An initial comparative map of copy number variations in the goat (Capra hircus) genome

<p>Abstract</p> <p>Background</p> <p>The goat (<it>Capra hircus</it>) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.</p> <p>Results</p> <p>We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P < 0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals.</p> <p>Conclusions</p> <p>We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.</p

Copper and tin isotopic analysis of ancient bronzes for archaeological investigation: development and validation of a suitable analytical methodology

Although in many cases Pb isotopic analysis can be relied on for provenance determination of ancient bronzes, sometimes the use of “non-traditional” isotopic systems, such as those of Cu and Sn, is required. The work reported on in this paper aimed at revising the methodology for Cu and Sn isotope ratio measurements in archaeological bronzes via optimization of the analytical procedures in terms of sample pre-treatment, measurement protocol, precision, and analytical uncertainty. For Cu isotopic analysis, both Zn and Ni were investigated for their merit as internal standard (IS) relied on for mass bias correction. The use of Ni as IS seems to be the most robust approach as Ni is less prone to contamination, has a lower abundance in bronzes and an ionization potential similar to that of Cu, and provides slightly better reproducibility values when applied to NIST SRM 976 Cu isotopic reference material. The possibility of carrying out direct isotopic analysis without prior Cu isolation (with AG-MP-1 anion exchange resin) was investigated by analysis of CRM IARM 91D bronze reference material, synthetic solutions, and archaeological bronzes. Both procedures (Cu isolation/no Cu isolation) provide similar δ 65Cu results with similar uncertainty budgets in all cases (±0.02–0.04 per mil in delta units, k = 2, n = 4). Direct isotopic analysis of Cu therefore seems feasible, without evidence of spectral interference or matrix-induced effect on the extent of mass bias. For Sn, a separation protocol relying on TRU-Spec anion exchange resin was optimized, providing a recovery close to 100 % without on-column fractionation. Cu was recovered quantitatively together with the bronze matrix with this isolation protocol. Isotopic analysis of this Cu fraction provides δ 65Cu results similar to those obtained upon isolation using AG-MP-1 resin. This means that Cu and Sn isotopic analysis of bronze alloys can therefore be carried out after a single chromatographic separation using TRU-Spec resin. Tin isotopic analysis was performed relying on Sb as an internal standard used for mass bias correction. The reproducibility over a period of 1 month (n = 42) for the mass bias-corrected Sn isotope ratios is in the range of 0.06–0.16 per mil (2 s), for all the ratios monitored

Parallel parametric linear programming solving, and application to polyhedral computations

International audienceParametric linear programming is central in polyhedral computations and in certain control applications.We propose a task-based scheme for parallelizing it, with quasi-linear speedup over large problems

An Efficient Parametric Linear Programming Solver and Application to Polyhedral Projection

International audiencePolyhedral projection is a main operation of the polyhedron abstract domain.It can be computed via parametric linear programming (PLP), which is more efficient than the classic Fourier-Motzkin elimination method.In prior work, PLP was done in arbitrary precision rational arithmetic.In this paper, we present an approach where most of the computation is performed in floating-point arithmetic, then exact rational results are reconstructed.We also propose a workaround for a difficulty that plagued previous attempts at using PLP for computations on polyhedra: in general the linear programming problems are degenerate, resulting in redundant computations and geometric descriptions

Scalable Minimizing-Operators on Polyhedra via Parametric Linear Programming

International audienceConvex polyhedra capture linear relations between variables. They are used in static analysis and optimizing compilation. Their high expressiveness is however barely used in verification because of their cost, often prohibitive as the number of variables involved increases. Our goal in this article is to lower this cost. Whatever the chosen representation of polyhedra – as constraints, as generators or as both – expensive operations are unavoidable. That cost is mostly due to four operations: conversion between representations, based on Chernikova’s algorithm, for libraries in double description; convex hull, projection and minimization, in the constraints-only representation of polyhedra. Libraries operating over generators incur exponential costs on cases common in program analysis. In the Verimag Polyhedra Library this cost was avoided by a constraints-only representation and reducingall operations to variable projection, classically done by Fourier-Motzkin elimination. Since Fourier-Motzkin generates many redundant constraints, minimization was however very expensive. In this article, we avoid this pitfall by expressing projection as a parametric linear programming problem. This dramatically improves efficiency, mainly because it avoids the post-processing minimization. We show how our new approach can be up to orders of magnitude faster than the previous approach implemented in the Verimag Polyhedra Library that uses only constraints and Fourier-Motzkin elimination, and on par with the conventional double description approach, as implemented in well-known libraries

My dysphoria blues: Or why I cannot write autoethnography

n this essay, I would like to ask if we are concerned with writing about difference or writing differently. I attempt to present an account of my on-going experience of dysphoria and consider how I write about that experience. I reveal how my writing has no epiphany, is repetitive and in its characterless depiction of others is a two-dimensional, monologue that fails the conventions of an evocative autoethnographic account. My writing is ‘bad writing’ but what should become of it? Does a concern with style, whether or not over content, based on taste preclude some stories and different ways of writing? Should I be excluded from academe and silenced, or can room be found for a tasteless account like mine? I end my essay by provocatively owning the label of bad writing

A new methodology for precise cadmium isotope analyses of seawater

Previous studies have revealed considerable Cdisotope fractionations in seawater, which can be used tostudy the marine cycling of this micronutrient element. Thelow Cd concentrations that are commonly encountered innutrient-depleted surface seawater, however, pose a particularchallenge for precise Cd stable isotope analyses. In thisstudy, we have developed a new procedure for Cd isotopeanalyses of seawater, which is suitable for samples as largeas 20 L and Cd concentrations as low as 1 pmol/L. Theprocedure involves the use of a 111Cd–113Cd double spike,co-precipitation of Cd from seawater using Al(OH)3, andsubsequent Cd purification by column chromatography. Tosave time, seawater samples with higher Cd contents can beprocessed without co-precipitation. The Cd isotope analysesare carried out by multiple collector inductively coupledplasma mass spectrometry (MC-ICP-MS). The performanceof this technique was verified by analyzing multiplealiquots of a large seawater sample that was collected fromthe English Channel, the SAFe D1 seawater referencematerial, and several samples from the GEOTRACESAtlantic intercalibration exercise. The overall Cd yield ofthe procedure is consistently better than 85% and themethodology can routinely provide ?114/110Cd data with aprecision of about ±0.5 ? (2sd, standard deviation) when atleast 20–30 ng of natural Cd is available for analysis.However, even seawater samples with Cd contents of only1–3 ng can be analyzed with a reproducibility of about ±3to ±5 ?. A number of experiments were furthermoreconducted to verify that the isotopic results are accurate to within the quoted uncertainty