Ontology highlight
ABSTRACT:
PROVIDER: PRJNA715957 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14027000_1.fastq.gz | Fastqsanger.gz | |||
| SRR14027000_2.fastq.gz | Fastqsanger.gz | |||
| SRR14027100_1.fastq.gz | Fastqsanger.gz | |||
| SRR14027100_2.fastq.gz | Fastqsanger.gz | |||
| SRR14071200_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:An animal’s ability to effectively capture prey and defend against predators is pivotal to its survival1. A key innovation in many predator-prey interactions is venom, which consists of many toxin proteins that shape its phenotype2. Its unusually direct relationship of gene-toxin-phenotype make it an appealing system for studies at the organismal level 3,4. In this work we use the sea anemone Nematostella vectensis as a model organism as it provides us with the opportunity to test for the first time how toxin-genotypes impact predator-prey interactions. Specifically, we compare a native-population5 and a transgenic line which both have significantly reduced levels of Nv1, the major toxin in adult Nematostella6, to animals with wildtype levels of Nv1. We demonstrate that the transgenic strain phenocopies native anemones lacking Nv1 as they both have impaired ability to defend themselves against grass shrimp, a native predator. Mummichog killifish, unexpectedly are attracted to Nematostella with wildtype-levels of Nv1, highlighting that Nv1 plays a complex role in shaping interspecific-interactions. Finally, we demonstrate an evolutionary tradeoff as the reduction of Nv1 levels causes faster growth and increased reproductive rates compared to Nematostella control lines. Overall, our results experimentally link organism’s venom to its physiology, reproduction and interspecific interactions.
2023-12-31 | PXD043447 | Pride
Project description:An animal’s ability to effectively capture prey and defend against predators is pivotal to its survival1. A key innovation in many predator-prey interactions is venom, which consists of many toxin proteins that shape its phenotype2. Its unusually direct relationship of gene-toxin-phenotype make it an appealing system for studies at the organismal level 3,4. In this work we use the sea anemone Nematostella vectensis as a model organism as it provides us with the opportunity to test for the first time how toxin-genotypes impact predator-prey interactions. Specifically, we compare a native-population5 and a transgenic line which both have significantly reduced levels of Nv1, the major toxin in adult Nematostella6, to animals with wildtype levels of Nv1. We demonstrate that the transgenic strain phenocopies native anemones lacking Nv1 as they both have impaired ability to defend themselves against grass shrimp, a native predator. Mummichog killifish, unexpectedly are attracted to Nematostella with wildtype-levels of Nv1, highlighting that Nv1 plays a complex role in shaping interspecific-interactions. Finally, we demonstrate an evolutionary tradeoff as the reduction of Nv1 levels causes faster growth and increased reproductive rates compared to Nematostella control lines. Overall, our results experimentally link organism’s venom to its physiology, reproduction and interspecific interactions.
2023-12-31 | PXD043484 | Pride
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 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 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:Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 20 days yielded both previously described (Wrinkly Spreader; WS) and novel colony morphotype (Wrinkly Fried Egg; WFE) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance. Results: For differential gene expression the WT SBW25 without predation was used as a baseline. For the WS condition, a total of 881 differentially expressed genes (DEGs) were identified, of which 424 were upregulated and 457 were downregulated. In the WFE condition, a total of 908 DEGs were identified, of which 475 were upregulated and 434 were downregulated. Among all DEGs, 335 upregulated and 313 downregulated genes were shared between the WS1 and WFE conditions Conclusions: Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period of time. Together, the differential expression results suggest expression of features that would be expected to increase biofilm formation in WFE according to previous studies. However, increased expression of these traits may not lead to a stronger biofilm, but may still provide predation resistance. For example, fibrils may increase the effective profile size of a bacterial cell. Increased Fap-mediated biofilm formation also induces increased alginate synthesis in P. aeruginosa PA01, an exopolysaccharide that protects mucoid P. aeruginosa against macrophage killing. Interestingly, we found increased expression of alginate biosynthesis genes in both WFE and WS1 (algA, algF), suggesting alternate mechanisms leading to increased alginate production in these two strains.
2022-04-20 | GSE200723 | GEO
Project description:Myeloid cells in tumour-immune interactions.
Kareva I1, Berezovskaya F, Castillo-Chavez C.
Author information
Abstract
Despite highly developed specific immune responses, tumour cells often manage to escape recognition by the immune system, continuing to grow uncontrollably. Experimental work suggests that mature myeloid cells may be central to the activation of the specific immune response. Recognition and subsequent control of tumour growth by the cells of the specific immune response depend on the balance between immature (ImC) and mature (MmC) myeloid cells in the body. However, tumour cells produce cytokines that inhibit ImC maturation, altering the balance between ImC and MmC. Hence, the focus of this manuscript is on the study of the potential role of this inhibiting mechanism on tumour growth dynamics. A conceptual predator-prey type model that incorporates the dynamics and interactions of tumour cells, CD8(+) T cells, ImC and MmC is proposed in order to address the role of this mechanism. The prey (tumour) has a defence mechanism (blocking the maturation of ImC) that prevents the predator (immune system) from recognizing it. The model, a four-dimensional nonlinear system of ordinary differential equations, is reduced to a two-dimensional system using time-scale arguments that are tied to the maturation rate of ImC. Analysis shows that the model is capable of supporting biologically reasonable patterns of behaviour depending on the initial conditions. A range of parameters, where healing without external influences can occur, is identified both qualitatively and quantitatively.
2022-05-10 | MODEL2001310001 | BioModels