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    Wyświetlanie 1-5 z 5
    Tytuł:
    Complex analysis of genes involved in the inflammatory response: interleukin-1-induced differential transcriptome of cultured human hepatoma HepG2 cells.
    Autorzy:
    Koj, Aleksander
    Jura, Jolanta
    Powiązania:
    https://bibliotekanauki.pl/articles/1043427.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    proteome
    transcriptome
    microarray
    hepatoma cells
    gene expression
    inflammatory reaction
    acute phase response
    differential display
    Opis:
    The systemic inflammatory reaction (acute phase response) is induced by many noxious stimuli but in all cases the inflammatory cytokines, such as interleukin-1-beta (IL-1β) and interleukin-6 (IL-6), are involved. Liver cell response to inflammation manifested by a characteristic change in the profile of synthesized plasma proteins (acute phase proteins) has been extensively studied. Here we describe a model system of cultured human hepatoma HepG2 cells stimulated with IL-1β to evaluate the transcriptome induced by this cytokine during 24 h of treatment. By using differential display analysis we found IL-1β-induced upregulation of several genes coding for cellular trafficking/motor proteins, proteins participating in the translation machinery or involved in posttranscription/posttranslation modifications, proteases, proteins involved in cellular metabolism, activity modulators, proteins of the cell cycle machinery and also some new proteins so far functionally not classified.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 3; 573-582
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Deciphering the soybean molecular stress response via high-throughput approaches
    Autorzy:
    Tyczewska, Agata
    Gracz, Joanna
    Kuczyński, Jakub
    Twardowski, Tomasz
    Powiązania:
    https://bibliotekanauki.pl/articles/1038715.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    soybean
    transcriptome
    miRNA
    proteome
    stress conditions
    Opis:
    As a result of thousands of years of agriculture, humans had created many crop varieties that became the basis of our daily diet, animal feed and also carry industrial application. Soybean is one of the most important crops worldwide and because of its high economic value the demand for soybean products is constantly growing. In Europe, due to unfavorable climate conditions, soybean cultivation is restricted and we are forced to rely on imported plant material. The development of agriculture requires continuous improvements in quality and yield of crop varieties under changing or adverse conditions, namely stresses. To achieve this goal we need to recognize and understand the molecular dependencies underlying plant stress responses. With the advent of new technologies in studies of plant transcriptomes and proteomes, now we have the tools necessary for fast and precise elucidation of desirable crop traits. Here, we present an overview of high-throughput techniques used to analyze soybean responses to different abiotic (drought, flooding, cold stress, salinity, phosphate deficiency) and biotic (infections by F. oxysporum, cyst nematode, SMV) stress conditions at the level of the transcriptome (mRNAs and miRNAs) and the proteome.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 631-643
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Potential protein activity modifications of amino acid variants in the human transcriptome
    Autorzy:
    Zyla, Joanna
    Bulman, Robert
    Badie, Christophe
    Bouffler, Simon
    Powiązania:
    https://bibliotekanauki.pl/articles/1039132.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    RNA editing
    amino acid variants
    Opis:
    Background: The occurrence of widespread RNA and DNA sequence differences in the human transcriptome was reported in 2011. Similar findings were described in a second independent publication on personal omics profiling investigating the occurrence of dynamic molecular and related medical phenotypes. The suggestion that the RNA sequence variation was likely to affect disease susceptibility prompted us to investigate with a range of algorithms the amino acid variants reported to be present in the identified peptides to determine if they might be disease-causing. Results: The predictive qualities of the different algorithms were first evaluated by using nonsynonymous single-base nucleotide polymorphism (nsSNP) datasets, using independently established data on amino acid variants in several proteins as well as data obtained by mutational mapping and modelling of binding sites in the human serotonin transporter protein (hSERT). Validation of the used predictive algorithms was at a 75% level. Using the same algorithms, we found that widespread RNA and DNA sequence differences were predicted to impair the function of the peptides in over 57% of cases. Conclusions: Our findings suggest that a proportion of edited RNAs which serve as templates for protein synthesis is likely to modify protein function, possibly as an adaptive survival mechanism in response to environmental modifications.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 1; 57-61
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    RNA-Seq-based analysis of differential gene expression associated with hepatitis C virus infection in a cell culture
    Autorzy:
    Hojka-Osinska, Anna
    Budzko, Lucyna
    Zmienko, Agnieszka
    Rybarczyk, Agnieszka
    Maillard, Patrick
    Budkowska, Agata
    Figlerowicz, Marek
    Jackowiak, Paulina
    Powiązania:
    https://bibliotekanauki.pl/articles/1038741.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    RNA-Seq
    HCV
    transcriptome
    Opis:
    Hepatitis C virus (HCV) infection is one of the major causes of chronic liver diseases. Unfortunately, the mechanisms of HCV infection-induced liver injury and host-virus interactions are still not well recognized. To better understand these processes we determined the changes in the host gene expression that occur during HCV infection of Huh-7.5 cells. As a result, we identified genes that may contribute to the immune and metabolic cellular responses to infection. Pathway enrichment analysis indicated that HCV induced an increased expression of genes involved in mitogen-activated protein kinases signaling, adipocytokine signaling, cell cycle and nitrogen metabolism. In addition, the enrichment analyses of processes and molecular functions revealed that the up-regulated genes were mainly implicated in the negative regulation of phosphorylation. Construction of the pathway-gene-process network enabled exploration of a much more complex landscape of molecular interactions. Consequently, several essential processes altered by HCV infection were identified: negative regulation of cell cycle, response to endoplasmic reticulum stress, response to reactive oxygen species, toll-like receptor signaling and pattern recognition receptor signaling. The analyses of genes whose expression was decreased upon HCV infection showed that the latter were engaged in the metabolism of lipids and amino acids. Moreover, we observed disturbance in the cellular antiviral defense. Altogether, our results demonstrated that HCV infection elicits host response that includes a very wide range of cellular mechanisms. Our findings significantly broaden the understanding of complex processes that accompany HCV infection. Consequently, they may be used for developing new host-oriented therapeutic strategies.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 789-798
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods
    Autorzy:
    Schmidt, Marcin
    Handschuh, Luiza
    Zyprych, Joanna
    Szabelska, Alicja
    Olejnik-Schmidt, Agnieszka
    Siatkowski, Idzi
    Figlerowicz, Marek
    Powiązania:
    https://bibliotekanauki.pl/articles/1039855.pdf
    Data publikacji:
    2011
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    microarray
    data normalization
    enterocyte
    transcriptome analysis
    probiotic
    adhesion
    gene expression profiling
    Opis:
    Two-color DNA microarrays are commonly used for the analysis of global gene expression. They provide information on relative abundance of thousands of mRNAs. However, the generated data need to be normalized to minimize systematic variations so that biologically significant differences can be more easily identified. A large number of normalization procedures have been proposed and many softwares for microarray data analysis are available. Here, we have applied two normalization methods (median and loess) from two packages of microarray data analysis softwares. They were examined using a sample data set. We found that the number of genes identified as differentially expressed varied significantly depending on the method applied. The obtained results, i.e. lists of differentially expressed genes, were consistent only when we used median normalization methods. Loess normalization implemented in the two software packages provided less coherent and for some probes even contradictory results. In general, our results provide an additional piece of evidence that the normalization method can profoundly influence final results of DNA microarray-based analysis. The impact of the normalization method depends greatly on the algorithm employed. Consequently, the normalization procedure must be carefully considered and optimized for each individual data set.
    Źródło:
    Acta Biochimica Polonica; 2011, 58, 4; 573-580
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-5 z 5

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