Wyniki wyszukiwania

1

DNA microarray gene expression profile of Mycobacterium tuberculosis when exposed to osthole

100%

Wei J., Guo N., Liang J., Yuan P., Shi Q., Tang X., Yu L.

Polish Journal of Microbiology

|

2013

|

tom 62

|

nr 1

Tuberculosis (TB), affecting one-third of the global population, kills an estimated two to three million people every year. The development of drug resistance is becoming a serious threat to any attempt to control this disease, which underscores the need for new agents targeting Mycobacterium tuberculosis (M. tuberculosis). Osthole (7-methoxy-8-isopentenoxycoumarin) is a coumarin derivative present in many medicinal plants. Previous studies have shown that osthole possesses antimycobacterial effects, however, the action mechanism of osthole is unclear. In the study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of M.tuberculosis H37Rv triggered by exposure to osthole. Analysis of the microarray data revealed that a total of 478 genes were differentially regulated by osthole. Of these, 241 genes were upregulated, and 237 genes were downregulated. Some of the important genes that were significantly regulated are related to different pathways such as fumarate reductase, class I peroxidase, cell wall, nitrate respiration, and protein synthesis. Real-time quantitative RT-PCR was performed for chosen genes to validate the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of M. tuberculosis when exposed to osthole.

2

On methods of collecting data from DNA microarrays

100%

Bocianowski J., Gallavotti A., Krajewski P., Pe E.

Colloquium Biometryczne

|

2002

|

tom 32

3

Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods

100%

Schmidt M. T., Handschuh L., Zyprych J., Szabelska A., Olejnik-Schmidt A. K., Siatkowski I., Figlerowicz M.

Acta Biochimica Polonica

|

2011

|

tom 58

|

nr 4

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.

4

Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik

Application of epoxy functional silanes in the preparation of DNA microarrays

100%

Frydrych-Tomczak E., Uszczynska B., Ratajczak T., Markiewicz W. T., Figlerowicz M., Nowicki M., Maciejewski H., Chmielewski M. K.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

|

2014

|

tom 95

|

nr 1

5

Virulence and antibiotic resistance of Escherichia coli isolated from rooks

100%

Kmet V., Drugdova Z., Kmetova M., Stanko M.

Annals of Agricultural and Environmental Medicine

|

2013

|

tom 20

|

nr 2

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.

6

Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance

100%

Adamiec M., Drath M., Jackowski G.

Acta Biochimica Polonica

|

2008

|

tom 55

|

nr 1

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 24000 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.

7

Transcriptional pattern of TGF-beta1 inhibitory effect on mouse C2C12 myoblasts differentiation

84%

Wicik Z., Sadkowski T., Jank M., Motyl T.

Polish Journal of Veterinary Sciences

|

2010

|

tom 13

|

nr 4

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.

8

Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer - the DNA microarray assay

84%

Stojcev Z., Banasiewicz T., Kaszuba M., Sikorski A., Szczepkowski M., Bobkiewicz A., Paszkowski J., Krokowicz L., Biczysko M., Szmeja J., Jurkowska M., Majewski P., Mackiewicz A., Lamperska K., Drews M., Wojciechowicz J.

Acta Biochimica Polonica

|

2013

|

tom 60

|

nr 2

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.

9

Comparison of cellular and tissue transcriptional profiles in canine mammary tumor

84%

Pawlowski K. M., Krol M., Majewska A., Badowska-Kozakiewicz A., Mol J. A., Malicka E., Motyl T.

Journal of Physiology and Pharmacology. Supplement

|

2009

|

tom 60

|

nr 1

85-94

Tumor-derived cell lines are widely used as in vitro cancer models. Cell lines historically served as the primary experimental model systems for exploration of tumor cell biology and pharmacology. However, their ability to accurately reflect the phenotype and genotype of the parental histology remains questionable, given the prevalence of documented cell line-specific cytogenetic changes. Sometimes cell line studies are interpreted in the context of artifacts introduced by selection and establishment of cell lines in vitro. This complication has led to difficulties in the extrapolation of biology observed in cell lines to tumor biology in vivo. The aim of our study was to compare gene expression profiles in canine mammary tumor tissue and cell cultures derived from those tumors using cDNA microarrays. Tumors of two different origins were used; chondrosarcoma and adenocarcinoma and their primary cell cultures. It has been found that cell culture gene expression profiles closely resembled those of their corresponding in vivo tumor. In adenocarcinoma and chondrosarcoma only 6.0% and 2.7% of genes respectively, have shown significant difference in expression. In the most cases the difference concerned up-regulation of gene expression in cell lines, particularly genes involved in: protein metabolism and modification, signal transduction and nucleotide, nucleoside and nucleic acid metabolism. These experiments revealed that transcriptome of our primary cell culture corresponds to transcriptome of its parental tumor tissue and for this reason cell culture represents the reliable in vitro model for oncogenomic and pharmacogenomic studies.

10

The reverse-direction method links mass experimental data to human diseases

84%

Ogura H., Atsumi T., Bando H., Sabharwal L., Yamada M., Jiang J.-J., Nakamura A., Arima Y., Kamimura D., Murakami M.

Archivum Immunologiae et Therapiae Experimentalis

|

2014

|

tom 62

|

nr 1

11

Transcriptomic 'portraits' of canine mammary cancer cell lines with various phenotypes

84%

Krol M., Pawlowski K. M., Skierski J., Turowski P., Majewska A., Polanska J., Ugorski M., Morty R. E., Motyl T.

Journal of Applied Genetics

|

2010

|

tom 51

|

nr 2

169-183

In light of the high incidence of mammary cancer in dogs and completion of the canine genome sequencing, the new possibilities of gene profiling by using DNA microarrays give hope to veterinary oncology. The cell lines isolated from mammary tumors are a valuable tool in developing and testing new pathway-specific cancer therapeutics. Differential cytometric analysis of 6 canine mammary cancer cell lines was performed. We divided cell lines into 3 groups based on their phenotype: 2 lines with high proliferative potential, 2 lines with high antiapoptotic potential, and 2 lines with high metastatic potential. DNA microarray analysis revealed common genes for cell lines of each group. We found that genes encoding the receptors for growth hormone and ghrelin are related to high proliferation rate, while ABR (active BCR-related) and TMD1 (TM2 domain containing 1) genes are related to a high antiapoptotic potential of the cancer cells. Metastatic properties of mammary cancer cells seem to be associated with elevated expression of PGP (P glycoprotein), SEMA3B (semaphorin 3B), and STIM1 (stromal interaction molecule 1).

12

Calculation of reliable transcript levels of annotated genes on the basis of multiple probe-sets in Affymetrix microarrays

84%

Jaksik R., Polanska J., Herok R., Rzeszowska-Wolny J.

Acta Biochimica Polonica

|

2009

|

tom 56

|

nr 2

271-277

Microarray methods have become a basic tool in studies of global gene expression and changes in transcript levels. Affymetrix microarrays from the HGU133 series contain multiple probe-sets complementary to the same gene (4742 genes are represented by more than one probe-set in a microarray HGU133A). Individual probe-sets annotated to the same gene often show different hybridization signals and even opposite trends, which may result from some of them matching transcripts of more than one gene and from the existence of different splice-variant transcripts. Existing methods that redefine probe-sets and develop custom probe-set definitions use mathematical tools such as Matlab or the R statistical environment with the Bioconductor package (Gentleman et al., 2004, Genome Biol. 5: 280) and thus are directed to researchers with a good knowledge of bioinformatics. We propose here a new approach based on the principle that a probe-set which hybridizes to more than one transcript can be recognized because it produces a signal significantly different from others assigned to the particular gene, allowing it to be detected as an outlier in the group and eliminated from subsequent analyses. A simple freeware application has been developed (available at http://www.bioinformatics.aei.polsl.pl) that detects and removes outlying probe-sets and calculates average signal values for individual genes using the latest annotation database provided by Affymetrix. We illustrate this procedure using microarray data from our experiments aiming to study changes of transcription profile induced by ionizing radiation in human cells.

13

DNA microarrays, a novel approach in studies of chromatin structure

84%

Widlak P.

Acta Biochimica Polonica

|

2004

|

tom 51

|

nr 1

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.

14

Gene expression profiling of lipoarabinomannan-treated mouse macrophage cultures infected with Mycobacterium bovis BCG

84%

Krzyzowska M., Malewski T., Hamasur B., Augustynowicz-Kopec E., Schollenberger A., Pawlowski A., Niemialtowski M.

Polish Journal of Microbiology

|

2008

|

tom 57

|

nr 2

The mannosylated lipoarabinomanan (ManLAM) from mycobacterial species possesses strong anti-apoptotic action. Here we examined the ability of ManLAM isolated from Mycobacterium tuberculosis H37Rv to alter expression profiles of apoptosis-related genes in mouse macrophages infected with Mycobacterium bovis BCG Danish strain. ManLAM suppressed BCG-induced apoptosis and activities of caspase -1, -3, -8 and 9. Mouse Apoptosis Gene Array showed that ManLAM significantly down-regulated pro-apoptotic and proinflammatory genes: caspase -1, -3, -7, -8 and -9, TNF-α/TNFSF2, Fas/TNFRSF6, Bax-α, as well as IL-12 p35 and iNOS simultaneously up-regulating anti-apoptotic genes such as Bcl-2 and Mcl-1. The effect of ManLAM was contrary to BCG-induced up-regulation of pro-apoptotic and pro-inflammatory genes and consistent with the functional data.

15

DNA microarrays - future in oncology research and therapy

67%

Krol M., Pawlowski K. M., Otrebska D., Motyl T.

Journal of Pre-Clinical and Clinical Research

|

2008

|

tom 02

|

nr 2

16

Transcriptome sequencing: next generation approach to RNA functional analysis

67%

Zmienko A., Jackowiak P., Figlerowicz M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

|

2011

|

tom 92

|

nr 4

17

Virulence genes profiles and phylogenetic origin of Escherichia coli from acute and chronic intestinal diseases revealed by comparative genomic hybridization microarray

67%

Sobieszczanska B., Kasprzykowska U., Turniak M., Maciejewski H., Franiczek R., Duda -Madej A.

Polish Journal of Microbiology

|

2012

|

tom 61

|

nr 2

The association between Escherichia coli virulence factors and chronic intestinal disorders is mostly unknown. The presented study compared the distribution of virulence genes and phylogroups among E. coli isolated from chronic intestinal disorders such as Crohn’s disease and irritable bowel syndrome (IBS) with strains isolated from patients with acute diarrhea as a control group. The presence of 159 virulence genes corresponding to known E. coli pathotypes was determined among 78 E. coli archive strains isolated from IBS, acute diarrhea and Crohn’s disease using CGH microarray. E. coli isolated from IBS demonstrated a mosaic of virulence genes specific to enteropathogenic, enterotoxigenic, enterohemorrhagic E. coli strains and Shigella species. In contrast, virulence factors and phylogroups distribution among E. coli isolated from children with acute diarrhea was similar to extraintestinal E. coli strains that probably acquired some virulence genes. The acquisition of virulence genes might have an impact on diarrheagenic potential of these strains. On the other hand, E. coli isolated from children with Crohn’s disease seem to be similar to adherent-invasive E. coli strains (AIEC), as it lack most known virulence genes. The presented study showed that these analyzed groups of E. coli strains differed from each other with the respect to the distribution of virulence genes. The differences in gene content support the idea that the participation of E. coli in chronic intestinal diseases is mostly related to virulence potential of these strains.

Ograniczanie wyników

DNA microarray gene expression profile of Mycobacterium tuberculosis when exposed to osthole

On methods of collecting data from DNA microarrays

Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods

Application of epoxy functional silanes in the preparation of DNA microarrays

Virulence and antibiotic resistance of Escherichia coli isolated from rooks

Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance

Transcriptional pattern of TGF-beta1 inhibitory effect on mouse C2C12 myoblasts differentiation

Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer - the DNA microarray assay

Comparison of cellular and tissue transcriptional profiles in canine mammary tumor

The reverse-direction method links mass experimental data to human diseases

Transcriptomic 'portraits' of canine mammary cancer cell lines with various phenotypes

Calculation of reliable transcript levels of annotated genes on the basis of multiple probe-sets in Affymetrix microarrays

DNA microarrays, a novel approach in studies of chromatin structure

Gene expression profiling of lipoarabinomannan-treated mouse macrophage cultures infected with Mycobacterium bovis BCG

DNA microarrays - future in oncology research and therapy

Transcriptome sequencing: next generation approach to RNA functional analysis

Virulence genes profiles and phylogenetic origin of Escherichia coli from acute and chronic intestinal diseases revealed by comparative genomic hybridization microarray