Abstract: Techniques and methods are provided for isolating nucleic acids from a sample. The methods include adding a chelating agent to the sample to block nucleic acid binding sites on contaminants in the sample; heating the sample to remove hydrocarbons; and lysing the cells using freeze-thaw cycles.

Abstract: Methods for the rapid detection of the presence or absence of Mycoplasma genitalium (MG) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the target MG gene, along with kits are provided that are designed for the detection of MG.

Abstract: Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

Abstract: [Problem ] Provided is a means for detecting and quantifying a biological substance of interest with an improved accuracy by inhibiting non-specific adsorption of fluorescent nanoparticles and thereby reducing the background noise in immunostaining with fluorescent nanoparticles. [Means for Solution] Immunostaining is carried out upon diluting fluorescent nanoparticles with a fluorescent nanoparticle diluent which contains 1 to 5% (W/W) of a protein having a molecular weight of 40,000 or higher (e,g., BSA) and 1 to 3% (W/W) of a protein having a molecular weight of less than 40,000 (eg ., casein) and, when casein is used as a low-molecular-weight protein, it is preferred that the ?-casein content in the casein is 10% (W/W) or less and the ratio of ?-casein and ?-casein (?-casein:?-casein) contained in the casein is 40:60 to 60:40 ( taking the total amount of ?-casein and ?-casein as 100).

Abstract: The present invention provides an oligonucleotide probe for single nucleotide polymorphism detection to be used for a target nucleic acid where a single nucleotide polymorphism is present, the oligonucleotide probe comprising a reporter region, an anchor region, and a linker region. The reporter region comprises: an oligonucleotide consisting of a sequence perfectly matching when a nucleotide of the single nucleotide polymorphism is a first nucleotide, and mismatching when the nucleotide of the single nucleotide polymorphism is a nucleotide other than the first nucleotide; and a fluorescent dye quenching when the reporter region hybridize to the target nucleic acid.

Abstract: The present invention relates to a novel method for detecting instantaneously a biomarker immobilized to a solid surface and related uses. The method comprises exposing the biomarker to a probe having a magnetic label in a solution; applying a magnetic field to the solution, whereby a complex of the biomarker and the probe is formed on the solid surface; withdrawing the magnetic field; removing the solution from the solid surface; and detecting the complex instantaneously, wherein the presence of the complex on the solid surface indicates the presence of the biomarker.

Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods may allow amplification of DNA up to hundres of megabases in length.

Abstract: A method for amplifying a target nucleic acid including providing a system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Abstract: Improved methods for amplifying target nucleic acid sequences are provided by 1) first amplifying the number of copies of target nucleic acid sequences in a sample by a first nucleic acid amplification method, and then 2) applying a second nucleic amplification method to the amplified sample, or aliquot thereof, further amplifying the number of copies of target sequences. In embodiments, a first nucleic acid amplification method is a thermocycling method, and a second nucleic acid amplification method is an isothermal method.

Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for detecting genetic variations. In some embodiments, the technology is related to non-invasive assessment of aneuploidies.

Abstract: In an approach to magnetic flux density based DNA sequencing, a static magnetic field is provided. A chain of nucleotides is passed through the magnetic field. A change in magnetic flux density of the static magnetic field due to an ionic voltage associated with an individual nucleotide or base pair of the chain of nucleotides is measured. An identity of the nucleotide is determined based on the change in magnetic flux density.

Abstract: Described herein are methods, systems, and media for HLA typing an individual from nucleic acid or protein sequences. The methodology disclosed herein represents significant improvements over current methods of HLA typing.

Abstract: Embodiments may include a method of analyzing a nucleic acid molecule. The method may include attaching the nucleic acid molecule to a protein. The protein may be attached to a particle with a first diameter. The method may also include applying an electric field to move a first portion of the nucleic acid molecule into an aperture. The aperture may be defined by a first electrode, an insulator, and a second electrode. The aperture may have a second diameter less than the first diameter. The method may further include contacting the first portion of the nucleic acid molecule to both the first electrode and the second electrode. The method may include applying a voltage across the first electrode and the second electrode. The current through the electrodes and the portion of the nucleic acid molecule may be measured, and a nucleotide of the nucleic acid molecule may be identified.

Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Abstract: The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.

Abstract: Provided herein, among other things, are a variety of methods for transposase-mediated tagging and amplification of short DNA fragments, e.g., between about 150 bp and 1.5 Kb in length. In some aspects, the method includes tagging the DNA fragments with a first primer sequence using barcoded transposases followed by a primer extension reaction to introduce a second primer sequence, e.g., using random or gene-specific primers. Kits for performing this method are also provided.

Abstract: This disclosure provides methods and compositions for removing one or more high abundance species from a plurality of nucleic acid molecules. In some embodiments, the methods and compositions can be used for normalizing nucleic acid libraries. In some embodiments, molecular labels are used in conjunction with the methods and compositions disclosed herein to improve sequencing efficiency.

Abstract: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.

Abstract: Provided herein are methods of using FGF19 modulators and/or bile acid metabolism biomarkers.

Abstract: A process of identifying a plurality of biological samples having particular desired attributes by testing pooled samples and selecting, for intended uses such as transfusion, or for subsequent analysis that is thereby enriched for such samples, pooled samples which have, or may have, said desired attributes. The preferred number of samples per pool “d” is determined by selecting an integer value as d which produces the maximum or a value near the maximum of the product of: d times the expected number of unambiguous sample pools, where a sample pool is unambiguous if all of the samples have the desired attributes, and is otherwise ambiguous if at least one sample has the desired attributes. The value selected as d can be greater than the maximum product above, so as to enlarge the total number of samples assayed in determining the desired attributes.

Abstract: The invention relates to a method which is capable of determining, at an initial stage of differentiation, the differentiated state of undifferentiated stem cells. The invention provides a method for determining a differentiated state of a cell comprising detecting expression of FOXB2 gene of a stem cell, and determining the differentiated state based on the result, and a differentiation marker selected from mRNA or protein derived from the FOXB2 gene. The invention is applicable to quality management of the stem cells or to methods for preparation and isolation of the differentiated cells. Further, because the differentiated cells can be determined at an initial stage of culture, the invention is useful for an early stage screening of cells and for quality management of the stem cells, and reduction in culturing period and cost reduction in expenditure regarding a culture medium, or the like, can be expected.

Abstract: Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.

Abstract: A method of detecting circulatory nucleic acids from a transplanted tissue in a transplant recipient, the method comprising: amplifying circulatory nucleic acids from a transplanted tissue in a blood sample from the transplant recipient, and detecting amplification of a copy number deletion (CND) polymorphism from the transplanted tissue, and related methods for determining the status of a donor tissue transplanted into a recipient.

Abstract: The present invention provides methods for selecting an individual with psoriasis (Ps) or psoriatic arthritis (PsA) who should receive or who is likely to respond to a treatment with an anti-tumor necrosis factor alpha (anti-TNF?) therapy. In addition, provided herein are methods for selecting an individual with Ps or PsA who should receive or who is likely to respond to a therapy that is not an anti-TNF? therapy, e.g., a non-anti-TNF? therapy for the treatment of Ps or PsA. Specifically, the methods of the present invention relate to detecting the presence of distinct alleles of the PDE3A-SLCO1C1 locus which are associated with a clinical response to an anti-TNF? therapy or a non-anti-TNF therapy in patients with Ps or PsA.

Abstract: The invention relates to a method for predicting graft alterations in a transplanted patient, comprising a step of determining the expression levels of bactericidal/permeability-increasing protein (BPI), chemokine (C motif) ligand 1 (XCL1) and thioredoxin domain containing 3 (TXNDC3) genes in a biological sample obtained from said transplanted patient.

Abstract: The invention relates to novel markers of preterm birth, methods for assessing the status of preterm birth using the markers, and methods for the diagnosis and therapy of preterm birth.

Abstract: Disclosed herein are methods of increasing the expression rate of epigenetic markers such as ELOVL2, KLF14, and PENK with administration of a therapeutic agent (e.g., vitamin C or its derivatives, analogs, metabolites, prodrugs, or pharmaceutically acceptable salts thereof). Also described herein are methods of modulating the methylation pattern of epigenetic markers such as ELOVL2, KLF14, and PENK with administration of a therapeutic agent (e.g., vitamin C or its derivatives, analogs, metabolites, prodrugs, or pharmaceutically acceptable salts thereof).

Abstract: The present invention relates to kits and methods for monitoring therapy and/or for adapting therapy of an epithelial cancer patient, and for determining malignancy grade or progression of a tumor of a patient suffering from an epithelial tumor.

Abstract: A method is provided for selecting a subject diagnosed with cancer as a candidate for treatment with a PARP1 inhibitor, or both a PARP1 inhibitor and a chemotherapeutic agent such as an alkylating agent. The method includes detecting the presence or absence of a mutation in a non-coding region of a PARP1 gene, wherein the presence of a mutation in the PARP1 gene indicates that the cancer can be treated with the PARP1 inhibitor, optionally in conjunction with the chemotherapeutic agent. In a specific, non-limiting example, the PARP1 inhibitor is verliparib (ABT-888).

Abstract: The method for predicting the anti-tumor response in a human or animal having a tumor to multiple kinase inhibitors, using any multiple kinase inhibitor, comprises selection of genes encoding for protein kinases targeted by the said tyrosine kinase inhibitor, for each one of these genes, providing at least one nucleic acid probe which hybridizes to said gene under stringent conditions, thus providing an array of nucleic acid probes, having a biological sample containing cancer cells from said human or animal, extracting DNA from the sample, fragmenting into DNA fragments, optionally labeling the DNA fragments, submitting the optionally labeled DNA fragments to hybridization with the array of nucleic acid probes, recovering and quantifying for all the genes the gains or losses in gene copy numbers, wherein gains and losses of gene copy numbers of each selected gene are used to determine whether the tumor is sensitive or not to said kinase inhibitor.

Abstract: The invention relates to a method for predicting the localization of a primary tumour, wherein said method comprises the use of genomic profile data, and wherein the method is capable of predicting the type of cancer by a classification score ranking among a variety of the possible tumour types.

Abstract: Gene expression profiling in multiple myeloma patients identifies genes that distinguish between patients with subsequent early death or long survival after treatment. Poor survival is linked to over-expression of genes such as ASPM, OPN3 and CKS1B which are located in chromosome 1q. Given the frequent amplification of 1q in many cancers, it is possible that these genes can be used as powerful prognostic markers and therapeutic targets for multiple myeloma and other cancer.

Abstract: Described herein is the use of Agouti Signaling Protein (ASIP), in addition to certain other melanocortin signaling network (MSN) genes, as prognostic and predictive biomarkers for the progression of breast cancer. In particular, the novel biomarkers can be used to determine if a female breast cancer patient is at risk of progressing to metastatic disease and thus also be used to direct treatment of the patient.

Abstract: The present disclosure is directed to methods of detecting XRN2 expression levels, copy number and mutation status, particularly in cancer cells. The methods permit physicians to tailor therapies to subject having certain genotypes/phenotypes, and to exclude therapies unlikely to be effective.

Abstract: A method to detect ovarian cancer is provided that employs probes and/or primers to detect certain RNA isoform transcripts, as well as kits therefor.

Abstract: The use of specific microRNAs (miRNAs) present in CSF as biomarkers for particular brain malignancies and disease activity.

Abstract: Modules, devices, systems and methods for measuring or detecting cysteine and/or methionine metabolite levels in a sample from a subject are disclosed. Various embodiments of the present invention concern modules, devices, systems and methods for prognosing or diagnosing cancer, for example, prostate, colon, ovarian or breast cancer; predicting the risk or probability of cancer recurrence; and/or for predicting, detecting and/or monitoring cystinuria or cystine stone disease.

Abstract: A method for identifying the source of animal waste is provided. The method includes taking DNA samples from a known group of animals, conducting DNA analysis on the DNA samples to prepare a genetic profile for each animal from the group, preparing a database of the genetic profiles, collecting a specimen of waste from an unknown source, conducting DNA analysis on the specimen, and comparing the DNA analysis from the specimen to the database to determine the source of the waste.

Abstract: Methods for the rapid detection of the presence or absence of Trichomonas vaginalis (TV) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the target TV gene, along with kits are provided that are designed for the detection of TV.

Abstract: The invention relates to methods and compositions for identifying soybean plants that are tolerant, have improved tolerance or are susceptible to Fusarium solani infection (the causative agent of sudden death syndrome or SDS). The methods use molecular genetic markers to identify, select and/or construct disease-tolerant plants or identify and counter-select disease-susceptible plants. Soybean plants that display tolerance or improved tolerance to Fusarium solani infection that are generated by the methods of the invention are also a feature of the invention.

Abstract: A saccharide-containing solution is prepared from a cellulosic biomass feedstock in a process, where the cellulosic biomass feedstock includes torrefied biomass material, and where the torrefied biomass material is hydrolyzed in an aqueous reactant by contacting it with the aqueous reactant that comprises hydrochloric acid with a concentration of 35 to 45% wt, based on the weight of the combination of hydrochloric acid and water, to yield a saccharide-containing solution.

Abstract: A process for the separation of a monosaccharide from an aqueous solution comprising the monosaccharide, in particular a hydrolysate of a polysaccharide containing biomass, characterized in that a) the solution comprises one or more salts or mineral acids, b) the solution is contacted with a zeolite adsorbent preferably of BEA zeotype for adsorbing the monosaccharide on the zeolite, c) the zeolite with the adsorbed monosaccharide is separated from the solution, d) the monosaccharide is separated from the zeolite absorbent. The process in a chromatographic process, in particular SMB, produces relatively highly concentrated and pure monosaccharide solution in water.

Abstract: Disclosed herein is a dispersing agent composition essentially comprising polyalkylene polyhydric compound, an organic acid and a non-ionic surfactant. The dispersing composition finds application in leather processing industry for tanning without adding any water or any other medium. It finds tremendous application potential in the tanning industry to ensure eco-benign leather processing that does not add to environmental pollution as no effluent is generated. The invention is therefore envisaged to play a crucial role in enhancing the economic and environmental benefits associated with tanning industry. The disclosure also relates to a process for preparing the composition and also the process of eco-benign tanning using the said composition.

Abstract: A method of sealing a slag drain in a direct smelting vessel is disclosed. Also disclosed are a method of maintaining a slag drain channel and a direct smelting vessel with a slag drain channel that extends through a sleeve of refractory material installed in the direct smelting vessel. The method for sealing the slag drain includes locating a pre-formed refractory material at an inlet end of the slag drain channel so that it is exposed to a molten bath contained within the direct smelting vessel and sealing the slag drain channel with sealing material downstream of the pre-formed refractory material.

Abstract: Provided is a smelting method capable of effectively promoting a reduction reaction on pellets formed using nickel oxide ore as starting material to obtain a ferronickel alloy with a high nickel grade of at least 4%. The present invention is a method for smelting nickel oxide ore wherein ferronickel alloy with a nickel grade of at least 4%, the method comprising a pellet-producing step S1 for producing pellets from nickel oxide ore, and a reducing step S2 for reduction-heating of the obtained pellets in a smelting furnace. In the pellet-producing step S1, the pellets are produced by mixing nickel oxide ore with a specified amount of a carbonaceous reducing agent as starting materials. In the reducing step S2, the produced pellets are charged in a smelting furnace in which a carbonaceous reducing agent (furnace bottom carbonaceous reducing agent) has been spread over the entire furnace bottom and reduction-heating is performed.

Abstract: The present invention does not require a demanganese agent such as a sulfide or a combustible gas in the removal of manganese of cast iron. The method for removing manganese of cast iron according to the present invention is implemented by performing the removal of a manganese component by allowing a furnace to be in an oxygen atmosphere, and by blowing air into a molten cast iron in the furnace, while a carbon component in the molten cast iron is being maintained at an approximately constant amount. Alternatively, the method for removing manganese of cast iron according to the present invention is implemented by performing the removal of the manganese component by allowing the furnace to be in an oxygen atmosphere and by stirring the molten cast iron in the furnace, while the carbon component in the molten cast iron is being maintained at an approximately constant amount.

Abstract: A sandwich structure forming method including the steps of (1) providing a sandwich structure comprising a core positioned between a first liner sheet and a second liner sheet; (2) positioning the sandwich structure into a cavity of a die assembly; and (3) pressurizing the core to expand the sandwich structure into engagement with the die assembly.