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Engineered marine biofilms for ocean environment monitoring

ABSTRACT: Dinoroseobacter Shibae engineering for marine synthetic biology applications

PROVIDER: PRJEB90807 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR15158437.fastq.gz	Fastqsanger.gz
	ERR15158438.fastq.gz	Fastqsanger.gz
	ERR15158439.fastq.gz	Fastqsanger.gz
	ERR15157944_1.fastq.gz	Fastqsanger.gz
	ERR15157944_2.fastq.gz	Fastqsanger.gz

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Effect of changing light regimes on Dinoroseobacter shibae DFL12 growth

Project description:This SuperSeries is composed of the following subset Series: GSE25579: Time series analysis of the transition from dark to light growth of Dinoroseobacter shibae DFL12 GSE25581: Time series analysis of the transition from light to dark growth of Dinoroseobacter shibae DFL12 Refer to individual Series

2010-12-03 | E-GEOD-25591 | biostudies-arrayexpress

Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutant D. shibae clpX::Tn

Project description:Transcriptomes of Dinoroseobacter shibae DSM16493 wild type and clpX knockout mutant were recorded under white and blue light and in dark.

2023-05-10 | GSE219285 | GEO

Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn

Project description:Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn. Dinoroseobacter shibae DFL12T (DSM 16493T) and the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn were grown in artificial saltwater minimal medium (SWM) in baffled flasks shaking at 180 rpm and 30 °C and incubation was performed under light, dark and bluelight conditions. D. shibae wild type and mutant strain were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5).

2023-10-01 | GSE244289 | GEO

Dinoroseobacter shibae strain:DSM 16439 | isolate:DSM 16439

Project description:Dinoroseobacter shibae Dinoroseobacter shibae DSM 16439 transcriptome - FEBA_7_MM_RNA

| PRJNA426730 | ENA

Transcriptomic analysis of Dinoroseobacter shibae DFL12T in response to phage infection

Project description:Dinoroseobacter shibae DFL12T was cultured with/without phage R2C, and gene expression was analyzed at 60 min and 140 min during the incubation

2018-01-20 | GSE109415 | GEO

Dinoroseobacter shibae

Project description:Dinoroseobacter shibae overview

| PRJNA35939 | ENA

Project description:Dinoroseobacter shibae genomes

| PRJNA814221 | ENA

Adaption of Dinoroseobacter shibae to anaerobic conditions

Project description:To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions. Dinoroseobacter shibae wild type strain DSM 16493T was grown in a chemostate in saltwater mininmal medium (SWM) mimicking the conditions in the marine habitat under anaerobic conditions. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. Therefore, D. shibae was grown aerobically in the chemostate until the culture reached the exponential phase, than countinuously cultivaion was started. The dilution rate was 0.1 h-1, establishing the approximate half-maximum growth rate of D. shibae in the exponential phase. The anaerobic shift was initialised after 20 hours by stopping the aeration. The samples were harvested before (as reference) and 30 minutes after stopping the airation. Three biological replica were analyzed. Comparison: Identification of genes induced or repressed under aerobic conditions in the Dinoroseobacter shibae wild type strain DSM 16493T. Here we compared the transcriptome profile of D. shibae wild type strain DSM 16493T grown aerobically in the chemostate in exponential phase with the transcriptome profile of the D. shibae wild type strain DSM 16493T which was grown without aeration for 5, 10, 15, 20, 30, 60 and 120 min.

2013-08-30 | E-GEOD-47445 | biostudies-arrayexpress

Adaptation of Dinoroseobacter shibae to different kinds of oxidative stress

Project description:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. Living in the photic zone environment of marine ecosystems D. shibae is frequently exposed to oxygen. Oxic environments are hazardous and therefore effective defense mechanisms are required. In the present study, the adaptation of D. shibae to different kinds of oxidative stresses was investigated. Hydrogen peroxide, diamide and paraquat were used as agents to trigger peroxide, thiol and superoxide stress. To define and compare the peroxide, superoxide and thiol stress stimulons in D. shibae, GeLC-MS/MS based proteomic data of cytosolic and surface associated proteins were used. Furthermore, a strain deficient in the rhizobial iron regulator (RirA) was used to study the global impact of RirA on peroxide dependent protein expression.

2021-03-12 | PXD013791 | Pride

Biogenesis and DNA cargo of Dinoroseobacter shibae outer membrane vesicles suggests vesicle formation is coupled to replication

Project description:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. In the ocean, OMVs have about the same abundance as bacteria, a distinct depth distribution, and contain DNA from a variety of marine bacterial taxa. In the present study, we determined the abundance, size, and ultrastructure of membrane vesicles of D. shibae and analysed the protein inventory of the soluble and membrane fractions of cells and vesicles in order to study the origin of OMV membranes and content. The proteomic analyses were complemented by fatty acid analyses.

2020-12-16 | PXD014351 | Pride

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