Ontology highlight
ABSTRACT:
PROVIDER: PRJNA473050 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7216660_1.fastq.gz | Fastqsanger.gz | |||
| SRR7216660_2.fastq.gz | Fastqsanger.gz | |||
| SRR7216670_1.fastq.gz | Fastqsanger.gz | |||
| SRR7216670_2.fastq.gz | Fastqsanger.gz | |||
| SRR7216680_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 192 |
Similar Datasets
Project description:Antarctic fur seal (Arctocephalus gazella) HiC genome assembly
| PRJEB30577 | ENA
Project description:The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Polyomic data analysis revealed that a total of 81 genes in 42 transcription units (TUs) are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation as well as holo-Fur repression. We showed that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development was found. These results indicate that Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate E. coli responses to the availability of iron. [ChIP-exo]: A total of twelve samples were analyzed. WT and Fur-8-myc tagged cells were cultured in the presense and absence of iron with biological duplicates. To analyze static RNAP binding, rifampicin was also added to the media with biological duplicates. DPD = iron chelator.
2014-09-09 | E-GEOD-54899 | biostudies-arrayexpress
Project description:The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Polyomic data analysis revealed that a total of 81 genes in 42 transcription units (TUs) are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation as well as holo-Fur repression. We showed that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development was found. These results indicate that Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate E. coli responses to the availability of iron.
2014-09-09 | GSE54899 | GEO
Project description:The Western Antarctic Peninsula (WAP) is among the areas of the planet showing some of the most significant increases in air and water temperature. It is projected that increasing temperature will modulate communities of coastal ecosystems at species ecological performance and molecular composition. The main way that the organisms can cope with large thermal variation is by having a reversible phenotypic plasticity, which provides the organisms with a compensatory physiological response when facing challenging conditions. However, since Antarctic organisms have evolved in a very cold and stable environment. The giant Antarctic isopod Glyptonotus antarcticus is one of the most abundant in Antarctic waters. This species has a larval development inside of maternal marsupium, where juveniles have a short period to acclimate to environmental conditions after birth. In this sense, we hypothesize that juveniles exposed to unusual temperature increases even for short periods, would not respond adequately showing a narrow phenotypic plasticity. We assessed if early juveniles of G. antarcticus have the molecular plasticity when exposed to increased temperature at 5¡C during 1, 6, 12, and 24 hours in comparison to control 0¡C. Sequenced HIseq2000 libraries were compared between control and each treatment to detect differentially expressed transcripts. The main molecular pathways affected by thermal stress were antioxidants, proteases, endopeptidases, and ubiquitination transcripts which were up-regulated, and mitochondrial respiratory chain, cuticle, cytoskeleton, and a molt transcript which were down-regulated. Considering HSP transcript, only 3 were up-regulated at least in two points of the stress kinetic, without classical HSP70 and HSP90 transcripts. This study shows that juveniles of G. antarcticus do not show molecular phenotypic plasticity to cope with acute short-term heat stress, even for one or few hours of exposure without an eco-physiological capacity to respond. This may have consequences at the ecological population level, showing a reduced individual ability to survive decreasing population recruitment.
2021-09-01 | GSE180716 | GEO
Project description:Bacillus subtilis CU1065: WT vs fur, fur vs fur fsrA, fur vs fur fbpAB, fur vs fur fbpC, and fur vs fur fbpABC
| PRJNA137241 | ENA
Project description:As descirbed in the manuscript The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons we performed a control ChIP-chip experiment in an E. coli strain lacking the transcription factor Fur to identify regions Fur-independent enrichment.
2015-12-01 | GSE74931 | GEO
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning.
2010-12-30 | GSE22825 | GEO