Abstract: Provided herein are devices that facilitate the magnetic separation of an analyte from a sample, and methods of use thereof. In particular embodiments, devices and methods are provided for the trans-interfacial magnetic separation (TIMS) of analytes from a sample.

Abstract: Provided herein are devices that facilitate the magnetic separation of an analyte from a sample, and methods of use thereof. In particular embodiments, devices and methods are provided for the trans-interfacial magnetic separation (TIMS) of analytes from a sample.

Abstract: Provided herein are methods of producing lyophilized reagents with desired physical characteristics, and the lyophilized reagents produced thereby. In particular, lyophilized combinations of reagents are provided with specific physical geometries that provide optimized use in assays and devices.

Abstract: Provided herein are methods for rapid detection of RNA in a sample. The methods comprise providing a reaction mixture containing the sample, amplification reagents, and a polymerase enzyme having both RNA and DNA-dependent polymerase activity; reverse transcribing the RNA to DNA by incubating for a reverse transcription time of no longer than 5 minutes; and amplifying the DNA by performing a thermal cycling protocol comprising a plurality of amplification cycles, wherein each amplification cycle comprises at least a denaturation step and an annealing step.

Abstract: Provided herein are methods for enhancing the speed and/or efficiency of a nucleic acid capture using an affinity-tagged capture oligonucleotide (e.g., biotinylated DNA oligo) and an immobilized capture agent (e.g., immobilized avidin/streptavidin). In particular, experiments conducted during development of embodiments herein demonstrate that streptavidin capture of biotinylated nucleic acid complexes occurs more quickly and efficiently at elevated temperatures while simultaneously reducing the amount of nonspecific DNA captured.

Abstract: Provided herein are devices that facilitate the magnetic separation of an analyte from a sample, and methods of use thereof. In particular embodiments, devices and methods are provided for the trans-interfacial magnetic separation (TIMS) of analytes from a sample.

Abstract: Microorganisms that co-consume glucose with non-glucose carbohydrates, such as xylose, and methods of using same. The microorganisms comprise modifications that reduce or ablate the activity of a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) protein or modifications that reduce or ablate the activity of a phosphoglucose isomerase and a GntR. The PTS protein may be selected from an enzyme I (EI), an HPr, an FPr, and an enzyme IIGlc (EIIGlc). Additional modifications include reduction or ablation of the activity of a pyruvate formate lyase, a lactate dehydrogenase, and a fumarate reductase and inclusion of recombinant pyruvate decarboxylase and alcohol dehydrogenase genes. The microorganisms are particularly suited to co-consuming glucose and xylose in media containing these substrates and producing ethanol therefrom.

Abstract: Systems and methods for determining genetic variations of an organism for performing a physiological function. The systems include a number of modules that can be integrated into existing metabolic engineering algorithms. The methods include use of the modules. The physiological function may include growth, compound production, and/or metabolic reaction flux, among others.

Abstract: Microorganisms that co-consume glucose with non-glucose carbohydrates, such as xylose, and methods of using same. The microorganisms comprise modifications that reduce or ablate the activity of a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) protein or modifications that reduce or ablate the activity of a phosphoglucose isomerase and a GntR. The PTS protein may be selected from an enzyme I (EI), an HPr, an FPr, and an enzyme IIGlc (EIIGlc). Additional modifications include reduction or ablation of the activity of a pyruvate formate lyase, a lactate dehydrogenase, and a fumarate reductase and inclusion of recombinant pyruvate decarboxylase and alcohol dehydrogenase genes. The microorganisms are particularly suited to co-consuming glucose and xylose in media containing these substrates and producing ethanol therefrom.

Abstract: Microorganisms that co-consume glucose with non-glucose carbohydrates, such as xylose, and methods of using same. The microorganisms comprise modifications that reduce or ablate the activity of a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) protein or modifications that reduce or ablate the activity of a phosphoglucose isomerase and a GntR. The PTS protein may be selected from an enzyme I (EI), an HPr, an FPr, and an enzyme IIGlc (EIIGlc). Additional modifications include reduction or ablation of the activity of a pyruvate formate lyase, a lactate dehydrogenase, and a fumarate reductase and inclusion of recombinant pyruvate decarboxylase and alcohol dehydrogenase genes. The microorganisms are particularly suited to co-consuming glucose and xylose in media containing these substrates and producing ethanol therefrom.

Abstract: Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

Abstract: Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

Abstract: This disclosure relates generally to methods and kits useful for preparing samples, extracting nucleic acids from samples (e.g., biological samples), and/or detecting nucleic acids (e.g., pathogen nucleic acids) in samples (e.g., samples obtained from a subject). In particular, compositions, kits, and methods are provided comprising detergents and proteinases to treat biological samples prior to extraction of nucleic acids. Also described is use of cations for improved efficiency of nucleic acid hybridization. The prepared nucleic acid is suitable for PCR assays including those described for detection of Mycobacterium tuberculosis.

Abstract: Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

Abstract: Microorganisms that co-consume glucose with non-glucose carbohydrates, such as xylose, and methods of using same. The microorganisms comprise modifications that reduce or ablate the activity of a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) protein or modifications that reduce or ablate the activity of a phosphoglucose isomerase and a GntR. The PTS protein may be selected from an enzyme I (EI), an HPr, an FPr, and an enzyme IIGlc (EIIGlc). Additional modifications include reduction or ablation of the activity of a pyruvate formate lyase, a lactate dehydrogenase, and a fumarate reductase and inclusion of recombinant pyruvate decarboxylase and alcohol dehydrogenase genes. The microorganisms are particularly suited to co-consuming glucose and xylose in media containing these substrates and producing ethanol therefrom.

Abstract: Systems and methods for determining genetic variations of an organism for performing a physiological function. The systems include a number of modules that can be integrated into existing metabolic engineering algorithms. The methods include use of the modules. The physiological function may include growth, compound production, and/or metabolic reaction flux, among others.

Abstract: Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

Abstract: The invention relates to the novel discovery that antagonizing a C/CLP can be useful for the treatment of diseases associated with the upregulation of one or more C/CLP such as Th2-driven and/or IL-13 mediated inflammatory diseases. Accordingly the present invention provides C/CLP antagonists and also provides compositions and methods for the prevention, management, treatment or amelioration of an inflammatory condition associated with the upregulation of a C/CLP or one or more symptoms thereof and/or the inhibition of IL-13 mediated inflammation.

Abstract: The present invention relates to methods and compositions designed for the treatment, management, or prevention of a non-neoplastic hyperproliferative cell or excessive cell accumulation disorders, particularly those involving hyperproliferation of epithelial or endothelial cells. In one embodiment, the methods of the invention comprise the administration of an effective amount of one or more EphA2 agonistic agents that bind to EphA2 and increase EphA2 cytoplasmic tail phosphorylation and/or increase EphA2 autophosphorylation, in cells which EphA2 has been agonized. In another embodiment, the methods of the invention comprise the administration of an effective amount of one or more EphA2 agonistic agents that bind to EphA2 and reduce EphA2 activity (other than autophosphorylation). In another embodiment, the methods of the invention comprise administration of an effective amount of one or more EphA2 agonistic agents that bind to EphA2 and decrease a pathology-causing cell phenotype (e.g.