Geobacillus sp. E263 isolate:East pacific sediment
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PROVIDER: PRJNA553850 | ENA |
REPOSITORIES: ENA
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Project description:Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas.
2010-09-01 | GSE23883 | GEO
Project description:To investigate the transcriptional profile of GVE2 genes, the viral genes were identified by DNA microarray with Cy5- or Cy3-dUTP-labeled cDNAs prepared from uninfected and GVE2-infected Geobacillus sp. E263 at 4 h p.i.. After hybridization with the Cy3-dUTP-labeled cDNAs from GVE2-infected Geobacillus sp. E263 at 4 h p.i., Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263 as well as Cy3- dUTP-labeled yeast cDNAs and Hex DNA, many spots produced positive signals significantly above the background, while no signal appeared for the Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263., indicating that the positive signals represented the GVE2 gene transcripts detectable by DNA microarray. The DNA fragments, detected to be positive in the reverse transcripts at 4 h p.i., contained 74.2% of the presumptive GVE2 ORFs. Keywords: Transcriptional profile of thermophilic bacteriophage at 4 h p.i.
2006-08-26 | GSE5577 | GEO
Project description:Transcriptional profile comparison among Beijing and non-Beijing M. tuberculosis isolates. Three M. tuberculosis strains were compared. The laboratory reference strain, H37Rv, belongs to the Euro-American or lineage 4. Two clinical isolates of the East-Asian or lineage 2: 98_1663 is a pre-Beijing or Group 1 isolate, and HN878 is a Beijing or Group 5 isolate. Three replicates were performed for each comparison using two different biological samples.
2016-06-24 | E-GEOD-83677 | biostudies-arrayexpress
Project description:<p>Deep-sea hydrothermal vents are unique ecosystems that may release chemically distinct dissolved organic matter to the deep ocean. Here, we describe the composition and concentrations of polar dissolved organic compounds observed in low and high temperature hydrothermal vent fluids at 9°50′N on the East Pacific Rise. The concentration of dissolved organic carbon was 46 µM in the low temperature hydrothermal fluids and 14 µM in the high temperature hydrothermal fluids. In the low temperature vent fluids, quantifiable dissolved organic compounds were dominated by water-soluble vitamins and amino acids. Derivatives of benzoic acid and the organic sulfur compound 2,3-dihydroxypropane-1-sulfonate (DHPS) were also present in low and high temperature hydrothermal fluids. The low temperature vent fluids contain organic compounds that are central to biological processes, suggesting that they are a by-product of biological activity in the subseafloor. These compounds may fuel heterotrophic and other metabolic processes at deep-sea hydrothermal vents and beyond.</p>
2017-05-23 | MTBLS428 | MetaboLights
Project description:To investigate the transcriptional profile of GVE2 genes, the viral genes were identified by DNA microarray with Cy5- or Cy3-dUTP-labeled cDNAs prepared from uninfected and GVE2-infected Geobacillus sp. E263 at 4 h p.i.. After hybridization with the Cy3-dUTP-labeled cDNAs from GVE2-infected Geobacillus sp. E263 at 4 h p.i., Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263 as well as Cy3- dUTP-labeled yeast cDNAs and Hex DNA, many spots produced positive signals significantly above the background, while no signal appeared for the Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263., indicating that the positive signals represented the GVE2 gene transcripts detectable by DNA microarray. The DNA fragments, detected to be positive in the reverse transcripts at 4 h p.i., contained 74.2% of the presumptive GVE2 ORFs. Keywords: Transcriptional profile of thermophilic bacteriophage at 4 h p.i. A DNA microarray containing 82 DNA fragments of the viral genome was constructed following a PCR-based microarray method. Briefly, specific primer sets were designed to amplify approximately 500-bp fragment each using viral genome as template. All PCR products showing a single band of the appropriate size by gel electrophoresis were purified, and reconstituted in TE buffer at a final concentration of about 500 μg/ml for spotting in triplicates onto the silylated-glass slides (CEL Associates, Inc. USA) using a microarrayer (Smart Arrayer 48, CapitalBio). Eight DNA fragments from yeast genome and a randomly synthesized DNA fragment (Hex) were included as exogenous positive controls to normalize the microarry date. Distilled water was used as negative controls. Total RNAs were isolated from the uninfected and phage-infected Geobacillus sp. E263 cells at 4 h postinfection. The cDNAs from uninfected Geobacillus sp. E263 were labeled with Cy5 and the cDNAs from phage-infected Geobacillus sp. E263 labeled with Cy3. At the same time, the cDNAs from yeast and the Hex DNA were labeled with Cy3. The Cy5- or Cy3-dUTP-labeled cDNAs were resuspended in hybridization solution and hybridized with the microarrays for 16 to 18 h at 42°C. Then the microarrays were rinsed several times following the standard method. Following the washing steps, the microarrays were dried by low-speed centrifugation (500 g for 5 min), and immediately scanned using a GenePix 4000B array scanner (Axon Instruments, Inc.). Images obtained from scanning were analyzed by GenePix Pro 4.0 array analysis software (Axon Instruments, Inc.)
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