Report from the Second International Symposium on Animal Genomics for Animal Health: Critical Needs, Challenges and Potential Solutions

The second International Symposium on Animal Genomics for Animal Health held in Paris, France 31 May-2 June, 2010, assembled more than 140 participants representing research organizations from 40 countries. The symposium included a roundtable discussion on critical needs, challenges and opportunities, and a forward look at the potential applications of animal genomics in animal health research. The aim of the roundtable discussion was to foster a dialogue between scientists working at the cutting edge of animal genomics research and animal health scientists. Importantly, stakeholders were included to provide input on priorities and the potential value of animal genomics to the animal health community. In an effort to facilitate the roundtable discussion, the organizers identified four priority areas to advance the use of genome-enabled technologies in animal health research. Contributions were obtained through open discussions and a questionnaire distributed at the start of the symposium. This report provides the outcome of the roundtable discussion for each of the four priority areas. For each priority, problems are identified, including potential solutions and recommendations. This report captures key points made by symposium participants during the roundtable discussion and serves as a roadmap to steer future research priorities in animal genomics research

Genetic Analysis of Reproductive Traits and Antibody Response in PRRS Infected Sows

The genetic components of reproductive performance and antibody response of 641 commercial sows were assessed in a commercial herd that faced a PRRS outbreak. Antibody response after the PRRS outbreak was highly heritable and had high genetic correlations with reproductive traits. Many genomic regions were associated with antibody response in this study. These results indicate that there is a significant genomic component associated with PRRS antibody response and its high genetic correlations with reproductive traits during PRRS suggest that this trait could be used as an indicator trait to reduce the impact of PRRS on reproductive performance

Cloned, CD117 Selected Human Amniotic Fluid Stem Cells Are Capable of Modulating the Immune Response

Amniotic fluid stem (AFS) cells are broadly multipotent, can be expanded extensively in culture, are not tumorigenic and can be readily cryopreserved for cell banking. Mesenchymal stem cells (MSC) show immunomodulatory activity and secrete a wide spectrum of cytokines and chemokines that suppress inflammatory responses, block mixed lymphocyte reactions (MLR) and other immune reactions, and have proven therapeutic against conditions such as graft-versus-host disease. AFS cells resemble MSCs in many respects including surface marker expression and differentiation potential. We therefore hypothesized that AFS cells may exhibit similar immunomodulatory capabilities. We present data to demonstrate that direct contact with AFS cells inhibits lymphocyte activation. In addition, we show that cell-free supernatants derived from AFS cells primed with total blood monocytes or IL-1β, a cytokine released by monocytes and essential in mediation of the inflammatory response, also inhibited lymphocyte activation. Further investigation of AFS cell-free supernatants by protein array revealed secretion of multiple factors in common with MSCs that are known to be involved in immune regulation including growth related oncogene (GRO) and monocyte chemotactic protein (MCP) family members as well as interleukin-6 (IL-6). AFS cells activated by PBMCs released several additional cytokines as compared to BM-MSCs, including macrophage inflammatory protein-3α (MIP-3α), MIP-1α and Activin. AFS cells also released higher levels of MCP-1 and lower levels of MCP-2 compared to BM-MSCs in response to IL-1β activation. This suggests that there may be some AFS-specific mechanisms of inhibition of lymphocyte activation. Our results indicate that AFS cells are able to suppress inflammatory responses in vitro and that soluble factors are an essential component in the communication between lymphocytes and AFS cells. Their extensive self-renewal capacity, possibility for banking and absence of tumorigenicity may make AFS cells a superior source of stable, well characterized “off the shelf” immunomodulatory cells for a variety of immunotherapies

Grazing Collisions of Black Holes via the Excision of Singularities

We present the first simulations of non-headon (grazing) collisions of binary black holes in which the black hole singularities have been excised from the computational domain. Initially two equal mass black holes $m$ are separated a distance $\approx10m$ and with impact parameter $\approx2m$. Initial data are based on superposed, boosted (velocity $\approx0.5c$) solutions of single black holes in Kerr-Schild coordinates. Both rotating and non-rotating black holes are considered. The excised regions containing the singularities are specified by following the dynamics of apparent horizons. Evolutions of up to $t \approx 35m$ are obtained in which two initially separate apparent horizons are present for $t\approx3.8m$. At that time a single enveloping apparent horizon forms, indicating that the holes have merged. Apparent horizon area estimates suggest gravitational radiation of about 2.6% of the total mass. The evolutions end after a moderate amount of time because of instabilities.Comment: 2 References corrected, reference to figure update

Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

<p>Abstract</p> <p>Background</p> <p>Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45–55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple.</p> <p>Results</p> <p>Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes.</p> <p>Conclusion</p> <p>Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.</p

Mechanisms governing interannual variability of upper-ocean temperature in a global ocean hindcast simulation

Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 1918-1938, doi:10.1175/jpo3089.1.The interannual variability in upper-ocean (0–400 m) temperature and governing mechanisms for the period 1968–97 are quantified from a global ocean hindcast simulation driven by atmospheric reanalysis and satellite data products. The unconstrained simulation exhibits considerable skill in replicating the observed interannual variability in vertically integrated heat content estimated from hydrographic data and monthly satellite sea surface temperature and sea surface height data. Globally, the most significant interannual variability modes arise from El Niño–Southern Oscillation and the Indian Ocean zonal mode, with substantial extension beyond the Tropics into the midlatitudes. In the well-stratified Tropics and subtropics, net annual heat storage variability is driven predominately by the convergence of the advective heat transport, mostly reflecting velocity anomalies times the mean temperature field. Vertical velocity variability is caused by remote wind forcing, and subsurface temperature anomalies are governed mostly by isopycnal displacements (heave). The dynamics at mid- to high latitudes are qualitatively different and vary regionally. Interannual temperature variability is more coherent with depth because of deep winter mixing and variations in western boundary currents and the Antarctic Circumpolar Current that span the upper thermocline. Net annual heat storage variability is forced by a mixture of local air–sea heat fluxes and the convergence of the advective heat transport, the latter resulting from both velocity and temperature anomalies. Also, density-compensated temperature changes on isopycnal surfaces (spice) are quantitatively significant.This work was supported in part from NOAA Office of Global Programs ACCP Grant NA86GP0290, NSF Grant OCE96-33681, and the WHOI Ocean and Climate Change Institute

Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array

Background The genetic architecture of complex traits in farmed animal populations is of interest from a scientific and practical perspective. The use of genetic markers to predict the genetic merit (breeding values) of individuals is commonplace in modern farm animal breeding schemes. Recently, high density SNP arrays have become available for Atlantic salmon, which facilitates genomic prediction and association studies using genome-wide markers and economically important traits. The aims of this study were (i) to use a high density SNP array to investigate the genetic architecture of weight and length in juvenile Atlantic salmon; (ii) to assess the utility of genomic prediction for these traits, including testing different marker densities; (iii) to identify potential candidate genes underpinning variation in early growth. Results A pedigreed population of farmed Atlantic salmon (n = 622) were measured for weight and length traits at one year of age, and genotyped for 111,908 segregating SNP markers using a high density SNP array. The heritability of both traits was estimated using pedigree and genomic relationship matrices, and was comparable at around 0.5 and 0.6 respectively. The results of the GWA analysis pointed to a polygenic genetic architecture, with no SNPs surpassing the genome-wide significance threshold, and one SNP associated with length at the chromosome-wide level. SNPs surpassing an arbitrary threshold of significance (P &#60; 0.005, ~ top 0.5 % of markers) were aligned to an Atlantic salmon reference transcriptome, identifying 109 SNPs in transcribed regions that were annotated by alignment to human, mouse and zebrafish protein databases. Prediction of breeding values was more accurate when applying genomic (GBLUP) than pedigree (PBLUP) relationship matrices (accuracy ~ 0.7 and 0.58 respectively) and 5,000 SNPs were sufficient for obtaining this accuracy increase over PBLUP in this specific population. Conclusions The high density SNP array can effectively capture the additive genetic variation in complex traits. However, the traits of weight and length both appear to be very polygenic with only one SNP surpassing the chromosome-wide threshold. Genomic prediction using the array is effective, leading to an improvement in accuracy compared to pedigree methods, and this improvement can be achieved with only a small subset of the markers in this population. The results have practical relevance for genomic selection in salmon and may also provide insight into variation in the identified genes underpinning body growth and development in salmonid species

Establishment of a taxonomic and molecular reference collection to support the identification of species regulated by the Western Australian Prevention List for Introduced Marine Pests

Introduced Marine Pests (IMP, = non-indigenous marine species) prevention, early detection and risk-based management strategies have become the priority for biosecurity operations worldwide, in recognition of the fact that, once established, the effective management of marine pests can rapidly become cost prohibitive or impractical. In Western Australia (WA), biosecurity management is guided by the “Western Australian Prevention List for Introduced Marine Pests” which is a policy tool that details species or genera as being of high risk to the region. This list forms the basis of management efforts to prevent introduction of these species, monitoring efforts to detect them at an early stage, and rapid response should they be detected. It is therefore essential that the species listed can be rapid and confidently identified and discriminated from native species by a range of government and industry stakeholders. Recognising that identification of these species requires very specialist expertise which may be in short supply and not readily accessible in a regulatory environment, and the fact that much publicly available data is not verifiable or suitable for regulatory enforcement, the WA government commissioned the current project to collate a reference collection of these marine pest specimens. In this work, we thus established collaboration with researchers worldwide in order to source representative specimens of the species listed. Our main objective was to build a reference collection of taxonomically vouchered specimens and subsequently to generate species-specific DNA barcodes suited to supporting their future identification. To date, we were able to obtain specimens of 75 species (representative of all but four of the pests listed) which have been identified by experts and placed with the WA Government Department of Fisheries and, where possible, in accessible museums and institutions in Australasia. The reference collection supports the fast and reliable taxonomic and molecular identification of marine pests in WA and constitutes a valuable resource for training of stakeholders with interest in IMP recognition in Australia. The reference collection is also useful in supporting the development of a variety of DNA-based detection strategies such as real-time PCR and metabarcoding of complex environmental samples (e.g. biofouling communities). ThePrevention List is under regular review to ensure its continued relevance and that it remains evidence and risk-based. Similarly, its associated reference collection also remains to some extent a work in progress. In recognition of this fact, this report seeks to provide details of this continually evolving information repository publicly available to the biosecurity management community worldwid

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio