Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database.

John of Worcester and the science of history

Although the ‘chronicle of chronicles’ compiled at Worcester c1095-c1140 is now firmly attributed to John of Worcester, rather than Florence, major questions remain. A central issue is that the semi-autograph manuscript of the chronicle (now Oxford, Corpus Christi College, Ms 157) underwent several alterations to its structure and contents, as codicological evidence demonstrates. These included the incorporation of important illuminations, which have been surprisingly little considered in their overall manuscript context. This article focuses on these illuminations, and will argue that their presence in this version of the chronicle makes it something even more distinctive than the learned, revisionist chronological work of Marianus Scotus upon which it was based. John of Worcester’s chosen images are linked not only to his political narrative but also to theological works and to cutting-edge science, newly translated from Arabic. The presence of such miniatures in a twelfth-century chronicle is unique, and they are central to the final form given to the Worcester chronicle by John of Worcester himself in this key manuscript. Their analysis thus brings into focus the impressive assembly of materials which the chronicle offered to readers, to shape their understanding of ongoing events.