Transcriptomic profiling of host-parasite interactions in the microsporidian <i>Trachipleistophora hominis</i>

BACKGROUND: Trachipleistophora hominis was isolated from an HIV/AIDS patient and is a member of a highly successful group of obligate intracellular parasites. METHODS: Here we have investigated the evolution of the parasite and the interplay between host and parasite gene expression using transcriptomics of T. hominis-infected rabbit kidney cells. RESULTS: T. hominis has about 30 % more genes than small-genome microsporidians. Highly expressed genes include those involved in growth, replication, defence against oxidative stress, and a large fraction of uncharacterised genes. Chaperones are also highly expressed and may buffer the deleterious effects of the large number of non-synonymous mutations observed in essential T. hominis genes. Host expression suggests a general cellular shutdown upon infection, but ATP, amino sugar and nucleotide sugar production appear enhanced, potentially providing the parasite with substrates it cannot make itself. Expression divergence of duplicated genes, including transporters used to acquire host metabolites, demonstrates ongoing functional diversification during microsporidian evolution. We identified overlapping transcription at more than 100 loci in the sparse T. hominis genome, demonstrating that this feature is not caused by genome compaction. The detection of additional transposons of insect origin strongly suggests that the natural host for T. hominis is an insect. CONCLUSIONS: Our results reveal that the evolution of contemporary microsporidian genomes is highly dynamic and innovative. Moreover, highly expressed T. hominis genes of unknown function include a cohort that are shared among all microsporidians, indicating that some strongly conserved features of the biology of these enormously successful parasites remain uncharacterised. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1989-z) contains supplementary material, which is available to authorized users

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have <21, 000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. © 2012 Macmillan Publishers Limited. All rights reserved

Defensive responses by a social caterpillar are tailored to different predators and change with larval instar and group size

Gregariousness in animals is widely accepted as a behavioral adaptation for protection from predation. However, predation risk and the effectiveness of a prey’s defense can be a function of several other factors, including predator species and prey size or age. The objective of this study was to determine if the gregarious habit of Malacosoma disstria caterpillars is advantageous against invertebrate natural enemies, and whether it is through dilution or cooperative defenses. We also examined the effects of larval growth and group size on the rate and success of attacks. Caterpillars of M. disstria responded with predator-specific behaviors, which led to increased survival. Evasive behaviors were used against stinkbugs, while thrashing by fourth instar caterpillars and holding on to the silk mat by second instar caterpillars was most efficient against spider attacks. Collective head flicking and biting by groups of both second and fourth instar caterpillars were observed when attacked by parasitoids. Increased larval size decreased the average number of attacks by spiders but increased the number of attacks by both stinkbugs and parasitoids. However, increased body size decreased the success rate of attacks by all three natural enemies and increased handling time for both predators. Larger group sizes did not influence the number of attacks from predators but increased the number of attacks and the number of successful attacks from parasitoids. In all cases, individual risk was lower in larger groups. Caterpillars showed collective defenses against parasitoids but not against the walking predators. These results show that caterpillars use different tactics against different natural enemies. Overall, these tactics are both more diverse and more effective in fourth instar than in second instar caterpillars, confirming that growth reduces predation risk. We also show that grouping benefits caterpillars through dilution of risk, and, in the case of parasitoids, through group defenses. The decreased tendency to aggregate in the last larval instar may therefore be linked to decreasing predation risk

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing &amp;gt;3200 variants in &amp;gt;470 genes from &amp;gt;3100 publications

Reality Monitoring and Metamemory in Adults with Autism Spectrum Conditions.

Studies of reality monitoring (RM) often implicate medial prefrontal cortex (mPFC) in distinguishing internal and external information, a region linked to autism-related deficits in social and self-referential information processing, executive function, and memory. This study used two RM conditions (self-other; perceived-imagined) to investigate RM and metamemory in adults with autism. The autism group showed a deficit in RM, which did not differ across source conditions, and both groups exhibited a self-encoding benefit on recognition and source memory. Metamemory for perceived-imagined information, but not for self-other information, was significantly lower in the autism group. Therefore, reality monitoring and metamemory, sensitive to mPFC function, appear impaired in autism, highlighting a difficulty in remembering and monitoring internal and external details of past events.This research was supported by a James S. McDonnell Scholar Award to J.S.S., and an Economic and Social Research Council Award to R.A.C

Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote

Background: The microsporidian Encephalitozoon cuniculi possesses one of the most reduced and compacted eukaryotic genomes. Reduction in this intracellular parasite has affected major cellular machinery, including the loss of over fifty core spliceosomal components compared to S. cerevisiae. To identify expression changes throughout the parasite’s life cycle and also to assess splicing in the context of this reduced system, we examined the transcriptome of E. cuniculi using Illumina RNA-seq. Results We observed that nearly all genes are expressed at three post-infection time-points examined. A large fraction of genes are differentially expressed between the first and second (37.7%) and first and third (43.8%) time-points, while only four genes are differentially expressed between the latter two. Levels of intron splicing are very low, with 81% of junctions spliced at levels below 50%. This is dramatically lower than splicing levels found in two other fungal species examined. We also describe the first case of alternative splicing in a microsporidian, an unexpected complexity given the reduction in spliceosomal components. Conclusions Low levels of splicing observed are likely the result of an inefficient spliceosome; however, at least in one case, splicing appears to be playing a functional role. Although several RNA decay genes are encoded in E. cuniculi, the lack of a few key players could be reducing decay levels and therefore increasing the proportion of unspliced transcripts. Significant proportions of genes are differentially expressed in the first forty-eight hours but not after, indicative of genetic changes that precede the intracellular to infective stage transition.Botany, Department ofNon UBCScience, Faculty ofReviewedFacult

Splicing and Transcription Differ between Spore and Intracellular Life Stages in the Parasitic Microsporidia

Abstract Microsporidia are a diverse group of highly derived fungal relatives that are intracellular parasites of many animals. Both transcription and introns have been shown to be unusual in microsporidia: The complete genome of the human parasite Encephalitozoon cuniculi has only a few very short introns, and two distantly related microsporidian spores have been shown to harbor transcripts encoding several genes that overlap on different strands. However, microsporidia alternate between two life stages: the intracellular proliferative stage and the extracellular and largely metabolically dormant infectious spore. To date, most studies have focused on the spore. Here, we have compared transcription profiles for a number of genes from both life stages of microsporidia and found major differences in both the prevalence of overlapping transcription and splicing. Specifically, spore transcripts in E. cuniculi have longer 5# untranslated regions, overlap more frequently with upstream genes, and have a significantly higher number of transcription initiation sites compared with intracellular transcripts from the same species. In addition, we demonstrate that splicing occurs exclusively in the intracellular stage and not in spore messenger RNAs (mRNAs) in both E. cuniculi and the distantly related Antonospora locustae. These differences between the microsporidian life stages raise questions about the functional importance of transcripts in the spore. We hypothesize that at least some transcripts in spores are a product of the cell&apos;s transition into a dormant state and that these unusual mRNAs could play a structural role rather than an informational one