Vannella sp. KDN1
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome analyses of Naegleria sp., Effects of photosynthetic traits of bacterial prey on predatory amoebae.
| PRJDB6846 | ENA
Project description:Transcriptome analyses of Acanthamoeba sp., Effects of photosynthetic traits of bacterial prey on predatory amoebae.
| PRJDB6847 | ENA
Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic.
2013-11-19 | GSE52455 | GEO
Project description:Bdellovibrio bacteriovorus HD100 is a predatory bacterium which attacks a wide range of gram negative bacterial pathogens and is proposed to be a potential living antibiotic. In the current study, we evaluated the effects of indole, a bacterial signaling molecule commonly produced within the gut, on the predatory ability of B. bacteriovorus HD100. Indole significantly delayed predation on E. coli MG1655 and S. enterica KACC 11595 at physiological concentrations (0.25 to 1 mM) and completely inhibited predation when present at 2 mM. Microscopic analysis revealed that indole blocked the predator from attacking the prey. Furthermore, indole was not toxic to the predator but slowed down its motility. Microarray and RT-qPCR analyses confirmed this as the gene group showing the greatest down-regulation in the presence of 1 and 2 mM indole was flagellar assembly and motility genes. Aside from this group, indole also caused a wide spectrum changes in gene expression including the general down-regulation of genes involved in ribosome assembly and RNA translation. Furthermore, indole addition to the predatory culture after the entrance of B. bacteriovorus into the prey periplasm slowed down bdelloplast lysis. In conclusion, indole is an important gut-related signaling molecule that can have significant impacts on the predation efficiency and predator behavior. These findings should be taken into consideration especially if B. bacteriovorus is to be applied as a probiotic or living antibiotic. Bdellovibrio bacteriovorus HD100 was incubated for 30 min at 30°C in HEPES buffer supplemented with 0,1, and 2 mM indole. RNA was then extracted from each sample and purified. 100 ng of RNA from each sample were used for microarray experiment. For zero and 1 mM indole treatments, three independant samples were tested while for 2 mM indole treatment, two samples were tested. A total of 8 arrays were used.
2013-11-19 | E-GEOD-52455 | biostudies-arrayexpress
Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis
2009-12-09 | GSE9269 | GEO
Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent âHIâ manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis 3 replicates of attack phase cells and 3 replicates of 30 minutes post-infection cells were analysed on individual arrays. Replicate 3 was normalized separately.
2010-05-18 | E-GEOD-9269 | biostudies-arrayexpress
Project description:To investigate the gene expression levels of Medicago truncatula roots after beneficial fungi Gongronella sp. w5 inoculated.Gongronella sp. w5 promoted M. truncatula growth and caused the accumulation of sucrose in M. truncatula root tissue at 16 day-post-inoculation (dpi) without invading into the root cells. The transport of photosynthetic product sucrose to the rhizosphere by M. truncatula root cells was accelerated by upregulating the SWEET gene.
2020-08-11 | GSE155951 | GEO
Project description:Prey-specialised spiders are adapted to capture specific prey items, including dangerous prey such as ants, termites or other spiders. It has been observed that the venoms of specialists are often prey-specific and less complex than those of generalists, but venom composition has not been studied in detail in prey-specialised spiders. Here, we investigated the venom of the prey-specialised white-tailed spider (Lamponidae: Lampona sp.), which utilises specialised morphological and behavioural adaptations to capture spider prey. We hypothesised Lampona spiders also possess venomic adaptations, specifically, its venom is more effective to focal spider prey due to the presence of prey-specific toxins. We analysed the venom composition using proteo-transcriptomics and taxon-specific toxicity using venom bioassays. Our analysis identified 208 putative toxin sequences, comprising 103 peptides <10 kDa and 105 proteins >10 kDa. Most peptides belonged to one of two families characterised by scaffolds containing eight or ten cysteine residues. Protein toxins showed similarity to galectins, leucine-rich repeat proteins, trypsins and neprilysins. The venom of Lampona was shown to be spider-specific, as it was more potent against the preferred spider prey than against alternative prey represented by a cricket. In contrast, the venom of a related generalist (Gnaphosidae: Gnaphosa sp.) was similarly potent against both prey types. Prey-specific Lampona toxins were found to form part of the protein (>10 kDa) fraction of the venom. These data provide insights into the molecular adaptations of venoms produced by prey-specialised spiders.
2023-02-08 | PXD033502 | Pride
Project description:In this study transcriptomic data of three life history stages of Orciraptor agilis was generated: 1) Gliding cells in absence of food ('gliding'), 2) Cells attached to the cell wall of its algal prey during perforation ('fattacking'), 3) Cells after acquisition of the algal plastid material ('digesting'). Furthermore, RNA-seq of the algal prey Mougeotia sp. was also performed. A de novo transcriptome assembly of the algal reads was performed in order to identify and substract algal reads of the Orciraptor samples by mapping the Orciraptor reads to the algal transcriptome. After this filtering step the remaining Orciraptor reads from all libraries were pooled for a de novo transcriptome assembly of Orciraptor agilis. This transcriptome was the basis for a comparative transcriptomic study in which transcript expression was compared between the three life history stages.
2022-06-13 | E-MTAB-11291 | biostudies-arrayexpress