A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis

The rapid development of new technologies for the high throughput (HT) study of proteins has increased the demand for comprehensive plasmid clone resources that support protein expression. These clones must be full-length, sequence-verified and in a flexible format. The generation of these resources requires automated pipelines supported by software management systems. Although the availability of clone resources is growing, current collections are either not complete or not fully sequence-verified. We report an automated pipeline, supported by several software applications that enabled the construction of the first comprehensive sequence-verified plasmid clone resource for more than 96% of protein coding sequences of the genome of F. tularensis, a highly virulent human pathogen and the causative agent of tularemia. This clone resource was applied to a HT protein purification pipeline successfully producing recombinant proteins for 72% of the genes. These methods and resources represent significant technological steps towards exploiting the genomic information of F. tularensis in discovery applications

A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis

The rapid development of new technologies for the high throughput (HT) study of proteins has increased the demand for comprehensive plasmid clone resources that support protein expression. These clones must be full-length, sequence-verified and in a flexible format. The generation of these resources requires automated pipelines supported by software management systems. Although the availability of clone resources is growing, current collections are either not complete or not fully sequence-verified. We report an automated pipeline, supported by several software applications that enabled the construction of the first comprehensive sequence-verified plasmid clone resource for more than 96% of protein coding sequences of the genome of F. tularensis, a highly virulent human pathogen and the causative agent of tularemia. This clone resource was applied to a HT protein purification pipeline successfully producing recombinant proteins for 72% of the genes. These methods and resources represent significant technological steps towards exploiting the genomic information of F. tularensis in discovery applications

A Biomedically Enriched Collection of 7000 Human ORF Clones

We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance

Portable X-ray fluorescence as a rapid technique for surveying elemental distributions in soil

Case studies from two sites demonstrate how concentration distributions of hazardous contaminants can be rapidly measured and visualized using portable XRF (X-ray fluorescence) coupled with geostatistical interpolation tools. In this study, lead is used as an exemplar due to its well-known detrimental effect on human health through long-term exposure. A portable Thermo Scientific NITON X-ray fluorescence (XRF) instrument was used for real-time in-situ concentration measurements, which were linked to GPS coordinates of the sampling locations. A 52 point mixed sampling density survey was performed at a site near Maynooth, Co. Kildare, and a second 58 survey undertaken at Dublin City University (DCU). At Maynooth, high concentrations of Pb (above 110 mg/kg) were found close to the site where a local canal meets a road. At the DCU site, results indicate high Pb concentrations (above 160 mg/kg) near a busy main road. Geostatistical techniques were used to generate concentration prediction and critical threshold contour surfaces for both sites. Linked with GPS coordinates for each sampling location, this technology enables the distribution of multiple elements to be mapped over wide areas in a relatively short time. Supplemental materials are available for this article. Go to the publisher's online edition of Spectroscopy Letters to view the supplemental file

Portable XRF as a rapid technique for surveying elemental distributions in soil

Case studies from two sites demonstrate how concentration distributions of hazardous contaminants can be rapidly measured and visualised using portable XRF coupledwith geostatistical interpolation tools. In this study, lead is used as an exemplar due toits well-known detrimental effect on human health through long-term exposure. Aportable X-ray fluorescence instrument was used for real-time in-situ concentrationmeasurements, which were linked to GPS coordinates of the sampling locations.Geostatistical techniques were used to generate concentration prediction and criticalthreshold contour surfaces for both sites. This technology enables the distribution ofmultiple elements to be mapped over wide areas in a relatively short time

Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae

The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These studies rely on availability of cloned open reading frame (ORF) collections that can be used for cell-free or cell-based protein expression. Several yeast ORF collections are available, but their use and data interpretation can be hindered by reliance on now out-of-date annotations, the inflexible presence of N- or C-terminal tags, and/or the unknown presence of mutations introduced during the cloning process. High-throughput biochemical and genetic analyses would benefit from a “gold standard” (fully sequence-verified, high-quality) ORF collection, which allows for high confidence in and reproducibility of experimental results. Here, we describe Yeast FLEXGene, a S. cerevisiae protein-coding clone collection that covers over 5000 predicted protein-coding sequences. The clone set covers 87% of the current S. cerevisiae genome annotation and includes full sequencing of each ORF insert. Availability of this collection makes possible a wide variety of studies from purified proteins to mutation suppression analysis, which should contribute to a global understanding of yeast protein function