizją cyfrową w celu pozyskiwania wiedzy o oglądalności poszczególnych programów.
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Role of the Synergistic Interactions of Environmental Pollutants in the Development of Cancer
PublicationThere is a growing awareness that the large number of environmental pollutants we are exposed to on a daily basis are causing major health problems. Compared to traditional studies that focus on individual pollutants, there are relatively few studies on how pollutants mixtures interact. Several studies have reported a relationship between environmental pollutants and the development of cancer, even when pollutant levels are below...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Testing the usability of decisional DNA in robotics
PublicationW pracy poddano dyskusji i nalizie obszary mozliwych zastowac reprezentacji wiedzy zwanej Decisional DNA w zagadnieniach zwiazanych z robotyka.
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Preparation of DNA films for studies under vacuum conditions
PublicationExperiments were carried out to determine the optimum conditions required for the preparation of uniform films of supercoiled plasmid DNA to be used in irradiation experiments under high vacuum conditions. Investigations reveal that significant damage to the DNA molecules occurs due to the evacuation process when films were formed from DNA samples in ultra high purity water only. A variety of bases were tested for their possible...
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Early models of DNA damage formation
PublicationPrzeanalizowano jedne z pierwszych modeli opisujących uszkodzenia nici DNA. Przeanalizowano uszkodzenia powstające w pojedynczych i podwójnych niciach, pod wpływem czynników fizycznych i chemicznych.
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Isoform-specific inhibition of DNA topoisomerase II as the mechanism of action of novel anticancer agent C-1305
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Low-energy interactions related to atmospheric and extreme conditions
PublicationThis Topical Issue, entitled “Low-Energy Interactions Related to Atmospheric and Extreme Conditions”, showcases a collection of eighteen articles that reported recent theoretical and experimental findings pertaining to the following topics: – low-energy interactions of charged particles (electrons [1–7], protons [8], positrons [9]), and photons [10] with atoms and molecules of biological [1–4,7,8], astrochemical [10], industrial,...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Syntheses, Structures and Reactivity of Terminal Phosphido Complexes of Iron(II) Supported by a β-Diketiminato Ligand
PublicationWe report the synthesis of the first series of terminal phosphido iron complexes supported by a β‐diketiminato ligand (Dippnacnac) and their catalytic activity in dehydrocoupling of secondary phosphines. Anionic and neutral mono‐ or diphosphido complexes were obtained from the reaction of [(Dippnacnac)FeCl2Li(dme)2] with the R2PLi (R = iPr, tBu, Cy, Ph) phosphides by tuning the stoichiometric ratio, polarity of the solvent, and...
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Badanie i porównanie zdolności wybranych leków i związków przeciwnowotworowych do międzyłańcuchowego sieciowania DNA mitochondrialnego i jądrowego w komórkach nowotworowych
PublicationCelem pracy było zbadanie zdolności przeciwnowotworowych związków do indukowania międzyłańcuchowych wiązań sieciujących DNA mitochondrialne w ludzkich komórkach nowotworowych oraz porównanie ze zdolnością do sieciowania DNA jądrowego. Pochodna 4-metylo-1-nitroakrydyny C-1748, Ledakrin i mitomycyna C wykazują zdolność do sieciowania mtDNA i jDNA w komórkach raka okrężnicy HCT-8 w sposób zależny od dawki; C-1748 w komórkach raka...
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Toward Intelligent Recommendations Using the Neural Knowledge DNA
PublicationIn this paper we propose a novel recommendation approach using past news click data and the Neural Knowledge DNA (NK-DNA). 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 news recommendation tasks on the MIND benchmark dataset. By taking advantages of NK-DNA, deep...
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The Decisional DNA-Based Smart Bike for Internet of Things
PublicationIn this paper, we introduce a novel application of the Internet of Things, the Decisional DNAbased Smart Bike. The Decisional DNA is a domain-independent, flexible and standard knowledge representation structure; it allows its domains to acquire and store experiential knowledge and formal decision events in an explicit way. By using Decisional DNA, the sensor-equipped bicycle is able to learn its user’s weight, riding habits, etc....
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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A case study of constructing decisional DNA on finanse
PublicationPrzedstawiono koncepcję i rozwiązanie analityczne opisu rynku finansowego przy pomocy reprezentacji wiedzy zwanej ''decyzyjne DNA''.
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Barriers of cross-cultural interactions according to the research findings
PublicationThe aims of this article are to label major cultural barriers and to present results of empirical findings referring to barriers to intercultural interactions in foreign subsidiaries of transnational corporations (TNCs). The qualitative research was conducted in TNCs'foreign subsidiaries operating in Poland in winter 2009/2010. The article describes how respondents perceive the problems in cooperation with foreigners, their sources,...
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Barriers of Cross-cultural Interactions According to the Research Findings
PublicationThe aim of this article is to label major cultural barriers and to present results of empiricalfindings referring to barriers to intercultural interactions in foreign subsidiaries oftransnational corporations (TNCs). The qualitative research was conducted in TNCs'foreign subsidiaries operating in Poland in the winter of 2009/2010. The articledescribes how the respondents perceived the problems in cooperation with foreigners,defines...
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Optoelectronic investigation of nanodiamond interactions with human blood
PublicationWe present optoelectronic investigation of in vitro interactions of whole human blood with different nanodiamond biomarkers. Plasmo-chemical modifications of detonation nanodiamond particles gives the possibility for controlling their surface for biological applications. Optical investigations reveal the biological activity of nanodiamonds in blood dependent on its surface termination. We compare different types of nanodiamonds:...
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Interactions using passive optical proximity detector
PublicationIn this paper we evaluated the possible application of a passive, optical sensor as an interface for human-smart glasses interactions. The designed proximity sensor is composed of set of photodiodes and the appropriate hardware and software components. First, experiments were performed for the estimations of such parameters as distance to an object, its width and velocity. Achieved results were satisfactory. Therefore, next, a...
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Decisional DNA and Optimization Problem
PublicationMany researchers have proved that Decisional DNA (DDNA) and Set of Experience Knowledge Structure (SOEKS or SOE) is a technology capable of gathering information and converting it into knowledge to help decision-makers to make precise decisions in many ways. These techniques have a feature to combine with different tools, such as data mining techniques and web crawlers, helping organization collect information from different sources...
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Empirical investigation on labour market interactions in an enlarged Europe
PublicationThis 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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Decisional DNA: the concept and its implementation platforms
PublicationOmowiono kopncepcje zarzadzania wiedza oparta na decyzyjnym DNA gdzie wiedza jest reprezentowana poprzez zbiory doswiadczen. Przedstawiono obecne oraz przyszle zastosowania omawianej koncepcji.
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Metylacja DNA w rozwoju, diagnostyce i terapii nowotworów
PublicationDotychczas kowalencyjna modyfikacja DNA, jaką jest zarówno naturalna metylacja DNA, jak i addukty DNA egzogennych niskocząsteczkowych związków chemicznych, były ropatrywane z punktu widzenia genomu. W świetle obecnej wiedzy dotyczącej epigenomu można sądzić, że stosunkowo niewielkie modyfikacje czy to w postaci metylacji cytozyny, czy adduktu DNA mogą mieć znaczący wpływ na działanie komórki, a co za tym idzie także jej transformację...
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Therapeutic intervention by the simultaneous inhibition of DNA repair and type I or type II DNA topoisomerases: one strategy, many outcomes
PublicationMany anticancer drugs reduce the integrity of DNA, forming strand breaks. This can cause mutations and cancer or cell death if the lesions are not repaired. Interestingly, DNA repair-deficient cancer cells (e.g., those with BRCA1/2 mutations) have been shown to exhibit increased sensitivity to chemotherapy. Based on this observation, a new therapeutic approach termed 'synthetic lethality' has been developed, in which radiation...
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Intramolecular interactions in crystals of tris(2,6-diisopropylphenoxy)silanethiol and its sodium salts
PublicationHydrolytically 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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Framework for Product Innovation Using SOEKS and Decisional DNA
PublicationProduct 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...