Transcriptomic analysis of thermally stressed Symbiodinium reveals differential expression of stress and metabolism genes

Endosymbioses between dinoflagellate algae (Symbiodinium sp.) and scleractinian coral species form the foundation of coral reef ecosystems. The coral symbiosis is highly susceptible to elevated temperatures, resulting in coral bleaching, where the algal symbiont is released from host cells. This experiment aimed to determine the transcriptional changes in cultured Symbiodinium, to better understand the response of cellular mechanisms under future temperature conditions. Cultures were exposed to elevated temperatures (average 31°C) or control conditions (24.5°C) for a period of 28 days. Whole transcriptome sequencing of Symbiodinium cells on days 4, 19, and 28 were used to identify differentially expressed genes under thermal stress. A large number of genes representing 37.01% of the transcriptome (∼23,654 unique genes, FDR < 0.05) with differential expression were detected at no less than one of the time points. Consistent with previous studies of Symbiodinium gene expression, fold changes across the transcriptome were low, with 92.49% differentially expressed genes at ≤2-fold change. The transcriptional response included differential expression of genes encoding stress response components such as the antioxidant network and molecular chaperones, cellular components such as core photosynthesis machinery, integral light-harvesting protein complexes and enzymes such as fatty acid desaturases. Differential expression of genes encoding glyoxylate cycle enzymes were also found, representing the first report of this in Symbiodinium. As photosynthate transfer from Symbiodinium to coral hosts provides up to 90% of a coral’s daily energy requirements, the implications of altered metabolic processes from exposure to thermal stress found in this study on coral-Symbiodinium associations are unknown and should be considered when assessing the stability of the symbiotic relationship under future climate conditions

Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses

Insects are the most diverse group of animals on the planet, comprising over 90% of all metazoan life forms, and have adapted to a wide diversity of ecosystems in nearly all environments. They have evolved highly sensitive chemical senses that are central to their interaction with their environment and to communication between individuals. Understanding the molecular bases of insect olfaction is therefore of great importance from both a basic and applied perspective. Odorant binding proteins (OBPs) are some of most abundant proteins found in insect olfactory organs, where they are the first component of the olfactory transduction cascade, carrying odorant molecules to the olfactory receptors. We carried out a search for OBPs in the genome of the parasitoid wasp Nasonia vitripennis and identified 90 sequences encoding putative OBPs. This is the largest OBP family so far reported in insects. We report unique features of the N. vitripennis OBPs, including the presence and evolutionary origin of a new subfamily of double-domain OBPs (consisting of two concatenated OBP domains), the loss of conserved cysteine residues and the expression of pseudogenes. This study also demonstrates the extremely dynamic evolution of the insect OBP family: (i) the number of different OBPs can vary greatly between species; (ii) the sequences are highly diverse, sometimes as a result of positive selection pressure with even the canonical cysteines being lost; (iii) new lineage specific domain arrangements can arise, such as the double domain OBP subfamily of wasps and mosquitoes.Rothamsted Research receives grant-aided support from the BBSRC of the UK. The authors thank Prof. David M. Shuker, University of Edinburgh, UK, who provided us with N. vitripennis. FGV was supported by a predoctoral fellowship SFRH/BD/22360/2005 from the ‘Fundac¸a˜o para a Cieˆncia e a Tecnologı´a’ (Portugal). This work was funded by grants BFU2007-62927 and BFU2010-15484 from the ‘Direccio´n General de Investigacio´n Cientı´fica y Te´cnica’ (Spain) to JR. JR was partially supported by ICREA Academia (Generalitat de Catalunya). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Empirical distribution of k-word matches in biological sequences

This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are firstly that it does not assume that homologous segments are contiguous, and secondly that the algorithm is computationally extremely fast, the runtime being proportional to the size of the sequence under scrutiny. Existing applications of the D_2 statistic include the clustering of related sequences in large EST databases such as the STACK database. Such applications have typically relied on heuristics without any statistical basis. Rigorous statistical characterisations of the distribution of D_2 have subsequently been undertaken, but have focussed on the distribution's asymptotic behaviour, leaving the distribution of D_2 uncharacterised for most practical cases. The work presented here bridges these two worlds to give usable approximations of the distribution of D_2 for ranges of parameters most frequently encountered in the study of biological sequences.Comment: 23 pages, 10 figure

Valuing Compromise for the Common Good

Pursuing the common good in a pluralist democracy is not possible without making compromises. Yet the spirit of compromise is in short supply in contemporary American politics. The permanent campaign has made compromise more difficult to achieve, as the uncompromising mindset suitable for campaigning has come to dominate the task of governing. To begin to make compromise more feasible and the common good more attainable, we need to appreciate the distinctive value of compromise and recognize the misconceptions that stand in its way. A common mistake is to assume that compromise requires finding the common ground on which all can agree. That undermines more realistic efforts to seek classic compromises, in which each party gains by sacrificing something valuable to the other, and together they serve the common good by improving upon the status quo. Institutional reforms are desirable, but they, too, cannot get off the ground without the support of leaders and citizens who learn how and when to adopt a compromising mindset

A comparative view of early development in the corals Favia lizardensis, Ctenactis echinata, and Acropora millepora - morphology, transcriptome, and developmental gene expression

Fasta file of sequences of PCR products. (TXT 7 kb

Use of curved adhesively bonded anchorage for a pultruded composite cable

International audienceIn order to join a plane composite cable to the main structure of a composite footbridge designed within (Caron, 2009), it was decided to investigate structural adhesive bonding. This technique is indeed particularly adapted to composite materials. However structural adhesive bonding induces stress concentrations at the edges of the adhesive joint, which have been studied by a large number of researchers in order to reduce these phenomena and increase the capacity and service life of the bonded joint (Kinloch, 1987). These studies are all concerned with optimizing shear stress transfer in adhesively bonded joints. This paper investigates the role of hydrostatic pressure on the ultimate capacities of common civil engineering adhesives. The conclusions led us to study a new joint geometry, the " curved " bonded joint that naturally creates compressive stresses on the edge of the bonded joint. Several experimental investigations are presented within this paper to illustrate the optimization. These are quasi-static tests that compare classical shear lap joints to curved joints. Additional testing is currently in progress, but the curved bonded joint seems to hold good prospects and a patent has been filed

Use of a curved adhesively bonded anchorage for a pultruded composite cable

7th International Conference on FRP Composites in Civil Engineering (CICE), VANCOUVER, CANADA, 20-/08/2014 - 22/08/2014In order to join a plane composite cable to the main structure of a composite footbridge designed within (Caron, 2009), it was decided to investigate structural adhesive bonding. This technique is indeed particularly adapted to composite materials. However structural adhesive bonding induces stress concentrations at the edges of the adhesive joint, which have been studied by a large number of researchers in order to reduce these phenomena and increase the capacity and service life of the bonded joint (Kinloch, 1987). These studies are all concerned with optimizing shear stress transfer in adhesively bonded joints. This paper investigates the role of hydrostatic pressure on the ultimate capacities of common civil engineering adhesives. The conclusions led us to study a new joint geometry, the 'curved' bonded joint that naturally creates compressive stresses on the edge of the bonded joint. Several experimental investigations are presented within this paper to illustrate the optimization. These are quasi-static tests that compare classical shear lap joints to curved joints. Additional testing is currently in progress, but the curved bonded joint seems to hold good prospects and a patent has been filed

Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes

Endosymbioses between dinoflagellate algae (Symbiodinium sp.) and scleractinian coral species form the foundation of coral reef ecosystems. The coral symbiosis is highly susceptible to elevated temperatures, resulting in coral bleaching, where the algal symbiont is released from host cells. This experiment aimed to determine the transcriptional changes in cultured Symbiodinium, to better understand the response of cellular mechanisms under future temperature conditions. Cultures were exposed to elevated temperatures (average 31°C) or control conditions (24.5°C) for a period of 28 days. Whole transcriptome sequencing of Symbiodinium cells on days 4, 19, and 28 were used to identify differentially expressed genes under thermal stress. A large number of genes representing 37.01% of the transcriptome (∼23,654 unique genes, FDR < 0.05) with differential expression were detected at no less than one of the time points. Consistent with previous studies of Symbiodinium gene expression, fold changes across the transcriptome were low, with 92.49% differentially expressed genes at ≤2-fold change. The transcriptional response included differential expression of genes encoding stress response components such as the antioxidant network and molecular chaperones, cellular components such as core photosynthesis machinery, integral light-harvesting protein complexes and enzymes such as fatty acid desaturases. Differential expression of genes encoding glyoxylate cycle enzymes were also found, representing the first report of this in Symbiodinium. As photosynthate transfer from Symbiodinium to coral hosts provides up to 90% of a coral's daily energy requirements, the implications of altered metabolic processes from exposure to thermal stress found in this study on coral-Symbiodinium associations are unknown and should be considered when assessing the stability of the symbiotic relationship under future climate conditions.This study was supported by the Australian Research Council Centre of Excellence for Coral Reef Studies (CE140100020) and Australian Research Council Discovery Projects (DP130101421 and DP160100271)

Differential Gene Expression at Coral Settlement and Metamorphosis - A Subtractive Hybridization Study

A successful metamorphosis from a planktonic larva to a settled polyp, which under favorable conditions will establish a future colony, is critical for the survival of corals. However, in contrast to the situation in other animals, e.g., frogs and insects, little is known about the molecular basis of coral metamorphosis. We have begun to redress this situation with previous microarray studies, but there is still a great deal to learn. In the present paper we have utilized a different technology, subtractive hybridization, to characterize genes differentially expressed across this developmental transition and to compare the success of this method to microarray.\ud \ud Methodology/Principal Findings\ud \ud Suppressive subtractive hybridization (SSH) was used to identify two pools of transcripts from the coral, Acropora millepora. One is enriched for transcripts expressed at higher levels at the pre-settlement stage, and the other for transcripts expressed at higher levels at the post-settlement stage. Virtual northern blots were used to demonstrate the efficacy of the subtractive hybridization technique. Both pools contain transcripts coding for proteins in various functional classes but transcriptional regulatory proteins were represented more frequently in the post-settlement pool. Approximately 18% of the transcripts showed no significant similarity to any other sequence on the public databases. Transcripts of particular interest were further characterized by in situ hybridization, which showed that many are regulated spatially as well as temporally. Notably, many transcripts exhibit axially restricted expression patterns that correlate with the pool from which they were isolated. Several transcripts are expressed in patterns consistent with a role in calcification.\ud \ud Conclusions\ud \ud We have characterized over 200 transcripts that are differentially expressed between the planula larva and post-settlement polyp of the coral, Acropora millepora. Sequence, putative function, and in some cases temporal and spatial expression are reported

Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species

Reef-building corals and some other cnidarians form symbiotic relationships with members of the dinoflagellate family Symbiodinaceae. As Symbiodinaceae is a highly diverse taxon, the physiological interactions between its members and their hosts are assumed to differ between associations. The presence of different symbiont types is known to affect expression levels of specific host genes, but knowledge of the effects on the transcriptome more broadly remains limited. In the present study, transcriptome profiling was conducted on the tropical corallimorpharian, Ricordea yuma, following the establishment of symbiosis with either the \u27homologous\u27 symbiont Symbiodinium goreaui (also known as Cladocopium goreaui; ITS2 type C1) or \u27heterologous\u27 symbionts (predominantly S. trenchii, which is also known as Durusdinium trenchii; ITS2 type D1a) isolated from a different corallimorpharian host (Rhodactis indosinensis). Transcriptomic analyses showed that genes encoding host glycogen biosynthesis pathway components are more highly induced during colonization by the homologous symbiont than by the heterologous symbiont. Similar patterns were also observed for several other genes thought to facilitate symbiotic nutrient exchange, including those involved in lipid translocation/storage and metabolite transport. The gene expression results presented here imply that colonization by homologous or heterologous Symbiodinium types may have very different metabolic consequences for the Ricordea host, supporting the notion that even though some cnidarians may be able to form novel symbioses after bleaching, the metabolic performance of these may be compromised.This article has an associated First Person interview with the first author of the paper