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Search results for: DNAK
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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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Berry fruit juices protect lymphocytes against DNA damage and ROS formation induced with heterocyclic aromatic amine PhIP
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Comparison of immune response in sheep immunized with DNA vaccine encoding Toxoplasma gondii GRA7 antigen in different adjuvant formulations
PublicationPraca przedstawia badania dotyczące odpowiedzi immunologicznej owiec immunizowanych plazmidowym DNA kodującym antygen granul GRA7 Toxoplasma gondii w trzech różnych formulacjach adjuvanta. Sześćdziesiąt owiec było szczepionych domięśniowo z DNa plazmidów. Dwanaście otrzymało liposomową formę plazmidu pVAXIgGRA7, 12 formulację z Emulsigen P plazmidu pVAXIgGRA7 1 12 formulację z Emulsigen D plazmidu pVAXIgGRA7. Wszystkie zwierzęta...
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Termodynamika oddziaływań i przejść strukturalnych DNA w układach wodnych na podstawie symulacji metodą dynamiki molekularnej
PublicationKwas deoksyrybonukleinowy jest jednym z najistotniejszych elementów każdej żywej komórki ze względu na rolę głównego nośnika informacji genetycznej. Posiada on instrukcje potrzebne do wzrostu, budowy, funkcjonowania oraz namnażania się wielu żywych organizmów, w tym także wirusów. Okazuje się, że w zależności od warunków środowiskowych, DNA może przyjmować wiele różnych struktur drugorzędowych, z których większość stanowi formy...
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Beyond Antioxidant Activity: Redox Properties of Catechins May Affect Changes in the DNA Methylation Profile—The Example of SRXN1 Gene
PublicationThe role of catechins in the epigenetic regulation of gene expression has been widely studied; however, if and how this phenomenon relates to the redox properties of these polyphenols remains unknown. Our earlier study demonstrated that exposure of the human colon adenocarcinoma HT29 cell line to these antioxidants affects the expression of redox-related genes. In particular, treatment with (−)-epigallocatechin (EGC) downregulated...
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Physicochemical profile of Os (III) complexes with pyrazine derivatives: From solution behavior to DNA binding studies and biological assay
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Transport of Particles in Intestinal Mucus under Simulated Infant and Adult Physiological Conditions: Impact of Mucus Structure and Extracellular DNA
PublicationThe final boundary between digested food and the cells that take up nutrients in the small intestine is a protective layer of mucus. In this work, the microstructural organization and permeability of the intestinal mucus have been determined under conditions simulating those of infant and adult human small intestines. As a model, we used the mucus from the proximal (jejunal) small intestines of piglets and adult pigs. Confocal...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublicationIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Evaluation and comparison of random amplification of polymorphic DNA, pulsed field gel electrophoresis and ADSRRS-fingerprinting for typing Serratiamarcescens outbreaks.
PublicationADSRRS-fingerprinting, nowa metoda genotypowania oparta na supresji reakcji PCR została zastosowana do badań epidemiologicznych izolatów S. marcescens,pochodzących z trzech różnych epidemii Szpitala Publicznego w Gdańsku. Wyniki uzyskane metodą ADSRRS-fingerprinting porównano z wynikami uzyskanymi technikami RAPD-fingerprinting i PFGE.
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Flow cytometry analysis of DNA DSBs in telomerase positive and negative cell lines after treatment with TXT2 and TXT4
Open Research DataFlow cytometry analysis of DNA DSBs in telomerase positive (A549, H460) and negative (NHBE2594, U2OS) cell lines after treatment with equitoxic concentrations of TXT2 and TXT4. MTX and DMSO were used as positive and negative controls, respectively.
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Study of the ability of TXT-compounds to promote telomeric G4 DNA thermal stabilization using FRET melting assay
Open Research DataThe data set contains a DNA melting screen obtained from the FRET melting assay. Thermal stabilities of G-quadruplex structures were analysed in the presence and in absence of ligands. TMPyP4 and MTX were used as references. Measurements were carried out in triplicate using a LightCycler 480 thermocycler (Roche Life Science) with a filter setting of...
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The extended version of restriction analysis approach for the examination of the ability of low-molecular-weight compounds to modify DNA in a cell-free system
PublicationOne of the primary requirements in toxicology is the assessment of ability of chemicals to induce DNA covalent modification. There are several well-established methods used for this purpose such as 32P-Postlabeling or HPLC-MS. However, all of these approaches have difficult to overcome limitations, which prevents their use in genotoxin screening. Here, we describe the simple protocol exploiting specificity of restriction enzymes...
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Helicobacter pylori infection is associated with oxidatively damaged DNA in human leukocytes and decreased level of urinary 8-oxo-7,8-dihydroguanine
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Substantial decrease of urinary 8-oxo-7,8-dihydroguanine, a product of the base excision repair pathway, in DNA glycosylase defective mice
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Small field radiotherapy of head and neck cancer patients is responsible for oxidatively damaged DNA/oxidative stress on the level of a whole organism
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Quantification of DNA Modifications Using Two-Dimensional Ultraperformance Liquid Chromatography Tandem Mass Spectrometry (2D-UPLC-MS/MS)
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Prediction of skin color, tanning and freckling from DNA in Polish population: linear regression, random forest and neural network approaches
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The immune responses of sheep after DNA immunization with Toxoplasma gondii MAG1 antigen - with and without co-expression of ovine interleukin 6
PublicationW niniejszej pracy porównano odpowiedź immunologiczną owiec, którym podano domięśniowo plazmid DNA zawierający gen kodujący białko macierzy cyst tkankowych (MAG1) Toxoplasma gondii - pojedynczo bądź z DNA plazmidu kodującego owczą interleukinę 6 (IL-6). Dzięki wykorzystaniu plazmidu zawierającego gen mag1 odnotowano podwyższony poziom przeciwciał IgG1 oraz IgG2 w surowicach szczepionych zwierząt.
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Evaluation of immune responses in sheep induced by DNA immunization with genes encoding GRA1, GRA4, GRA6 and GRA7 antigens of Toxoplasma gondii
PublicationW niniejszej pracy oszacowano odpowiedź immunologiczną owiec szczepionych domięśniowo szczepionkami DNA zawierającymi geny kodujące cztery antygeny granul o dużej gęstości (GAR1, GRA4, GRA6 oraz GRA7) Toxoplasma gondii. Wykazano, iż wykorzystanie DNA plazmidu pGRA7 indukuje znaczący poziom przeciwciał IgG-2 anty-GRA7 oraz IFN-gammma, podczas gdy iniekcja pGRA1, pGRA4 oraz pGRA6 stymuluje odpowiedź przeciwciał IgG1 z ograniczoną...
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Modulation of immune response to Toxoplasma gondii in sheep by immunization with a DNA vaccine encoding ROP1 antigen as a fusion protein with ovine CD154
PublicationNiniejszy artykuł prezentuje porównanie skuteczności działania w immunizacji owiec dwóch antytoksoplazmozowych szczepionek DNA: kodującej białko ROP1 Toxoplasma gondii oraz kodującej w/w antygen i owczą cząsteczkę CD154 lokalizowaną na powierzchni aktywowanych komórek T. Otrzymane wyniki badań pokazały, iż domięśniowe podanie szczepionki DNA zawierającej gen kodujący ROP1 i CD154 znacząco wzmacnia odpowiedź immunologiczną szczepionych...
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Numeryczna analiza wpływu budowy podpory mostu na rzece Wiśle na przepływ i rozmycie dna koryta rzeki
PublicationW artykule opisano wyniki hydraulicznej analizy wpływu jednego z filarów mostu w Kwidzynie na zmianę pola prędkości przepływu i warunków transportu rumowiska w rzece Wiśle, powodujących lokalne rozmywanie dna koryta rzeki w rejonie filara zlokalizowanego w nurcie rzeki. Bezpośrednią przyczyną podjęcia badań były zaobserwowane podczas budowy mostu lokalne rozmycia dna w sąsiedztwie podpory nr 24.
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DNA-damaging imidazoacridinone C-1311 induces autophagy followed by irreversible growth arrest and senescence in human lung cancer cells
PublicationImidazoacridinone 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) is an antitumor inhibitor of topoisomerase II and FMS-like tyrosine kinase 3 receptor. In this study, we describe the unique sequence of cellular responses to C-1311 in human non-small cell lung cancer (NSCLC) cell lines, A549 and H460. In A549 cells, C-1311 (IC80 = 0.08 µM) induced G1 and G2/M arrests, whereas H460 cells (IC80 = 0.051 µM) accumulated...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Presence of Chlamydophila pneumoniae DNA in blood cells is a frequent event in patients with the late stage of primary cutaneous lymphomas and with atopic dermatitis
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Relationships between acute reactions to radiotherapy in head and neck cancer patients and parameters of radiation-induced DNA damage and repair in their lymphocytes
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Decreased integrity of exercise-induced plasma cell free nuclear DNA – negative association with the increased oxidants production by circulating phagocytes
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Decreased integrity of exercise-induced plasma cell free nuclear DNA – negative association with the increased oxidants production by circulating phagocytes
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Repeated bouts of exhaustive exercise increase circulating cell free nuclear and mitochondrial DNA without development of tolerance in healthy men
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European Multicenter Evaluation of High-Density DNA Probe Arrays for Detection of Hepatitis B Virus Resistance Mutations and Identification of Genotypes
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Detection of MGMT, RASSF1A, p15INK4B, and p14ARF promoter methylation in circulating tumor-derived DNA of central nervous system cancer patients
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A Novel Biological Role for Peptidyl-Arginine Deiminases: Citrullination of Cathelicidin LL-37 Controls the Immunostimulatory Potential of Cell-Free DNA
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Changes in Epigenetic Patterns Related to DNA Replication in Vicia faba Root Meristem Cells under Cadmium-Induced Stress Conditions
PublicationExperiments on Vicia faba root meristem cells exposed to 150 µM cadmium chloride (CdCl2) were undertaken to analyse epigenetic changes, mainly with respect to DNA replication stress. Histone modifications examined by means of immunofluorescence labeling included: (1) acetylation of histone H3 on lysine 56 (H3K56Ac), involved in transcription, S phase, and response to DNA damage during DNA biosynthesis; (2) dimethylation of histone...
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Introduction of a multiplex amplicon sequencing assay to quantify DNA methylation in target cytosine markers underlying four selected epigenetic clocks
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Modulation of immune response to Toxoplasma gondii in sheep by immunization with a DNA vaccine encoding ROP1 antigen as a fusion protein with ovine CD154
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The immune responses of sheep after DNA immunization with, Toxoplasma gondii MAG1 antigen—with and without co-expression of ovine interleukin 6
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UV-induced electron transfer between triethylamine and 5-bromo-2′-deoxyuridine. A puzzle concerning the photochemical debromination of labeled DNA
Publication5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublicationThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublicationOkreślono molekularne właściwości białek SSB-podobnych z Thermus thermophi-lus i T. aquaticus. Zbadano aktywność białek oraz termostabilność. Ponadto, dowiedziono homodimeryczność obu białek i ustalono minimalną sekwencję wiążącą ssDNA.
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One-tube cell lysis and DNA extraction procedure for PCR based detection of Mycobacterium ulcerans in aquatic insects, molluscs and fish.
PublicationMycobacterium ulcerans jest bakterią wywołującą choroby skóry u ludzi i zwierząt. W trakcie prowadzonych badań opracowano prostą w wykonaniu metodę ekstrakcji DNA Mycobacterium ulcerans z próbek środowiskowych oraz klinicznych. Opracowana metoda izolacji DNA może być przydatna w badaniu źródeł infekcji oraz dróg szerzenia się Mycobacterium ulcerans.
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Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities.
PublicationCelem pracy było scharakteryzowanie odziaływania związku C-1305 z DNA w porównaniu do innych inhibitorów topoizomerazy II. Badania pokazują, że C-1305 odziaływuje preferencyjnie z parami CG, interkaluje do DNA i zaburza sąsiednie otoczenie w bardzo charakterystyczny sposób, który nie został zaobserwowany u pozostałych 22 badanych związków.
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ArchBGal32cB 441Glu mutein gene analysis dataset
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The influence of G2 arrest abrogation on the long-term cytotoxicity of different genotoxic lesions
PublicationJak się uważa, zdolność komórek nowotworowych z uszkodzeniami DNA do zatrzymywania progresji w cyklu komórkowym w fazie G2 wydłuża czas na reperację tych uszkodzeń i zwiększa zdolność do przeżycia tych komórek. W pracy badaliśmy wpływ skrócenia bloku w fazie G2 w komórkach dwóch typów białaczek, poddanych działaniu związków przeciwnowotworowych indukujących różne typy uszkodzeń DNA, na efekt cytotoksyczny tych związków. Zwiększenie...
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System for characterisation and multidimensional imaging of seafloor using multibeam sonar data
PublicationMultibeam sonars are widely used in applications like high resolution bathymetry measurements, underwater object detection and imaging, etc. Also, they are the promising tool in seafloor characterisation and classification, having several advantages over conventional single beam echosounders. The proposed approach to seafloor classification relies on the combined use of three different techniques. In each of them, a set of descriptors...
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Novel anticancer strategy aimed at targeting shelterin complexes by the induction of structural changes in telomeric DNA: hitting two birds with one stone.
PublicationThe ends of chromosomes in mammals are composed of telomeric DNA containing TTAGGG repeats, which bind specific proteins called shelterins. This telomeric DNA together with shelterins form a cap that protects the ends of chromosomes from being recognized as sites of DNA damage and from chromosomal fusions. Many very successful antitumor drugs used in the treatment of cancer patients bind to DNA, some of them with a prominent sequence...
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A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model
PublicationWe have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the...
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Urinary Measurement of Epigenetic DNA Modifications: A Non-Invasive Assessment of the Whole-Body Epigenetic Status in Healthy Subjects and Colorectal Cancer Patients
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Discovery and characterization of RecA protein of thermophilic bacterium Thermus thermophilus MAT72 phage Tt72 that increases specificity of a PCR-based DNA amplification
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The changes of antioxidant defense system caused by quercetin administration do not lead to DNA damage and apoptosis in the spleen and bone marrow cells of rats
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