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Wyszukujesz frazę "transcriptome" wg kryterium: Wszystkie pola

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    Wyświetlanie 1-22 z 22
    Tytuł:
    Consequences of mitochondrial translation perturbation for the whole cell transcriptome
    Autorzy:
    Adamowicz, A.
    Kwasniak, M.
    Janska, H.
    Powiązania:
    https://bibliotekanauki.pl/articles/81252.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    gene encoding
    mitochondrial protein
    whole cell
    transcriptome
    abiotic stress
    biotic stress
    chromosome complex
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptome sequencing: next generation approach to RNA functional analysis
    Autorzy:
    Zmienko, A.
    Jackowiak, P.
    Figlerowicz, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/81137.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    RNA molecule
    functional analysis
    RNA sequence
    transcriptome
    isoform
    DNA microarray
    qualitative change
    quantitative change
    gene expression
    hybridization
    oligonucleotide probe
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data
    Autorzy:
    Farhadian, M.
    Rafat, S.A.
    Hasanpur, K.
    Ebrahimie, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/80629.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    transcriptome
    lactation
    milk production
    microarray
    expression analysis
    cDNA synthesis
    RNA sequence
    gene expression
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2018, 99, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    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:
    Transcriptome and proteome changes accompanying increased vigor of osmoprimed rape (Brassica napus L.) seeds
    Autorzy:
    Kubala, S.
    Lechowska, K.
    Wojtyla, L.
    Kosmala, A.
    Quinet, M.
    Lutts, S.
    Garnczarska, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/81285.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    osmopriming
    seed germination
    stress tolerance
    Brassica napus
    rapeseed
    transcriptome
    proteomics
    gene encoding
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    De novo sequencing and comparative transcriptome analysis of white petals and red labella in Phalaenopsis for discovery of genes related to flower color and floral differentiation
    Autorzy:
    Yang, Y.
    Wang, J.
    Ma, Z.
    Sun, G.
    Zhang, C.
    Powiązania:
    https://bibliotekanauki.pl/articles/58306.pdf
    Data publikacji:
    2014
    Wydawca:
    Polskie Towarzystwo Botaniczne
    Tematy:
    sequencing
    RNA sequence
    transcriptome
    Phalaenopsis
    gene
    flower
    colour
    floral differentiation
    diversity
    Opis:
    Phalaenopsis is one of the world’s most popular and important epiphytic monopodial orchids. The extraordinary floral diversity of Phalaenopsis is a reflection of its evolutionary success. As a consequence of this diversity, and of the complexity of flower color development in Phalaenopsis, this species is a valuable research material for developmental biology studies. Nevertheless, research on the molecular mechanisms underlying flower color and floral organ formation in Phalaenopsis is still in the early phases. In this study, we generated large amounts of data from Phalaenopsis flowers by combining Illumina sequencing with differentially expressed gene (DEG) analysis. We obtained 37 723 and 34 020 unigenes from petals and labella, respectively. A total of 2736 DEGs were identified, and the functions of many DEGs were annotated by BLAST-searching against several public databases. We mapped 837 up-regulated DEGs (432 from petals and 405 from labella) to 102 Kyoto Encyclopedia of Genes and Genomes pathways. Almost all pathways were represented in both petals (102 pathways) and labella (99 pathways). DEGs involved in energy metabolism were significantly differentially distributed between labella and petals, and various DEGs related to flower color and floral differentiation were found in the two organs. Interestingly, we also identified genes encoding several key enzymes involved in carotenoid synthesis. These genes were differentially expressed between petals and labella, suggesting that carotenoids may influence Phalaenopsis flower color. We thus conclude that a combination of anthocyanins and/or carotenoids determine flower color formation in Phalaenopsis. These results broaden our understanding of the mechanisms controlling flower color and floral organ differentiation in Phalaenopsis and other orchids.
    Źródło:
    Acta Societatis Botanicorum Poloniae; 2014, 83, 3
    0001-6977
    2083-9480
    Pojawia się w:
    Acta Societatis Botanicorum Poloniae
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Revealing the core transcriptome modulating plant growth phase in Arabidopsis thalianaby RNA sequencingand coexpression analysis of the FHY3 FAR1 mutant
    Autorzy:
    Wang, W.
    Zhao, G.
    Wu, S.
    Hua, W.
    Zhang, T.
    Ruan, R.
    Cheng, Y.
    Powiązania:
    https://bibliotekanauki.pl/articles/2130692.pdf
    Data publikacji:
    2020
    Wydawca:
    Polskie Towarzystwo Botaniczne
    Tematy:
    weekly transcriptome analysis
    plant development
    different expression genes
    (DEGs)
    immune response
    Opis:
    Plants must continually calibrate their growth in response to the environment throughout their whole life cycle. Revealing the regularity of plant early growth and development is of great significance to plant genetic modification. It was previously demonstrated that loss of two key light signaling transcription factors, FHY3 and FAR1, can cause a stunted stature in the plant adult stage, and numerous defense response genes can be continuously activated. In this study, we performed a time-course transcriptome analysis of the early 4 weeks of leaf samples from wild plants and their fhy3 and far1 transcription factors. By comparative transcriptome analysis, we found that during the early 4 weeks of plant growth, plants primarily promoted morphogenesis by organizing their microtubules in the second week. In the third week, plants began to trigger large- scale defense responses to resist various external stresses. In the fourth week, increased photosynthetic efficiency promoted rapid biomass accumulation. Weighted gene coexpression network analysis of FHY3 and FAR1 revealed that the two light signaling transcription factors may be originally involved in the regulation of genes during embryonic development, and in the later growth stage, they might regulate gene expression of some defense-related genes to balance plant growth and immunity. Remarkably, our yeast two-hybrid and bimolecular fluorescence complementation experiments showed that FAR1 interacts with the immune signaling factor EDS1. Taken together, this study demonstrates the major biological processes occurring during the early 4 weeks of plant growth. The light signaling transcription factors, FHY3 and FAR1, may integrate light signals with immune signals to widely regulate plant growth by directly interacting with EDS1.
    Źródło:
    Acta Societatis Botanicorum Poloniae; 2020, 89, 2
    0001-6977
    2083-9480
    Pojawia się w:
    Acta Societatis Botanicorum Poloniae
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptome analysis of enzyme activities regulating ROS metabolism in olive (Olea europaea L.) reproductive tissues
    Autorzy:
    Zafra, A.
    Carmona, R.
    Jimenez-Quesada, M.
    Traverso, J.
    Castro, A.
    Rodriguez-Garcia, M.
    Bautista, R.
    Claros, M.
    Alche, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/80459.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    transcriptome
    enzyme activity
    reactive oxygen species
    metabolism
    olive
    Olea europaea
    reproductive tissue
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    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:
    Transcriptomic analysis of different tissues in Korean arborvitae
    Autorzy:
    Mu, H.
    Gao, Y.
    Cheng, F.
    Lin, L.
    Wang, G.
    Xia, F.
    Powiązania:
    https://bibliotekanauki.pl/articles/2077762.pdf
    Data publikacji:
    2019
    Wydawca:
    Polska Akademia Nauk. Instytut Dendrologii PAN
    Tematy:
    Thuja koraiensis
    transcriptome
    tissue specific
    Opis:
    Korean arborvitae (Thuja koraiensis) is an evergreen shrub or small tree native to Korea and the extreme Changbai Mountain of China threatened by habitat loss. Due to the limited genomic sources of Ko- rean arborvitae, it is important to explore transcriptome to understand this economically important plant. We used RNA-seq technology to characterize the transcriptome of root, stem and leaf in Korean arborvitae, respectively. Based on the bioinformatics analysis of assembled transcriptome data, transcriptional path- ways and differentially expressed genes (DEGs) were identified. There were 152.26 million reads generated, and 446,568 unigenes with a mean size of 423.51 nt obtained via de novo assembly. Of these, 204,091 unigenes (45.70%) were further annotated by comparison to public protein databases. A total of 63,495 unigenes (14.22%) were associated into 130 pathways by searching against the KEGG database. DEGs analysis identified 11,890, 5,900 and 10,136 DEGs from the comparison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. Besides, photosynthesis, plant hormone signal transduction and metabolism and biosynthesis of sugar and amino acids were changed in different tissues. We obtained 446,568 unigenes in Korean arborvitae and 11,890, 5,900 and 10,136 DEGs from the compar- ison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. These results will aid in understanding and carrying out future studies on the molecular basis of Korean arborvitae and contribute to future artificial production and applications.
    Źródło:
    Dendrobiology; 2019, 81; 31-39
    1641-1307
    Pojawia się w:
    Dendrobiology
    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:
    Analysis of the transcriptome of Potentilla sericea under cadmium stress conditions
    Autorzy:
    Wu, J.
    Fan, W.
    Gao, P.
    Yang, Q.
    Zhang, J.
    Wang, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/2130579.pdf
    Data publikacji:
    2021
    Wydawca:
    Polskie Towarzystwo Botaniczne
    Tematy:
    glutathione metabolism
    sulfur metabolism
    Opis:
    Cadmium (Cd) stress significantly affects plant growth and development. Potentilla sericea is typically grown in gardens or as ground cover. In this study, the Cd response of P. sericea was analyzed based on physiological examinations and transcriptome analyses that uncovered the gene expression changes in P. sericea roots induced by a 7-day treatment with 90 μmol/L Cd2+. A total of 53,225 unigenes were identified, including 11,684 differentially expressed genes (DEGs; 8,083 upregulated and 3,601 downregulated). Additionally, 44 gene ontology terms and 127 Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched among these DEGs. Genes related to glutathione metabolism, plant hormone signal transduction, peroxisome processes, sulfur metabolism, and flavonoid biosynthesis pathways were confirmed as relevant to the Cd response of P. sericea. The molecular biology-related data described here may be useful for the future breeding of transgenic P. sericea plants with increased resistance to heavy metal stresses.
    Źródło:
    Acta Societatis Botanicorum Poloniae; 2020, 89, 4
    0001-6977
    2083-9480
    Pojawia się w:
    Acta Societatis Botanicorum Poloniae
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    ROSMETER: a bioinformatic tool for the identification of reactive oxygen species (ROS) transcriptomic imprints
    Autorzy:
    Rosenwasser, S.
    Sela, N.
    Fluhr, R.
    Friedman, H.
    Powiązania:
    https://bibliotekanauki.pl/articles/80882.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    reactive oxygen species
    subcellular localization
    leaf
    transcriptome
    abiotic stress
    biotic stress
    molecular mechanism
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    RNA-seq reveals differentially expressed genes in cucumber MSC lines possessing mitochondrial DNA rearrangements
    Autorzy:
    Mroz, T.
    Pryszcz, L.
    Skarzynska, A.
    Kielkowska, A.
    Havey, M.
    Bartoszewski, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/80502.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    cucumber
    gene expression
    mitochondrial DNA
    transcriptome
    wild-type line
    oxidoreductase
    rearrangement
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Gene expression pattern in canine mammary osteosarcoma
    Autorzy:
    Pawlowski, K.
    Majewska, A.
    Szyszko, K.
    Dolka, I.
    Motyl, T.
    Krol, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/32248.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    bone tumour
    canine mammary osteosarcoma
    gene expression
    mammary osteosarcoma
    microarray
    osteosarcoma
    transcriptome
    tumour
    sarcoma
    proliferation
    aggressive tumour
    gene list
    Opis:
    Canine mammary sarcomas are usually very aggressive and easily metastasize. Unfortunately the biology of this type of tumor is not well known because they are a very rare type of tumors. The aim of this study was to find differences in gene expression patterns in canine mammary osteosarcomas (malignant) versus osteomas (benign) using DNA microarrays. Our microarray experiment showed that 11 genes were up-regulated in osteosarcoma in comparison to osteoma whereas 36 genes were down-regulated. Among the up-regulated genes were: PDK1, EXT1, and EIF4H which are involved in AKT/PI3K and GLI/Hedgehog pathways. These genes play an important role in cell biology (cancer cell proliferation) and may be essential in osteosarcoma formation and development. Analyzing the down-regulated genes, the most interesting seemed to be HSPB8 and SEPP1. HSPB8 is a small heat shock protein that plays an important role in cell cycle regulation, apoptosis, and breast carcinogenesis. Also SEPP1 may play a role in carcinogenesis, as its down-regulation may induce oxidative stress possibly resulting in carcinogenesis. The preliminary results of the present study indicate that the up-regulation of three genes EXT1, EIF4H, and PDK1 may play an essential role in osteosarcoma formation, development and proliferation. In our opinion the cross-talk between GLI/Hedgehog and PI3K/AKT pathways may be a key factor to increase tumor proliferation and malignancy.
    Źródło:
    Polish Journal of Veterinary Sciences; 2011, 14, 1
    1505-1773
    Pojawia się w:
    Polish Journal of Veterinary Sciences
    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
    Tytuł:
    Global transcriptome analysis reveals genes associated with seedling advance growth traits in a selfed family of Chinese fir (Cunninghamia lanceolata)
    Autorzy:
    Deng, H.
    Hu, D.
    Wei, R.
    Yan, S.
    Wang, R.
    Zheng, H.
    Powiązania:
    https://bibliotekanauki.pl/articles/2130183.pdf
    Data publikacji:
    2022
    Wydawca:
    Polska Akademia Nauk. Instytut Dendrologii PAN
    Tematy:
    Chinese fir
    selfing
    RNA-Seq
    growth trait
    hub gene
    Opis:
    Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a major timber conifer species in southern China. In this study, we aimed to capture the rarely advanced phenomenon for selfing in this species and illustrated the underlying molecular mechanism, especially the hub gene-regulated networks and pathways, by global transcriptome analysis assays (RNA-Seq). Self-pollination trials revealed a wide variation of selfing effects among parents. Parent cx569 produced a selfed family with the best growth performance at the seedling stage. The growth-based extremely advanced (AD) (n=3) and depressed (DE) variants (n=3; different types) were then subjected to comparative RNA-Seq. The transcriptome data revealed more than 5000 differentially expressed genes (DEGs) for each comparison group (AD versus DE). Weighted gene co-expression network analysis (WGCNA) further identified more than 80 important DEGs that were significantly associated with growth traits in each comparison group. A subsequent enrichment analysis showed that the identified DEGs belonged to six main types, including xylem metabolism-related, sugar and energy metabolism-related, plant hormone signal transduction-related, stress response-related, cytochrome-related, and transcription factor genes. Ten hub genes represented by the ERF071, MYB-relate 305, WRKY6, WRKY31, PER3, LAC4, CESA8, CESA9, GID1, and PR1 genes were co-identified between AD and DE variants. These genes exhibited rather different expression patterns between AD and DE variants, especially of the transcription factor ERF071 gene that presented a low transcript level in the AD seedlings with only 4.45% activity compared to DE's. While, the plant hormone signal transduction GID1 gene was significantly upregulated in AD by about 20-fold when compared to DE's, and fold change of the lignin biosynthesis-related PER3, CESA9 and LAC4 gene expression parallel reached to 10–15 times in an upregulation pattern in AD seedlings. The set of hub gene-linked interaction networks and pathways revealed in this study may be responsible for the rarely advanced phenomenon for selfing at the seedling stage in Chinese fir.
    Źródło:
    Dendrobiology; 2022, 87; 27-46
    1641-1307
    Pojawia się w:
    Dendrobiology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Differential transcriptomic analysis by RNA-seq of GSNO-responsive genes between Arabidopsis roots and leaves
    Autorzy:
    Begara-Morales, J.
    Sanchez-Calvo, B.
    Luque, F.
    Laterrier, M.
    Valderrama, R.
    Mata-Perez, C.
    Padilla, M.
    Carreras, A.
    Corpas, F.
    Barroso, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/81065.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    transcriptome
    RNA sequence
    S-nitrosoglutathione
    nitric oxide
    stress condition
    physiological condition
    gene expression
    root
    leaf
    Arabidopsis
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Expression patterns of molecular chaperone genes in Antarctic psychrophilic yeast, Glaciozyma antarctica PI12 in response to heat stress
    Autorzy:
    Yusof, Nur Athirah
    Wong, Clemente Michael Vui Ling
    Murad, Abdul Munir Abdul
    Abu Bakar, Farah Diba
    Mahadi, Nor Muhammad
    Rahman, Ahmad Yamin Abdul
    Zainuddin, Nursyafiqi
    Najimudin, Mohd Nazalan Mohd
    Powiązania:
    https://bibliotekanauki.pl/articles/2041852.pdf
    Data publikacji:
    2019
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Antarctic
    psychrophile
    molecular chaperone
    heat-stress
    transcriptome
    Źródło:
    Polish Polar Research; 2019, 40, 3; 273-292
    0138-0338
    2081-8262
    Pojawia się w:
    Polish Polar Research
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses
    Autorzy:
    Jazayeri, Seyed Mehdi
    Pooralinaghi, Mahtab
    Torres-Navarrete, Yenny
    Oviedo-Bayas, Byron
    Espinoza Guerra, Italo
    Herrera Jacome, Dario
    Quinaluisa Morán, César
    Salas Macias, Carlos
    Montes Escobar, Karime
    Ghafoor, Seyed Mohammad Hossein Ale Seyed
    Veiskarami, Gholamhasan
    Jandaghi, Pouria
    Villamar Torres, Ronald Oswaldo
    Powiązania:
    https://bibliotekanauki.pl/articles/16648150.pdf
    Data publikacji:
    2022
    Wydawca:
    Polska Akademia Nauk. Czasopisma i Monografie PAN
    Tematy:
    SSR
    model plant
    transcription factor
    RNA-Seq
    halophyte
    Opis:
    Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2022, 103, 4; 355-384
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Isolation of biosynthesis related transcripts of 2,3,5,4-tetrahydroxy stilbene-2-O-beta-D-glucoside from Fallopia multiflora by suppression subtractive hybridization
    Autorzy:
    Zhao, W.
    Sheng, S.
    Liu, Z.
    Lu, Di.
    Zhu, K.
    Li, X.
    Zhao, S.
    Yao, Y.
    Powiązania:
    https://bibliotekanauki.pl/articles/58239.pdf
    Data publikacji:
    2014
    Wydawca:
    Polskie Towarzystwo Botaniczne
    Tematy:
    isolation
    biosynthesis
    transcriptome
    2,3,5,4'-tetrahydroxy stilbene-2-O-beta-D-glucoside
    Fallopia multiflora
    hybridization
    gene expression
    medicinal plant
    Chinese herb
    Opis:
    2,3,5,4'-tetrahydroxy stilbene-2-O-ß-D-glucoside (THSG) exerts multiple pharmacodynamic actions, found in Fallopia multiflora, but the biosynthesis pathway of THSG is still unclear. To clear this ambiguity, we constructed suppression subtractive hybridization (SSH) libraries to screen the genes involved in THSG biosynthesis from two F. multiflora varieties, which vary significantly in THSG content. Twelve non-redundant differentially expressed sequence tags were obtained and the full lengths of 4 unreported fragments were amplified by rapid amplification of cDNA ends. We totally got 7 fulllength transcripts, and all of them were aligned to the transcriptome and digital gene expression tag profiling database of four F. multiflora tissues (root, stem and leaf from Deqing F. multiflora and another root from Chongqing F. multiflora; data unpublished) using local BLAST. The results showed that there was a significant, organ specific difference in the expression of fragments and full-length sequences. All the sequences were annotated by aligning to nucleotide and protein databases. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that THSG biosynthesis was correlated with multiple life activities.
    Źródło:
    Acta Societatis Botanicorum Poloniae; 2014, 83, 2
    0001-6977
    2083-9480
    Pojawia się w:
    Acta Societatis Botanicorum Poloniae
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-22 z 22

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