Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans
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ABSTRACT:
ORGANISM(S): Steinernema carpocapsae Caenorhabditis elegans
PROVIDER: GSE156356 | GEO | 2020/08/18
REPOSITORIES: GEO
Similar Datasets
Project description:Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans
| PRJNA657600 | ENA
Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.
2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress
Project description:Steinernema carpocapsae genomic variation
| PRJNA351254 | ENA
Project description:Schistosomes are obligate helminths responsible for over 218 million cases of human schistosomiasis in 78 countries around the world. Infection occurs when free-swimming cercariae penetrate human skin and initiate developmental progression into parasitic obligate worms that consume red blood cells. Transcriptomic studies of infectious cercariae reveal abundant mRNAs associated with energy metabolism and host invasion. However, the cercaria is mostly transcriptionally quiescent, suggesting that most mRNAs are primed prior to cercarial escape from the snail host. The use of transcriptomics to understand protein expression presumes that transcription and translation are functionally coupled and the cercarial stage has categorically been treated as a single unit for -omic analysis. Per contra, the relationship between transcription and translation in infectious cercariae has not been described. To understand the correlation between transcription and translation in cercariae, we separately measured nascent translation levels in cercarial heads, cercarial tails and in the developing schistosomula, the next stage of its life cycle. The loss of the cercarial tail is essential for the transformation from a cercaria to a schistosomulum. We observed that translation was initially limited and the translation rate accelerated during the first 72-hours after tail loss. When we tested nascent translation in cercarial heads, cercarial tails, whole cercariae, and 4-hour schistosomula, we found that translation is significantly upregulated in the cercarial tail when compared to the cercarial head and that translation was undetectable in heads using immunofluorescent image quantification (p = .0005). These data represent a major shift in how we understand the cercarial stage. The cercarial head is mostly transcriptionally and translationally quiescent while being sufficient for progression into a schistosomulum. In addition, transcription and translation are not linked in Schistosoma mansoni cercaria. Thus, our current conceptual approach of treating the cercaria as a single functional unit for -omic studies may be insufficient to understand cercarial development.
| S-EPMC6816793 | biostudies-literature
Project description:Steinernema carpocapsae Raw sequence reads
| PRJNA938950 | ENA
Project description:Young adult N2 Caenorhabditis elegans were infected with Enterococcus faecalis or Enterococcus faecium for 8 h to determine the transcriptional host response to each enterococcal species. Analysis of differential gene expression in C. elegans young adults exposed to four different bacteria: heat-killed Escherichia coli strain OP50 (control), wild-type E. faecalis MMH594, wild-type E. faecium E007, or Bacillus subtilis PY79 (sigF::kan). Samples were analyzed at 8 hours after exposure to the different bacteria. These studies identified C. elegans genes induced by pathogen infection. Brain-heart infusion agar plates (10 ug/ml kanamycin) were used.
2018-02-14 | GSE95636 | GEO
Project description:We report small RNA sequencing of the entomopathogenic nematode Steinernema carpocapsae. The nematodes were grown in liquid culture in homogenates of pig kidney/fat and infective juveniles were gathered. Then Galleria mellonella insect haemolymph was added to simulate insect infection, control nematodes weren't added haemolymph. Nematodes were collected after two hours after haemolymph addition. infective juveniles S. carpocapsae were incubated with and without haemolymph, three replicates
2016-09-05 | E-GEOD-85256 | biostudies-arrayexpress
Project description:Steinernema carpocapsae Transcriptome or Gene expression
| PRJNA525359 | ENA
Project description:Steinernema carpocapsae strain:ALL Genome sequencing and assembly
| PRJNA202318 | ENA
Project description:Observers are better at discriminating upright bodies than inverted bodies, and this body inversion effect (BIE) is reliable with whole figures (bodies with heads), but not with bodies presented without heads or the heads occluded suggesting that heads may be key to BIEs. Some studies present whole figures and bodies without heads between groups, and BIEs are not found for bodies without heads [1]. Other studies present whole figures and bodies without heads in the same blocks and BIEs are found with bodies without heads [2]. Does seeing the heads of whole figures induce BIEs in bodies without heads? Here, participants discriminated bodies with either whole figures and bodies without heads presented within blocks, or in separate blocks with bodies without heads presented first. We tested body identity and posture discrimination and measured participants' gaze. BIEs were found with whole figures and bodies without heads in both identity and posture discrimination, and in both study designs. However, efficiency scores were better for the whole figures than the bodies without heads, but only when whole figures appeared in separate blocks. The magnitude of the BIE was overall stronger for whole figures compared to bodies without heads, but only in identity discrimination. BIE magnitudes were similar in the identity and posture tasks. Participants were better at identity discrimination, yet, there was greater looking at heads and less at bodies. During posture discrimination, greater looking at bodies and less at heads was associated with better performance. Faces might influence BIEs but are not essential. Configural representations of bodies without heads are sufficient for BIEs in posture and identity discrimination.
| S-EPMC8853516 | biostudies-literature