Whole genome sequencing of Sphingobium sp. Z007
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PROVIDER: PRJEB12244 | ENA |
REPOSITORIES: ENA
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Project description:Sphingobium sp. strain RSMS was described earlier as an efficient degrader of tributyl phosphate, an organic pollutant. This report describes the generation and annotation of the genome sequence of Sphingobium sp. strain RSMS, which will facilitate future studies to identify genetic elements responsible for the degradation of tributyl phosphate.
| S-EPMC7561683 | biostudies-literature
Project description:Purpose: The goal of this study was to compare gene expression in whole embryos to identify transcriptomic changes that result from maternal exposure to predation risk. Methods: Whole embryo mRNA profiles of 3 day post-fertilizationstickleback embrosof mothers exposed to simulated predation risk and control embryos were generated by RNA-sequencing of pooled embryos using Illumina Hiseq2000. The sequence reads that passed quality filters were aligned to the stickleback reference genome and analyzed at the gene level (EdgeR) and at the transcript level (Cufflinks/Cuffdiff). Subsets of embryos were also measured for embryo length and eye diameter, and data were analyzed with a general linear model (SPSS). Results: We mapped ~22 million sequence reads per sample to the stickleback reference genome (BROADS1, Ensembl database version 71.1, Feb 2006) and identified 17440 transcripts with the Tophat workflow. Differential expression analysis using both EdgeR and Cufflinks/Cuffdiff identified 455 transcripts were differentially expressed in embryos of mothers exposed to simulated predation risk as compared to control embryos, with an FDR <0.05 (Cuffdiff) or <0.10 (EdgeR). Gene ontology and pathway analysis (DAVID, IPA) of the differentially expressed gene list revealed enrichment of genes involved in growth, metabolism, neurogenesis, and epigenetics. Embryos of mothers exposed to predation risk had elevated expression of growth and metabolism genes and were also larger than control embryos, suggesting at least some of the genes differentially expressed in this study are involved in the transfer of maternal experience to offspring. Conclusions: Our results suggest that early stickleback embryos respond to maternal exposure to predation risk via changes in gene expression, and a general acceleration of the developmental program. Further study is needed to elucidate the myriad molecular interactions between genes that are differentially-regulated as a result of maternal exposure to predation risk and to understand their relationships to previously-observed maternal effects in this system. Whole embryo mRNA profiles of 3dpf stickleback embryos of mothers exposed to simulated predation risk [E] and control mothers [C] were generated by barcoded, multiplexed high-throughput RNA-sequencing on Illumina Hiseq-2000.
2014-06-07 | E-GEOD-56160 | biostudies-arrayexpress
Project description:Sphingobium sp. strain PNB can completely degrade phenanthrene, naphthalene, and biphenyl as the sole carbon and energy source. The strain is also capable of cometabolizing benzo[a]pyrene, pyrene, acenaphthene, fluoranthene, etc. Here, we report the 5.69-Mb assembly and annotation of the genome sequence of strain PNB, obtained using Illumina sequencing.
| S-EPMC8638569 | biostudies-literature
Project description:Global transcriptional profiles of Saccharomyces cerevisiae were studied following changes in growth conditions to high hydrostatic pressure and low temperature. These profiles were quantitatively very similar, encompassing 561 co-upregulated genes and 161 co-downregulated genes. In particular, expression of the DAN/TIR cell wall mannoprotein genes, which are generally expressed under hypoxia, were markedly upregulated by high pressure and low temperature, suggesting the overlapping regulatory networks of transcription. In support of the role of the mannoproteins in cell wall integrity, cells acquired resistance against treatment with SDS, Zymolyase and lethal level of high pressure when preincubated under high pressure and low temperature. Keywords: stress response
2007-10-05 | GSE9136 | GEO
Project description:An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.
2017-01-20 | GSE87706 | GEO
Project description:Small distortions in transcriptional networks might lead to drastic phenotypical changes, especially in cellular developmental programs such as competence for natural transformation. Here, we report a pervasive circuitry rewiring for competence and predation interplay in commensal streptococci. Canonically, in model species of streptococci such as Streptococcus pneumoniae and Streptococcus mutans, the pheromone-based two-component system BlpRH is a central node that orchestrates the production of antimicrobial compounds (bacteriocins) and incorporates signal from the competence activation cascade. However, the human commensal Streptococcus salivarius does not contain a functional BlpRH pair and in this species, the competence signaling system ComRS directly couples bacteriocin production and competence commitment. This network shortcut might account for an optimal reaction against microbial competitors and could explain the high prevalence of S. salivarius in the human digestive tract. Moreover, the broad spectrum of bacteriocin activity against pathogenic bacteria showcases the commensal and genetically tractable S. salivarius species as a user-friendly model for natural transformation and bacterial predation.
2018-01-10 | GSE100416 | GEO
Project description:Shewanella piezotolerans WP3 wild-type strain under high hydrostatic pressure
| PRJNA324485 | ENA
Project description:Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrio’s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a “predatosome” of genes specifically upregulated during predation and implicates some of those important in HI growth.
2009-12-09 | GSE16034 | GEO
Project description:Bdellovibrio is a Gram-negative bacterium that preys upon other Gram-negative bacteria, including many pathogens, and as such has potential as a biocontrol agent. Little is known of the molecular and genetic control of Bdellovibrioâ??s attack upon its prey and of the nature of the HI phenotype. Here, we apply microarray technology to monitor changes of gene expression during the initial stages of prey infection to determine which predatory genes are important in this stage and to gain insight into possible regulatory mechanisms controlling the predation process. Comparison to gene expression during HI growth reveals a â??predatosomeâ?? of genes specifically upregulated during predation and implicates some of those important in HI growth. 3 replicates of attack phase cells and 3 replicates of Host-Independent grown cells were analysed on individual arrays.
2010-05-18 | E-GEOD-16034 | biostudies-arrayexpress