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    Wyświetlanie 1-9 z 9
    Tytuł:
    Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).
    Autorzy:
    Brzeziński, Krzysztof
    Janowski, Robert
    Podkowiński, Jan
    Jaskólski, Mariusz
    Powiązania:
    https://bibliotekanauki.pl/articles/1044143.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    Southern blot
    S-adenosyl-L-homocysteinase
    Northern blot
    biological methylation
    screening of cDNA library
    phylogeny
    Opis:
    The coding sequences of two S-adenosyl-L-homocysteine hydrolases (SAHases) were identified in yellow lupine by screenig of a cDNA library. One of them, corresponding to the complete protein, was sequenced and compared with 52 other SAHase sequences. Phylogenetic analysis of these proteins identified three groups of the enzymes. Group A comprises only bacterial sequences. Group B is subdivided into two subgroups, one of which (B1) is formed by animal sequences. Subgroup B2 consist of two distinct clusters, B2a and B2b. Cluster B2b comprises all known plant sequences, including the yellow lupine enzyme, which are distinguished by a 50-residue insert. Group C is heterogeneous and contains SAHases from Archaea as well as a new class of animal enzymes, distinctly different from those in group B1.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 2; 477-483
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Wykorzystanie spektrometrii mas do analizy modyfikacji nukleotydów i adduktów DNA
    Application of mass spectrometry methods for analysis of modified nucleotides and DNA adducts
    Autorzy:
    Hanus, J.
    Jelonek, K.
    Pietrowska, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/171867.pdf
    Data publikacji:
    2011
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    kancerogeneza
    diagnostyka molekularna
    spektrometria mas
    nukleotydy
    uszkodzenia DNA
    addukty DNA
    metylacja DNA
    carcinogenesis
    molecular diagnostics
    mass spectrometry
    nucleotides
    DNA damage
    DNA adducts
    DNA methylation
    Opis:
    Chemically modified nucleotides, which are not normally present in genetic material, are called DN A adducts. This type of DN A modifications (damage) is directly related to processes of mutagenesis and carcinogenesis. Elevated levels of DN A adducts present in genetic material reflect exposure of humans to carcinogenic factors and are markers of increased risk of cancer [1]. For this reason different methods useful for quantitative and qualitative analyses of DN A adducts are used in the field of cancer prevention and research (Tab. 1). Enzymatically-catalyzed methylation of cytosine, observed mostly in so called CpG islands, is a frequent endogenous modification of genetic material. Such a DN A methylation is a key factor involved in regulation of gene expression, and methylation status of oncogenes and tumor supressor genes is an important biomarker of carcinogenesis. As such, analytical methods for assessment of DN A methylation are of great importance for molecular diagnostics of cancer. During the last decade significant progress has been made in methods available for quantitative, qualitative and structural analyses of biological molecules. Among intensively developed tools for bioanalyses are methods of mass spectrometry. Spectrometers that are based on two methods of ionization, namely electrospray ionization (ESI ) [30] and matrix-assisted laser desorption-ionization (MALDI ) [48], are particularly suitable for analyses of biological macromolecules: proteins and nucleic acids. Currently available mass spectrometers, together with microscale methods for sample preparation and separation, significantly increased sensitivity and accessible mass range of analyses. New generation of “user-friendly” instruments is developed to bring the techniques directly into the workplaces of biological and clinical investigators. This review demonstrates representative examples of mass spectrometry techniques used for qualitative analyses of nucleotide modifications and adducts present in genetic material of humans. In this field several methods base on spectrometers with electrospray ionization. Generated ions are separated according to their mass-to-charge ratio in an analyzer by electric fields; among different ion analyzers frequently used in this methods are single or triple quadrupole and ion traps (Fig. 1). Among other methods available for assessment of DN A adducts is so called Accelerator Mass Spectrometry (Fig. 2) [41]. The most frequently applied method for the assessment of DN A methylation is based on methylation-specific PCR reaction. Products of such PCR reactions are analyzed using MALDI mass spectrometry [54] (Fig. 3). In summary, new powerful methods of mass spectrometry that made available qualitative analyses of damage and modifications of human genetic material found their important place in modern biological and medical laboratories.
    Źródło:
    Wiadomości Chemiczne; 2011, 65, 3-4; 191-205
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Integrated statistical and rule-mining techniques for dna methylation and gene expression data analysis
    Autorzy:
    Mallik, S.
    Mukhopadhyay, A.
    Maulik, U.
    Powiązania:
    https://bibliotekanauki.pl/articles/1396742.pdf
    Data publikacji:
    2013
    Wydawca:
    Społeczna Akademia Nauk w Łodzi. Polskie Towarzystwo Sieci Neuronowych
    Tematy:
    statistical analysis
    gene marker
    methylation
    genetic algorithm
    DNA
    Opis:
    For determination of the relationships among significant gene markers, statistical analysis and association rule mining are considered as very useful protocols. The first protocol identifies the significant differentially expressed/methylated gene markers, whereas the second one produces the interesting relationships among them across different types of samples or conditions. In this article, statistical tests and association rule mining based approaches have been used on gene expression and DNA methylation datasets for the prediction of different classes of samples (viz., Uterine Leiomyoma/class-formersmoker and uterine myometrium/class-neversmoker). A novel rule-based classifier is proposed for this purpose. Depending on sixteen different rule-interestingness measures, we have utilized a Genetic Algorithm based rank aggregation technique on the association rules which are generated from the training set of data by Apriori association rule mining algorithm. After determining the ranks of the rules, we have conducted a majority voting technique on each test point to estimate its class-label through weighted-sum method. We have run this classifier on the combined dataset using 4-fold cross-validations, and thereafter a comparative performance analysis has been made with other popular rulebased classifiers. Finally, the status of some important gene markers has been identified through the frequency analysis in the evolved rules for the two class-labels individually to formulate the interesting associations among them.
    Źródło:
    Journal of Artificial Intelligence and Soft Computing Research; 2013, 3, 2; 101-115
    2083-2567
    2449-6499
    Pojawia się w:
    Journal of Artificial Intelligence and Soft Computing Research
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Structural enzymology at the legume-microbe interface: S-adenosyl-L-homocysteine hydrolase of rhizobia
    Autorzy:
    Manszewski, T.
    Singh, K.
    Imiolczyk, B.
    Jaskolski, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/80810.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    S-adenosyl-L-homocysteine hydrolase
    rhizobia
    biological methylation
    methyl group
    enzymatic hydrolysis
    enzymatic process
    crystal structure
    phylogenetic analysis
    biochemical analysis
    legume plant
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 1
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Konformacyjne właściwości modyfikowanych reszt aminokwasowych
    Conformational properties of modified amino acid residues
    Autorzy:
    Wałęsa, R.
    Buczek, A.
    Broda, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/143003.pdf
    Data publikacji:
    2014
    Wydawca:
    Stowarzyszenie Inżynierów i Techników Przemysłu Chemicznego. Zakład Wydawniczy CHEMPRESS-SITPChem
    Tematy:
    dehydrofenyloalanina
    N-metylowanie
    analiza konformacyjna
    obliczenia DFT
    wpływ rozpuszczalnika
    dehydrophenylalanine
    N-methylation
    conformational analysis
    DFT calculations
    solvent impact
    Opis:
    Konformacyjnie usztywnione aminokwasy są szeroko stosowane przy konstruowaniu peptydowych analogów o lepszych właściwościach farmako-kinetycznych. Jednym z sposobów modyfikacji peptydów jest wprowadzenie reszt a,b-dehydroaminokwasowych w łańcuch peptydowy. Podwójne wiązanie Ca=Cb usztywnia łańcuch boczny i umożliwia występowanie izomerii geometrycznej Z/E. Innym rodzajem modyfikacji jest zastąpienie amidowej grupy –NH grupą –NCH3, czyli tzw. N-metylowanie. Autorzy określili wpływ tych dwóch modyfikacji strukturalnych na konformację łańcucha peptydowego. Przeprowadzone badania pozwoliły ustalić, że reszta a,b-dehydrofenyloalaniny aminokwasów konformacji H. Wykazano również, że polarny rozpuszczalnik zwiększa wyraźnie udział konfiguracji cis wiązania amidowego w N-metylowanych peptydach.
    Conformationally constrained amino acids are widely used in the design of peptide analogues with better pharmacokinetic properties. One of the methods of peptide modification is the introduction of a, b -dehydroamino acid residues into peptide chain. The double bond Ca=Cb constrains side chain and enables occurrence of geometrical isomerism Z/E. The other type of modification is the replacement of amide group –NH with group –NCH3, i.e. so called N-methylation. The Authors have determined the impact of these two structural modifications on peptide chain conformation. Conducted research has lead to the conclusion that -dehydrophenylalanine residue has the ability to exhibit atypical for standard amino acids H conformation. It has also been shown that polar solvent clearly increase percentage of cis configuration of amide bond in N-methylated peptides.
    Źródło:
    Chemik; 2014, 68, 4; 329-334
    0009-2886
    Pojawia się w:
    Chemik
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The analysis of Fanconi anemia/BRCA pathway genesin laryngeal carcinoma
    Autorzy:
    Szaumkessel, Marcin
    Powiązania:
    https://bibliotekanauki.pl/articles/1401931.pdf
    Data publikacji:
    2014
    Wydawca:
    Index Copernicus International
    Tematy:
    Fanconi anemia/BRCA pathway
    DNA repair
    Laryngeal carcinoma
    DNA methylation
    microRNA
    mRNA level
    FANCA gene
    Opis:
    Summary of Doctoral Thesis/Streszczenie pracy doktorskiej
    Źródło:
    Polski Przegląd Otorynolaryngologiczny; 2014, 3, 4; 250-252
    2084-5308
    2300-7338
    Pojawia się w:
    Polski Przegląd Otorynolaryngologiczny
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Metody określania struktury polisacharydów
    Methods for determining polysaccharides structure
    Autorzy:
    Samaszko-Fiertek, J.
    Kuźma, M.
    Dmochowska, B.
    Ślusarz, R.
    Madaj, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/172410.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    polisacharydy
    monosacharydy
    degradacja oksydacyjna
    analiza metylacyjna
    acetoliza
    NMR
    magnetyczny rezonans jądrowy
    MS
    polysaccharides
    monosaccharides
    oxidative degradation
    methylation analysis
    acetolysis
    nuclear magnetic resonance (NMR)
    Opis:
    Sequencing of polysaccharides is difficult to achieve because of the heterogeneous nature of the polysaccharide structure, high molecular weight (the size of a polysaccharide varies between approximately 16,000 and 16,000,000 daltons (Da)), and polydispersity of the polymer chains. The following information is essential to determine the primary structure of a polysaccharide: • monosaccharide composition: nature and molar ratios of the monosaccharide building blocks; • relative configuration of monosaccharides: d or l; • anomeric configuration: α- or β-configuration of the glycosidic linkage; • ring size: presence and distinction of furanosidic and pyranosidic rings; • linkage patterns: linkage positions between the monosugars and branches; • sequences of monosaccharide residues in the repeating units; • substitutions: position and nature of OH–modifications, such as O–phosphorylation, acetylation, O-sulfation, etc.; • molecular weight and molecular weight distribution. A polysaccharide extracted from plant materials or food products is usually purified before being subjected to structural analysis. The first step of characterizing a polysaccharide is the determination of its purity, which is reflected by its chemical composition, including total sugar content, level of uronic acids, proteins, ash, and moisture of the preparation. The second step is the determination of monosaccharide composition, which will unveil structural information such as the number of monosaccharides present in the polysaccharide and how many of each sugar unit. NMR spectroscopy has become the most powerful and noninvasive physicochemical technique for determining polysaccharide structures. It can provide detailed structural information of carbohydrates, including identification of monosaccharide composition, elucidation of α- or β-anomeric configurations, establishment of linkage patterns, and sequences of the sugar units in oligosaccharides and/or polysaccharides. Monosaccharide composition can be determined also by analysis of totally acid hydrolyzed polysacharide using high performance liquid chromatography (HPLC) or gas chromatography (GC). The ring size and glycosidic linkage positions of sugar units in a polysaccharide could be established by methylation analysis and/or cleavage reduction. The anomeric configuration is conventionally determined by oxidation, and this method can be combined with mass spectrometry to obtain more structural information.
    Źródło:
    Wiadomości Chemiczne; 2016, 70, 5-6; 299-318
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    LBP gene methylation involved in mRNA expression and resistance to E. coli F18 in weaned piglets
    Autorzy:
    Gan, L.N.
    Bao, W.B.
    Wu, S.L.
    Qin, W.Y.
    Sun, L.
    Zhao, C.X.
    Powiązania:
    https://bibliotekanauki.pl/articles/2087872.pdf
    Data publikacji:
    2017
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    LBP gene
    methylation analysis of the LBP region
    E.coli F18 strain
    weaned piglets
    Źródło:
    Polish Journal of Veterinary Sciences; 2017, 4; 643-650
    1505-1773
    Pojawia się w:
    Polish Journal of Veterinary Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Comparative analysis of CpG islands in two genotypes of African swine fever virus
    Autorzy:
    Yu, Y.-Y.
    X, M.-S.
    Liu, Q.
    Powiązania:
    https://bibliotekanauki.pl/articles/16539329.pdf
    Data publikacji:
    2022
    Wydawca:
    Polska Akademia Nauk. Czasopisma i Monografie PAN
    Tematy:
    African Swine Fever Virus (ASFV)
    genotype
    DNA methylation
    CpG island
    Opis:
    African swine fever (ASF) is an acute, hemorrhagic, and devastating viral infectious disease that causes important economic losses to the swine industry. Currently, there are no effective vaccines or drugs available. Epigenetic mechanisms, especially cytosine methylation of cytosine-phosphate-guanine (CpG) islands, have a significant impact on the life cycle of several viruses. Hence, drugs targeting DNA methylation may potentially be used for the treatment of ASF. Here, we selected the inner core, core shell, inner membrane, capsid, and external envelope membrane, to analyze the characteristics of CpG islands in the ASF virus (ASFV) genomes. Furthermore, we analyzed the promoters and CpG islands in the upstream regions of these genes. Results showed that the CpG islands of seven genes were conserved in the genomes of two genotype of ASFV strains, whereas the CpG islands of other genes were relatively conserved (ASFV strains differed mainly in the quantity of CpG islands). The different distribution of CpG islands in the genomes of different ASFV strains may affect their methylation status, which may in turn affect the regulation of viral gene expression, leading to different clinical outcomes. In addition, the predicted promoter regions based on the upstream sequences of most genes overlapped with CpG island positions. Methylation of the binding sites of the promoter regions inhibits the binding of the transcription factors to the promoters, thus inhibiting the activation of the promoters and limiting the synthesis of viral proteins. The results of this study provide a basis for exploring new antiviral therapeutic strategies from an epigenetic perspective.
    Źródło:
    Polish Journal of Veterinary Sciences; 2022, 25, 3; 455-462
    1505-1773
    Pojawia się w:
    Polish Journal of Veterinary Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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