Abstract: Degenerate primers for amplifying fragments of the nucleotide sequences of mutL and dnaJ genes of a lactic acid bacterium of Lactobacillus casei group are provided. Methods and kits for discriminating interspecies and intraspecies of a lactic acid bacteria of Lb. casei group are also provided.

Abstract: Methods of diagnosing and treating patients afflicted with acne, including diagnosing one as having acne if the individual possesses RT4, RT5, RT7, RT8, RT9, or RT10. Methods for treating acne include administering an effective amount of a drug specifically targeting RT4, RT5, RT7, RT8, RT9, or RT10, such as small molecules, antisense molecules, siRNAs, biologics, antibodies, phages, vaccines, or combination thereof.

Abstract: Disclosed herein are methods of detecting a target RNA, methods of diagnosing an individual with a disease or condition when a target RNA associated with the disease or condition is detected, and methods of conveying via a communication medium data from the detection of a target RNA.

Abstract: A measuring method for amplicon length is provided. A qPCR master mix, a forward primer, a reverse primer, a hybridization probe, a double-stranded DNA binding dye, and nucleic acid samples are added into reaction wells for qPCR reaction, and the fluorescence intensity of each of a hybridization probe and a double-stranded DNA binding dye varying with cycle number is respectively measured. Afterwards, amplicon length is obtained by applying a calculating method.

Abstract: A method of determining whether a given single nucleotide is methylated or not methylated characterised by the steps of (a) contacting the single nucleotide with one or more hybridisation probe types each of which in its unused form comprises (1) a first oligonucleotide to which is attached one or more first detectable elements in an essentially undetectable state and which further comprises (i) double- and single-stranded regions and (ii) a region resistant to exonucleolytic degradation attached to the end of the double-stranded region adjacent the single-stranded region and (2) a second single-stranded oligonucleotide to which is attached one or more second detectable elements also in an essentially undetectable state and which is adapted to be at least in part the nucleotide sequence compliment of the single-stranded region of the first oligonucleotide; (b) for the relevant probe type causing (i) the single nucleotide to bind to the region resistant to exonucleolytic degradation and the single-stranded reg

Abstract: The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subject's genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.

Abstract: Disclosed are a sensor capable of detecting zinc oxide nanowires in water with high selectivity and sensitivity and a method for the detection of zinc oxide nanowires in water using the sensor. The sensor and method can provide powerful tools for analyzing the toxicity of zinc oxide nanowires to the environment and humans due to their ability to detect zinc oxide nanowires in water with high selectivity and sensitivity.

Abstract: The invention relates to a reaction vessel, a device and a method for detecting specific interactions between molecular target and probe molecules. The present invention especially relates to a reaction vessel which has a shape and size typical of a laboratory reaction vessel and in which a supporting element with probe molecules immobilised thereon on predetermined regions is arranged on its base surfaces.

Abstract: This invention provides methods of using labeled primers or probes for nucleic acid target detection and to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, and sets of oligonucleotide primers for use in such methods, as well as methods of quantitative PCR coupled with nanopore detection.

Abstract: Described herein are systems for analysis of biopolymers and complexes containing biopolymers based on optical measurement of ion flux through pores. Also described are methods of using such devices for analysis of biopolymers and complexes containing biopolymers, including methods of determining the nucleotide sequences of polynucleotides.

Abstract: The invention relates to mutant forms of Msp. The invention also relates to polynucleotide characterisation using Msp.

Abstract: The invention relates to improving the movement of a target polynucleotide with respect to a transmembrane pore when the movement is controlled by a polynucleotide binding protein. The invention also relates to improved transmembrane pores and polynucleotide binding proteins.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.

Abstract: The present invention includes, but is not limited to, methods, assays, and compositions for preparing libraries of nucleic acid molecules from biological samples, and for detecting and measuring the abundances of nucleic acid molecules, including RNA and DNA. The methods, assays, and compositions of the present invention provide in whole or in part for the detecting and measuring the abundances of nucleic acid molecules, and particularly but not limited to those nucleic acids that have structures that cannot be determined reliably by routine alignment to a reference sequence or concatenation of smaller sequences by matching homologous ends.

Abstract: A sequencing instrument optical system having a combined light source with multiple collinear excitation beams having different respective excitation wavelengths, a sequencing surface having DNA templates and nucleobase labels configured to emit a respective emission light at a different respective emission wavelength upon excitation by one or more of the excitation beams, a color camera configured to detect the emission light of each of the nucleobase labels, a first optical pathway configured to direct the collinear excitation beams from the combined light source to the sequencing surface, and a second optical pathway configured to direct the emission light from the sequencing surface to the color camera.

Abstract: Materials, methods, and systems for determining the position, i.e. the sequence within a double stranded nucleic acid, where a protein is bound are disclosed and described. Materials can include dsDNA, dsRNA, and dsDNA-mimics. Materials are first reacted with Osmium tetroxide 2,2?-bipyridine to partially osmylate the nucleic acid (osmylated or labeled polymer) and monitored by HPLC or CE in order to stop the labeling before it reaches 50%. This preserves the double stranded structure of the nucleic acid and leaves the protein bound to it during the labeling. Labeling occurs randomly at the whole length of the polymer but leaves the region where the protein binds intact. Methods are provided to describe preparation of the osmylated polymers, their purification, and characterization. Labeled polymers may be subject to voltage-driven translocation via nanopores of appropriate width so that the polymer can traverse.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: There is disclosed a method comprising the steps of: carrying out a plurality of expression assays, each expression assay comprising the steps of: carrying out an intervention on a biological system, measuring an expression profile of non-coding RNAs in the biological system resulting from the intervention, and storing an expression data set derived from the measured expression profile, the said expression assays concerning either or both a plurality of different interventions and a plurality of different biological systems; and analysing the resulting expression data sets to determine correlations between the effect on the expression profile of non-coding RNAs of the respective intervention in groups of two or more expression assays concerning either or both different interventions or different biological systems.

Abstract: Male subjects having an increased risk of developing Alzheimer's disease are identified by determining a fraction of cells that have lost chromosome Y in a biological sample obtained from the male subject. The fraction is compared to a predefined threshold and the male subject is predicted to have an increased risk of developing Alzheimer's disease based on the comparison between the fraction and the predefined threshold.

Abstract: The present invention concerns predictive mRNA biomarkers, which are used in combination with HLA-DRB4 for forecasting the treatment with MTX (methotrexate). The present invention further concerns a method for forecasting the treatment with MTX (methotrexate), comprising detection of the predictive mRNA biomarkers in combination with HLA-DRB4 in patient samples, whereby the patients are classified into responders or non-responders.

Abstract: The present invention relates to methods for treating or preventing a mitral valve disease in a subject in need thereof, comprising administering to the subject an effective amount of a therapeutic agent. The therapeutic agent is capable of suppressing serotonin receptor signaling. The methods may be combined with a mitral valve surgery, serotonin transporter polymorphism genotyping, MV disease diagnosis, and/or an adjunct assay. Also provided are related medicaments, pharmaceutical compositions, and methods for preparing the medicaments.

Abstract: Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

Abstract: The invention relates to a method of assigning treatment to a breast and/or ovarian cancer patient. More specifically, the invention relates to a method for classification of breast and/or ovarian cancer as BRCA-like or sporadic-like by determining a level of expression of a set of genes and comparing said level of expression to a reference. A patient that is classified as BRCA-like is treated with a DNA-damage inducing agent.

Abstract: The present invention provides a novel use of hsvI-miR-H18 or hsv2-miR-H9-5p, which is microRNA, for the diagnosis of prostate cancer. According to hsvI-miR-H18 or hsv2-miR-H9-5p of the present invention, it is possible to accurately diagnose even a subject in the PSA gray zone in which accurate diagnosis though PSA is difficult. The present invention can be applied to various biological samples, and exerts accurate diagnostic ability even when a supernatant of the solution excluding, particularly, cell-derived materials is used, and thus a diagnostic procedure is simple and convenient. According to the present invention, the prostate cancer can be accurately and promptly diagnosed at low costs.

Abstract: The invention provides a method of determining T cell function in a subject in need of immunotherapy comprising: i) providing a blood sample comprising a population of T cells from the subject; ii) activating the T cells in the sample; and iii) assaying an expression level of one or more T cell activation markers using quantitative real time PCR (qPCR) after activating the T cells in the sample.

Abstract: Techniques for diagnosis of aggressive prostate cancer include determining a level of expression of each of the genes encoding (FOXM1) Forkhead box protein M1 and Centromere protein F (CENPF) in a test sample. If the level of expression of each of the FOXM1 and CENPF genes in the test sample is at least 35% higher than the corresponding level in a control sample, then it is determined that the subject has an aggressive form of prostate cancer or has a high risk of prostate cancer progressing to an aggressive form. Alternatively, if at least 50% of prostate cancer cells in the sample express both FOXM1 protein and CENPF protein at a composite score of at least 100 for each, then the above diagnosis is made. Composite score is calculated by multiplying a percent staining value by a staining intensity value.

Abstract: It is intended to provide a rapid, convenient, and highly accurate method for determining the prognosis of cancer. The present invention provides a method for determining the prognosis of a renal cell carcinoma patient, comprising: (1) treating genomic DNA prepared from a renal tissue of a subject with bisulfite; (2) amplifying the bisulfite-treated DNA by PCR; (3) subjecting the obtained PCR amplification product to ion exchange chromatography; (4) obtaining the retention time of a detection signal obtained by the chromatography; and (5) determining the renal cell carcinoma of the subject as having poor prognosis when the result of the step (4) is shorter than a retention time serving as a reference.

Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as gastric cancer.

Abstract: Methods and kits for identifying a subject having pre-cancerous advanced polyps or colorectal cancer based on the expression profile(s) of specific mRNA biomarkers. Methods and kits for diagnosing, preventing, managing therapy, monitoring and identifying predisposition to colorectal cancer.

Abstract: A method for detecting genes sensitive to low-level ionizing radiation and genes detected by the method. More specifically, genes sensitive to low-level ionizing radiation, discovered in a carcinogenic entity and verified in a normal entity are detected by subjecting a cancerous AKR/J mouse and a normal ICR mouse to low-level radiation. Thymus is collected therefrom, and glycometabolism-related genes are classified via microarray processing of the thymus. The genes are amplified and the levels of gene expression are measured. Thus, a gene having a specific reaction to radiation can be accurately detected by preventing the interference of confounding variables.

Abstract: A method for detecting genes sensitive to low-level ionizing radiation and genes detected by the method. More specifically, genes sensitive to low-level ionizing radiation, discovered in a carcinogenic entity and verified in a normal entity are detected by subjecting a cancerous AKR/J mouse and a normal ICR mouse to low-level radiation. Thymus is collected therefrom, and glycometabolism-related genes are classified via microarray processing of the thymus. The genes are amplified and the levels of gene expression are measured. Thus, a gene having a specific reaction to radiation can be accurately detected by preventing the interference of confounding variables.

Abstract: Disclosed are biomarkers, methods and assay systems for the identification of cancer patients who are predicted to respond, or not respond to the therapeutic administration of radiation therapy to treat cancer. Thus, the invention provides a diagnostic paradigm to select cancer patients who will benefit from radiation therapy. In particular, the invention provides a novel 41-gene biomarker model associated with clinical outcome following radiotherapy across multiple histological tumor types, including the biomarker Cyclophilin B (PPIB).

Abstract: The present invention provides polypeptide and antibody for assessing predisposition of myelodysplastic syndrome or myeloid tumor, and method for screening therapeutic drugs therefor. The polypeptide comprises at least a portion of the U2AF35 gene, at least a portion of the ZRSR2 gene, at least a portion of the SFRS2 gene, or at least a portion of the SF3B1 gene, and is able to serve as a marker for evaluating predisposition for myelodysplastic syndromes or a myelogenous tumor.

Abstract: Methods and kits to determine the presence of exogenous alleles within a native haplotype are provided. Introduction of foreign alleles into livestock genomes has provided the ability to introduce specific desirable traits. The present disclosure provides methods to identify the presence of exogenous alleles that foreign to a haplotype at a target locus, and identify specific markers that are native to the haplotype. Identification of exogenous genes at a target locus, flanked by native markers is indicative that the exogenous gene is present through molecular engineering. Conversely, the presence of an exogenous gene that are only partially flanked by native markers is indicative that the allele is present due to sexual breeding.

Abstract: A method for identifying a subject of Acropora genus to an Acropora species comprises of detecting one or more microsatellite loci in the genome of the subject, wherein the microsatellite loci are selected from the group consisting of a microsatellite locus 8346m3 and others. A method for quantifying an index of level of chimerism of a coral colony restored by transplanting an Acropora first coral colony of an Acropora species into a second coral colony in need of restoration that belongs to the same species as the first coral colony comprises of identifying one or more microsatellite loci whose PCR fragment size, amplified with genomic DNA derived from the first coral colony as template, is different from the PCR fragment size amplified with genomic DNA derived from the second coral colony.

Abstract: Disclosed are compositions, kits, and methods for detecting, characterizing, and/or identifying one or more protozoa. Various types of polymerase chain reaction techniques in connection with specifically designed primers can be used to detect a variety of, e.g., pathogenic, protozoa in samples.

Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.

Abstract: Disclosed herein are methods of detecting HIV-2 nucleic acids in a sample (such as from a sample infected with or suspected to be infected with HIV-2). In some examples, the methods include LAMP or RT-LAMP, while in other examples, the methods include hybridization of a probe to an HIV-2 nucleic acid, including, but not limited to real-time PCR. Sets of LAMP primers for detection of HIV-2 Group A and Group B nucleic acids are provided herein. Sets of probes and primers for real-time PCR detection of HIV-2 nucleic acids are also provided herein. Finally, primers for amplification of HIV-2 nucleic acids are provided. Also disclosed are isolated HIV-2 nucleic acids, vectors including the HIV-2 nucleic acids, and cells transformed with vectors including HIV-2 nucleic acids.

Abstract: Disclosed are compositions including primers and probes, which are capable of interacting with the disclosed nucleic acids, such as the nucleic acids encoding the reverse transcriptase or protease of HIV as disclosed herein. Thus, provided is an oligonucleotide comprising any one of the nucleotide sequences set for in SEQ ID NOS:1-89, and 96-104. Also provided are the oligonucleotides consisting of the nucleotides as set forth in SEQ ID NOS:1-89, and 96-104. Each of the disclosed oligonucleotides is a probe or a primer. Also provided are mixtures of primers and probes and for use in RT-PCR and primary PCR reactions disclosed herein. Provided are methods for the specific detection of several mutations in HIV. Mutations in both the reverse transcriptase and the protease of HIV can be detected using the methods described herein.

Abstract: The present invention relates to a novel hyperhalophilic strain and use thereof for the degradation of carbon-containing substrates, in particular making it possible to prepare novel polymers.

Abstract: A method of producing a sugar liquid includes a step of filtering a saccharified liquid derived from cellulose-containing biomass, through a nanofiltration membrane and/or reverse osmosis membrane; and a two-step washing step of washing the nanofiltration membrane and/or reverse osmosis membrane after the filtration, with an acid washing liquid and then with an alkali washing liquid; is provided. The method of producing a sugar liquid in which a cellulose-derived sugar liquid is processed through a nanofiltration membrane and/or reverse osmosis membrane is/are effectively washed in a contaminated separation membrane(s).

Abstract: The present invention provides processes for deconstructing biomass using a solvent produced in a bioreforming reaction.

Abstract: The present invention provides aqueous composition comprising a multi-stage acrylic emulsion polymer having a first stage polymer of from 0.5 to 4 wt. %, based on the total weight of monomers used to make the first stage polymer, of a copolymerized carboxylic acid or salt group containing monomer, and having 10 to 30 wt. %, on total solids of the multi-stage acrylic emulsion polymer, of a second stage polymer of from 3 to 15 wt. % of a copolymerized hydroxyl group containing monomer, the first stage polymer having a glass transition temperature (Tg) by dynamic mechanical analysis (DMA) of less than ?10° C. and the second stage polymer having a Tg (DMA) of greater than 80° C.; and (ii) from 25 to 75 wt. %, based on the total solids weight of the multi-stage acrylic polymer, of a polyurethane.

Abstract: A method for preparing coal which is to be injected into a blast furnace includes: a step (S1) for analyzing the ash of coal in a raw-coal stage and determining the contents (wt %) of At Si, Ca and Mg in the ash; a step (S2) for deriving the ash melting point of the coal on the basis of the obtained data: a step (S3) for selecting a metal species to be supported on the coal and deriving the amount thereof to be supported on the basis of the obtained data so as to adjust the melting point of the ash of the coal to 1200 to 1400° C.; a step (S4) for making the metal supported on the coal in the derived amount by an ion-exchange method; and a step (S5) for carbonizing the coal obtained in the step (4).

Abstract: Methods and systems for producing direct reduced iron having increased carbon content, comprising: providing a reformed gas stream from a reformer; delivering the reformed gas stream to a carbon monoxide recovery unit to form a carbon monoxide-rich gas stream and a hydrogen-rich gas stream; and delivering the carbon-monoxide-rich gas stream to a direct reduction furnace and exposing partially or completely reduced iron oxide to the carbon monoxide-rich gas stream to increase the carbon content of resulting direct reduced iron. The carbon monoxide-rich gas stream is delivered to one of a transition zone and a cooling zone of the direct reduction furnace. Optionally, the method further comprises mixing the carbon monoxide-rich gas stream with a hydrocarbon-rich gas stream.

Abstract: A hardening method for an annular workpiece made of metal includes a heating process that heats the annular workpiece to a hardening temperature; an analyzing process that obtains a diameter of the annular workpiece heated to the hardening temperature, and divides the heated annular workpiece into at least a small diameter portion and a large diameter portion based on the obtained diameter; and a cooling process that injects cooling liquid under an injection condition toward the annular workpiece that has been divided into at least the large diameter portion and the small diameter portion in the analyzing process such that a dimensional difference between the large diameter portion and the small diameter portion decreases, the injection condition for the large diameter portion being different from the injection condition for the small diameter portion.

Abstract: Processes for producing continuous bulk forms of iron-silicon alloys and bulk forms produced thereby. Such a bulk form is continuous in a longitudinal direction thereof and has a continuous cross-sectional form transverse to the longitudinal direction. The bulk form is formed of an Fe—Si alloy and has a crystallographic texture that comprises <111> and {110} fibers that are inclined relative to the longitudinal direction. The bulk form may be produced by a process that includes deforming a solid body formed of an Fe—Si alloy with a cutting tool in a single step to continuously produce a continuous bulk form from material obtained from the solid body.

Abstract: It is an object of the present invention to provide a rolled material, which is a material for high strength spring, and also can exhibit excellent corrosion fatigue properties after quenching and tempering even when suppressing the addition amount of an alloying element; and a wire for high strength spring obtained from such a rolled material. The rolled material for high strength spring of the present invention includes, in % by mass: C: 0.39 to 0.65%, Si: 1.5 to 2.5%, Mn: 0.15 to 1.2%, P: exceeding 0% and 0.015% or less, S: exceeding 0% and 0.015% or less, Al: 0.001 to 0.1%, Cu: 0.10 to 0.80%, Ni: 0.10 to 0.80%, and O: exceeding 0% and 0.0010% or less, with the balance being iron and inevitable impurities, wherein the number of oxide inclusions having an average diameter of 25 ?m or more is 30 or less per 100 g of a steel material, and an amount of nondiffusible hydrogen is 0.40 ppm by mass or less.