Oil biodegradation studies Svalbard
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB85177 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14226700_1.fastq.gz | Fastqsanger.gz | |||
| ERR14226700_2.fastq.gz | Fastqsanger.gz | |||
| ERR14226701_1.fastq.gz | Fastqsanger.gz | |||
| ERR14226701_2.fastq.gz | Fastqsanger.gz | |||
| ERR14226702_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 324 |
Similar Datasets
Project description:Microbial community dynamics during biodegradation of crude oil and its response to biostimulation in Svalbard seawater at low temperature
| PRJEB48192 | ENA
Project description:As apex predators, cetaceans are recognized as sentinels for the health of marine ecosystems. The ability to identify the impacts of anthropogenic contamination on the health of a species requires long term monitoring to establish baseline health parameters. This makes health measurements that can be sampled from free ranging animals highly desirable. In the current study, we investigate the utility of skin gene expression profiling to monitor the physiological, health, and contaminant exposure status in bottlenose dolphins. Remote integument biopsies were obtained from bottlenose dolphins at three locations in the northern Gulf of Mexico prior to oil exposure (May 2010) and during summer and winter of the two years (2010-2011) following their exposure to oil from the Deepwater Horizon oil spill. A bottlenose dolphin-specific oligonucleotide microarray was used to characterize the skin transcriptomes of 94 individuals from three genetically distinguishable populations in Barataria Bay, Louisiana, Chandeleur Sound, Louisiana, and Mississippi Sound, Mississippi. Location did not significantly affect the transcriptome patterns of the dolphins included in the study. In contrast, season had a profound effect on gene expression, with nearly one-third of all genes on the array differing significantly in expression between winter and the warmer seasons (p<0.01, fold-change >1.5). Gene ontology enrichment analysis revealed that processes related to cell proliferation, motility and differentiation dominated the seasonal differences in expression, which likely reflects the differences in ambient temperature to which the skin is exposed, and possibly changes in blood flow. More subtle differences were seen between spring and summer transcriptomes (1.5% differentially expressed), with two presumed oil-exposed animals presenting gene expression profiles more similar to the summer (exposed) animals than the other spring animals. Xenobiotic pathway components also showed some seasonal trends, which may reflect crosstalk between xenobiotic pathways and those regulating corticoids, hormones, and cytokines. Seasonal effects have not previously been considered in studies assessing gene expression in cetaceans, but clearly must be taken into account when applying transcriptomic analyses to investigate their exposure or health status.
2016-11-29 | GSE58471 | GEO
Project description:Peptides were qualitatively characterized in supraoptic nuclei (SON)of dromedary camels by liquid chromatography-mass spectrometry/mass spectrometry. Samples collected in winter and summer were analyzed separately. Qualitative seasonal differences were noted. The presence of the PMCH hormone by detection of a single peptide, Neuropeptide-glutamic acid-isoleucine (EIGDEENSAKFPI-amide), only in winter SON. SCG1- and SCG2- derived peptides were detected in both seasons, but more peptides identified in winter than summer for either of the proteins. Peptides from SCG3 were detected only in winter SON samples. We found evidence of alternative splicing of the tachykinin precursor 1 in dromedary between seasons. In summer, we detected neurokinin A (isoforms 2,4, and 6) as well as peptide DADSSVEKQVALLKALYGLGQISHKMAYE confirming prohormone variant without neurokinin A (dromedary isoforms 3 and 7), while in winter SON we detected peptides supporting prohormone variants with neurokinin A (isoforms 2, 4, 6). Substance P was detected only in winter samples. The MS data supported some of our transcriptomics results.
2019-11-11 | PXD013869 | Pride
Project description:Investigation of transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in winter (Dec. 22-23, 2011) and summer (July 30-31, 2012). We investigated seasonal and diurnal transcriptome dynamics of Japanese cedar (Cryptomeria japonica) by analyzing shoot samples collected at four-hour interval for two days in winter and summer, respectively. We first collected sequence data of expressed genes from shoots to designed microarray probes. Microarray analysis revealed the significant difference of transcripts between summer and winter, and the diurnal transcriptome dynamic in summer.Statistical analysis indicated that about 7.7 % of unique genes showed diurnal rhythms with more than two-fold of peak-to-trough amplitude in summer.
2014-09-29 | GSE53945 | GEO
Project description:A double cropping system has been commercially adopted in subtropical regions in southern China, where there is abundant sunshine and heat resources. In this viticulture system, the first growing season normally starts as a summer cropping cycle; then, the vine is pruned and forced by hydrogen cyanamide, resulting in a second crop in January of the next year. Due to climate differences between the two growing seasons,the transcriptome varies greatly between summer- and winter- grape berries. In this study, we conducted RNA-seq for two table grape varieties (Vitis vinifera cv. Victoria and V. vinifera cv. Muscat Superior) at three developmental stages (pre-veraison, post-veraison and full maturity).The transcriptome between summer- and winter- grape berries were compared.
2018-11-30 | GSE122411 | GEO
Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.
2011-04-15 | GSE24353 | GEO
Project description:Atmospheric fine particulate matter (PM2.5) causes severe haze in China and is regarded as a threat to human health. The health effects of PM2.5 vary location by location due to the variation in size distribution, chemical com position, and sources. In this study, the cytotoxicity effect, oxidative stress, and gene expression regulation of PM2.5 in Chengdu and Chongqing, two typical urban areas in southern China, were evaluated. Urban PM2.5 in summer and winter significantly inhibited cell viability and increased reactive oxygen species (ROS) levels in A549 cells. Notably, PM2.5 in winter exhibited higher cytotoxicity and ROS level than summer. Moreover, in this study, PM2.5 commonly induced cancer-related gene expression such as cell adhesion molecule 1(PECAM1), interleukin 24 (IL24), and cytochrome P450 (CYP1A1); meanwhile, PM2.5 commonly acted on cancer-related biological functions such as cell-substrate junction, cell-cell junction, and focal adhesion. In partic ular, PM2.5 in Chengdu in summer had the highest carcinogenic potential among PM2.5 at the two sites in summer and winter. Importantly, cancer-related genes were uniquely targeted by PM2.5, such as epithelial splicing regu latory protein 1 (ESRP1) and membrane-associated ring-CH-type finger 1 (1-Mar) by Chengdu summer PM2.5; collagen type IX alpha 3 chain (COL9A3) by Chengdu winter PM2.5; SH2 domain-containing 1B (SH2D1B) by Chongqing summer PM2.5; and interleukin 1 receptor-like 1 (IL1RL1) and zinc finger protein 42 (ZNF423) by Chongqing winter PM2.5. Meanwhile, important cancer-related biological functions were specially induced by PM2.5, such as cell cycle checkpoint by Chengdu summer PM2.5; macromolecule methylation by Chengdu win ter PM2.5; endoplasmic reticulum-Golgi intermediate compartment membrane by Chongqing summer PM2.5;and cellular lipid catabolic process by Chongqing winter PM2.5. Conclusively, in the typical urban areas of southern China, both summer and winter PM2.5 illustrated significant gene regulation effects. This study contrib utes to evaluating the adverse health effects of PM2.5 in southern China and providing public health suggestions for policymakers.
2022-10-30 | GSE216512 | GEO