Abstract: A system including an optical signal detector and a controller operatively coupled to the optical signal detector and configured to determine an operational performance status of the optical signal detector. The optical signal detector includes a detection channel having a light source and a sensor, where the detection channel is configured to emit and focus light generated by the light source at a detection zone and to receive and focus light on the sensor. The optical performance status of the optical signal detector is based on a measured characteristic of light focused on the sensor while a non-fluorescent surface is in the detection zone and/or a measured characteristic of light focused on the sensor while a void is in the detection zone.

Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).

Abstract: A system and method for self-checking a fluorometer for failure or deteriorated performance includes fluorescent reference standards mounted on a support to move with respect to one or more fixed fluorometers. The intensity of the fluorescent emission of the fluorescent reference standard is initially measured with the fluorometer, and, after a prescribed interval of usage of the fluorometer, a test measurement of the intensity of the fluorescent emission of the fluorescent standard is taken with the fluorometer. The test measurement is compared to the initial measurement, and failure or deteriorated performance of the fluorometer is determined based on a deviation of the test measurement from the initial measurement.

Abstract: A method for moving a processing vial between locations of an instrument. The method includes the steps of dispensing a fluid into a processing vial with a disposable pipette tip frictionally fitted onto a probe of a pipettor, stripping the disposable pipette tip from the probe of the pipettor, and then engaging a cap in a frictional fit with the probe of the pipettor. While the cap is engaged in a frictional fit with the probe of the pipettor, coupling the cap to the processing vial to form a cap/vial assembly, where the cap seals the processing vial. The pipettor moves the cap/vial assembly from a first location of an instrument to a second location of the instrument. At the second location of the instrument, the cap/vial assembly is ejected from the probe of the pipettor, thereby depositing the cap/vial assembly at the second location.

Abstract: A method of reading machine-readable labels on sample receptacles held by a sample rack. In the method, an absolute position of the sample rack is measured as the sample rack moves between first and second positions in a housing. During movement between the first and second positions, an image is acquired of a machine-readable label associated with each sample receptacle held by the sample rack. The image of each machine-readable label is thereafter decoded.

Abstract: An automated method for analyzing a plurality of samples within a housing of a self-contained system. The system is loaded with a plurality of samples, after which a first assay is performed on a first sample subset and a second assay performed on a second sample subset. The two assays include exposing the samples to a target capture reagent having a solid support for directly or indirectly immobilizing a target nucleic acid that may be present in one or more of the samples. The two assays may be performed with the same or different target capture reagents and target nucleic acids, but the receptacles for performing the exposing step have substantially identical geometries. Following the exposing step, an amplification reaction for amplifying a region of the target nucleic acid is performed with each sample. The amplification reactions of the two assays are performed in receptacles having different geometries.

Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Abstract: Provided are compositions, kits, and methods for the identification of Salmonella. In certain aspects and embodiments, the compositions, kits, and methods may provide improvements in relation to specificity, sensitivity, and speed of detection.

Abstract: Compositions, reaction mixtures, kits and methods used in amplifying and detecting nucleic acids from various species of the class Mollicutes. Particular regions of the 23S rRNA or its gene have been identified as preferred targets for nucleic acid amplification reactions of a sample suspected containing at least one species of Mollicutes. Some oligomers comprise tag regions, target closing regions, promoter sequences, and/or binding moieties. Samples can be from any source suspected of containing a species of the class Mollicutes. Preferred sample sources include bioreactors, cell lines, cell culture wares and pharmaceutical manufacturing wares.

Abstract: The invention provides a lysis reagent for lysing red blood cells, thereby releasing a target, such as RNA from a parasitic organism, in a form suitable for analysis. The reagent includes at least ammonium chloride and an anionic detergent, and may include an anti-coagulant. The reagent serves to lyse red blood cells, protect the released target from degradation in the lysate, and is compatible with subsequent steps for analysis of the target such as target capture, amplification, detection, or sequencing.

Abstract: A receptacle having a plurality of interconnected chambers arranged to permit multiple process steps or processes to be performed independently or simultaneously. The receptacles are manufactured to separate liquid from dried reagents and to maintain the stability of the dried reagents. An immiscible liquid, such as an oil, is included to control loading of process materials, facilitate mixing and reconstitution of dried reagents, limit evaporation, control heating of reaction materials, concentrate solid support materials to prevent clogging of fluid connections, provide minimum volumes for fluid transfers, and to prevent process materials from sticking to chamber surfaces. The receptacles can be adapted for use in systems having a processing instrument that includes an actuator system for selectively moving fluid substances between chambers and a detector. The actuator system can be arranged to concentrate an analyte present in a sample.

Abstract: Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a 16S rRNA or its encoding gene from bacterial species associated with bacterial vaginosis. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

Abstract: A receptacle for minimizing evaporation of a fluid includes a single-piece body, a fluid-tight seal, a penetrable septum, and a lid coupled to the body. The body includes a first chamber having a first opening. The fluid-tight seal is affixed to a surface of the body that defines the first opening. The fluid-tight seal covers the first opening and is frangible. The septum covers the first opening and the fluid-tight seal. The lid has an opening axially aligned with the first opening. The septum comprises slits forming flaps The first chamber can be the only chamber containing a fluid, or the single-piece body may also include another chamber containing the fluid. The other chamber can be in fluid communication with the first chamber via a conduit. The fluid-tight seal can also cover the opening of the second chamber.

Abstract: Oligonucleotide primer useful for synthesizing a cDNA copy of HIV-1 nucleic acids from a broad range of HIV-1 subtypes, including M group and O group variants.

Abstract: Populations of target capture probes are provided that are useful for nucleic acid separation and purification. The probes of the population comprise a first region that is at least about 12 residues in length and comprises a poly(r) sequence comprising (i) a randomized sequence comprising G and A nucleotides, or (ii) a non-randomized repeating (A and G) sequence; and a second region comprising a first specific binding partner (SBP), wherein the SBP is capable of specifically binding a second specific binding partner (SBP2). Related combinations, methods, uses, kits, and reaction mixtures are also provided.

Abstract: System, apparatuses, and methods for performing automated reagent-based analysis are provided. Also provided are methods for automated attachment of a cap to a reaction receptacle, and automated removal of a cap from a capped reaction receptacle.

Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).