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Wyniki wyszukiwania dla: DDNA
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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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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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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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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublikacjaModeling an effective mechanism for design and control strategies for the implementation of a flexible manufacturing system (FMS) has been a challenge. Consequently, to overcome this issue various techniques have applied in the past but most of these models are effective only for some specific situation or an element of FMS. In this study, the knowledge representation technique of Decisional DNA (DDNA) is applied to FMS to develop...
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublikacjaPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Representing and Managing Experiential Knowledge with Decisional DNA and its Drimos® Extension
PublikacjaThe 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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A Framework for Enhancing Supplier Selection Process by Using SOEKS and Decisional DNA
PublikacjaAbstract. Supplier selection process is one of the significant stages in supply chain management for industrial manufactured products. It plays an integral role in the success of any manufacturing organization and is an important part starting right from selecting raw material to dispatch of finished products. This paper contributes to enhance the supplier selection process by proposing a multi-criteria decision making framework...
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cDNA fingerprint from the hepatopancreatic glands of pond snails (Lymnaea stagnalis) exposed to benzo[a]pyrene
PublikacjaIdentification of differentially expressed genes that could be potentially used as biomarkers of PAH exposure of common invertebrate animal (like freshwater snail) would be a valuable resource for investigators interested in toxicology and biomonitoring of aquatic environments. Therefore, the aim of this research was to investigate effects of waterborne benzo[a]pyrene (B[a]P) exposure on mRNA expression in the pond snail’s (Lymnaea...
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LS-DYNA simulations of the impacts of a 38-ton Heavy Goods Vehicle into a road cable barrier
PublikacjaNowadays, more and more attention is being paid to safety on roads and motorways. It is due to the continuous development of road and motorway network and a significant increase of the number of vehicles on roads. To meet the expectations of improving road safety in Poland, the Road Innovations Development (RID) research programme was implemented in 2016. The aim of the RID 3A - Road Safety Equipment (RoSE) project is a comprehensive...
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DNA modification by 1-nitroacridine derivatives. Comparison of 32P-Postlabeling and restriction enzyme analysis method for the detection of DNA adducts formed by 1-nitroacridines C-1748 and C-857
Publikacja4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych akrydyny, zsyntetyzowanych na Politechnice Gdańskiej. Metoda 32P-postlabellingu wykazała, że pochodne C-1748 i C-857 tworzą od 4-6 adduktów DNA w systemie komórkowym i bezkomórkowym o innym rozkładzie plam chromatograficznych, jednakże niezależnym od zastosowanego systemu aktywacyjnego. Metoda enzymatycznej analizy restrykcyjnej pozwoliła natomiast śledzić kinetykę...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA 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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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublikacjaDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms
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Altered levels of circulating nuclear and mitochondrial DNA in patients with Papillary Thyroid Cancer
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Diagnostyka zakażeń Candida spp. oparta o amplifikację DNA techniką PCR
PublikacjaZakażenia wywoływane przez oportunistyczne grzyby z rodzaju Candida są poważnym problemem klinicznym. Niezbędne jest poszukiwanie nowych szybkich, czułych i pewnych metod do identyfikacji gatunkowej tych drobnoustrojów. W artykule przedstawiono opisane w literaturze metody diagnostyki molekularnej drożdżaków z rodzaju Candida oparte o amplifikację DNA techniką PCR.
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Prediction based on integration of Decisional DNA and a feature selection algorithm Relief-F
PublikacjaThe paper presents prediction model based on Decisional DNA and Set of experienced integrated with Relief_F algorithm for feature selection
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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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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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The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions
PublikacjaPrzeanalizowano wpływ temperatury na formowanie warstw DNA. Sprawdzono wpływ stabilizatorów na jakość otrzymanych próbek. Stwierdzono, że optymalnymi warunkami przygotowywania filmów do badań w warunkach próżniowych jest - 10 st. C przy minimalnej zawartości NaOH.
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Decisional DNA with embedded Relief-F linear regression for knowledge and experience management
PublikacjaOmowiono zastowania Decyzyjnego DNA, regresji liniowej oraz funkcji RELIEF-F w procesach formalnego modelowania i wspomagania zarzadzania wiedza oraz zarzadzania doswiadczeniem.
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Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
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Photostability pf Cy3 and Cy5-labeled DNA in the presence of metallic silver particles
PublikacjaZbadano wpływ cząstek metalicznego srebra na fotostabilność oligomerów DNA kowalencyjnie związanych z Cy3 lub Cy5. Zbliżenie fluoroforów do cząstek srebra powodowało zwiększenie intensywności fluorescencji i pojawienie się frakcji emisji bardziej odpornej na wybielanie.
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublikacjaBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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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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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublikacjaMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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How acidic amino acid residues facilitate DNA target site selection
PublikacjaDespite 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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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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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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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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Wpływ dodatku kwasu deoksyrybonukleinowego (DNA) na właściwości mechaniczne żeli żelatynowych
PublikacjaKwasy 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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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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Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method
PublikacjaApplications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers –...
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Integrating Experience-Based Knowledge Representation and Machine Learning for Efficient Virtual Engineering Object Performance
PublikacjaMachine learning and Artificial Intelligence have grown significant attention from industry and academia during the past decade. The key reason behind interest is such technologies capabilities to revolutionize human life since they seamlessly integrate classical networks, networked objects and people to create more efficient environments. In this paper, the Knowledge Representation technique of Set of Experience...
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Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublikacjaAb initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant...
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Bio-inspired Decisional DNA in Machinas and other Man-made Systems: The Way Forward
PublikacjaArtificial bio-inspired intelligent techniques and systems supporting smart, knowledge-based solutions of real world problems which are currently researched very extensively by research teams around the world, have enormous potential to enhance automation of decision making and problem solving for a number of diverse areas including design, manufacturing, Information Technology (IT), social communities of practice, and economics...
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublikacjaA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublikacjaW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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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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Preparation of DNA films for studies under vacuum conditions. The influence of cations in buffer solutions
PublikacjaBadania zostały przeprowadzone w celu określenia optymalnych warunków wymaganych do przygotowania jednolitych filmów superskręconego plazmidowego DNA do wykorzystania w doświadczeniach napromieniowania w warunkach wysokiej próżni. Badania pokazują, że znaczne szkody w DNA powstają w wyniku odpompowywania filmów DNA z roztworów zawierających jedynie czysta wodę.
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DNA variants in Helicobacter pylori infected patients with chronic gastritis, dysplasia and gastric cancer
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DNA Variants in Helicobacter Pylori Infected Patients with Chronic Gastritis, Dysplasia and Gastric Cancer
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Epigenetic Basis of Regeneration: Analysis of Genomic DNA Methylation Profiles in the MRL/MpJ Mouse
PublikacjaEpigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the...
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Decisional DNA for modeling and reuse of experiential clinical assessments in breast cancer diagnosis and treatment
PublikacjaClinical Decision Support Systems (CDSS) are active knowledge resources that use patient data to generate case specific advice. The fast pace of change of clinical knowledge imposes to CDSS the continuous update of the domain knowledge and decision criteria. Traditional approaches require costly tedious manual maintenance of the CDSS knowledge bases and repositories. Often, such an effort cannot be assumed by medical teams, hence...
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Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic
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Endogenous oxidative DNA base modifications analysed with repair enzymes and GC/MS technique
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Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Noncanonical DNA Bases
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Supplementation with antioxidant vitamins prevents oxidative modification of DNA in lymphocytes of HIV-infected patients
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