Onset and breakdown of cnidarian-dinoflagellate symbiosis : a survey of the host transcriptomic response and characterization of the sphingosine rheostat during symbiont colonization and hyperthermal stress

The symbiosis between cnidarians, such as corals and sea anemones, and photosynthetic dinoflagellates belonging to the genus Symbiodinium spp. is one of the most productive in the marine environment. This mutualistic endosymbiosis allow reef-building corals to lay down the foundation of coral reef ecosystems, which supports a highly biodiverse community of marine organisms. The relationship between the cnidarian host and algal symbiont changes over time, from the initial contact through symbiont removal. The breakdown of the partnership can be brought on by numerous environmental stressors; most notably by elevated temperatures associated with climate change. The cellular and molecular mechanisms underlying these key events in cnidarian-dinoflagellate symbiosis are still poorly understood. Lipids play a central role in symbiosis by providing cellular structure, energy storage, signaling platforms. Specifically, the signaling lipids from the sphingosine rheostat, sphingosine and sphingosine-1-phosphate (S1P), play a pivotal role in determining cell fate. Increased sphingosine drives apoptotic activity within the cell while S1P promotes cell survival. The research presented in this dissertation addresses (1) the role of signaling sphingolipids at different stages of cnidarian-dinoflagellate symbiosis and (2) the transcriptional patterns of coral larvae undergoing onset of symbiosis while exposed to elevated seawater temperatures. In Chapter 2, the proposed cnidarian sphingosine rheostat model was functionally characterized in the sea anemone Aiptasia pallida. This study identified differential response of the sphingosine rheostat with symbiont recolonization and long-term symbiont maintenance, suggesting a role in host-symbiont interactions. In Chapter 3, a heat stress experiment revealed a biphasic sphingosine rheostat response in A. pallida where acute stress inhibits rheostat expression and activity that is recovered and shifted toward cell death with longer-term heat stress. This response was not linked to symbiont loss, but has implications for a more generalized heat stress response for long-term acclimation in cnidarians. In Chapter 4, coral Acropora digitifera larvae displayed different phenotypes and transcriptional profiles with the combined stress of elevated temperature and symbiont uptake. Larval survival, symbiont colonization and algal density were highly reduced from this treatment. These transcriptional patterns indicate immune suppression, membrane reorganization and oxidative stress. Furthermore, sphingolipid signaling differed at the onset of heat stress. Overall, the work presented here indicates that the sphingosine rheostat mediates host-symbiont interactions until symbiosis dysfunction and that the determinants of symbiosis can be altered with climate-induced stress.Keywords: RNA-Seq, sphingolipids, coral, symbiosis, Aiptais

Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus

Background Oribatid mites are a specious order of microarthropods within the subphylum Chelicerata, compromising about 11,000 described species. They are ubiquitously distributed across different microhabitats in all terrestrial ecosystems around the world and were among the first animals colonizing terrestrial habitats as decomposers and scavengers. Noted for their biosynthesis capacities and biochemical diversity, the majority of oribatid mites possess a pair of exocrine opisthonotal oil-glands used for chemical defense and communication. Genomic resources are lacking for oribatids despite their species richness and ecological importance. Results We used a comparative genomic approach to investigate the developmental, sensory and glandular biosynthetic gene repertoire of the clonal, all-female oribatid mite species Archegozetes longisetosus Aoki, a model species used by numerous laboratories for the past 30 years. Here, we present a 190-Mb genome assembly constructed from Nanopore MinION and Illumina sequencing platforms with 23,825 predicted protein-coding genes. Genomic and transcriptional analyses revealed patterns of reduced body segmentation and loss of segmental identity gene abd-A within Acariformes, and unexpected expression of key eye development genes in these eyeless mites across developmental stages. Consistent with the soil dwelling lifestyle, investigation of the sensory genes revealed a species-specific expansion of gustatory receptors, the largest chemoreceptor family in the genome used in olfaction, and evidence of horizontally transferred enzymes used in cell wall degradation of plant and fungal matter, both components of the Archegozetes longisetosus diet. Using biochemical and genomic data, we were able to delineate the backbone biosynthesis of monoterpenes, an important class of compounds found in the major exocrine gland system of Oribatida – the oil glands. Conclusions With the Archegozetes longisetosus genome, we now have the first high-quality, annotated genome of an oribatid mite genome. Given the mite’s strength as an experimental model, the new sequence resources provided here will serve as the foundation for molecular research in Oribatida and will enable a broader understanding of chelicerate evolution

Adaptation and validation of the Nigerian Igbo Multidimensional Scale of Perceived Social Support in patients with chronic low back pain

Social support may be important in the perpetuation of symptoms in chronic low back pain (CLBP). The multidimensional scale of perceived social support (MSPSS) is one of the best measures of social support with applicability in Africa. The aims of this study were to translate, culturally adapt, test-retest, and assess cross-sectional psychometric properties of the Igbo-MSPSS. Methods: Forward and backward translation of the MSPSS was done by clinicians and non-clinician translators and evaluated by a specialist review committee. The adapted measure was piloted amongst twelve adults with CLBP in rural Nigeria. Cronbach's alpha and McDonald's omega coefficient were used for investigating internal consistency. Intra-class correlation coefficient (ICC: two-way random effects model, average of raters' measurements, absolute definition of agreement) reflecting both the degree of correlation and agreement between measurements was used for the statistical investigation of test-retest reliability. Criterion validity of the adapted measure was investigated with the eleven-point box scale, back performance scale, Roland Morris Disability Questionnaire, and World Health Organisation Disability Assessment Schedule amongst 200 people with CLBP in rural Nigeria using Spearman's correlation analyses. Exploratory factor analyses conducted using Kaiser criterion and parallel analysis as methods for determining dimensionality were used to determine the structural validity of the adapted measure amongst the same sample of 200 rural dwellers. Results: Igbo-MSPSS had excellent internal consistency (0.88) and ICC of 0.82. There were moderate correlations with measures associated with the social support construct. The same item-factor pattern in the three-dimensional structure (with Kaiser criterion) as in the original measure and a two-dimensional structure (with parallel analysis) were produced. Conclusions: Igbo-MSPSS is a measure of social support with some evidence of validity and reliability and can be used clinically or for research. Future studies are required to confirm its validity and reliability

The Role of Complement in Cnidarian-Dinoflagellate Symbiosis and Immune Challenge in the Sea Anemone Aiptasia pallida

The complement system is an innate immune pathway that in vertebrates, is responsible for initial recognition and ultimately phagocytosis and destruction of microbes. Several complement molecules including C3, Factor B, and mannose binding lectin associated serine proteases (MASP) have been characterized in invertebrates and while most studies have focused on their conserved role in defense against pathogens, little is known about their role in managing beneficial microbes. The purpose of this study was to (1) characterize complement pathway genes in the symbiotic sea anemone Aiptasia pallida, (2) investigate the evolution of complement genes in invertebrates, and (3) examine the potential dual role of complement genes Factor B and MASP in the onset and maintenance of cnidarian-dinoflagellate symbiosis and immune challenge using qPCR based studies. The results demonstrate that A. pallida has multiple Factor B genes (Ap_Bf-1, Ap_Bf-2a, and Ap_Bf-2b) and one MASP gene (Ap_MASP). Phylogenetic analysis indicates that the evolutionary history of complement genes is complex, and there have been many gene duplications or gene loss events, even within members of the same phylum. Gene expression analyses revealed a potential role for complement in both onset and maintenance of cnidarian-dinoflagellate symbiosis and immune challenge. Specifically, Ap_Bf-1 and Ap_MASP are significantly upregulated in the light at the onset of symbiosis and in response to challenge with the pathogen Serratia marcescens suggesting that they play a role in the initial recognition of both beneficial and harmful microbes. Ap_Bf-2b in contrast, was generally downregulated during the onset and maintenance of symbiosis and in response to challenge with S. marcescens. Therefore, the exact role of Ap_Bf-2b in response to microbes remains unclear, but the results suggest that the presence of microbes leads to repressed expression. Together, these results indicate functional divergence between Ap_Bf-1 and Ap_Bf-2b, and that Ap_Bf-1 and Ap_MASP may be functioning together in an ancestral hybrid of the lectin and alternative complement pathways. Overall, this study provides information on the role of the complement system in a basal metazoan and its role in host-microbe interactions.Keywords: Symbiodinium, symbiosis, Serratia marcescens, Aiptasia, cnidarians, complement, innate immunit

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding of these processes will require extending beyond the sequenced coral genome (Acropora digitifera) to encompass diverse coral species and related anthozoans. Toward that end, we have assembled and annotated reference transcriptomes to develop catalogs of gene sequences for three scleractinian corals (Fungia scutaria, Montastraea cavernosa, Seriatopora hystrix) and a temperate anemone (Anthopleura elegantissima). High-throughput sequencing of cDNA libraries produced ∼20–30 million reads per sample, and de novo assembly of these reads produced ∼75,000–110,000 transcripts from each sample with size distributions (mean ∼1.4 kb, N₅₀ ∼2 kb), comparable to the distribution of gene models from the coral genome (mean ∼1.7 kb, N₅₀ ∼2.2 kb). Each assembly includes matches for more than half the gene models from A. digitifera (54–67%) and many reasonably complete transcripts (∼5300–6700) spanning nearly the entire gene (ortholog hit ratios ≥0.75). The catalogs of gene sequences developed in this study made it possible to identify hundreds to thousands of orthologs across diverse scleractinian species and related taxa. We used these sequences for phylogenetic inference, recovering known relationships and demonstrating superior performance over phylogenetic trees constructed using single mitochondrial loci. The resources developed in this study provide gene sequences and genetic markers for several anthozoan species. To enhance the utility of these resources for the research community, we developed searchable databases enabling researchers to rapidly recover sequences for genes of interest. Our analysis of de novo assembly quality highlights metrics that we expect will be useful for evaluating the relative quality of other de novo transcriptome assemblies. The identification of orthologous sequences and phylogenetic reconstruction demonstrates the feasibility of these methods for clarifying the substantial uncertainties in the existing scleractinian phylogeny.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: http://www.g3journal.org/Keywords: database, coral, nonmodel system, phylogenomic

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.journal articl

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Background: The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods: This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings: Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation: This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding: Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant