Abstract: An array of micro-chambers (220) with ISFETs (300) disposed therein for monitoring single cell activity in the microarray to determine the presence or absence of microorganisms in a sample (390).

Abstract: An array of micro-chambers (220) with ISFETs (300) disposed therein for monitoring single cell activity in the microarray to determine the presence or absence of microorganisms in a sample (390).

Abstract: An array of micro-chambers (220) with individual ion sensitive field effect transistors (ISFETs) (300) disposed therein for monitoring single cell activity in the microarray to determine the presence or absence of microorganisms in a sample (390). In addition to the presence or absence of a single cell, certain further embodiments contemplate monitoring cell behavior. Cell behavior includes the entire range of cell activity as well as cell response to changes in environmental conditions of changes in response due to the addition of sample constituents.

Abstract: A high-sensitivity, low-background immuno-amplification assay is provided, which offers a streamlined workflow suitable for high-throughput assays of clinically relevant samples, such as blood and other bodily fluids. The assay comprises the use of two proximity members that each comprise an analyte-specific binding component conjugated to an oligonucleotide. Binding an analyte brings the oligonucleotide moieties of the proximity members in sufficiently close contact that the oligonucleotides form an amplicon. The presence of the analyte then is detected through amplification of the amplicon and detection of the amplified nucleic acids. The sensitivity of the assay of the present invention is improved by preventing spurious or non-specific amplicon formation by proximity members that are not complexed with an analyte.

Abstract: Presented herein are methods for the detection of the presence or absence of one or more microorganisms in a sample. The method deploys a plurality of probe sets to detect a plurality of microorganisms. The probes in the probe set are detectably labeled. At least one probe set has probes labeled with a combination of detectable labels. The number of detectable labels used in the plurality of probe sets numbers less than the number of microorganisms being detected by the probe set.

Abstract: Presented herein are methods and compositions for generating sequence-specific, secondary amplification products during Loop-mediated Isothermal Amplification (LAMP). Conventional LAMP produces a preponderance of high molecular weight DNA structures concatenated into self-complementary hairpins, which are not amenable to detection by routine probe-based hybridization methods, making multiplex detection of two or more targets or sequence variants in closed-tube formats extremely difficult. Provided herein, for example, are methods for generating secondary LAMP products bearing a fragment of the original target sequence embedded within low-molecular weight products that are devoid of competitive hairpin structures, the lack of which enhances probe-based detection of target sequences. These secondary products can, for example, be produced in real-time, during the LAMP process, and can provide the option of detecting multiple target sequences within a single tube using, e.g.

Abstract: Provided herein are methods and kits for the improved detection of rare mutations within a high background. Exemplary embodiments relate to kits and methods that include amplification primers, a blocking oligonucleotide, and one or more allele-specific detector probes, useful in the specific detection of rare allelic variants or mutations.

Abstract: An array of micro-chambers 220) with individual ion sensitive field effect transistors (ISFETs) (300) disposed therein for monitoring single cell activity in the microarray to determine the presence or absence of microorganisms in a sample (390). In addition to the presence or absence of a single cell, certain further embodiments contemplate monitoring cell behavior. Cell behavior includes the entire range of cell activity as well as cell response to changes in environmental conditions of changes in response due to the addition of sample constituents.

Abstract: A high-sensitivity, low-background immuno-amplification assay is provided, which offers a streamlined workflow suitable for high-throughput assays of clinically relevant samples, such as blood and other bodily fluids. The assay comprises the use of two proximity members that each comprise an analyte-specific binding component conjugated to an oligonucleotide. Binding an analyte brings the oligonucleotide moieties of the proximity members in sufficiently close contact that the oligonucleotides form an amplicon. The presence of the analyte then is detected through amplification of the amplicon and detection of the amplified nucleic acids. The sensitivity of the assay of the present invention is improved by preventing spurious or non-specific amplicon formation by proximity members that are not complexed with an analyte.

Abstract: Provided herein are methods and kits for modulating the amplification efficiency of nucleic acids, which are useful in multiplex reactions where the amplification efficiency of one or more nucleic acids in the mixture are desired to be modulated relative to one or more other nucleic acids. Embodiments relate to molecular diagnostics, including detecting sequence variants, such as SNPs, insertions deletions, and altered methylation patterns, as well as the modulation of the amplification efficiency of internal control sequences to provide more accurate control sequences for amplification reactions.

Abstract: Presented herein are methods for determining the presence of a non-mutated Mycobacterium rpoB gene core region. For example, presented herein are methods that permit the determination of whether a Mycobacterium is rifampin-resistant by determining whether or not the Mycobacterium rpoB gene core region comprises a mutation. In accordance with such methods, multi-drug-resistant strains of Mycobacterium also can be identified.

Abstract: Presented herein are methods for the detection of the presence or absence of one or more microorganisms in a sample. The method deploys a plurality of probe sets to detect a plurality of microorganisms. The probes in the probe set are detectably labeled. At least one probe set has probes labeled with a combination of detectable labels. The number of detectable labels used in the plurality of probe sets numbers less than the number of microorganisms being detected by the probe set.

Abstract: The invention employs an unlabeled signal primer comprising a 5? adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3? end of which hybridizes to the complement of the 5? adapter sequence of the signal primer to produce a 5? overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5? overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.

Abstract: Presented herein are methods and compositions for generating sequence-specific, secondary amplification products during Loop-mediated Isothermal Amplification (LAMP). Conventional LAMP produces a preponderance of high molecular weight DNA structures concatenated into self-complementary hairpins, which are not amenable to detection by routine probe-based hybridization methods, making multiplex detection of two or more targets or sequence variants in closed-tube formats extremely difficult. Provided herein, for example, are methods for generating secondary LAMP products bearing a fragment of the original target sequence embedded within low-molecular weight products that are devoid of competitive hairpin structures, the lack of which enhances probe-based detection of target sequences. These secondary products can, for example, be produced in real-time, during the LAMP process, and can provide the option of detecting multiple target sequences within a single tube using, e.g.

Abstract: Mass spectrometry techniques for determining the status of sepsis in an individual are provided. A biomarker profile resolved from a biological sample, taken from the individual, using a mass spectrometry technique is compared to a reference biomarker profile. A single such comparison classifies the individual as belonging to or not belonging to a reference population. The individual's biomarker profile and the reference biomarker profile comprise a plurality of ions each having a mass-to-charge ratio of about 100 Daltons to about 1000 Daltons. The plurality of ions can be detected by electrospray ionization mass spectrometry in positive mode. The comparison uses a decision rule, such as a classification tree, that determines the status of sepsis in the individual without requiring knowledge of the identity of the biomarkers in the biomarker profile from the individual and without requiring knowledge of the identity of the biomarkers in the reference biomarker profile.

Abstract: Mass spectrometry techniques for determining the status of sepsis in an individual are provided. A biomarker profile resolved from a biological sample, taken from the individual, using a mass spectrometry technique is compared to a reference biomarker profile. A single such comparison classifies the individual as belonging to or not belonging to a reference population. The individual's biomarker profile and the reference biomarker profile comprise a plurality of ions each having a mass-to-charge ratio of about 100 Daltons to about 1000 Daltons. The plurality of ions can be detected by electrospray ionization mass spectrometry in positive mode. The comparison uses a decision rule, such as a classification tree, that determines the status of sepsis in the individual without requiring knowledge of the identity of the biomarkers in the biomarker profile from the individual and without requiring knowledge of the identity of the biomarkers in the reference biomarker profile.

Abstract: The invention employs an unlabeled signal primer comprising a 5? adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3? end of which hybridizes to the complement of the 5? adapter sequence of the signal primer to produce a 5? overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5? overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.

Abstract: The invention employs an unlabeled signal primer comprising a 5? adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3? end of which hybridizes to the complement of the 5? adapter sequence of the signal primer to produce a 5? overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5? overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.

Abstract: The early prediction or diagnosis of sepsis advantageously allows for clinical intervention before the disease rapidly progresses beyond initial stages to the more severe stages, such as severe sepsis or septic shock, which are associated with high mortality. Early prediction or diagnosis is accomplished by comparing an individual's profile of biomarker expression to profiles obtained from one or more control, or reference, populations, which may include a population that develops sepsis. Recognition of features in the individual's biomarker profile that are characteristic of the onset of sepsis allows a clinician to diagnose the onset of sepsis from a bodily fluid isolated from the individual at a single point in time. The necessity of monitoring the patient over a period of time is, therefore, avoided, advantageously allowing clinical intervention before the onset of serious symptoms of sepsis.

Abstract: Methods for detecting, immobilizing or localizing primer extension products of a Strand Displacement Amplification reaction which are coupled to, and an indication of, amplification of the target sequence. The primer extension products are secondary, target-specific DNA products generated concurrently with SDA of the target sequence and can therefore be used to detect and/or measure target sequence amplification in real-time. In general, the secondary amplification products are not amplifiable and remain inert in the SDA reaction after they are formed without interfering with amplification of the target sequence. The secondary amplification products may be designed or modified to contain special features to facilitate their detection, immobilization or localization.