Abstract: The present disclosure describes various improved methods for imaging at least one target in a sample, including methods employing an adapter strand oligonucleotide and a bridge strand oligonucleotide. Some methods also employ bouncer oligonucleotides and/or blocker oligonucleotides. Some methods also use two partial docking strands to detect proximity of the partial docking strands to each other.

Abstract: Disclosed is a method of quantifying a biomarker with high sensitivity using photo-oxidation induced amplification. The method includes performing an enzyme-substrate reaction of a measurement sample including an enzyme labeled on any one selected from among an antibody, an aptamer, and a nucleic acid specifically bound to the biomarker, optically measuring one or more optical properties selected from among amounts of color formation, light emission, and fluorescence of a product during a photo-oxidation induced amplification process while the product resulting from the enzyme-substrate reaction is continuously exposed to light to thus perform the photo-oxidation induced amplification process, indexing a time-varying pattern of the measured optical properties, and quantifying a concentration of the biomarker included in the measurement sample by comparing an index extracted during the indexing with an index of a reference sample.

Abstract: The invention provides DNA compositions that relate to transgenic insect resistant maize plants. Also provided are assays for detecting the presence of the maize DAS-59122-7 event based on the DNA sequence of the recombinant construct inserted into the maize genome and the DNA sequences flanking the insertion site. Kits and conditions useful in conducting the assays are provided.

Abstract: The present invention relates to a method, a device, and an apparatus for analyzing the expression of a gene in single cells. Specifically, the present invention relates to: a device for gene expression analysis, characterized by including a support, in which a nucleic acid probe having a test nucleic acid capture sequence and a known sequence, and further containing a cell recognition tag sequence which differs depending on the difference in position on the surface of the support or in the vicinity of the surface thereof, and a common primer sequence having a known sequence is two-dimensionally distributed and immobilized on the surface of the support or in the vicinity of the surface thereof; and a method and an apparatus using the device for gene expression analysis.

Abstract: Disclosed herein are primers and probes related to the detection of SARS-CoV-2 via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of SARS-CoV-2 in test samples and/or to diagnose Covid-19. Specifically, the present disclosure describes primers and probes that bind to the N gene, ORF1ab, or E gene of SARS-CoV-2 coronavirus for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.

Abstract: Disclosed are compositions and methods for enriching a non-host sequence from a host sample. Also disclosed are compositions and methods for detecting a non-host sequence in a host sample. For example, a pathogen can be enriched and detected in a sample taken from a human without knowing what the pathogen is.

Abstract: Methods and systems are provided for point-of-care nucleic acid amplification and detection. One embodiment of the point-of-care molecular diagnostic system includes a cartridge and an instrument. The cartridge can accept a biological sample, such as a urine or blood sample. The cartridge, which can comprise one or more of a loading module, lysis module, purification module and amplification module, is inserted into the instrument which acts upon the cartridge to facilitate various sample processing steps that occur in order to perform a molecular diagnostic test.

Abstract: A method for detecting a target nucleic acid sequence in a sample in the presence of at least protein capable of binding to single-stranded DNA is provided, comprising contacting said sample with at least one oligonucleotide probe comprising a fluorophore, a quencher and a region complementary to said target nucleic acid sequence. The sequence of the oligonucleotide probe comprises at least 20% RNA nucleotides, modified RNA nucleotides and/or PNA nucleotides.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: The present invention provides compositions and methods based on genetic polymorphisms that are associated with coronary heart disease (particularly myocardial infarction), aneurysm/dissection, and/or response to drug treatment, particularly statin treatment. For example, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by these nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and variant proteins, and methods of using the nucleic acid molecules and proteins as well as methods of using reagents for their detection.

Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.

Abstract: Systems, methods, and compositions for monitoring and analyzing nucleic acid hybridization state using L-DNA probes are described. The methods include adding L-DNA probes that can be fluorescently detected to a system including D-DNA. The L-DNA probes include primer, target, and antisense nucleotide sequences, and fluorescent dye compounds. The L-DNA probes are particularly useful for monitoring and analyzing various parameters during DNA amplification using the polymerase chain reaction.

Abstract: The invention provides methods and compositions generally useful to the use of polymerase chain reaction (PCR) amplification of trace DNA sequences from formalin-fixed paraffin-embedded (FFPE) biopsy samples and specifically relevant to the identification of multi-drug resistant H. pylori in such biopsy samples.

Abstract: A bottleneck in the Next Generation Sequencing (NGS) workflow is the quantification of libraries for accurate pooling and loading of the sequencing instrument flow cell or chip. Disclosed herein are methods that improve performance and reduce time compared to existing methods.

Abstract: The disclosed invention include nucleic acid oligomers that may be used as amplification oligomers, including primers, as capture probes for sample preparation, and detection probes for detection of 16S rRNA from Atopobium vaginae in samples by using methods of specific nucleic acid amplification and detection.

Abstract: A method of detecting a target polynucleotide sequence in a given nucleic acid analyte characterised by the steps of: a. annealing the analyte to a single-stranded probe oligonucleotide A0 to create a first intermediate product which is at least partially double-stranded and in which the 3? end of A0 forms a double-stranded complex with the analyte target sequence; b. pyrophosphorolysing the first intermediate product with a pyrophosphorolysing enzyme in the 3?-5? direction from the 3? end of A0 to create partially digested strand A1 and the analyte; c. (i) annealing A1 to a single-stranded trigger oligonucleotide B and extending the A1 strand in the 5?-3? direction against B; or (ii) circularising A1 through ligation of its 3? and 5? ends; or (iii) ligating the 3? end of A1 to the 5? end of a ligation probe oligonucleotide C; in each case to create an oligonucleotide A2; d. priming A2 with at least one single-stranded primer oligonucleotide and creating multiple copies of A2, or a region of A2; and e.

Abstract: Described herein is a method for isolating microbial DNA from a sample that comprises host DNA and microbial DNA. In some embodiments, the method may comprise: obtaining a tagged DNA sample, wherein the tagged DNA sample contains host DNA and microbial DNA, both comprising an appended universal adaptor; b) hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by in vitro transcribing, in the presence of an affinity-tagged ribonucleotide, a library of fragmented host DNA that has been ligated to an RNA promoter adaptor; c) binding the product of step b) with a capture agent that is tethered to a substrate, in the presence of RNA oligonucleotides that are complementary to or have the same sequence as one or more strands of the universal adaptor, thereby capturing the host DNA on the substrate; and d) collecting the unbound DNA, wherein the unbound DNA comprises the microbial DNA.

Abstract: Provided herein is technology relating to the amplification-based detection of nucleic acids and particularly, but not exclusively, to methods and compositions for minimizing variability in the activity between different samples or manufacturing lots of DNA polymerases, such as Taq DNA polymerase.

Abstract: A method for real-time quantitative detection of single-type, target nucleic acid sequences amplified using a PCR in a microwell, comprising introducing in the microwell a sample comprising target nucleic acid sequences, magnetic primers, and labelling probes; performing an amplification cycle to form labelled amplicons; attracting the magnetic primers to a surface through a magnetic field to form a layer including labelled amplification products and free magnetic primers; and detecting the labelled amplification products in the layer with a surface-specific reading method.

Abstract: A method of evaluating a sequence variation in a sample is provided. In some embodiments, the method may involve: amplifying a nucleic acid product from an initial sample; fragmenting an amount of the nucleic acid product to produce fragments; attaching an adaptor to each end of the fragments to produce adaptor-tagged fragments; sampling no more than 10% of the tagged fragments and amplifying them; sequencing at least some of the copies of the fragments to produce a plurality of sequence reads; grouping sequence reads for copies of fragments that have the same fragmentation breakpoints; deriving a consensus sequence for each of the read groups; and aligning the consensus sequences with a reference sequence.