Daniel Russell

Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA

ABSTRACT Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.

Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements

Mycobacteriophages BPs, Angel and Halo are closely related viruses isolated from Mycobacterium smegmatis, and possess the smallest known mycobacteriophage genomes, 41,901 bp, 42,289 bp and 41,441 bp, respectively. Comparative genome analysis reveals a novel class of ultra-small mobile genetic elements; BPs and Halo each contain an insertion of the proposed mobile elements MPME1 and MPME2, respectively, at different locations, while Angel contains neither. The close similarity of the genomes provides a comparison of the pre- and post-integration sequences, revealing an unusual 6 bp insertion at one end of the element and no target duplication. Nine additional copies of these mobile elements are identified in a variety of different contexts in other mycobacteriophage genomes. In addition, BPs, Angel and Halo have an unusual lysogeny module in which the repressor and integrase genes are closely linked. The attP site is located within the repressor-coding region, such that prophage formation results in expression of a C-terminally truncated, but active, form of the repressor.

Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp.

The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, Hau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage Hau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species.

Emblematic structures in Renaissance French culture

The emblem and the device (or impresa as it was called in Italy) were the most direct and telling manifestations of a mentality that played a significant role in the discourse and art in Western Europe between the late Middle Ages and the mid-eighteenth century. In the history of Western symbolism, the emblematic sign forms a bridge between late medieval allegory and the Romantic metaphor. These intricate combinations of picture and text, where the picture completes the ellipses of an epigrammatic text, and where the text fixes the intention of the pictured signs, provide useful clues to the way pictures in general were read and textual descriptions visualized in early modern Europe. Daniel Russell demonstrates how the emblematic forms emerged from the way illustrations were used in late medieval French manuscript culture, how the forms were later disseminated in France, and how they functioned within early modern French culture and society. He also attempts to show how the guiding principles behind the composition of emblems influenced the production of courtly decoration, ceremony, and propaganda, as well as the composition of literary texts as different as Maurice Sc|ves Delie, Montaignes Essais, and Du Bartass Sepmaine.

Characterization of prophages containing “evolved” Dit/Tal modules in the genome of Lactobacillus casei BL23

Lactic acid bacteria (LAB) have many applications in food and industrial fermentations. Prophage induction and generation of new virulent phages is a risk for the dairy industry. We identified three complete prophages (PLE1, PLE2, and PLE3) in the genome of the well-studied probiotic strain Lactobacillus casei BL23. All of them have mosaic architectures with homologous sequences to Streptococcus, Lactococcus, Lactobacillus, and Listeria phages or strains. Using a combination of quantitative real-time PCR, genomics, and proteomics, we showed that PLE2 and PLE3 can be induced—but with different kinetics—in the presence of mitomycin C, although PLE1 remains as a prophage. A structural analysis of the distal tail (Dit) and tail associated lysin (Tal) baseplate proteins of these prophages and other L. casei/paracasei phages and prophages provides evidence that carbohydrate-binding modules (CBM) located within these “evolved” proteins may replace receptor binding proteins (RBPs) present in other well-studied LAB phages. The detailed study of prophage induction in this prototype strain in combination with characterization of the proteins involved in host recognition will facilitate the design of new strategies for avoiding phage propagation in the dairy industry.

Deviceful Settings: The English Renaissance Emblem and Its Contexts

This volume, containing papers from the Third International Emblem Conference held in Pittsburgh in 1993, focuses on the 17th-century emblem in England. It focuses on the contexts within which emblems were used, rather than on the emblem books themselves.

Complete Genome Sequences of Lactobacillus Phages J-1 and PL-1

ABSTRACT Lactobacillus phages J-1 and PL-1 were isolated during the 1960s from abnormal fermentations of Yakult. The genomes are almost identical, but PL-1 has a deletion in the genetic switch region and also differs in a gene coding for a putative tail protein.

The emblem and authority

How should one characterize a person who makes emblems? This is no trivial matter, for the nature of an activity is often revealed in the name given to those who perform that activity. A menuisier, an ebeniste, and a charpentier all work with wood, but in different ways that lead to different products; if they happen to be doing the same kind of work, we will expect the results to be slightly different according to the experience and attitudes that they bring severally to the task, experience and attitudes summarized in the nouns that characterize them professionally.

Nouvelles directions dans l'étude de l'emblème français

In a general way, in continuity with a 1990 article, emblems and emblematics are the symptom of a Renaissance epistemological shift. This stays of contemporary interest especially as the cultural importance of emblems to the Renaissance is now largely recognised.