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Wyświetlanie 1-15 z 33
Tytuł:
Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer - the DNA microarray assay
Autorzy:
Stojcev, Zoran
Banasiewicz, Tomasz
Kaszuba, Michał
Sikorski, Adam
Szczepkowski, Marek
Bobkiewicz, Adam
Paszkowski, Jacek
Krokowicz, Łukasz
Biczysko, Maciej
Szmeja, Jacek
Jurkowska, Monika
Majewski, Przemysław
Mackiewicz, Andrzej
Lamperska, Katarzyna
Drews, Michał
Wojciechowicz, Jacek
Powiązania:
https://bibliotekanauki.pl/articles/1039574.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
HNPCC
DNA microarray
colon cancer
Opis:
Detection of mutations in families with a hereditary predisposition to colon cancer gives an opportunity to precisely define the high-risk group. 36 patients operated on for colon cancer, with familiar prevalence of this malignancy, were investigated using the DNA microarrays method with the potential detection of 170 mutations in MLH1, MSH2, MSH6, CHEK2, and NOD2 genes. In microarrays analysis of DNA in 9 patients (25% of the investigated group), 6 different mutations were found. The effectiveness of genetic screening using the microarray method is comparable to the effectiveness of other, much more expensive and time-consuming methods.
Źródło:
Acta Biochimica Polonica; 2013, 60, 2; 195-198
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
DNA microarrays, a novel approach in studies of chromatin structure.
Autorzy:
Widłak, Piotr
Powiązania:
https://bibliotekanauki.pl/articles/1043314.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
chromatin
genomics
epigenomics
DNA microarray
nucleosomes
Opis:
The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes - for the new field termed functional genomics. Gene expression profiling - the primary application of DNA microarrays technology - generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.
Źródło:
Acta Biochimica Polonica; 2004, 51, 1; 1-8
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The methods of normalization used in the analysis of two-color microarrays
Metody normalizacji w analizie dwukolorowych mikromacierzy
Autorzy:
Siatkowski, I.
Zyprych, J.
Handschuh, L.
Figlerowicz, M.
Powiązania:
https://bibliotekanauki.pl/articles/9613.pdf
Data publikacji:
2009
Wydawca:
Uniwersytet Przyrodniczy w Lublinie. Katedra Zastosowań Matematyki i Informatyki
Tematy:
normalization method
analysis
microarray analysis
bioconductor
Źródło:
Colloquium Biometricum; 2009, 39
1896-7701
Pojawia się w:
Colloquium Biometricum
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Transcriptional pattern of TGF-beta1 inhibitory effect on mouse C2C12 myoblasts differentiation
Autorzy:
Wicik, Z.
Sadkowski, T.
Jank, M.
Motyl, T.
Powiązania:
https://bibliotekanauki.pl/articles/30377.pdf
Data publikacji:
2010
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
transforming growth factor-beta 1
myogenesis
microarray
DNA microarray
differentiation
myoblast
mouse
mice
muscle cell
myosin heavy chain
Opis:
The aim of the present study was to define the effect of TGF-β1 on C2C12 myoblasts myogenesis. TGF-β1 together with its receptor is a negative auto-paracrine regulator of myogenesis, which influences the proliferation, differentiation, and functions of muscle cells. TGF-β1 exerts highly significant inhibitory effect on differentiation of C2C12 mouse myoblasts manifested by the impairment of cell fusion and very low expression of myosin heavy chain. The study of differentiating C2C12 mouse myoblasts treated with TGF-β1 revealed 502 genes (436 down-regulated and 66 up-regulated) with statistically different expression. TGF-β1-regulated genes were identified to be involved in 29 biological processes, 29 molecular functions groups and 59 pathways. The strongest inhibiting effect of TGF-β1 was observed in the cadherin and Wnt pathways. The key-genes that could play the role of TGF-β1 targets during myoblasts differentiation was identified such as: Max, Creb1, Ccna2, Bax, MdfI, Tef, Tubg1, Cxcl5, Rho, Calca and Lgals4.
Źródło:
Polish Journal of Veterinary Sciences; 2010, 13, 4
1505-1773
Pojawia się w:
Polish Journal of Veterinary Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
How the RNA isolation method can affect microRNA microarray results
Autorzy:
Podolska, Agnieszka
Kaczkowski, Bogumil
Litman, Thomas
Fredholm, Merete
Cirera, Susanna
Powiązania:
https://bibliotekanauki.pl/articles/1039846.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
microarray
microRNA isolation method
microRNA
small RNA fraction
pig
Opis:
The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.
Źródło:
Acta Biochimica Polonica; 2011, 58, 4; 535-540
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Microarray Inspector: tissue cross contamination detection tool for microarray data
Autorzy:
Stępniak, Piotr
Maycock, Matthew
Wojdan, Konrad
Markowska, Monika
Perun, Serhiy
Srivastava, Aashish
Wyrwicz, Lucjan
Świrski, Konrad
Powiązania:
https://bibliotekanauki.pl/articles/1039460.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
microarray
transcription profiling
contamination analysis
adipose tissue
cancer
data quality
Opis:
Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.
Źródło:
Acta Biochimica Polonica; 2013, 60, 4; 647-655
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Pathogenesis of middle ear acquired cholesteatoma in the light of the research using high throughput, “omics”, technologies of molecular biology
Autorzy:
Makuszewska, Maria
Bartoszewicz, Robert
Niemczyk, Kazimierz
Powiązania:
https://bibliotekanauki.pl/articles/1399639.pdf
Data publikacji:
2019
Wydawca:
Index Copernicus International
Tematy:
aquired cholesteatoma
gene expression
microarray
molecular biology
pathogenesis
proteomic analysis
Opis:
Cholesteatoma is described as cystic lesion consisting of keratinizing squamous cell epithelium, filed with keratin debris, surrounded by inflammatory fibrous tissue, gradually expanding in the middle ear and causing destruction of neighboring bones. This paper presents brief review of existing hypotheses explaining its etiology in the light of the researches using high throughput, “omics”, technologies of molecular biology. Classic theories of pathogenesis of acquired cholesteatoma as: immigration, squamous metaplasia, basal cell hyperplasia or invagination theory have not been able to explain fully all pathological processes observed in cholesteatoma tissue. This also concerns the newer concepts that cholesteatoma is a result of mucosal traction generated by interaction of migrating opposing surfaces, a natural attempt by the body to cure the underlying inflammation in the cavity or chronic wound healing process triggered by micro defects in the basement membrane of the epithelium in the retraction pocket. Introduction of high-throughput, “omics”, technologies of molecular biology to the studies under cholesteatoma pathogenesis allowed identification of cholesteatoma-related gene expression signatures using full-genome microarrays as well as proteomic analysis of cholesteatoma. Those studies confirmed known pathological processes observed in cholesteatoma tissue such as: high proliferative activity, decreased signal transduction, active immunological response, alterations in the extracellular matrix, increased expression of proinflammatory cytokines, neovascularization and may others. This technique allows precise and complete insight into molecular mechanisms in those processes. However, it is still unknown what is the cause that trigger epithelial hyperplasia, inhibited migration and inflammatory response in the preexisting retraction pocket.
Źródło:
Polski Przegląd Otorynolaryngologiczny; 2019, 8, 3; 14-19
2084-5308
2300-7338
Pojawia się w:
Polski Przegląd Otorynolaryngologiczny
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Characterization of Biofilms From Selected Synthetic Materials Used in Water Distribution System
Autorzy:
Biedroń, I.
Traczewska, T.
Konieczny, T.
Płaza, G.
Powiązania:
https://bibliotekanauki.pl/articles/952367.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Inżynierii Ekologicznej
Tematy:
biofilm
metabolic profile
drinking water
bacteria consortia
phenotypic microarray
PM
Opis:
Materials like polyvinyl chloride (PVC), polypropylene (PP), ultra high molecular weight polyethylene (UHMW-PE) are used for the construction of drinking water supply systems. It was found that regardless of the type of material the distribution network is built of, microorganisms formed biofilms on every available surface. The pipes material plays a key role in terms of biofilm formation. Important factors are the surface roughness, adhesives, plasticizers, stabilizers, which can be a source of nutrients for bacteria. The metabolic activity of microorganisms on polymer materials, induces migration of compounds from the material into water. The aim of this study was to present the differences in the structure and the metabolic profile of biofilm formed on the technical materials.
Źródło:
Journal of Ecological Engineering; 2017, 18, 1; 284-293
2299-8993
Pojawia się w:
Journal of Ecological Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of epoxy functional silanes in the preparation of DNA microarrays
Autorzy:
Frydrych-Tomczak, E.
Uszczynska, B.
Ratajczak, T.
Markiewicz, W.T.
Figlerowicz, M.
Nowicki, M.
Maciejewski, H.
Chmielewski, M.K.
Powiązania:
https://bibliotekanauki.pl/articles/80900.pdf
Data publikacji:
2014
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA microarray
gene expression
organofunctional silane
oligonucleotide
atomic force microscopy
goniometer
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2014, 95, 1
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of genes involved in response to doxorubicin and a GD2 ganglioside-specific 14G2a monoclonal antibody in IMR-32 human neuroblastoma cells
Autorzy:
Horwacik, Irena
Durbas, Małgorzata
Boratyn, Elżbieta
Sawicka, Anna
Węgrzyn, Paulina
Krzanik, Sylwia
Górka, Anna
Drożniak, Joanna
Augustyniak, Ewa
Kowalczyk, Aleksandra
Rokita, Hanna
Powiązania:
https://bibliotekanauki.pl/articles/1038977.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
doxorubicin
GD2 ganglioside
microarray
14G2a
neuroblastoma
mimitin
Opis:
Neuroblastoma is the most common extra-cranial solid tumor of childhood and it is characterized by the presence of a glycosphingolipid, GD2 ganglioside. Monoclonal antibodies targeting the antigen are currently tested in clinical trials. Additionally, several research groups reported results revealing that ganglioside-specific antibodies can affect cellular signaling and cause direct cytotoxicity against tumor cells. To shed more light on gene expression signatures of tumor cells, we used microarrays to analyze changes of transcriptome in IMR-32 human neuroblastoma cell cultures treated with doxorubicin (DOX) or a mouse monoclonal antibody binding to GD2 ganglioside 14G2a (mAb) for 24 h. The obtained results highlight that disparate cellular pathways are regulated by doxorubicin and 14G2a. Next, we used RT-PCR to verify mRNA levels of selected DOX-responsive genes such as RPS27L, PPM1D, SESN1, CDKN1A, TNFSF10B, and 14G2a-responsive genes such as SVIL, JUN, RASSF6, TLX2, ID1. Then, we applied western blot and analyzed levels of RPS27L, PPM1D, sestrin 1 proteins after DOX-treatment. Additionally, we aimed to measure effects of doxorubicin and topotecan (TPT) and 14G2a on expression of a novel human NDUFAF2 gene encoding for mimitin protein (MYC-induced mitochondrial protein) and correlate it with expression of the MYCN gene. We showed that expression of both genes was concomitantly decreased in the 14G2a-treated IMR-32 cells after 24 h and 48 h. Our results extend knowledge on gene expression profiles after application of DOX and 14G2a in our model and reveal promising candidates for further research aimed at finding novel anti-neuroblastoma targets.
Źródło:
Acta Biochimica Polonica; 2015, 62, 3; 423-433
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Chemical regulation of photorespiratory hydrogen peroxide-induced cell death in catalase deficient (cat2) Arabidopsis plants
Autorzy:
Kerchev, P.
Denecker, J.
Muhlenbock, P.
Van Breusegem, F.
Powiązania:
https://bibliotekanauki.pl/articles/80515.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
photorespiration
hydrogen peroxide
cell death
catalase
Arabidopsis
molecular structure
microarray
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:
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:
Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance*
Autorzy:
Adamiec, Małgorzata
Drath, Maria
Jackowski, Grzegorz
Powiązania:
https://bibliotekanauki.pl/articles/1040834.pdf
Data publikacji:
2008
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
hierarchical clustering
plastoquinone
elevated irradiance
gene expression
transcription factors
DNA microarray
Opis:
DNA microarray technology was applied to gain insight into the role of the redox state of PQ pool as a retrograde factor mediating differential expression of Arabidopsis nuclear genes during the acclimation to changing irradiance. DNA microarray chips containing probes corresponding to 24 000 Arabidopsis nuclear genes were screened with cRNA samples prepared from leaves of plants exposed for 5 h to low irradiance (control) vs. medium, high and excessive irradiances (MI, HI and EI, respectively). Six hundred and sixty three genes were differentially expressed as a result of an exposure to at least one elevated irradiance. Among 663 differentially expressed genes a total of 50 were reverted by DCMU - 24 ones modulated at medium irradiance, 32 ones modulated at high irradiance and a single one modulated at excessive irradiance. We postulate that their expression is regulated by redox state of plastoquinone (PQ) pool. Thus the PQ-mediated redox regulation of expression of Arabidopsis nuclear genes is probably limited to the irradiance window representing non-stressing conditions. We found that the promoter regions of the PQ-regulated genes contained conserved elements, suggesting transcriptional control by a shared set of trans-acting factors which participate in signal transduction from the redox state of the PQ pool.
Źródło:
Acta Biochimica Polonica; 2008, 55, 1; 161-174
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Elevated CO2 mitigates the impact of a combination of heat wave and drought in Arabidopsis thaliana
Autorzy:
Zinta, G.
AbdElgawad, H.
Domagalska, M.
Vergauwen, L.
Nijs, I.
Beemster, G.
Asard, H.
Janssens, I.
Powiązania:
https://bibliotekanauki.pl/articles/80475.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
carbon dioxide
heat wave
drought stress
Arabidopsis thaliana
photosynthesis
microarray analysis
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:
Virulence and antibiotic resistance of Escherichia coli isolated from rooks
Autorzy:
Kmet, V.
Drugdova, Z.
Kmetova, M.
Stanko, M.
Powiązania:
https://bibliotekanauki.pl/articles/51141.pdf
Data publikacji:
2013
Wydawca:
Instytut Medycyny Wsi
Tematy:
virulence
antibiotic resistance
Escherichia coli
isolation
rook
polymerase chain reaction
DNA microarray
Opis:
With regard to antibiotic resistance studies in various model animals in the urban environment, the presented study focused on the rook, many behavioural and ecological aspects of which are important from an epidemiological point of view. A total of 130 Escherichia coli strains isolated from rook faeces during a two-year period (2011–2012) were investigated for antibiotic resistance and virulence. Resistance to ampicillin (60%) and streptomycin (40%) were the most frequent, followed by resistance to fluoroquinolones (ciprofloxacin-22% and enrofloxacin-24%), tetracycline (18%), cotrimoxazol (17%) and florfenicol (14%). Ceftiofur resistance occured in 10.7 % of strains and cefquinom resistance in 1.5 % of strains. Twenty-five E.coli strains with a higher level of MICs of cephalosporins (over 2mg/L of ceftazidime and ceftriaxon) and fluoroquinolones were selected for detection of betalactamase genes (CTX-M, CMY), plasmid-mediated quinolone resistance qnrS, integrase 1, and for APEC (avian pathogenic E.coli) virulence factors (iutA, cvaC, iss, tsh, ibeA, papC, kpsII). Genes of CTX-M1, CMY-2, integrase 1, papC, cvaC, iutA were detected in one strain of E.coli, and qnrS, integrase 1, iss, cvaC, tsh were detected in another E.coli. DNA microarray revealed the absence of verotoxin and enterotoxin genes and pathogenicity islands. The results show that rooks can serve as a reservoir of antibiotic-resistant E. coli with avian pathogenic virulence factors for the human population, and potentially transmit such E.coli over long distances.
Źródło:
Annals of Agricultural and Environmental Medicine; 2013, 20, 2
1232-1966
Pojawia się w:
Annals of Agricultural and Environmental Medicine
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 33

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