Abstract: The present invention relates to a simple and easy-to-use method for the rapid determination of the presence of an antibiotic in a waste such as e.g. liquid or solid waste streams from plants. The present invention also relates to a kit comprising an as say and a manual for the rapid determination of the presence of an antibiotic in a waste.

Abstract: A nanodot for detecting glucose concentration includes a silicon oxide core, a self-assembled monolayer having a 3-glycidoxypropyl trimethoxysilane group, and a glucose oxidase particle. The self-assembled monolayer joins the silicon oxide core by a covalent bond, and the glucose oxidase particle joins the 3-glycidoxypropyl trimethoxysilane group of the self-assembled monolayer by a conjugated bond. Moreover, a method for detecting glucose concentration by the nanodot includes oxidizing a glucose molecule in a glucose solution by the glucose oxidase particle of the nanodot, producing a hydrogen peroxide molecule; fluorescent quenching the nanodot by the hydrogen peroxide molecule, resulting in a change in fluorescent intensity of the nanodot; and detecting the change in fluorescent intensity of the nanodot.

Abstract: This disclosure relates to novel morphinan compounds and their derivatives, pharmaceutically acceptable salts, solvates, and hydrates thereof. This disclosure also provides compositions comprising a compound of this disclosure and the use of such compositions in methods of treating diseases and conditions that are beneficially treated by administering a ?i receptor agonist that also has NMDA antagonist activity.

Abstract: An isolated polynucleotide encoding a modified luciferase polypeptide and substrates. The OgLuc variant polypeptide has at least 60% amino acid sequence identity to SEQ ID NO: 1 and at least one amino acid substitution at a position corresponding to an amino acid in SEQ ID NO: 1. The OgLuc variant polypeptide has at least one of enhanced luminescence, enhanced signal stability, and enhanced protein stability relative to the corresponding polypeptide of the wild-type Oplophorus luciferase.

Abstract: The invention generally relates to methods and kits for capturing sperm nucleic acids from or in a biological sample. In one embodiment the method the method comprises, contacting the sample with a lysis solution, having a protamine-DNA complex, to lyse the cell and applying a protamine-specific binding element. This results in the protamine-specific binding element binding to the protamine-DNA to form a complex which may be captured, purified, or detected. Also provided are kits for carrying out the disclosed methods.

Abstract: Disclosed herein are methods of extracting genetic material from a diverse population of one or more types of microbes in a sample. Microbes can be prokaryotes or eukaryotes and may include bacteria, archaea, fungi, protozoa, helminths, parasites, viruses, phages, and others. Extraction may be from a single sample and subsequent identification may be through a molecular method such as qPCR, PCR, RFLP, SSCP, allele specific PCR, targeted sequencing, pull down sequencing, whole shotgun sequencing, or other methods.

Abstract: A method of detection of a target nucleic acid is provided. The method includes fractionating a sample into a plurality of sample volumes wherein more than 50% of the fractions contain no more than 1 target nucleic acid molecule per sample volumes, and subjecting the plurality of sample volumes to conditions for amplification. The method further includes detecting a change in ion concentration in a sample volume wherein a target nucleic acid is present, counting the number of fractions with an amplified target nucleic acid, and determining the quantity of target nucleic acid in the sample.

Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Abstract: A method of detecting a presence of Francisella tularensis (F. tularensis). The method includes amplifying a first nucleic acid from said specimen using a first plurality of primers, said first plurality of primers comprising SEQ ID NO 4 and SEQ ID NO 5. When the first nucleic acid is detected, then the presence of F. tularensis is determined.

Abstract: The invention concerns methods for detecting exposure to a RIP II family toxin in a biological sample. The method is based on identifying the enzymatic activity of the toxin on 28sRNA and employs sensitive and specific amplification steps that allow detection in clinical samples.

Abstract: A system and method for strain typing without need for isolation in pure form and subsequent longitudinal strain tracking. The method includes the steps of locating one or more genetic regions present in a target. The genetic regions contain genetic loci that vary among two or more variants (i.e., strains) of the target. A device detects a unique sequence of each of the genetic loci. After a sample of biological material having the genetic loci is obtained, the device generates an amplicon for the genetic regions present in the target. The amplicons are hybridized to complimentary probes, resulting in hybridized probes and non-hybridized probes, which are detected. The detected hybridized probes are assigned an identifier. The device transforms the identifiers into a pattern. The pattern is recorded and compared to one or more other patterns recorded to determine if the pattern is different from the one or more other patterns.

Abstract: The present invention relates to a method for selecting a target region of interest (ROI) in a target nucleic acid molecule using a nucleic acid probe comprising a 3? sequence capable of hybridising to a target nucleic acid molecule and acting as a primer for the production of a complement of the target ROI (i.e. by target templated extension of the primer), and a sequence capable of templating the circularisation and ligation of the extended probe comprising the reverse complement of the target ROI and a portion of the probe. The circularised molecule thus obtained contains the reverse complement of the target ROI and may be subjected to further analysis and/or amplification etc. The probe may be provided as an oligonucleotide comprising a stem-loop structure or as a partially double-stranded construct and comprises a single-stranded 3? end region containing the target-binding site.

Abstract: The present application relates to a biosensor for detecting analytes, various kits and methods of use thereof. In particular, the biosensor's mode of operation is based on binding of analytes to a nucleic acid sequence which triggers rolling circle amplification and detection of the amplified product as the indicator of the presence of the analytes.

Abstract: Methods of measuring chimerism in a biological sample use informative copy number variations (CNV) in genetically distinct cell populations. Chimerism describes the co-existence of cells originating from more than one individual. Assessing CNV polymorphisms in genomic DNA provides a useful in-vitro method of measuring chimerism. The accuracy of the methods can be validated using an internal validation step.

Abstract: Provided is a method of detecting a chromosome abnormality in an embryo by using blastocyst culture. The method comprises: detecting embryonic circulating cell-free DNA in early embryonic in-vitro culture, i.e., blastocyst culture, performing uniform whole genome amplification on trace DNA, and then using a method, such as next generation sequencing, to perform analysis on the amplified DNA product, so as to determine a chromosome condition of an embryo, namely, whether aneuploidy or partial aneuploidy of chormosomes occurs.

Abstract: The present invention provides a method for multiplex detection of target DNA. Specifically the invention provides a solid substrate comprising a plurality of DNA probes, wherein each probe contains at least two linear nucleotide chains (LNCs). The present invention is particularly useful in multiplex reactions wherein multiple target sequences are detected in one reaction. Kits useful in the multiple target detection are also provided.

Abstract: A fluidic card assembly comprising a fluidic card housing (1) and a biochip (3) located in the fluidic card housing. The fluidic card housing (1) includes a chamber (2) with a base wall, into which at least one fluidic channel extends. The biochip (3) is at least partially located in the chamber. A seal (7) is provided for sealing the biochip in the chamber (2) when the biochip is urged into the chamber. The fluidic channel has a serpentine form.

Abstract: Disclosed is a method of producing a two dimensional microarray using a three dimensional or structured microarray. The invention involves forming defined functionalized areas by layering an inert material over the surface structures of the three dimensional microarray. Sufficient of the inert material and of the top of the surface structures are then removed to expose defined areas of the surface structures within the inert material.

Abstract: The invention provides methods and nucleic acid molecules for determining the presence of DNA molecules from an origin of interest in a subject.

Abstract: The present teachings relate to a method of generating calibration information during a real-time polymerase chain reaction (RT-PCR) or other amplification reaction. A sample well plate or other support can contain one or more dyes or other reference materials that are subjected to the same RT-PCR thermal cycles or other conditions used to conduct amplification or other reactions on a biological sample. A set of maxima values and a set of minimum values, and/or other calibration information useful for adjusting emission data for sample dyes can be recorded, for example, for 10 cycles, 20 cycles, or each cycle of a complete RT-PCR run. Such testing of dye response under realistic operating conditions can enable more accurate characterization of plate, dye, filter, or instrument response and therefore more accurate calibration corrections and other and/or adjustments.

Abstract: A method of isolating DNA and RNA from a single cell sample effectively is provided. By the method of isolating, it is possible to isolate DNA and RNA from a single cell sample, and thus genome information and transcriptome information can be simultaneously collected and/or analyzed.

Abstract: This disclosure is related to a method for determining the identity of a nucleotide residue of a single-stranded DNA or RNA, or sequencing DNA or RNA, in a solution using an ion-sensing field effect transistor and reversible nucleotide terminators.

Abstract: A method for template-directed sequencing-by-synthesis of an array of target polynucleotide can include: (a) providing an array of target polynucleotides in a fluidic vessel; (b) contacting the array of polynucleotides with a solution comprising (i) polymerization complex and (ii) reversibly terminating and differently labeled A,C,G, and T/U nucleotides; (c) incorporating one of the differently labeled nucleotides, using the polymerization complex, into a chain complementary to at least one of the array of polynucleotides; (d) binding imaging tags to the differently labeled nucleotides of step (c); (e) imaging and storing the identity and position of the imaging tags of step (d); (f) reversing termination (b)-(e); (g) repeating steps (b)-(e) and assembling a sequence for each of the array of target polynucleotides from the stored identity and position of the imaging tags, optionally as a homogeneous or one pot reaction. Additional methods of sequencing target polynucleotides are described herein.

Abstract: The invention relates to a method for determining the clonality of a master cell bank (MCB) in which a transgene has been inserted. The method involves a combination of sequencing methodology and bioinformatic analysis, performed on multiple subclones originating from a common MCB, to establish a reliable set of reference transgene insertion regions in one reference subclone, and corresponding sets of comparative transgene insertion regions in one or more other subclones originating from the same MCB. Based on the degree of congruity between reference and comparative transgene insertion regions, the MCB is determined to be either monoclonal or polyclonal.

Abstract: Aspects of the invention include methods for preparing an enriched sequencing library. In some embodiments, the methods involve preparing a sequencing library that is enriched for AT-rich sequences. In certain embodiments, the methods involve determining a presence or an absence of cancer, determining a cancer stage, monitoring cancer progression, and/or determining a cancer classification in a subject by analyzing an enriched sequencing library.

Abstract: An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.

Abstract: Microarray platforms and methods of fabricating said microarrays without traditional high aspect ratio barriers used to define individual array elements are described herein. Self-assembled nanoshells were stabilized with a polymerized scaffold to enhance the stability in physiological conditions and serve as an optical transducer upon molecular recognition events. Soft photolithography combined with surface chemistry was developed for covalent immobilization of nanoshells onto the pre-patterned arrayed microspots for rapid multiplexed detection of membrane-binding analytes. This robust fabrication methodology is amenable for general lipid structures, and thus facilitates the integration of stable membrane architectures into diagnostic and prognostic platforms. In particular, the microarray platform may be used in diverse applications ranging from the detection of pathogens, such bacterial toxin in biological matrices, to cellular membrane studies.

Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices.

Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: Methods and oligonucleotides are provided for detecting an internal control nucleic acid for qualitative and/or quantitative purposes.

Abstract: Cumulus cell (CC) gene expression is being explored as an additional method to morphological scoring to choose the embryo with the highest chance to pregnancy. The present invention relates to a novel method of identifying biomarker genes for evaluating the competence of a mammalian oocyte in giving rise to a viable pregnancy after fertilization, based on the use of live birth and embryonic development as endpoint criteria for the oocytes to be used in an exon level analysis of potential biomarker genes. The invention further provides CC-expressed biomarker genes thus identified, as well as prognostic models based on the biomarker genes identified using the methods of the present invention.

Abstract: Disclosed is a method of identifying a greater risk for developing bronchopulmonary dysplasia (BPD) in a preterm infant. The method comprises obtaining a genomic DNA sample from the preterm infant's mother, identifying the nucleotide of rs2280789 SNP in the RANTES gene and the nucleotide of rs1800566 SNP in the NQO1 gene, and determining the preterm infant as being at risk of developing BPD when the genotype of rs2280789 SNP carries C nucleotide and the genotype of rs1800566 SNP carries T nucleotide.

Abstract: The present invention is related to detecting respiratory diseases using molecular markers as prognostic tool of the evolution of respiratory infection cases. Concretely, during the differential diagnostic of respiratory infections caused by the Syncytial Respiratory Virus and human Metapneumovirus, it will be established the expression pattern of the severity markers of IL-3, IL-33 and IL12p40. The expression pattern of the molecular markers can be defined in biological samplers using ELISA assays, flow cytometry or PCR in real time. The confirmation of the etiological agent of the infection in combination to the pattern definition of the molecular markers IL-3, IL-33 and IL12p40 will indicate a prognostic of the disease severity.

Abstract: Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of genetic variations.

Abstract: Various embodiments include methods of diagnosing susceptibility to epilepsy in an individual or methods of managing treatment of a neurological condition in an individual, comprising: obtaining a sample from the individual; assaying the sample to determine the presence or absence of one or more biomarkers of epilepsy; and diagnosing susceptibility to epilepsy in the individual based on the presence of one or more biomarkers of epilepsy. Various embodiments further include kits for diagnostic use, comprising a diagnostic panel of one or more of the biomarkers: Let-7d-5p, miR-340-3p, miR-484, miR-151, miR-350, miR-770-5p, miR-139-3p, miR-2985, miR-101a-5p, miR-206-3p, miR-760-3p, miR-383-5p, miR-294, and miR-328a-5p.

Abstract: Methods and kits are provided for diagnosing, monitoring, or predicting preeclaimpsia in a pregnant woman, trisomy 18 and trisomy 21 in a fetus, as well as for detecting pregnancy in a woman, by quantitatively measuring in the maternal blood the amount of one or more RNA species derived from a set of genetic loci and comparing the amount of the RNA species with a standard control.

Abstract: The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject.

Abstract: A gene expression platform, which is a combination of a set of genes that are correlated with response to a PD-1 antagonist in multiple tumor types and a normalization gene set, is disclosed. A method and system of using the gene expression platform to derive gene signature biomarkers of anti-tumor response to a PD-1 antagonist and to test patient samples for predictive gene signature biomarkers are also disclosed.

Abstract: A method of analyzing tissue in a subject having or suspected of having cancer includes obtaining an expression profile from a sample of tissue obtained from the subject, wherein the expression profile comprises the level of at least one esophageal adenocarcinoma associated lincRNA selected from the group consisting of linc-PRKD, lincRTL, lincMIA, lincNAV, and lincTMEM.

Abstract: Provided herein is technology relating to genetic determinants of disease and particularly, but not exclusively, to methods, compositions, and systems for identifying single nucleotide polymorphisms that are functionally associated with a disease.

Abstract: The present invention relates to a method for determining sensitivity to a simultaneous inhibitor against poly ADP ribose polymerase (PARP) and Tankyrase. According to the present invention, a colorectal treatment effect can be maximized by sorting patients having sensitivity to the simultaneous inhibitor against PARP and Tankyrase.

Abstract: The present disclosure relates to methods of collecting exosomes and microvesicles (EMV) from urine, isolating corresponding mRNA, and analyzing expression patterns in order to diagnose and treat various urothelial cancers. In particular, various expression patterns are analyzed through a unique diagnostic formula.

Abstract: The present disclosure involves a process to identify a patient likely to have OSCC by taking a sample containing miRNA from epithelial cells from the patient's oral cavity and determining the relative level of expression of miRNA sequences which have different levels of expression in epithelial cell OSCC tissue than in benign tissue. The epithelial cells are those that form the mucosal epithelium that consists mainly of keratinocytes with some immune cells. It involves determining the relative level of expression of at least miRNA sequences hsa-miR-130-3p, hsa-miR-7-5p, hsa-miR-101-3p and hsa-miR-146b-5p. It also involves discriminating between benign oral lesions and OSCC using a sample of epithelial cells of the lesion and determining the relative level of expression of miRNA sequences which have different levels of expression in epithelial cell OSCC tissue than in benign tissue. It uses the relative level of expression of at least miRNA sequences hsa-miR-196a-5p and hsa-miR-873-5p.

Abstract: Diagnostic methods for identifying cancer bearing subjects appropriate for treatment with CPX-351 include genetic and ex vivo testing of cells from a candidate subject. Combination treatment with CPX-351 and FLT-3 inhibitors improve CPX-351 uptake and toxicity.

Abstract: A method of detecting the level of 5-hydroxymethylcytosines (5-hmc) in a DNA molecule of a cell having a 5-hmc prevalence lower than 0.002% of total DNA bases is provided. The method comprising: (a) attaching a 5-hmc labeling agent to the DNA molecule; and (b) subjecting the DNA molecule to an imaging method suitable for detecting the labeling agent, thereby detecting the level of 5-hmc in the DNA molecule. Also provided is a method of diagnosing cancer in a subject in need thereof, the method comprising: (a) providing a DNA sample of a cell of the subject; (b) detecting the level of 5-hmc in the DNA sample as described herein; wherein a significant decrease in the level of 5-hmc in the DNA sample, as compared to a control DNA sample from a healthy subject is indicative that the subject has cancer.

Abstract: Embodiments concern methods and compositions for characterizing or evaluating neoplastic pancreatic cells using miRNAs that are measured and used in calculations to determine a risk score for a patient.