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Effects of the Three Gorges Dam on bacterioplankton

ABSTRACT: By taking three metagenomic approaches to reveal the microplankton communities from composition to functional properties in this study. It should make a significant advance in understanding the impacts of human activities on ecosystem functions, from the angle of dam influences on the microbial functions.

PROVIDER: PRJEB14607 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1474560_1.fastq.gz	Fastqsanger.gz
	ERR1474560_2.fastq.gz	Fastqsanger.gz
	ERR1474561_1.fastq.gz	Fastqsanger.gz
	ERR1474561_2.fastq.gz	Fastqsanger.gz
	ERR1474562_1.fastq.gz	Fastqsanger.gz

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DNA adenine methyltransferase (Dam) overexpression impairs Photorhabdus luminescens motility and virulence

Project description:Dam, the most described bacterial DNA-methyltransferase, is widespread in gamma-proteobacteria. Dam DNA methylation can play a role in various genes expression and is involved in pathogenicity of several bacterial species. In the entomopathogenic bacterium Photorhabdus luminescens, a dam ortholog was identified. Overexpression of dam in P. luminescens did not impair growth ability in vitro. In contrast, compared to a control strain harboring an empty plasmid, a significant decrease in motility was observed in the dam-overexpressing strain. In addition, the dam-overexpressing P. luminescens strain showed a delayed virulence compared to that of the control strain after injection in larvae of the lepidopteran Spodoptera littoralis. These results reveal that Dam plays a major role during P. luminescens insect infection.

2017-10-04 | GSE100650 | GEO

Basal gene expression in dam, dam mutS, and mutS mutant E. coli strains

Project description:We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains. Keywords: Basal gene expression comparison

2005-07-14 | GSE2928 | GEO

Dam-specific RNA-seq

Project description:Dam-specific RNA-seq

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Dam-specific RNA-seq

Project description:To determine the transcription start site and the abundance of dam mRNA, we conducted mRNA-specific RNA-Seq experiments. Essentially two strategies were tested. First strategy: We obtained the cDNA with a specific RT-PCR in order to get the mRNA from our dam construct (see DNA-seq of DamID reporter cassette). An enrichment, in which we used a Biotinylated dam oligo and Streptavidin magnetic beads, was needed. Then, similar to SHAPE-seq, the ssDNA ligation was performed with CircLigase. The last step was the PCR reaction in order to prepare the cDNA libraries to be sequenced. Second strategy: Similar to the first one, but the specificity was introduced at the PCR, not at the RT. Thereby, busk cDNA was prepared with random hexamers. The enrichment step was not needed.

2018-03-22 | E-MTAB-5363 | biostudies-arrayexpress

RNA-seq analysis for E.coli dnd and dam derivatives

Project description:To get a global view of PT modification’s function in ∆dam mutant, we did an RNA-seq to compare the gene expression change after dam knocks out and test whether PT could restore the changes.

2020-05-21 | GSE135938 | GEO

DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association. Comparison of Dam::LMN-1 and Dam::EMR-1 DNA assotiation in wild type strains and Dam::LMN-1 DNA association in wild type, lem-2(tm1582) and emr-1(gk119) mutant backgrounds.

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Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli

Project description:We used Affymetrix microarrays to determine the cisplatin-induced gene expression changes in E. coli deficient in dam and mismatch repair (dam, dam mutS, and mutS mutant strains). E. coli deficient in dam are hypersensitive to cisplatin. However introducing an additional mutation in mismatch repair (i.e., a mutation in mutS or mutL) abrogates this sensitivity and essentially restores wildtype levels of resistance. Keywords: Drug-induced expression

2005-07-27 | GSE2999 | GEO

Neisseria gonorrhoeae drg::cm versus wild type and Neisseria gonorrhoeae drg::dam versus wild type

Project description:Transcriptional profiling of N. gonorrhoeae comparing wild type cells to cells with inactivated by chloramphenicol cassette (cm) dam replacing gene (drg) or wild type cells comparing to cells with inserted dam gene. The Goal was to study the role of drg or dam presence in overall expression profile.

2017-02-09 | GSE60347 | GEO

Dam(ID)-profiling in B cells

Project description:Both chromatin access, and binding of AID in B cells are of major scientific interest. Therefore DamID was setup in B cells. AID specific binding could not be identified. In contrast to binding, DAM profiling provide a upmost useful tool in defining chromatin access in vivo.

2016-05-12 | GSE81342 | GEO

16s metagenomics of dam water.

Project description:16s metagenomics of dam water from 3 sources.

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