Ontology highlight
ABSTRACT:
PROVIDER: PRJNA471544 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7167830_1.fastq.gz | Fastqsanger.gz | |||
| SRR7167830_2.fastq.gz | Fastqsanger.gz | |||
| SRR7167831_1.fastq.gz | Fastqsanger.gz | |||
| SRR7167831_2.fastq.gz | Fastqsanger.gz | |||
| SRR7167832_1.fastq.gz | Fastqsanger.gz |
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Project description:Brucella dynamically engage macrophages while trafficking to an intracellular replicative niche as macrophages, the first line of innate host defense, attempt to eliminate organisms. Brucella melitensis, B. neotomae, and B. ovis are highly homologous, yet exhibit a range of host pathogenicity and specificity. RAW 264.7 macrophages infected with B. melitensis, and B. ovis exhibit divergent patterns of bacterial persistence and clearance; conversely, B. melitensis and B. neotomae exhibit similar patterns of infection. Evaluating early macrophage interaction with Brucella spp. allows discovery of host entry and intracellular translocation mechanisms, rather than bacterial replication. Microarray analysis of macrophage transcript levels following a 4 hr Brucella spp. infection revealed 130 probe sets altered compared to uninfected macrophages; specifically, 72 probe sets were increased and 58 probe sets were decreased with any Brucella spp. Interestingly, much of the inflammatory response was not regulated by the number of Brucella gaining intracellular entry, as macrophage transcript levels were often equivalent among B. melitensis, B. ovis, and B. neotomae infections. An additional 33 probe sets were identified with altered macrophage transcript levels among Brucella spp. infections that may correlate with species specific host defenses and intracellular survival. Gene ontological categorization unveiled genes altered among species are involved in cell growth and maintenance, response to external stimuli, transcription regulation, transporter activity, endopeptidase inhibitor activity and G-protein mediated signaling. Host transcript profiles provide a foundation to understand variations in Brucella spp. infections, while structure of the macrophage response and intracellular niche of Brucella spp. will be revealed through piecewise consideration of host signaling pathways. Keywords: Macrophage, intracellular pathogen, Brucella melitensis, Brucella neotomae, Brucella ovis, inflammatory immune response, species specificity
2010-01-01 | GSE8385 | GEO
Project description:The potato cyst nematodes (PCN), Globodera pallida and Globodera rostochiensis, are important parasites of potato. PCN have complex, biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study is to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible or partially resistant potato genotypes. For this purpose, two microarray experiments were designed: i) a comparison of eggs, infective second stage juveniles (J2) and sedentary parasitic stage J2s (SJ2); ii) a comparison of SJ2 at eight days after inoculation (DAI) in the susceptible cultivar (Desiree) and two partially resistant lines. The data set in this submission came from experiment (I). The results show differential expression of G. pallida genes during the stages studied, including previously characterized effectors. Also, a large number of genes changed their expression between the SJ2 in the susceptible cultivar compared to those infecting partially resistant lines; the number of genes with modified expression were smaller when two partially resistant lines were compared. Additionally, a histopathological study was performed at several time points (7, 14 and 30 DAI) showing the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison to the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison to the susceptible cultivar.
2012-04-12 | E-MTAB-999 | biostudies-arrayexpress
Project description:The potato cyst nematodes (PCN), Globodera pallida and Globodera rostochiensis, are important parasites of potato. PCN have complex, biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study is to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible or partially resistant potato genotypes. For this purpose, two microarray experiments were designed: i) a comparison of eggs, infective second stage juveniles (J2) and sedentary parasitic stage J2s (SJ2); ii) a comparison of SJ2 at eight days after inoculation (DAI) in the susceptible cultivar (Desiree) and two partially resistant lines. The data set in this submission came from experiment (ii). (Experiment (I) has also been deposited in ArrayExpress under accession E-MTAB-999). The results show differential expression of G. pallida genes during the stages studied, including previously characterized effectors. Also, a large number of genes changed their expression between the SJ2 in the susceptible cultivar compared to those infecting partially resistant lines; the number of genes with modified expression were smaller when two partially resistant lines were compared. Additionally, a histopathological study was performed at several time points (7, 14 and 30 DAI) showing the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison to the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison to the susceptible cultivar.
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Project description:Globodera spp. WGS sequencing and assembly, and targeted sequencing of HYP loci
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Project description:Aims: To assess the virulence of multiple Aeromonas spp. using two models, a neonatal mouse assay and a mouse intestinal cell culture. Methods and Results: Transcriptional responses to both infection models were evaluated using microarrays. After artificial infection with a variety of Aeromonas spp., mRNA extracts from the two models were processed and hydridized to murine microarrays to determine host gene response. Definition of virulence was determined based on host mRNA production in murine neonatal intestinal tissue and mortality of infected animals. Infections of mouse intestinal cell cultures were then performed to determine whether this simpler model system's mRNA responses correlated to neonatal results and therefore be predictive of virulence of Aeromonas spp. Virulent aeromonads up-regulated transcripts in both models including multiple host defense gene products (chemokines, regulation of transcription and apoptosis, cell signaling). Avirulent species exhibited little or no host response in neonates. Mortality results correlated well with both bacterial dose and average fold change of up-regulated transcripts in the neonatal mice. Conclusions: Cell culture results were less discriminating but showed promise as potentially being able to be predictive of virulence. Jun oncogene up-regulation in murine cell culture is potentially predictive of Aeromonas virulence. Significance and Impact of the Study: Having the ability to determine virulence of waterborne pathogens quickly would potentially assist public health officials to rapidly assess exposure risks. Keywords: Aeromonas; Virulence; Gene expression; Host response
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Project description:A mutualistic relationship between reef-building corals and endosymbiotic algae (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. If, and to what extent, differences in algal symbiont clade contents can exert effects on the coral host transcriptome is currently unknown. In this study, we monitored algal physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered coral fragments using a custom cDNA gene expression microarray. Combining these analyses with results from algal and host genotyping revealed a striking symbiont effect on both the acclimated coral host transcriptome and the magnitude of the thermal stress response. This is the first study that links coral host transcriptomic patterns to the clade content of their algal symbiont community. Our data provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-algal partnerships.
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Project description:Aims: To assess the virulence of multiple Aeromonas spp. using two models, a neonatal mouse assay and a mouse intestinal cell culture. Methods and Results: Transcriptional responses to both infection models were evaluated using microarrays. After artificial infection with a variety of Aeromonas spp., mRNA extracts from the two models were processed and hydridized to murine microarrays to determine host gene response. Definition of virulence was determined based on host mRNA production in murine neonatal intestinal tissue and mortality of infected animals. Infections of mouse intestinal cell cultures were then performed to determine whether this simpler model system's mRNA responses correlated to neonatal results and therefore be predictive of virulence of Aeromonas spp. Virulent aeromonads up-regulated transcripts in both models including multiple host defense gene products (chemokines, regulation of transcription and apoptosis, cell signaling). Avirulent species exhibited little or no host response in neonates. Mortality results correlated well with both bacterial dose and average fold change of up-regulated transcripts in the neonatal mice. Conclusions: Cell culture results were less discriminating but showed promise as potentially being able to be predictive of virulence. Jun oncogene up-regulation in murine cell culture is potentially predictive of Aeromonas virulence. Significance and Impact of the Study: Having the ability to determine virulence of waterborne pathogens quickly would potentially assist public health officials to rapidly assess exposure risks. Experiment Overall Design: Two infection models were assessed, live, whole animals (neonatal Swiss Webster mice) and a murine small intestinal cell culture. Biological replicates (n=5) were infected with different Aeromonas species/strains and compared to uninfected controls.
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