We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA-amino acid binding structures.

The Poxvirus Bioinformatics Resource Center (PBRC) has been established to provide informational and analytical resources to the scientific community to aid research directed at providing a better understanding of the Poxviridae family of viruses. The PBRC was specifically established as the result of the concern that variola virus, the causative agent of smallpox, as well as related viruses, might be utilized as biological weapons. In addition, the PBRC supports research on poxviruses that might be considered new and emerging infectious agents such as monkeypox virus. The PBRC consists of a relational database and web application that supports the data storage, annotation, analysis and information exchange goals of the project. The current release consists of over 35 complete genomic sequences of various genera, species and strains of viruses from the Poxviridae family. Sequence and annotation information for these viruses has been obtained from sequences publicly available from GenBank as well as sequences not yet deposited in GenBank that have been obtained from ongoing sequencing projects. In addition to sequence data, the PBRC provides comprehensive annotation and curation of virus genes; analytical tools to aid in the understanding of the available sequence data, including tools for the comparative analysis of different virus isolates; and visualization tools to help better display the results of various analyses. The PBRC represents the initial development of what will become a more comprehensive Viral Bioinformatics Resource Center for Biodefense that will be one of the National Institute of Allergy and Infectious Diseases' ‘Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases’. The PBRC website is available at http://www.poxvirus.org.

Exserohilum rostratum was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of Exserohilum infection had been reported, and very little was known about this dematiaceous fungus, which usually infects plants. Here, we report using whole-genome sequencing (WGS) for the detection of single nucleotide polymorphisms (SNPs) and phylogenetic analysis to investigate the molecular origin of the outbreak using 22 isolates of E. rostratum retrieved from 19 case patients with meningitis or epidural/spinal abscesses, 6 isolates from contaminated NECC vials, and 7 isolates unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of 8 SNPs were detected among the outbreak genomes, with no more than 2 SNPs separating any 2 of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by ϳ136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in E. rostratum. Beginning in September, 2012, the United States experienced one of the largest outbreaks of health care-associated infections ever reported. More than 13,000 people were exposed to three lots of contaminated methylprednisolone acetate (MPA) produced by a single compounding pharmacy, and Ͼ750 developed fungal infections following their MPA injections (1-3). Infections included meningitis, as well as localized epidural, paraspinal, and peripheral joint infections, complicated by arachnoiditis and abscess formation (4, 5). Although several fungal species were implicated in the outbreak, the vast majority of infections were caused by Exserohilum rostratum, a saprobic mold found in soil and plant debris worldwide (2, 6-10). Most species of Exserohilum are plant pathogens. Exserohilum rostratum and the species formerly known as Exserohilum longirostratum and Exserohilum mcginnisii are morphologically similar and are the only species known to cause human infections; however, their taxonomic status remains under investigation (11-13).DNA fingerprinting has been used as an epidemiological tool to answer questions pertaining to strain relatedness (14, 15). However, no methodologies for DNA fingerprinting of E. rostratum existed at the time of the outbreak. While whole-genome sequencing (WGS) is a relatively new tool of molecular epidemiology, it has quickly been embraced as a mechanism for inferring phylogenetic relationships among organisms. This has translated to the recent use of whole-genome single nucleotide polymorphism (SNP) typing (whole-genome sequence typing [WGST]) as a mechanism for inferring relatedness of both bacteria (16)(17)(18)(19) and fungi (20, 21) during outbreak investigations. One of the benefits of WGST is that prior knowledge of the genome i...