Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.

A genealogy of the kings of England in papal Avignon: British Library, Egerton MS. 1500

This is one of three articles in eBLJ (2013) dedicated to the "Abreujamen de las estorias", British Library Egerton MS 1500. The other two articles are: Federico Botana,' The Making of "L'Abreujamen de las estorias": British Library Egerton MS 1500', eblj (2013), article 16. Alexander Ibarz, 'The Provenance of the "Abreujamens de las estorias" (London, British Library, Egerton MS. 1500) and the Identification of Scribal Hands (c. 1323)' eblj (2013), article 17. Leglu's article, eblj (2013), article 18, examines the various political agendas that emerge in the depiction of the kings of Britain and England, from Brutus to Edward II.

Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA

Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-29-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5- HmdC, 5-formyl-29-deoxycytidine (5-FodC), 5-carboxyl-29-deoxycytidine (5-CadC), 5-hydroxymethyl-29-deoxyuridine (5- HmdU), and the (59S) diastereomer of 8,59-cyclo-29-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tetfamily dioxygenase enzymes in Arabidopsis.

Derivation of an urban materials spectral library through emittance and reflectance spectroscopy

Recent advances in thermal infrared remote sensing include the increased availability of airborne hyperspectral imagers (such as the Hyperspectral Thermal Emission Spectrometer, HyTES, or the Telops HyperCam and the Specim aisaOWL), and it is planned that an increased number spectral bands in the long-wave infrared (LWIR) region will soon be measured from space at reasonably high spatial resolution (by imagers such as HyspIRI). Detailed LWIR emissivity spectra are required to best interpret the observations from such systems. This includes the highly heterogeneous urban environment, whose construction materials are not yet particularly well represented in spectral libraries. Here, we present a new online spectral library of urban construction materials including LWIR emissivity spectra of 74 samples of impervious surfaces derived using measurements made by a portable Fourier Transform InfraRed (FTIR) spectrometer. FTIR emissivity measurements need to be carefully made, else they are prone to a series of errors relating to instrumental setup and radiometric calibration, which here relies on external blackbody sources. The performance of the laboratory-based emissivity measurement approach applied here, that in future can also be deployed in the field (e.g. to examine urban materials in situ), is evaluated herein. Our spectral library also contains matching short-wave (VIS–SWIR) reflectance spectra observed for each urban sample. This allows us to examine which characteristic (LWIR and) spectral signatures may in future best allow for the identification and discrimination of the various urban construction materials, that often overlap with respect to their chemical/mineralogical constituents. Hyperspectral or even strongly multi-spectral LWIR information appears especially useful, given that many urban materials are composed of minerals exhibiting notable reststrahlen/absorption effects in this spectral region. The final spectra and interpretations are included in the London Urban Micromet data Archive (LUMA; http://LondonClimate.info/LUMA/SLUM.html).

Sir Bernard Spilsbury: a survey and catalogue of his autopsy case cards from the Wellcome Library, London

During his lifetime, Sir Bernard Spilsbury was referred to as the ‘‘father of forensic medicine.’’ He became a household name as a result of several famous cases. Several articles have been written about his life and work, but an objective assessment has proved difficult because of the lack of available material that Spilsbury himself produced. His main legacy has been a series of case cards, but for many years these were unavailable to the researcher. In 2008, a collection of some 4000 of Spilsbury’s case cards was bought by The Wellcome Library in London and therefore entered the public domain. In this article, we report our study of 650 of these cards. We discuss trends in Spilsbury’s work and several specific cases in more detail. These cards allow an objective view to be taken of Spilsbury’s everyday work, and we feel that some reappraisal of his legacy is now timely

The Italian Academies, 1525-1700: a themed collection database, London, British Library

A database of books published by Italian Academies between 1525 and 1700. The Italian Academies Themed Collection provides a detailed searchable database for locating printed material relating to the Italian learned Academies active in Avellino, Bari, Benevento, Bologna, Brindisi, Caltanissetta, Catania, Catanzaro, Enna, L’Aquila, Lecce, Mantua, Naples, Padua, Palermo, Rome, Salerno, Siena, Syracuse, Trapani, and Venice in the period 1525-1700 and now held in the collections of the British Library.

The Environmental Data Abstraction Library (EDAL): a modular approach to processing and visualising large environmental data

The Environmental Data Abstraction Library provides a modular data management library for bringing new and diverse datatypes together for visualisation within numerous software packages, including the ncWMS viewing service, which already has very wide international uptake. The structure of EDAL is presented along with examples of its use to compare satellite, model and in situ data types within the same visualisation framework. We emphasize the value of this capability for cross calibration of datasets and evaluation of model products against observations, including preparation for data assimilation.

The Devil’s Daughters and a question of translation between Occitan and Anglo-Norman French: ‘De las .vii. filhas del diable’ (British Library Add. MS 17920).

The evidence for vernacular-to-vernacular translation is hard to demonstrate in medieval Romance languages. This article analyses a hypothesis published a century ago that there is an identifiable Anglo-Norman source for an Occitan prose text. Both texts spring from a Latin exemplum in which the seven capital vices are personified as the Devil's daughters, married off to seven social categories (the clergy, knights, peasants, etc.). Although the hypothesis is disproved, it remains that the dialogue between Anglo-Norman French and Occitan has been overlooked, and deserves further exploration.

AmalgamScope: merging annotations data across the human genome

The past years have shown an enormous advancement in sequencing and array-based technologies, producing supplementary or alternative views of the genome stored in various formats and databases. Their sheer volume and different data scope pose a challenge to jointly visualize and integrate diverse data types. We present AmalgamScope a new interactive software tool focusing on assisting scientists with the annotation of the human genome and particularly the integration of the annotation files from multiple data types, using gene identifiers and genomic coordinates. Supported platforms include next-generation sequencing and microarray technologies. The available features of AmalgamScope range from the annotation of diverse data types across the human genome to integration of the data based on the annotational information and visualization of the merged files within chromosomal regions or the whole genome. Additionally, users can define custom transcriptome library files for any species and use the file exchanging distant server options of the tool.

A library at Antium?

This chapter considers the implications of accepting the 'Antium' crux in Galen's recently discovered Peri Alphas ( = De Indolentia). It examines what we know about the Roman imperial villa library at Antium, and what this new testimony can add.

Genomic signals of migration and continuity in Britain before the Anglo-Saxons

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 x) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Categories & order systems: Claude Parent and The Serving Library intersections of architecture, art and editorial design

This paper discusses the work of Claude Parent and The Serving Library, considering the critiques generated by their intersecting of architecture, art and editorial design. Through focus on the ways in which hosting environment, architecture and forms of expanded publishing can serve to dissolve disciplinary boundaries and activities of production, spectatorship and reception, it draws on the lineage of 1960s/70s Conceptual Art in considering these practices as a means through which to escape medium specificity and spatial confinement. Relationships between actual and virtual space are then read against this broadening of aesthetic ideas and the theory of critical modernity.

Genomic evidence for the Pleistocene and recent population history of Native Americans

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Everything is about to happen: an ongoing archive of artists’ books, as part of The Library Vacine

Group exhibition of artists books curated by Gregorio Magnani, including Frozen Tears I - III (2003-7). Including books by Kasper Andreasen, Linus Bill and Adrien Horni, blisterZine, Daniel Gustav Cramer, Arnaud Desjardin, Michael Dean, Karl Holmqvist, Louis Luthi, Sara MacKillop, Dan Mitchell, Kristen Mueller, Sophie Nys, Simon Popper, Preston is my Paris, Alessandro Roma, Karin Ruggaber, John Russell, Erik Steinbrecher, Peter Tillessen, Erik van der Weijde