Abstract: Provided herein are methods of preparing a template nucleic acid for next-generation sequencing. The methods comprise performing primer extension using c7dGTP instead of dGTP, which then allows for the input nucleic acids to be selectively digested by c7dGTP-resistant restriction enzymes, thereby enriching the template nucleic acid prior to next-generation sequencing library preparation.

Abstract: The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.

Abstract: Disclosed are methods for diagnosing Bacterial Vaginosis in a subject comprising performing an assay for the detection of any one or more of Lactobacillus sp., Gardneralla vaginalis, and Eggerthella sp. in a subject sample. Also disclosed are methods and compositions for detecting Lactobacillus sp., Gardneralla vaginalis, and/or Eggerthella nucleic acid in a sample.

Abstract: A miRNA marker for the treatment and/or diagnosis of Alzheimer's disease (AD), and the miRNA marker is a miRNA23 cluster. The miRNA23 cluster is used in the diagnosis and treatment of AD. The expression of the miRNA23 cluster is detected using primers for the microRNA marker through AD model cells, AD model animals and natural aging animals, and blood of AD patients, and it is found that the expression of the miRNA23 cluster is significantly reduced during the progression of AD, which reduces neuronal apoptosis by inhibiting the GSK-3?-mediated tau protein phosphorylation. Therefore, the miRNA23 cluster can be used as a novel biomarker and therapeutic target for the early, non-invasive diagnosis and treatment of AD.

Abstract: The present disclosure provides methods for detecting a single-stranded target RNA. The present disclosure provides methods of cleaving a precursor C2c2 guide RNA array into two or more C2c2 guide RNAs. The present disclosure provides a kit for detecting a target RNA in a sample.

Abstract: Methods for rapidly concentrating a food sample for efficient detection of bacteria are disclosed. A microfiltration approach followed by centrifugation was used to concentrate the cells with an enzyme (e.g., a protease) added at the beginning of the process to facilitate more efficient micro-filtering. The enzyme was found to have no significant effect on cell viability.

Abstract: The present invention provides a method for detecting fungal DNA in a turf grass sample with a loop-mediated isothermal amplification (LAMP) assay which contains primers for fungal DNA of at least one turf pathogenic fungi selected from Sclerotinia homoeocarpa, Rhizoctonia solani spp., Pythium ashanidematum, Gaeumannomyces graminis spp., Microdochium nivale spp., Magnaporthe poae, Colletotrihum graminicola, Colletotrichum cereale and Pytium ultimum var. ultimum, comprising: subjecting the turf sample to a LAMP reaction wherein the LAMP reaction uses a primer set of four or more nucleic acid sequences with each primer in the set having from 15 to 50 nucleic acids The primers useful in the present method are selected from specifically selected internal transcribed spacer regions or genes of the target fungi to provide improved assay results.

Abstract: A biochip for the integration of all steps in a complex process from the insertion of a sample to the generation of a result, performed without operator intervention includes microfluidic and macrofluidic features that are acted on by instrument subsystems in a series of scripted processing steps. Methods for fabricating these complex biochips of high feature density by injection molding are also provided.

Abstract: A biochip for the integration of all steps in a complex process from the insertion of a sample to the generation of a result, performed without operator intervention includes microfluidic and macrofluidic features that are acted on by instrument subsystems in a series of scripted processing steps. Methods for fabricating these complex biochips of high feature density by injection molding are also provided.

Abstract: A sample processing tubule is provided including, from a proximate to a distal end, an opening through which a sample is introducible, at least three segments, and an reagent introduction port operatively connected to a distal segment of the at least three segments. The reagent introduction port enables the addition of a reagent in the distal segment of the tubule, enabling the user to create a customizable assay tubule.

Abstract: The invention relates to a single nucleotide polymorphism (SNP) marker related to a Chinese horse short stature trait. The SNP molecular marker is located at the 501th position of a sequence shown in SEQ ID NO.1, polymorphism is G/A, and the SNP marker corresponds to base pair 18,205,998 on chromosome 8 in a horse. The SNP marker related to the Chinese horse short stature trait and use thereof provided by the present invention have the following advantages that: (1) the molecular marker is not restricted by the age, sex and the like of Chinese horses, is used in early breeding of the Chinese horses, performs accurate screening immediately at birth, and significantly promotes the breeding process of dominant pony varieties of the Chinese horse; (2) a method for detecting SNP of a Chinese horse TBX3 gene is accurate, reliable, and easy to operate.

Abstract: This invention is directed to a method for detecting near and distant interactions between cells, organelles and other large structures. This method can also be used for specific detection and quantification of Antibody or other binding moiety protein-protein and macro-molecular interactions, as well as quantitative analysis of multiple proteins and their modifications.

Abstract: The present invention provides methods, compositions and kits for enriching and determining nucleotide sequences of a plurality of target loci from a sample comprising nucleic acids. The methods comprise one or more cycles of primer extension followed by PCR amplification of target sequences using nested target-specific primers.

Abstract: The present disclosure relates to systems and methods for high efficiency electronic sequencing of nucleic acids and molecular detection.

Abstract: A method including steps of (a) providing an array of sites, wherein each site comprises a mixture of different nucleic acid templates; (b) extending primers hybridized to the different nucleic acid templates at each of the sites with different nucleotide analogs having different reversible blocking moieties, respectively, thereby producing different primer extension products at each site; (c) detecting the different primer extension products to distinguish the different nucleotide analogs at each site; and (d) removing the different reversible blocking moieties from the primer extension products at each of the sites using a first treatment that is selective for a first of the different reversible blocking moieties and a second treatment that is selective for a second of the different reversible blocking moieties.

Abstract: Provided are methods of producing a product nucleic acid. The methods include combining a template deoxyribonucleic acid (DNA), a polymerase, a template switch oligonucleotide, and dNTPs into a reaction mixture. The components are combined into the reaction mixture under conditions sufficient to produce a product nucleic acid that includes the template DNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.

Abstract: The present invention relates to a method for amplifying at least one target RNA in a fixed and, optionally, expanded biological sample. In an embodiment of the invention, the method comprises incubating the fixed biological sample with a pair of polynucleotides complementary to non-overlapping and proximal sequences of a target RNA, wherein the polynucleotide pair hybridizes to the target RNA; ligating the polynucleotide pair using a ligase; and amplifying the ligation product. The invention further provides methods for detecting and optionally quantifying and/or sequencing the amplification product. As the method comprises hybridizing polynucleotide pairs to a target RNA in a fixed biological sample, the target RNA can be hybridized in situ.

Abstract: Disclosed is a method of quality control of nucleic acid amplification using quality control oligonucleotide. The method comprises a nucleic acid detection step and a determination step. The nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe. In the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step.

Abstract: The present invention provides methods for rapidly identifying an RNA viral infection using an isothermal nucleic acid amplification reaction that can be carried out extracted RNA in the context of a crude biological sample.

Abstract: Genomic DNA contains embedded ribonucleotides (rNMPs) that are incorporated during DNA replication and repair, or formed during DNA damage. The modifications have been linked to genome instability and disease, but no method currently exists to profile their locations genome-wide. rNMP incorporation has been extensively studied in recent years; however, locating sites of rNMP incorporation in genomic DNA has not yet been possible. Disclosed herein is a unique method for mapping rNMPs in genomic DNA that exploits the unique ligation mechanism of Arabidopsis thaliana tRNA ligase (AtRNL), normally involved in tRNA maturation. As disclosed herein AtRNL captures 2?,3?-cyclic phosphate or 2?-phosphate termini of DNA derived from alkaline cleavage of a DNA oligonucleotide (oligo) at an embedded rNMP, ligating the 2?-phosphate end to the 5?-phosphate terminus of the same DNA molecule and producing a ssDNA circle containing an embedded rNMP.