Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Injurious tail biting in pigs: How can it be controlled in existing systems without tail docking?

Tail biting is a serious animal welfare and economic problem in pig production. Tail docking, which reduces but does not eliminate tail biting, remains widespread. However, in the EU tail docking may not be used routinely, and some 'alternative' forms of pig production and certain countries do not allow tail docking at all. Against this background, using a novel approach focusing on research where tail injuries were quantified, we review the measures that can be used to control tail biting in pigs without tail docking. Using this strict criterion, there was good evidence that manipulable substrates and feeder space affect damaging tail biting. Only epidemiological evidence was available for effects of temperature and season, and the effect of stocking density was unclear. Studies suggest that group size has little effect, and the effects of nutrition, disease and breed require further investigation. The review identifies a number of knowledge gaps and promising avenues for future research into prevention and mitigation. We illustrate the diversity of hypotheses concerning how different proposed risk factors might increase tail biting through their effect on each other or on the proposed underlying processes of tail biting. A quantitative comparison of the efficacy of different methods of provision of manipulable materials, and a review of current practices in countries and assurance schemes where tail docking is banned, both suggest that daily provision of small quantities of destructible, manipulable natural materials can be of considerable benefit. Further comparative research is needed into materials, such as ropes, which are compatible with slatted floors. Also, materials which double as fuel for anaerobic digesters could be utilised. As well as optimising housing and management to reduce risk, it is important to detect and treat tail biting as soon as it occurs. Early warning signs before the first bloody tails appear, such as pigs holding their tails tucked under, could in future be automatically detected using precision livestock farming methods enabling earlier reaction and prevention of tail damage. However, there is a lack of scientific studies on how best to respond to outbreaks: the effectiveness of, for example, removing biters and/or bitten pigs, increasing enrichment, or applying substances to tails should be investigated. Finally, some breeding companies are exploring options for reducing the genetic propensity to tail bite. If these various approaches to reduce tail biting are implemented we propose that the need for tail docking will be reduced. © 2014 The Animal Consortium.

Introducing the CTA concept

The Cherenkov Telescope Array (CTA) is a new observatory for very high-energy (VHE) gamma rays. CTA has ambitions science goals, for which it is necessary to achieve full-sky coverage, to improve the sensitivity by about an order of magnitude, to span about four decades of energy, from a few tens of GeV to above 100 TeV with enhanced angular and energy resolutions over existing VHE gamma-ray observatories. An international collaboration has formed with more than 1000 members from 27 countries in Europe, Asia, Africa and North and South America. In 2010 the CTA Consortium completed a Design Study and started a three-year Preparatory Phase which leads to production readiness of CTA in 2014. In this paper we introduce the science goals and the concept of CTA, and provide an overview of the project. © 2013 Elsevier B.V. All rights reserved.

An R-matrix approach for plasma modelling and the interpretation of astrophysical observation

Over the last decade an Auburn-Rollins-Strathclyde consortium has developed several suites of parallel R-matrix codes [1, 2, 3] that can meet the fundamental data needs required for the interpretation of astrophysical observation and/or plasma experiments. Traditionally our collisional work on light fusion-related atoms has been focused towards spectroscopy and impurity transport for magnetically confined fusion devices. Our approach has been to provide a comprehensive data set for the excitation/ionization for every ion stage of a particular element. As we progress towards a burning fusion plasma, there is a demand for the collisional processes involving tungsten, which has required a revitalization of the relativistic R-matrix approach. The implementation of these codes on massively parallel supercomputers has facilitated the progression to models involving thousands of levels in the close-coupling expansion required by the open d and f sub-shell systems of mid Z tungsten. This work also complements the electron-impact excitation of Fe-Peak elements required by astrophysics, in particular the near neutral species, which offer similar atomic structure challenges. Although electron-impact excitation work is our primary focus in terms of fusion application, the single photon photoionisation codes are also being developed in tandem, and benefit greatly from this ongoing work.

Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer

The Colorectal Cancer (CRC) Subtyping Consortium (CRCSC) recently published four consensus molecular subtypes (CMS’s) representing the underlying biology in CRC. The Microsatellite Instable (MSI) immune group, CMS1, has a favorable prognosis in early stage disease, but paradoxically has the worst prognosis following relapse, suggesting the presence of factors enabling neoplastic cells to circumvent this immune response. To identify the genes influencing subsequent poor prognosis in CMS1, we analyzed this subtype, centered on risk of relapse.
In a cohort of early stage colon cancer (n=460), we examined, in silico, changes in gene expression within the CMS1 subtype and demonstrated for the first time the favorable prognostic value of chemokine-like factor (CKLF) gene expression in the adjuvant disease setting [HR=0.18, CI=0.04-0.89]. In addition, using transcription profiles originating from cell sorted CRC tumors, we delineated the source of CKLF transcription within the colorectal tumor microenvironment to the leukocyte component of these tumors. Further to this, we confirmed that CKLF gene expression is confined to distinct immune subsets in whole blood samples and primary cell lines, highlighting CKLF as a potential immune cell-derived factor promoting tumor immune-surveillance of nascent neoplastic cells, particularly in CMS1 tumors. Building on the recently reported CRCSC data, we provide compelling evidence that leukocyte-infiltrate derived CKLF expression is a candidate biomarker of favorable prognosis, specifically in MSI-immune stage II/III disease.

M Dwarf Flare Continuum Variations on One-second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. The NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color-color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 104 K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100. Based on observations obtained with the Apache Point Observatory 3.5 m telescope, which is owned and operated by the Astrophysical Research Consortium, based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias, and observations, and based on observations made with the ESO Telescopes at the La Silla Paranal Observatory under programme ID 085.D-0501(A).

Schizophrenia risk from complex variation of complement component 4

Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia.

Automated retinal image quality assessment on the UK Biobank dataset for epidemiological studies

Morphological changes in the retinal vascular network are associated with future risk of many systemic and vascular diseases. However, uncertainty over the presence and nature of some of these associations exists. Analysis of data from large population based studies will help to resolve these uncertainties. The QUARTZ (QUantitative Analysis of Retinal vessel Topology and siZe) retinal image analysis system allows automated processing of large numbers of retinal images. However, an image quality assessment module is needed to achieve full automation. In this paper, we propose such an algorithm, which uses the segmented vessel map to determine the suitability of retinal images for use in the creation of vessel morphometric data suitable for epidemiological studies. This includes an effective 3-dimensional feature set and support vector machine classification. A random subset of 800 retinal images from UK Biobank (a large prospective study of 500,000 middle aged adults; where 68,151 underwent retinal imaging) was used to examine the performance of the image quality algorithm. The algorithm achieved a sensitivity of 95.33% and a specificity of 91.13% for the detection of inadequate images. The strong performance of this image quality algorithm will make rapid automated analysis of vascular morphometry feasible on the entire UK Biobank dataset (and other large retinal datasets), with minimal operator involvement, and at low cost.

Nonsteroidal Anti-Inflammatory Drug Use is Not Associated With Reduced Risk of Barrett’s Esophagus

OBJECTIVES: Regular use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with a reduced risk of esophageal adenocarcinoma. Epidemiological studies examining the association between NSAID use and the risk of the precursor lesion, Barrett’s esophagus, have been inconclusive.

METHODS: We analyzed pooled individual-level participant data from six case-control studies of Barrett’s esophagus in the Barrett’s and Esophageal Adenocarcinoma Consortium (BEACON). We compared medication use from 1474 patients with Barrett’s esophagus separately with two control groups: 2256 population-based controls and 2018 gastroesophageal reflux disease (GERD) controls. Study-specific odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression models and were combined using a random effects meta-analytic model.

RESULTS: Regular (at least once weekly) use of any NSAIDs was not associated with the risk of Barrett’s esophagus (vs. population-based controls, adjusted OR = 1.00, 95% CI = 0.76–1.32; I2=61%; vs. GERD controls, adjusted OR = 0.99, 95% CI = 0.82–1.19; I2=19%). Similar null findings were observed among individuals who took aspirin or non-aspirin NSAIDs. We also found no association with highest levels of frequency (at least daily use) and duration (≥5 years) of NSAID use. There was evidence of moderate between-study heterogeneity; however, associations with NSAID use remained non-significant in “leave-one-out” sensitivity analyses.

CONCLUSIONS: Use of NSAIDs was not associated with the risk of Barrett’s esophagus. The previously reported inverse association between NSAID use and esophageal adenocarcinoma may be through reducing the risk of neoplastic progression in patients with Barrett’s esophagus.

Occurrence of the pinewood nematode, Bursaphelenchus xylophilus in Portugal and perspectives of the disease spread in Europe.

In 1999, the pinewood nematode (PWN) , Bursaphelenchus xylophilus was found and identified for the first time in Portugal and in Europe. Following detection, Portuguese authorities initiated the implementation of eradication measures during 1999 and 2000, following an alert provided to European Community officials; as a result, the nematode was confirmed to be confined in the Setúbal region, near Lisbon. A task force from the follow-up group (GANP) created by the Secretary of State for the Rural Development established a national eradication programme (PROLUNP) to (1) Contain PWN within the initial geographic limits; (2) Implement eradication measures; and (3) Monitor PWN at a national level. Research is presently being conducted both at universities as well as research institutes, focusing on the characterization ofBursaphelenchus species associated with maritime pine, as well as on the insect vector, Monochamus galloprovincialis. Recent reports indicate that the nematode may be present in Siberia (Russia), which would present a threat to Eastern European forestry. Efforts are presently being developed by several European countries to establish a research consortium to detect and study the possible presence of PWN, for a new PRAs. A recent workshop held in Portugal, in 2001, has been an oportunity for sharing experiences and techniques on detection and control. There is clearly a greater awareness of this issue in Europe.

Estudo da variação da abundância e diversidade de procariotas em sedimentos subsuperficiais marinhos

Os sedimentos marinhos subsuperficiais profundos são, atualmente, um ambiente ainda pouco conhecido do ponto de vista microbiológico, nomeadamente quanto aos processos metabólicos que nele têm lugar e quanto à sua possível influência nos ciclos biogeoquímicos. O acesso a amostras colhidas em sedimentos profundos, particularmente no âmbito dos programas IODP (International Ocean Discovery Program) e ECORD (European Consortium for Ocean Research Drilling) tem permitido recolher informação sobre a estrutura das comunidades de procariotas bem como sobre alguns dos fatores que regulam a sua distribuição e atividade. Este estudo teve como objetivo caracterizar a distribuição e a diversidade estrutural das comunidades de procariotas em sedimentos subsuperficiais profundos colhidos no Arco Izu-Bonin-Mariana, no mar das Filipinas, com recurso a métodos independentes de cultivo (PCR-DGGE) e à contagem de células por microscopia de epifluorescência. Os resultados apontam para a existência de comunidades de Bacteria e Archaea diversas. Os valores do índice de diversidade de Shannon-Weaver (H’) calculados com base nos perfis de DGGE (Bacteria) foram significativamente mais elevados (3,035 – 1,971) nas camadas superficiais (< 140 mafm) do que nos sedimentos (2,519 - 1,049) correspondentes a profundidades superiores entre 163 e 879 mafm. A abundância máxima (8,66 x 106 células.gps-1) foi registada à profundidade de 67 mafm e valor mínimo (2,26 x 106 células.gps-1) foi observado em amostras colhidas a 879 mafm de profundidade. Abundância e diversidade apresentaram correlação negativa com a profundidade e com o teor de sulfato. Os resultados indicam que ao longo da coluna de sedimento se estabelecem comunidades de procariotas estruturalmente diferentes e adaptadas ao ambiente geoquímico prevalecente, nomeadamente em termos dos aceitadores de eletrões disponíveis. O estudo do microbioma destas amostras representativas do ambiente sedimentar subsuperficial profundo será continuado e detalhado, com recurso a técnicas de sequenciação avançada.