Project description:Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture. For each of the four condition, two replicates were analysed on an A. lipoferum 4B whole genome expression array designed by Roche Nimblegen, Inc. (Madison, WI, USA), based on the genome sequence (Wisniewski-DyM-CM-) et al. 2011), as follows: two replicates of 5 probes (length, 60 nucleotides) per gene, covering 6,242 genes and using a total of 62,178 probes.

2014-01-01 | E-GEOD-42450 | biostudies-arrayexpress

Mycobacterium avium subsp. paratuberculosis 4B strain:4B

Project description:Mycobacterium avium subsp. paratuberculosis 4B Genome Sequencing

| PRJNA72215 | ENA

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti

Project description:Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

2021-03-17 | MTBLS576 | MetaboLights

Acidovorax citrulli strain:HPP21-9-4B

Project description:Acidovorax citrulli strain:HPP21-9-4B Genome sequencing

| PRJNA774969 | ENA

Sensitivity of MiaPaCa2 cells to E2F inhibitor Ly101-4B.

Project description:MiaPaCa2 cells where screened with a set of original compounds with anticancer activity available at our laboratory. From these compounds we identified the nucleoside analogue ly101-4B as a strong inhibitor of the E2F activity. We confirmed its activity by studying its effect on MiaPaCa2's cell viability , caspase 3/7 activity and LDH release, to measure cell growth, apoptosis and necrosis after treatment with LY101-4B 25 µM. Then, to investigate the mechanism of action of ly101-4B we performed a transcriptomic analysis by using an Affymetrix approach (Genechip® Human Gene 1.0 ST Arrays).

2019-02-28 | GSE109853 | GEO

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