Northern Arizona University

The Translational Genomics Research Institute

University of California

Arizona Board of Regents, a Body Corporate

Universite Du Luxembourg

James M Schupp

Paul S Keim

David Engelthaler

Rebecca E Colman

Antonino Catanzaro

Timothy Rodwell

John D Gillece

Robert Scott Spurgiesz

David R Smith

Elizabeth Driebe

Lance B Price

Erin Kelley

Paul Wilmes

Jason Sahl

Viacheslav Fofanov

David Smith

Nathan Hicks

David Wagner

Emilie Muller

Antonio Catanzaro

David M Engelthaler

The present invention provides methods of detecting a biothreat agent in a sample, comprising detecting at least one biothreat-specific amplicon in the sample. The methods also encompass confirming the absence of the biothreat agent by detecting Near Neighbor specific amplicons to avoid false positive results.

Methods and assays for detection and subtyping of microbial pathogens

The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.

Single molecule-overlapping read analysis for minor variant mutation detection in pathogen samples

Methods for the production of lipids and biofuels with a culture ofspp. grown on a medium such as wastewater or sewage sludge are provided. Thespp. may be cultured with additional microorganisms that contribute to the accumulation of lipids from the growth medium such as Zoog!oea spp.,spp.,spp.,spp., ODI genera incertae sedis. Further discloses are transformed organisms comprising genes isolated from, as well as methods and processes for producing lipids, fatty acids, or biofuels in vitro using the protein products of the isolated genes.

Isolated genes and transgenic organisms for producing biofuels

Some embodiments of the invention include a method of preparing a sample for sequencing that includes receiving a sample and amplifying at least one marker within the sample. In some embodiments, amplification of the first marker may include mixing the sample with a first oligonucleotide that comprises a first universal tail sequence and a second oligonucleotide that comprises a second universal tail sequence. In some aspects of the invention, the first universal tail sequence and the second universal tail sequence are different sequences.

Systems and methods for universal tail-based indexing strategies for amplicon sequencing

The present invention provides methods and kits that may be used to detect and quantify the presence ofspecies. The methods include quantification real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes.

Method of detecting and quantifying coccidioides species

MLVA methods for strain discrimination amongstrains are disclosed. Nine VNTR loci have been identified from genomic sequences ofstrains and primer pairs suitable for amplifying the VNTR by PCR are disclosed. Polymorphisms at these loci were used to resolve genotypes into distinct groups. This sub-typing scheme is useful for the epidemiological study ofand may be applied to the local detection of the pathological causative agent of tuberculosum.

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MLVA methods for strain discrimination amongstrains are disclosed. Nine VNTR loci have been identified from genomic sequences ofstrains and primer pairs suitable for amplifying the VNTR by PCR are disclosed. Polymorphisms at these loci were used to resolve genotypes into distinct groups. This sub-typing scheme is useful for the epidemiological study ofand may be applied to the local detection of the pathological causative agent of

High resolution typing system for pathogenic Mycobaterium tuberculosum

Growing community of inventors

Flagstaff, AZ, United States of America

James M Schupp