4,428 research outputs found
ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples
The ability to specifically and sensitively target genotypes of interest is critical
for the success of many PCR-based analyses of environmental or clinical samples that
contain multiple templates.Next-generation sequence data clearly show that such
samples can harbour hundreds to thousands of operational taxonomic units; a richness
which precludes the manual evaluation of candidate assay specificity and sensitivity
using multiple sequence alignments. To solve this problem we have developed and
validated a free software tool which automates the identification of PCR assays
targeting specific genotypes in complex samples. ThermoPhyl uses user-defined
target and non-target sequence databases to assess the phylogenetic sensitivity and
specificity of thermodynamically optimised candidate assays derived from primer
design software packages. ThermoPhyl takes its name from its central premise of
testing Thermodynamically optimal assays for Phylogenetic specificity and
sensitivity and can be used for two primer (traditional PCR) or two primers with an
internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide
probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays.
PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a
traditional specific PCR assay and with a set of four genotype-specific qPCR assays
applied to estuarine sediment samples
Integrating Supplemental Jurisdiction and Diversity Jurisdiction: A Progress Report on the Work of the American Law Institute
Symposium: A Reappraisal of the Supplemental-Jurisdiction Statute: Title 28 U.S.C. § 1367
An Open Letter on Reforming the Process of Revising the Federal Rules
An Open Letter on Reforming the Process of Revising the Federal Rule
Promises of Confidentiality: Do Reporters Really Have to Keep Their Word
In an industry in which information is the ultimate commodity, a new dilemma that confronts the media world is whether the First Amendment protects news gatherers from sources who try to enforce promises of confidentiality. The debate raised in Cohen v. Cowles Media Co. pits the First Amendment freedoms of the press and speech against concepts of contracts and torts that are deeply rooted in our legal heritage. At least two reasons make promises of confidentiality important to the newsgathering profession. First, breaking a promise of confidentiality that has induced a source to provide information is dishonorable. Second, sources may disappear if it becomes known that the promises will not be kept
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