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Search results for: dna fingerprinting
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), 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 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Covalent DNA modification by products of myrosinase catalysed glucosinolate degradation in cell-free system
PublicationThe bioactive phytochemicals found in Brassica vegetables belonging to glucosinolates (GLS) and especially the products of their degradation isothiocyanates (ITC) and indoles are regarded as the most promising cancer chemopreventive compounds. These secondary metabolites constitute defence system repelling or preventing the development of agrophages attacking brassica plants. The antibiological properties of these compounds suggest...
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Electroanalytical and spectroscopic procedures for examination of interactions between double stranded DNA and intercalating drugs
PublicationPrzedstawiono metodę elektrochemicznego opisu oddziaływań dsDNA ze związkiem biologicznie czynnym w warunkach, w których zarówno badany związek jak i cząsteczka DNA są w roztworze elektrolitu. Opracowano warunki pomiaru, gdzie ani związek, ani DNA nie adsorbuje na elektrodzie. Wykazano, podobnie jak podczas badania innymi metodami, że oddziaływania są dwojakiego rodzaju: elektrostatyczne i poporzez interkalację.
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW 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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Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics
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One tube mutation detection using sensitive fluorescent dyeing of MutS protected DNA
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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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Melatonin as a major skin protectant: from free radical scavenging to DNA damage repair
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Aberrant repair of etheno–DNA adducts in leukocytes and colon tissue of colon cancer patients
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Oxidative stress and oxidative DNA damage is characteristic for mixed Alzheimer disease/vascular dementia
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Preliminary studies on DNA retardation by MutS applied to the detection of point mutations in clinical samples
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublicationNumerous 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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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo 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
PublicationBadania 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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Tracking Clonal Evolution of Multiple Myeloma Using Targeted Next-Generation DNA Sequencing
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Sample processing for DNA chip array-based analysis of enterohemorrhagic Escherichia coli (EHEC)
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A novel dual mode capacitor biosensor for real-time, label-free DNA detection
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Detection of bacteriophage infection and prophage induction in bacterial cultures by means of electric DNA chips
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Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons
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Cellular Turnover: A Potential Metabolic Rate–Driven Mechanism to Mitigate Accumulation of DNA Damage
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Influence of Selected Factors on the Survival Assessment and Detection of Giardia intestinalis DNA in Axenic Culture
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe 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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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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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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Zastosowanie zmodyfikowanej metody Prony'ego do detekcji dna morskiego i obiektów podwodnych
PublicationW artykule zaprezentowano zastosowanie nowej (zaproponowanej przez autorów) modyfikacji metody Prony'ego do określenia kierunku przyjścia sygnału echa fali akustycznej docierającego do odbiorczego przetwornika hydroakustycznego. Wykorzystanie zaproponowanej metody, umożliwia lepsze, niż za pomocą dotychczas znanych metod, określenie położenia wielu źródeł rewerberacji jednocześnie, zapewniając tym samym niezakłócone działanie w...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Zastosowanie immobilizowanego białka MutS do wychwytywania fragmentów DNA zawierających niesparowane zasady
PublicationBiałko MutS wiąże DNA zawierające błędnie sparowane oraz niesparowane zasady w DNA. Podjęto szereg prób wykorzystania tego białka jako narzędzia do detekcji nieznanych mutacji lub zagęszczania frakcji DNA z niesparowaną zasadą. Dotychczas żadna z metod oparta na użyciu białka MutS nie została wdrożona powszechnie do praktyki laboratoryjnej. Głównym powodem takiego stanu rzeczy jest stosunkowo silne powinowactwo MutS do DNA w pełni...
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Manufacturing collective intelligence by the means of Decisional DNA and virtual engineering objects, process and factory
PublicationEngineering 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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Decisional DNA for modeling and reuse of experiential clinical assessments in breast cancer diagnosis and treatment
PublicationClinical 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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Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublicationAb 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
PublicationArtificial 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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Set of Experience and Decisional DNA: Toward Brains for Cyber-physical Systems and Industry of the Future
PublicationThe concept of Decisional DNA is decade old. This article introduces the initial idea of Set of Experience Knowledge Structure, its advancement into Decisional DNA, and its potential for real life applications in divers domains. The most current and future research steps into Industry 4.0 are also presented and discussed
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From Individual to Collective: Intelligence Amplification with Bio-Inspired Decisional DNA and its Extensions
PublicationIn nature, deoxyribonucleic acid (DNA) contains the genetic instructions used in the development and functioning of all known living organisms. The idea behind our vision is to develop an artificial system, an architecture that would support discovering, adding, storing, improving and sharing information and knowledge among agents and organizations through experience. We propose a novel Knowledge Representation (KR) approach in...
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublicationOchratoxin A (OTA) is a hazardous contaminant of a large variety of plant and animal originated food. Herein, we report an interaction of OTA with calf thymus DNA (ct DNA) on the nanodiamond surface. We employed multispectroscopic techniques to elucidate the binding mechanism of OTA with ct DNA. The fluorescence and UV–Vis spectroscopy results show that OTA binds to ds ct DNA and forms complexes. We obtained the binding constants...
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DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis
PublicationThe human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization...
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Smart Decisional DNA Technology to Enhance Industry 4.0 Environment in Conjunction with Conventional Manufacturing
PublicationKnowledge-based support has become an indispensable part not only to the traditional manufacturing set-ups but also to the new fast-emerging Industry 4.0 scenario. In this regard, successful research has been performed and extensively reported to develop Decisional DNA based knowledge representation models of engineering object and engineering process called Virtual engineering object (VEO), Virtual engineering process (VEP) and...
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Effects of metallic silver particles on resonance energy transfer between fluorophores bound to DNA.
PublicationZbadano wpływ filmów wysepek metalicznego srebra na rezonansowe przekazywanie energii między fluoroforami związanymi z DNA. Donorem i akceptorem były odpowiednio 4´,6 diamidyno-2-fenylindon i jodek propydyny. Zmierzone dla tego układu czasy zaniku i widma fluorescencji pokazują, że sąsiedztwo cząstek srebra dramatycznie zwiększa promień Forstera, a tym samym i przekazywanie energii w znakowanym DNA.
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Electrochemical formation of the adduct between antitumor agent C_1311 and DNA nucleoside dG. 75.
PublicationPrzyjmuje się, że metaboliczna aktywacja przeciwnowotworowej pochodnej C_1311 jest procesem koniecznym dla jej aktywności przeciwnowotworowej. Wykazano wcześniej, że taka aktywacja prowadzi do kowalencyjnego wiązania się leku z DNA w komórce nowotworowej. Aby zbadać molekularny mechanizm powyższej reakcji metabolicznej przeprowadzono badania elektrochemicznego utleniania pochodnej C_1311. Wykazano w pracy, że dwa produkty elektrochemicznego...
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Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island film
PublicationOpisano fluorescencję barwnika CY5 połączonego z DNA w roztworze buforowym na wysepkach srebrowych.
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Interstrand crosslinking of DNA in tumor and fibroblast cells by C-1311 (Symadex) and other imidazoacridinones
PublicationImidazoakrydony, w tym pochodna C-1311 znajdująca się w pierwszej fazie badań klinicznych prowadzonych przez firmę Xanthus Life Sciences, należą do grupy bardzo aktywnych związków przeciwnowotworowych zsyntetyzowanych w Katedrze Technologii Leków i Biochemii PG. Za pomocą zmodyfikowanej metody Parsons'a wykazaliśmy, że C-1311 indukuje w sposób zależny od stężenia międzyłańcuchowe wiązania sieciujące w komórkach różnych nowotworów...
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The New LM-PCR/Shifter Method for the Genotyping of Microorganisms Based on the Use of a Class IIS Restriction Enzyme and Ligation Mediated PCR
PublicationThis study details and examines a novel Ligation-Mediated - Polymerase Chain Reaction (LM-PCR) method. Named the LM-PCR/Shifter, it relies on the use of a Class IIS restriction enzyme giving restriction fragments with different 4 base, 5' overhangs, this being the Shifter, and the ligation of appropriate oligonucleotide adapters. A sequence of 4-base, 5' overhangs of the adapter and a 4-base sequence of the 3' end of the primer(s)...
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From DNA damage to G2 arrest: the many roles of topoisomerase II. W: Prog-ress in Cell Cycle Research. Ed. Meijer L., Jezequel A., Roberge M. London: Plenum Publ. Comp. Ltd**2003 vol. 5 chapt. 30 s. 295-300 Od uszkodzeń DNA do bloku w G2: wiele ról dla topoizomerazy II.
PublicationInhibitory DNA topoizomerazy II sa jednymi z najbardziej szeroko stosowanymi lekami przeciwnowotworowymi. Związki te indukuja pekniecia nici DNA i bloku progresji cyklu komorkowego w fazie G2. Jednak topoizomeraza II jest nie tylko celem molekularnym dla lekow przeciwnowtworowych ale enzym ten pelniwazna role w odpowiedzi komorkowej na dzialanie wielu lekow uszkadzajacych DNA. Topoizomeraza tworzy kompleksy molekularne z bialkami...
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Oxidative DNA damage: assessment of the role in carcinogenesis, atherosclerosis, and acquired immunodeficiency syndrome1 1This article is part of a series of reviews on “Oxidative DNA Damage and Repair.” The full list of papers may be found on the homepage of the journal.
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Molecular epidemiology of Serratia marcescens in two hospitals in Danzig, Poland, over a 5-year period.Molecular epidemiology of Serratia marcescens in two hospitals in Gdańsk, Poland, over a 5-year period.
PublicationW pracy badano zmiany populacji Serratia marcescens w ciągu 5 lat w dwóch szpitalach klinicznych Gdańska. Posłużono się wartościami MIC, wynikami typowania genetycznego RAPD-PCR, PFGE i nową metodą ADSRRS-fingerprinting oraz analizą beta-laktamaz o rozszerzonym spektrum substratowym (ESBL). Dzięki określeniu lekowrażliwości na najnowsze antybiotyki beta-laktamowe wykryto fenotypy wykazujące derepresję cefalosporynazy AmpC u 23%...
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Cyclic voltammetry curves of the V2O5 nanorods (Na-ion batteries)
Open Research DataThe DataSet contains the next thirty cycles voltammetry curves for the V2O5 nanorods obtained by the sol-gel method. The cyclic voltammetry was measured using the AUTOLAB 302N potentiostat-galvanostat. The measurements were carried out in a voltage range of 2 V to 4 V vs. Na/Na+ at a scan rate of 1 mV/s. As an electrolyte 1M NaPF6 was applied.