Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays

Saizieu, Antoine de; Certa, Ulrich; Warrington, Janet A.; Gray, Christopher P.; Keck, Wolfgang; Mous, Jan

doi:10.1038/nbt0198-45

Cited by 204 publications

(106 citation statements)

References 12 publications

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“…Whole genome transcript profiling by RNA oligonucleotide microarrays (de Saizieu et al, 1998) allows observation of genome-wide gene transcription patterns in cultivated microorganisms; however, it may be unsuitable for natural mixed-taxon assemblages.…”

Section: Introductionmentioning

confidence: 99%

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

et al. 2009

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The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N 2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.

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Section: Introductionmentioning

confidence: 99%

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

et al. 2009

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“…The cDNA microarray method can analyze relative expression levels simultaneously using small sample amounts. 28,29 This has provided high-throughput gene expression profiling, which provides the possibility of finding critical genes for biologic processes without prior knowledge. The goal of the present study was to identify the most upregulated gene in prostate cancer cells after genistein treatment and to characterize the molecular and biochemical features of this gene.…”

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confidence: 99%

Genistein, a soy isoflavone, induces glutathione peroxidase in the human prostate cancer cell lines LNCaP and PC‐3

Suzuki

Koike

Matsui

et al. 2002

Intl Journal of Cancer

172

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Genistein is a major component of soybean isoflavone and has multiple functions resulting in antitumor effects. Prostate cancer is 1 of the targets for the preventive role of genistein. We examined the effect of genistein on human prostate cancer (LNCaP and PC-3) cells. Proliferation of both cell lines was inhibited by genistein treatment in a dose-dependent manner. To obtain the gene expression profile of genistein in LNCaP cells, we performed cDNA microarray analysis. The expression of many genes, including apoptosis inhibitor (survivin), DNA topoisomerase II, cell division cycle 6 (CDC6) and mitogen-activated protein kinase 6 (MAPK 6), was downregulated. Expression levels were increased more than 2-fold in only 4 genes. The glutathione peroxidase (GPx)-1 gene expression level was the most upregulated. Quantitative real-time polymerase chain reaction revealed significant elevation of transcript levels of GPx-1 in both LNCaP and PC-3 cells. Upregulation of gene expression levels accompanied elevation of GPx enzyme activities. In contrast, no significant changes were observed in the gene expression levels and enzyme activities of the other antioxidant enzymes, superoxide dismutase and catalase. GPx activation might be one of the important characteristics of the effects of genistein on prostate cancer cells.

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“…To further characterize the mechanisms of disease progression and to include the tubulointerstitial regions in our analysis, we undertook an investigation of gene expression using microchip arrays (13)(14)(15). This approach permitted the quantitative analysis of the expression of ϳ11,000 genes and expressed sequence tags.…”

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confidence: 99%

Global Gene Expression Analysis Reveals a Role for the α1 Integrin in Renal Pathogenesis

Sampson¹,

Ryan²,

Enke³

et al. 2001

Journal of Biological Chemistry

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Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays

Cited by 204 publications

References 12 publications

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

Genistein, a soy isoflavone, induces glutathione peroxidase in the human prostate cancer cell lines LNCaP and PC‐3

Global Gene Expression Analysis Reveals a Role for the α1 Integrin in Renal Pathogenesis

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