Abstract: The present invention is concerned with PCR-based detection methods and kits for the identification, differentiation, and quantification of different bacterial strains (e.g., Gram-negative bacterial strains), and also association of two or more PCR-positive genes to a single genome. The methods generally comprise carrying out PCR reactions using at least a first PCR primer set and/or probe for at least one target nucleic acid; and a second PCR primer set and/or probe for at least a second target nucleic acid. Positive PCR reaction products are then detected to determine test samples containing positive PCR reaction products for both the first and second target nucleic acids. This information can be used to calculate the gene association rate to determine whether the sample contains, for example, Shiga toxin-producing E. coli of the O-type serogroup.

Abstract: Homogenous DNA or RNA cell blocks used as a standard and comprising uniformly distributed cells, or ratio of cells, for use as a positive control for a biomarker in immunohistochemistry slide scanning and image analysis. The cell blocks are made using a Homogenous Cell Mixture (HCM) apparatus comprising a rotating multi-tiers that de-clump and filter single cells downward to mix with a fixation liquid-3% agarose. The uniform rotation of the tiers is under the operational control of a motorized mechanism, and results in a cell mixture comprising a constant density of cells, which is then transferred into molds to make formalin fixed paraffin embedded (FFPE) cell blocks. The size of the molds is also determined based upon a computation that factors in the total number of cells (e.g. density) in a cell block that a user desires, and the total cell volume for a specific cell type selected.

Abstract: An in vitro experimental standard comprising sections cut from a homogenous cell block for use as a positive control for biomarkers in immunohistochemistry experiments. The homogenous cell block is produced using a three layered vertical apparatus to create an evenly distributed suspension of FFPE cells, wherein the cells are mixed with 3% agarose while still rotating within the apparatus's middle layer. The injection of the cell mixture into a mold creates a homogeneous cell block where each cell, or ratio of different types of cells, is evenly distributed. The cell mixture within the cell block may further comprise: a mixture of the same type of cell with different genetic modifications; a mixture of the same type of cell with different protein or nucleic acids expression; and a mixture of different types of cells with different genetic backgrounds, and/or different expression level of genes and/or proteins.

Abstract: A solid composition comprising a homogenous cell block able to be used as a positive control for biomarkers in immunohistochemistry experiments, such as slide scanning and image analysis. The homogenous cell block is produced using a three layered vertical apparatus to create an evenly distributed suspension of FFPE cells, wherein the cells are mixed with 3% agarose while still rotating within the apparatus's middle layer. The injection of the cell mixture into a mold creates a homogeneous cell block where each cell, or ratio of different types of cells, is evenly distributed. The cell mixture within the cell block may further comprise: a mixture of the same type of cell with different genetic modifications; a mixture of the same type of cell with different protein or nucleic acids expression; and a mixture of different types of cells with different genetic backgrounds, and/or different expression level of genes and/or proteins.

Abstract: Provided is a DNA chip with micro-channel for DNA analysis, which has a structure in which a silicon layer (chip A) and a plastic layer (chip B) are laminated, wherein the chip A includes at least two PCR reactors connected in series in a micro-channel, and a filter between the PCR reactors, the chip B includes a reagent, a liquid delivery mechanism and a sensor in a micro-channel, and the reagent, liquid delivery mechanism and sensor can be changed according to a kind of an analyte and an object to be detected.

Abstract: A method of designing a primer for detecting a single nucleotide polymorphism (SNP), a method of detecting an SNP, a method of distinguishing SNPs, primers, detectable oligonucleotides, and kits.

Abstract: The present invention discloses methods of applications of indole-3-propionic acid, L-carnitine and O-acetyl-L-carnitine in one or more different reactive steps of a sequencing-by-synthesis workflow. The reactive steps employing these compounds include, but are not limited to, cleaving, imaging, incorporating bases and washing. The use of these new compounds provides improved sequencing performance including, but not limited to, lower error rates, higher sequence outputs and/or longer read lengths.

Abstract: The present invention provides novel compositions, kits and methods employing RNA 5? polyphosphatases, RNA 5? monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5? ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5? ends. The 5? tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses.

Abstract: Provided is a method for rapidly and easily detecting a mutated nucleic acid, which is contained in a small amount in a nucleic acid sample together with wild-type nucleic acids, with high specificity and high sensitivity. In the method of the present invention, amplification of a detection region comprising a target site by a nucleic acid amplification method is inhibited, by the steps of allowing a nucleic acid having a target site to coexist with a clamp probe comprising a photo-crosslinking nucleic acid and having a sequence complementary to the target site, and photo-crosslinking the nucleic acid having the target site with the clamp probe by photo-irradiation.

Abstract: Provided are an isolated oligonucleotide and a use thereof in nucleic acid sequencing, wherein the isolated oligonucleotide comprises a first strand, wherein the 5?-end nucleotide of the first strand has a phosphate group, and the 3?-end nucleotide of the first strand is a dideoxynucleotide, and a second strand, wherein the 5?-end nucleotide of the second strand does not have a phosphate group, and the 3?-end nucleotide of the second strand is a dideoxynucleotide, wherein the first strand is longer than the second strand in length, and a double-stranded structure is formed between the first strand and the second strand.

Abstract: A process for detecting Haemophilus influenzae nucleic acid in a sample includes producing an amplification product by amplifying a Haemophilus influenzae nucleotide sequence and measuring the amplification product to detect Haemophilus influenzae in the sample. Some embodiments allow direct serotype determination in a single step assay. Also provided are reagents and methods for detecting and distinguishing Haemophilus influenzae from other infectious agents. A kit is provided for detecting and quantifying Haemophilus influenzae in a sample.

Abstract: Compositions are provided that include a plurality of small molecules selected from the group consisting of an amide, urea or acetone having a molecular weight less than 300 g/mol; and dNTPs and a polymerase in a buffer suitable for use as an amplification buffer. Methods of use of the compositions are also described for reducing non-template DNA amplification.

Abstract: Dermatophytes which belong to one of the three genera Epidermophyton, Trichophyton and Microsporum are the main cause of fungal infections of skin, hair and nails. Traditional diagnostic procedures consist of microscopy and culture, but due to the slow growth rate of dermatophytes typically two to four weeks are needed before a final diagnosis is obtained. The present invention is a rapid DNA extraction method extracting nucleic acids from fungi (e.g. dermatophytes and other pathogenic fungi) which can be performed from directly on hair, nail or skin specimens from humans, from naturally or experimentally infected animals or from cultured fungal colonies for the use in PCR amplification and detection assays. The present invention also includes specific primer sets for detection of any dermatophyte and for species specific detection of Trichophyton rubrum and Epidermophyton floccosum by PCR and a kit for diagnosing fungal infections.

Abstract: A method of manufacturing a reference material for determining incorporation of a genetically modified (GM) plant into a sample or analyzing a mixing ratio from a tissue-cultured cell line that is obtained by incubating tissues of either a GM plant or a non-GM plant, and a method of determining incorporation of a GM plant into a sample and analyzing a mixing ratio using the reference material are provided. The reference material for determining the incorporation of a genetically modified (GM) plant a sample or analyzing a mixing ratio using the tissue-cultured cell lines that are obtained by incubating tissues of the GM plant and the non-GM plant can be useful in producing a countless number of populations having the same genetic traits via the tissue culture. Thus, when a culture capacity of the reference material is increased to a large volume, it is possible to obtain a large volume of the reference material having uniform qualities with no quality variation between batches.

Abstract: The present invention provides materials and methods for detecting, quantifying, and/or high-throughput-profiling microRNAs. Advantageously, the present invention is more sensitive and specific than other currently-available miRNA qPCR assays. In addition, the present invention is convenient, easy-to-perform, and cost-effective. In one embodiment, the present invention provides a universal primer for reverse transcription of all miRNAs, a universal reverse primer for PCR amplification reaction, and universal probes. In another embodiment, the present invention provides assays that allow simultaneous detection and/or quantification of a plurality of target miRNAs using a single reverse transcription reaction.

Abstract: The present invention relates to a process to perform a molecular risk assessment (MRA) upon a sample suspected to contain an enterohemorrhagic Escherichia coli (EHEC), comprising the steps: contacting said sample or DNA isolated therefrom with a pair of primers derived from the following target genes stx1, stx2, eae and/or espk; wherein the process is characterized in that if amplification products are detected for each of the target genes in the first step, in a second step said sample or DNA isolated therefrom is contacted with a pair of primers derived from the following target genes nleB, nleH1-2, nleE, ent/espL2, eae subtypes ?, ?, ? and ? and the target genes rfbE (0157), wbdl (0111), wzx (026); ihp1 (0145), wzx (0103); and detecting the presence or the absence of an amplification product for each of the target genes.

Abstract: Provided herein are products and processes for the amplification, detection and sequencing of short-stranded nucleic acid in the presence of a high background of long-stranded genomic material (e.g., host or maternal nucleic acids). The methods rely on the use of inside and outside primers introduced at varying concentrations, as well as universal amplification reactions that preferentially amplify short, low copy number nucleic acid.

Abstract: The present invention relates to systems and methods of monitoring velocity or flow in channels, especially in microfluidic channels. In some embodiments, the present invention relates to systems and methods of monitoring velocity or flow rate in systems and methods for performing a real-time polymerase chain reaction (PCR) in a continuous-flow microfluidic system.

Abstract: A detection method of nucleic acid is provided. The method includes: providing nucleic acid to be tested, making the nucleic acid to be tested react under asymmetric PCR conditions with a pair of primers for target nucleic acid amplification, DNA polymerase, adenine deoxyribonucleotide, guanine deoxyribonucleotide, cytosine deoxyribonucleotide and thymidine deoxyribonucleotide in a PCR buffer solution, mixing the reaction product and liquid that contains probe molecules, and judging whether the nucleic acid to be tested contains the target nucleic acid by observing the obtained mixture color or color change. A kit is also provided that can be used in the nucleic acid detection by the said method. Application of the method and the kit in inspection and quarantine is also provided. The method is a quick and easy, sensitive and a specific detection method of nucleic acid with direct observation using naked eyes. The method does not need additional equipment.

Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.