Lyngbya sp. PCC 8106
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ABSTRACT:
PROVIDER: PRJNA13409 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This marine bacterium was collected in the Mediterranean Sea.
| PRJNA13544 | ENA
Project description:In this study, we characterized the homeostasis of the marine cyanobacteria Synechococcus sp. PCC7002 (BMB04) growing in chemically characterized synthetic seawater with three different levels of iron limitation representative of the modern ocean. Using transcriptomic approach, we identified the sequence of physiological responses to increasing Fe limitation. Our results showed an increase in the number of dysregulated genes and in the complexity of the response to increasing Fe limitation. Genes involved in photosynthesis were strongly down-regulated under MiFeL, while membrane transporters were up-regulated. Genes involved in regulation of energy metabolism responded under strong Fe limitation, while fine metabolic regulation of co-factors expression and activation of specific cellular mechanisms to minimize oxidative stress were only observed under severe Fe limitation. Additionally, our results demonstrate the limitations in the construct of the bioreporter BMB04 that hamper its application in areas of the ocean strongly Fe limited.
2017-01-30 | GSE77354 | GEO
Project description:RNase III is a ribonucleases that recognizes and cleaves double-stranded RNA. RNase III has been known be involved in rRNA processing, but has many additional roles controlling both expression and RNA turnover of specific messages. Many organisms have just one RNase III while some have both a full length RNase III and a mini-III that lacks the double-stranded RNA binding domain. The cyanobacteria Synechococcus sp. PCC 7002 has three homologs of RNase III that are unessential even when deleted in combination. We were interested what coding regions these RNase III enzymes were influencing and if they had redundant or distinct specificities. To address these questions we collected samples for RNA-sequencing from WT, the single, double, and triple RNase III mutants in triplicate. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. We describe the role of two RNase III’s in 23S rRNA maturation, and show how the third is involved in copy number regulation of one of the six plasmids (pAQ3). Purified enzymes were capable of cleaving some E. coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.
2018-01-16 | GSE99279 | GEO
Project description:RNA samples from cells collected at twenty four time points in 48-hours diurnal cycles were analyzed, and they compared between each other for transcriptional profiles of global genes
2016-03-31 | GSE79714 | GEO
Project description:We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences. Chromatin pull down of hetR mutant strain UHM103 carrying pAM4375, which expresses HetR-6xHis, and a wild-type control. One dataset was collected.
2013-10-31 | E-GEOD-51886 | biostudies-arrayexpress
Project description:Synechocystis 6803 cells was grown photoautotrophically at 32 °C buffered in BG-11 and bubbled with 3% CO2. A relatively mild Ci stress was applied by switching the aeration from 3% CO2 to air alone. After incubation under designated conditions, a 100-ml aliquot of culture was immediately combined with an equal volume of ice-cold mixture of phenol and ethanol (1:10, w/v) in an ice bath. The resultant cells were collected by centrifugation at 1000 x g for 10 min at 4 °C. Total RNA was isolated with RNeasy Midi Kit (Qiagen, Valencia, CA) and further treated with the DNA-free kit (Ambion, Austin, TX). Fluorescently labeled cDNA was produced via a two-step indirect procedure involving cDNA synthesis from 16 µg of total RNA in a reverse transcriptase reaction incorporating aminoallyl-modified deoxynucleotide, followed by the second step involving chemical coupling of fluorescent dye to the introduced amino moieties of the synthesized cDNA. Labeled cDNA were adjusted to 14.75 µl, and the remainder of the hybridization components containing 2.5 µl of 10 µg µl-1 salmon sperm DNA, 8.75 µl of 20x SSC, 0.25 µl of 10% SDS, and 8.75 µl of formamide were added. The mixture was then heated for 2 min at 99 °C and maintained at 42 °C until hybridization. Hybridizations were preformed in a static incubator at 42 °C for 12-16 h then washed by placing in a 250-ml solution of 2x SSC and 0.1% SDS at 42 °C for 5 min with gentle agitation provided by rotation of a magnetic stir bar. The slide was transferred quickly to a 250-ml solution of 0.1x SSC and 0.1% SDS, incubated for 10 min at room temperature with gentle agitation, and washed five additional times in 0.1x SSC for 1 min at room temperature. Hybridization signals from the microarray were quantified using GenePix Pro 4.1 (Axon Instruments, Union City, CA). The quality control procedures were conducted in the image analysis software, and then data were saved to Acuity 3.1 (Axon Instruments). Keywords: time-course
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