Extraordinary diversity among members of the large gene family, 185/333, from the purple sea urchin, Strongylocentrotus purpuratus

<p>Abstract</p> <p>Background</p> <p>Recent analysis of immune-related genes within the sea urchin genome revealed a number of large gene families with vertebrate homologues, such as the Toll-like and NOD/NALP-like receptor families and C-type lectins in addition to a rudimentary complement system. Therefore, the immune response of the purple sea urchin appears to be more complex than previously believed. Another component of the sea urchin immune response is an unusual family of mRNAs, known as <it>185/333</it>, which is strongly upregulated in response to pathogen challenge. The work presented here indicates that this family of transcripts is derived from an unexpectedly diverse gene family.</p> <p>Results</p> <p>The <it>185/333 </it>genes are small (< 2 kb) with only two exons. Their extraordinary diversity was exemplified by 121 unique sequences identified from 171 cloned genes. Sequences from the second exons were aligned optimally by introducing large gaps, which defined blocks of sequence known as elements. Genes were defined by the presence or absence of elements. Phylogenetic analysis defined five intron types which, when combined with the exon element patterns resulted in 31 gene patterns, 14 of which were not described previously. Sequence diversity was present in all elements, and was higher in the intron than the exons. Repeats within the sequence facilitated multiple alignments, of which two were analyzed in detail. Although the two alignments differed in length, number of elements, and number of patterns, both were about equally accurate at describing the <it>185/333 </it>sequences. The genes were closely linked and flanked by short repeats. The repeats within and between the genes may promote their diversification through gene conversion, recombination, and meiotic mispairing.</p> <p>Conclusion</p> <p>The diversity of the <it>185/333 </it>gene family represents an intriguing addition to what is known about the <it>S. purpuratus </it>immune response, and provides further evidence that invertebrate immune systems are neither simple nor static.</p

Dynamic Evolution of Toll-Like Receptor Multigene Families in Echinoderms

The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates

The Sensitivity of the IceCube Neutrino Detector to Dark Matter Annihilating in Dwarf Galaxies

In this paper, we compare the relative sensitivities of gamma-ray and neutrino observations to the dark matter annihilation cross section in leptophilic models such as have been designed to explain PAMELA data. We investigate whether the high energy neutrino telescope IceCube will be competitive with current and upcoming searches by gamma-ray telescopes, such as the Atmospheric Cerenkov Telescopes (ACTs) (HESS, VERITAS and MAGIC), or the Fermi Gamma Ray Space Telescope, in detecting or constraining dark matter particles annihilating in dwarf spheroidal galaxies. We find that after ten years of observation of the most promising nearby dwarfs, IceCube will have sensitivity comparable to the current sensitivity of gamma-ray telescopes only for very heavy (m_X > 7 TeV) or relatively light (m_X < 200 GeV) dark matter particles which annihilate primarily to mu+mu-. If dark matter particles annihilate primarily to tau+tau-, IceCube will have superior sensitivity only for dark matter particle masses below the 200 GeV threshold of current ACTs. If dark matter annihilations proceed directly to neutrino-antineutrino pairs a substantial fraction of the time, IceCube will be competitive with gamma-ray telescopes for a much wider range of dark matter masses.Comment: 7 pages, 3 figures. v2: references added and minor revisions. v3: as published in PRD

High-Energy Neutrino Signatures of Dark Matter Decaying into Leptons

Decaying dark matter has previously been proposed as a possible explanation for the excess high energy cosmic ray electrons and positrons seen by PAMELA and the Fermi Gamma-Ray Space Telescope (FGST). To accommodate these signals however, the decays must be predominantly leptonic, to muons or taus, and therefore produce neutrinos, potentially detectable with the IceCube neutrino observatory. We find that, with five years of data, IceCube (supplemented by DeepCore) will be able to significantly constrain the relevant parameter space of decaying dark matter, and may even be capable of discovering dark matter decaying in the halo of the Milky Way.Comment: 4 pages, 1 figur

A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups

<p>Abstract</p> <p>Background</p> <p>As the amount of genome sequencing data grows, so does the problem of computational gene identification, and in particular, the splicing signals that flank exon borders. Traditional methods for identifying splicing signals have been created and optimized using sequences from model organisms, mostly vertebrate and yeast species. However, as genome sequencing extends across the animal kingdom and includes various invertebrate species, the need for mechanisms to recognize splice signals in these organisms increases as well. With that aim in mind, we generated a model for identifying donor and acceptor splice sites that was optimized using sequences from the purple sea urchin, <it>Strongylocentrotus purpuratus</it>. This model was then used to assess the possibility of alternative or cryptic splicing within the highly variable immune response gene family known as <it>185/333</it>.</p> <p>Results</p> <p>A donor splice site model was generated from <it>S. purpuratus </it>sequences that incorporates non-adjacent dependences among positions within the 9 nt splice signal and uses position weight matrices to determine the probability that the site is used for splicing. The <it>Purpuratus </it>model was shown to predict splice signals better than a similar model created from vertebrate sequences. Although the <it>Purpuratus </it>model was able to correctly predict the true splice sites within the <it>185/333 </it>genes, no evidence for alternative or trans-gene splicing was observed.</p> <p>Conclusion</p> <p>The data presented herein describe the first published analyses of echinoderm splice sites and suggest that the previous methods of identifying splice signals that are based largely on vertebrate sequences may be insufficient. Furthermore, alternative or trans-gene splicing does not appear to be acting as a diversification mechanism in the <it>185/333 </it>gene family.</p

An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification

Abstract Background The immune system of the purple sea urchin, Strongylocentrotus purpuratus, is complex and sophisticated. An important component of sea urchin immunity is the Sp185/333 gene family, which is significantly upregulated in immunologically challenged animals. The Sp185/333 genes are less than 2 kb with two exons and are members of a large diverse family composed of greater than 40 genes. The S. purpuratus genome assembly, however, contains only six Sp185/333 genes. This underrepresentation could be due to the difficulties that large gene families present in shotgun assembly, where multiple similar genes can be collapsed into a single consensus gene. Results To understand the genomic organization of the Sp185/333 gene family, a BAC insert containing Sp185/333 genes was assembled, with careful attention to avoiding artifacts resulting from collapse or artificial duplication/expansion of very similar genes. Twelve candidate BAC assemblies were generated with varying parameters and the optimal assembly was identified by PCR, restriction digests, and subclone sequencing. The validated assembly contained six Sp185/333 genes that were clustered in a 34 kb region at one end of the BAC with five of the six genes tightly clustered within 20 kb. The Sp185/333 genes in this cluster were no more similar to each other than to previously sequenced Sp185/333 genes isolated from three different animals. This was unexpected given their proximity and putative effects of gene homogenization in closely linked, similar genes. All six genes displayed significant similarity including both 5' and 3' flanking regions, which were bounded by microsatellites. Three of the Sp185/333 genes and their flanking regions were tandemly duplicated such that each repeated segment consisted of a gene plus 0.7 kb 5' and 2.4 kb 3' of the gene (4.5 kb total). Both edges of the segmental duplications were bounded by different microsatellites. Conclusions The high sequence similarity of the Sp185/333 genes and flanking regions, suggests that the microsatellites may promote genomic instability and are involved with gene duplication and/or gene conversion and the extraordinary sequence diversity of this family

Distinctive expression patterns of 185/333 genes in the purple sea urchin, Strongylocentrotus purpuratus: an unexpectedly diverse family of transcripts in response to LPS, β-1,3-glucan, and dsRNA

BACKGROUND: A diverse set of transcripts called 185/333 is strongly expressed in sea urchins responding to immune challenge. Optimal alignments of full-length 185/333 cDNAs requires the insertion of large gaps that define 25 blocks of sequence called elements. The presence or absence of individual elements also defines a specific element pattern for each message. Individual sea urchins were challenged with pathogen associated molecular patterns (PAMPs) (lipopolysaccharide, β-1,3-glucan, or double stranded RNA), and changes in the 185/333 message repertoire were followed over time. RESULTS: Each animal expressed a diverse set of 185/333 messages prior to challenge and a 0.96 kb message was the predominant size after challenge. Sequence analysis of the cloned messages indicated that the major element pattern expressed in immunoquiescent sea urchins was either C1 or E2.1. In contrast, most animals responding to lipopolysaccharide, β-1,3-glucan or injury, predominantly expressed messages of the E2 pattern. In addition to the major patterns, extensive element pattern diversity was observed among the different animals before and after challenge. Nucleotide sequence diversity of the transcripts increased in response to β-1,3-glucan, double stranded RNA and injury, whereas diversity decreased in response to LPS. CONCLUSION: These results illustrate that sea urchins appear to be able to differentiate among different PAMPs by inducing the transcription of different sets of 185/333 genes. Furthermore, animals may share a suite of 185/333 genes that are expressed in response to common pathogens, while also maintaining a large number of unique genes within the population

A nomenclature for echinoderm genes.

Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jsp Database URL https://www.echinobase.org/

Self-management for obesity and cardio-metabolic fitness: Description and evaluation of the lifestyle modification program of a randomised controlled trial

Background: Sustainable lifestyle modification strategies are needed to address obesity and cardiovascular risk factors. Intensive, individualised programs have been successful, but are limited by time and resources. We have formulated a group-based lifestyle education program based upon national diet and physical activity (PA) recommendations to manage obesity and cardio-metabolic risk factors. This article describes the content and delivery of this program, with information on compliance and acceptability. Methods: Overweight/obese adults (n = 153) with metabolic syndrome were recruited from the community and randomly allocated to intervention (INT) or control (CON). Written copies of Australian national dietary and PA guidelines were provided to all participants. INT took part in a 16-week lifestyle program which provided a curriculum and practical strategies on 1) dietary and PA information based on national guidelines, 2) behavioural self-management tools, 3) food-label reading, supermarkets tour and cooking, 4) exercise sessions, and 5) peer-group support. Compliance was assessed using attendance records and weekly food/PA logs. Participants' motivations, perceived benefits and goals were assessed through facilitated discussion. Program acceptability feedback was collected through structured focus groups. Results: Although completion of weekly food/PA records was poor, attendance at information/education sessions (77% overall) and exercise participation (66% overall) was high, and compared with CON, multiple markers of body composition and cardio-metabolic health improved in INT. Participants reported that the most useful program components included food-label reading, cooking sessions, and learning new and different physical exercises, including home-based options. Participants also reported finding self-management techniques helpful, namely problem solving and short-term goal setting. The use of a group setting and supportive 'peer' leaders were found to be supportive. More frequent clinical assessment was suggested for future programs. Conclusion: This group-based lifestyle program achieved improvements in body composition and cardio-metabolic and physical fitness similar to individualised interventions which are more resource intensive to deliver. It confirmed that active training in lifestyle modification is more effective than passive provision of guidelines. Such programs should include social support and self-management techniques. Continued clinical follow up may be required for long-term maintenance in individuals attempting lifestyle behaviour change. Program facilitation by peers may help and should be further investigated in a community-based model.Tahna L Pettman, Gary MH Misan, Katherine Owen, Kate Warren, Alison M Coates, Jonathan D Buckley and Peter RC How

Integration of attractive and defensive phytochemicals is unlikely to constrain chemical diversification in a perennial herb

Diversification of plant chemical phenotypes is typically associated with spatially and temporally variable plant–insect interactions. Floral scent is often assumed to be the target of pollinator-mediated selection, whereas foliar compounds are considered targets of antagonist-mediated selection. However, floral and vegetative phytochemicals can be biosynthetically linked and may thus evolve as integrated phenotypes. Utilizing a common garden of 28 populations of the perennial herb Arabis alpina (Brassicaceae), we investigated integration within and among floral scent compounds and foliar defense compounds (both volatile compounds and tissue-bound glucosinolates). Within floral scent volatiles, foliar volatile compounds, and glucosinolates, phytochemicals were often positively correlated, and correlations were stronger within these groups than between them. Thus, we found no evidence of integration between compound groups indicating that these are free to evolve independently. Relative to self-compatible populations, self-incompatible populations experienced stronger correlations between floral scent compounds, and a trend toward lower integration between floral scent and foliar volatiles. Our study serves as a rare test of integration of multiple, physiologically related plant traits that each are potential targets of insect-mediated selection. Our results suggest that independent evolutionary forces are likely to diversify different axes of plant chemistry without major constraints