Abstract: The subject matter discloses systems and methods for magnetic capturing of rare cells from a liquid sample. The system includes a capture chip (104) having a longitudinal channel (208) comprising a first part (304) and a second part (306). The capture chip (104) has a capture well (302) near an end of the second part (306) closer to an interfacing region between the first part (304) and the second part (306). The system includes a first set (126) of multiple rows of magnets for the magnetic capturing of the rare cells in the first part (304) of the longitudinal channel (208), where a first row (132) of the first set (126) of multiple rows has magnets that span a length of the first part (304) of the longitudinal channel (208) and each subsequent row of the first set (126) of multiple rows has one magnet less than a previous row.

Abstract: The invention provides compositions and methods related to selective inhibition of PPO11 and use for improving shelf life of a plant or parts thereof. In accordance with the invention, for example, compositions for topical application to a plant or part thereof, are provided that can reduce browning of the plant or part thereof to extend shelf life.

Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.

Abstract: Provided herein are a kit and method for detecting mutations in CTNNB1 and hTERT, and their use in detection and management of hepatocellular carcinoma (HCC). The kit comprises a first pair of primers, configured to specifically bind sequences flanking the genomic region for amplifying the genomic region in a first PCR reaction; and at least one clamp, each configured to bind to one first allele but not any second allele at an annealing temperature in the first PCR reaction to thereby selectively suppress amplification of the one first allele but still allow amplification of other second allele(s). Kits and methods for detecting mutations in CTNNB1 and hTERT are also provided. A method for detecting or monitoring recurrence of HCC is further disclosed, which comprises determining levels of five DNA markers, including CTNNB1 mutations, hTERT mutations, TP53 mutations, RASSF1A methylation, and GSTP1 methylation.

Abstract: Compositions, reaction mixtures, kits and methods used in amplifying and detecting nucleic acids from various species of the class Mollicutes. Particular regions of the 23S rRNA or its gene have been identified as preferred targets for nucleic acid amplification reactions of a sample suspected containing at least one species of Mollicutes. Some oligomers comprise tag regions, target closing regions, promoter sequences, and/or binding moieties. Samples can be from any source suspected of containing a species of the class Mollicutes. Preferred sample sources include bioreactors, cell lines, cell culture wares and pharmaceutical manufacturing wares.

Abstract: Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions.

Abstract: To provide a device for operating magnetic particles capable of treating large quantity, and retaining a gel-like medium layer stably, a vessel is formed so that an area perpendicular to a longitudinal direction in a large-diameter part packed with a liquid layer is larger than an area perpendicular to the longitudinal direction in the small-diameter part packed with a gel-like medium layer. Therefore, in the vessel, it is possible to reduce the diameter of the small-diameter part while keeping the capacity of the large-diameter part large. As a result, in the vessel, it is possible to treat large quantity in the liquid layer, and it is possible to retain the gel-like medium layer stably.

Abstract: A tissue dissociation device includes an inlet coupled to a first stage having a single channel having an upstream end and a downstream end; a plurality of serially arranged intermediate stages, wherein a first intermediate stage of the plurality is fluidically coupled to the downstream end of the first stage, and wherein each subsequent intermediate stage of the plurality has an increasing number of channels (with channels of smaller dimensions); and an outlet coupled to a last stage of the intermediate stages.

Abstract: This disclosure relates to novel compounds for use in various compositions, kits and methods, including, for example, use in polymerase storage buffers and in nucleic acid synthesis or amplification reactions such as a polymerase chain reaction (PCR). Methods for preparing the novel compounds are also described.

Abstract: The invention generally relates to methods of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe.

Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.

Abstract: A method of diagnosing bacterial vaginosis in a woman, which involves determining an amount of each of more than one BV-associated bacterium in a vaginal sample obtained from the female and assessing a BV status of the female based on the amount of each of the more than one BV-associated bacterium in the sample.

Abstract: Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a 16S rRNA or its encoding gene from bacterial species associated with bacterial vaginosis. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

Abstract: The present invention provides microfabricated substrates and methods of conducting reactions within these substrates. The reactions occur in plugs transported in the flow of a carrier-fluid.

Abstract: Provided are compositions and methods useful to the determination of whether a microbial contaminant is present in a biological therapeutic production process. Specifically, an artificial positive amplification control plasmid and unique quantitative PCR detection probe are provided, which enables the rapid and real-time detection of a false positive result.

Abstract: Methods and reagents suitable for conducing polymerase chain reaction are described. In particular, a nucleic acid amplification design strategy and thermal cycling profile to enable efficient amplification of multiple nucleic acid targets along with improved sensitivity is disclosed. The present disclosure also describes methods and devices for increasing the melting temperature (Tm) of a primer.

Abstract: This disclosure provides systems and methods for molecular identification and polymer (e.g., nucleic acid) sequencing using nanopores. The polymer may be passed through or in proximity to the nanopore and various subunits of the polymer may affect the current flowing through the nanopore. The various subunits may be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. In some cases, the polymerization of tagged nucleotides presents tag molecules to the nanopore that can be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. Also provided herein are systems and methods for sequencing both the sense and anti-sense strand of a double stranded nucleic acid molecule with a nanopore and methods for using ribonucleic acid (RNA) speed bump molecules to slow the passage of a nucleic acid molecule through or in proximity to a nanopore.

Abstract: A driving supporter includes an environment obtainer and a support controller configured to control a supporting device to perform driving support such that an own vehicle travels along a target traveling line. The environment obtainer includes a relative-positional-relationship obtainer configured to obtain a relative positional relationship between the own vehicle and an object detected based on object information obtained by an object-information obtainer. The support controller includes an offset-target-traveling-line setter configured to set, when the relative positional relationship is a specific relationship in which it is estimated that a steering operation in a direction in which the own vehicle avoids the object is to be performed, the target traveling line to an offset position that is shifted in a direction identical to a direction of a steering operation from the target traveling line located when the relative positional relationship is not the specific relationship.

Abstract: Disclosed herein are zinc fingers comprising CCHC zinc coordinating residues. Also described are zinc finger proteins and fusion proteins comprising these CCHC zinc fingers as well as polynucleotides encoding these proteins. Methods of using these proteins for gene editing and gene regulation are also described.

Abstract: A system and method for the detection and quantification of biomolecules by measuring a piezoelectric signal is described. The system comprises a plurality of elongate zinc oxide nanowires mounted generally parallel to each another on a semi conductive silicon substrate. The free ends of the nanowires are provided with biomolecules that are capable of associating with complementary biomolecules within a biological or water sample. Following incubation of the system in a sample, the association of molecules of interest with the immobilised biomolecules on the system results in the displacement of the zinc oxide nanowires. The displacement of the nanowires produces a piezoelectric voltage signal that is useful in diagnosing a pathogenic infection or the contamination of a sample.

Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).

Abstract: Provided herein are methods for generation and amplification of a single-stranded DNA circle in a single reaction vessel from a linear DNA without any intervening purification steps. The single-stranded DNA circle is generated via a template-independent single-stranded DNA ligation. Whole-genome amplification of linear chromosomal DNA in a single tube using ligation-assisted DNA amplification is also provided.

Abstract: Provided are methods and compositions for identifying a miRNA profile for a particular condition, such as pancreatic disease, and using the profile in assessing the condition of a patient.

Abstract: The present disclosure relates to RNA amidates and thioamidates useful for RNA interference applications. The RNA amidates and thioamidates contain at least one internucleoside linkage chosen from ribo-N3??P5? phosphoramidate (NP) and ribo-N3??P5? thiophosphoramidate (NPS) linkages, and optionally further containing at least one covalently conjugated lipid moiety. Compositions comprising the amidates and thioamidates are disclosed, as are methods for their use in modulating gene expression.

Abstract: Aspects of the present disclosure include systems that include reaction vessels and reaction vessel caps. In certain aspects, the reaction vessels include a reaction chamber and a groove disposed around a top opening of a reaction chamber. The system also includes a RV cap that includes a cap body, a RV plug, and a lower wall that includes an outer radial groove disposed above an outward projecting ridge of the lower wall. When the cap is inserted into the RV, the RV plug of the RV cap is sealingly inserted into the reaction chamber of the RV, a ridge of the RV mates with the outer radial groove of the RV cap, and an outward projecting ridge of the RV cap mates with the radial groove of the RV. Also provided are methods and sample analysis systems, which may employ the RV/RV cap systems of the present disclosure.

Abstract: The present invention relates to a method of predicting the propensity of tripeptides to from aggregates in solution. The present invention also provides tripeptides which are able to form aggregates in solution, as well as uses thereof. The present invention also provides nanostructures formed by self-aggregation of tripeptides of the present invention. The present invention also provides pH responsive aggregates as well as methods of screening for the ability of a tripeptide to form a pH dependent aggregate or gel.

Abstract: The present disclosure relates to modified or polymer conjugated MetAP2 inhibitors. The present disclosure also relates to methods of treating metabolically-driven diseases and disorders, such as certain cancers.

Abstract: Cartridges for the isolation of a biological sample and downstream biological assays on the sample are provided, as are methods for using such cartridges. In one embodiment, a nucleic acid sample is isolated from a biological sample and the nucleic acid sample is amplified, for example by the polymerase chain reaction. The cartridges provided herein can also be used for the isolation of non-nucleic acid samples, for example proteins, and to perform downstream reactions on the proteins, for example, binding assays. Instruments for carrying out the downstream biological assays and for detecting the results of the assays are also provided.

Abstract: Disclosed is a high-throughput sequencing method for methylated CpG island in trace DNA, comprising the steps of: 1) treating a DNA sample with bisulfite; 2) adding the treated sample obtained in step 1) to a PCR system containing a primer A for linear amplification; 3) adding an exonuclease having single-stranded DNA cleaving activity to the PCR product in step 2) and inactivating the exonuclease after the reaction; 4) adding the product in step 3) to a PCR system containing a primer B for linear amplification; 5) adding the product in step 4) to a PCR system containing the corresponding adapter primer C and adapter primer D for amplification; and 6) purifying the PCR product in step 5) to obtain a DNA library with a specific length and carrying out the sequencing.

Abstract: Described herein are methods and systems for detecting DNA or RNA using single molecules array or other techniques. DNA or RNA from the sample may be fragmented and exposed to a first type of binding ligand and a second type of binding ligand that comprise nucleic acid sequences complimentary at least a portion of a sequence contained in the target DNA or RNA. At least a portion of the fragmented DNA or RNA associates with at least one of the first type of binding ligand and/or the second type of binding ligand, wherein the first type of binding ligand and second type of binding ligand comprises nucleic acid sequences complimentary to a different portions of a sequence contained in the DNA or RNA. A portion of the sample exposed to the binding ligands is analyzed to determine the number of fragmented DNA or RNA sequences.

Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Abstract: Methods, devices, kits and compositions for detecting the presence or absence of hookworm in a fecal sample are disclosed herein. The methods, devices, kits and compositions of the present invention may be used to confirm the presence or absence of hookworm in a fecal sample from a mammal that may also be infected with one or more of roundworm, whipworm, and heartworm. Confirmation of the presence or absence of hookworm in the mammal may be made, for example, for the purpose of selecting an optimal course of treating the mammal and/or for the purpose of determining whether the mammal has been rid of the infection after treatment has been initiated.

Abstract: A method of identifying gene expression associated with recurrence free survival in a subject with cancer, comprising: a) assaying a sample from a subject diagnosed with cancer for the presence of altered gene expression of one or more genes selected from the group consisting of ADK, AP2B1, AVL9, CANX, DBT, DHRS7, DONSON, FAM190B, FGFR1, FOXN3, FZD5, GGH, GM2A, IGFBP5, ITSN2, LAMC1, LIFR, METTL7A, MT1F, MT1G, MT1P2, MT1X MT2A, NAB1, NCOA1, NCOR1, PAPOLA, PPME1, PPP1R13L, PRKAR2A, RABEP1, RBBP8, SGPL1, SIRT1, SNX2, SREK1, TAF1B, TMED5, and ZMIZ2; and b) identifying an outcome of decreased likelihood of recurrence free survival when altered gene expression relative to the level in a non-cancerous sample is present.

Abstract: A system and method for target material capture, the method comprising: receiving a set of target cells into an array of wells defined at a surface plane of a substrate; receiving a set of particles into the array of wells, thereby co-capturing the set of target cells and the set of particles; achieving a desired state for the array of wells upon receiving a washing fluid into a cavity in communication with the array of wells; receiving a lysis buffer into the cavity; receiving a partitioning fluid into the cavity, thereby displacing the lysis buffer from the cavity and partitioning each of the array of wells from adjacent wells, at the surface plane; and retaining intercellular material of the set of target cells, individually with the set of particles within the array of wells.

Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Legionella pneumophila 16S or 23S rRNA sequences or DNA encoding 16S or 23S rRNA. Methods are disclosed for detecting the presence of L. pneumophila in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 16S rRNA sequence or DNA encoding the 16S rRNA sequence, or of a 23S rRNA sequence or DNA encoding the 23S rRNA sequence to produce a detectable amplification product.

Abstract: Provided herein is reagent mixture comprising multiplexed amplification reagents and flap assay reagents for detecting, in a single reaction, mutant copies of the KRAS gene that contain any of the 34A, 34C, 34T, 35A, 35C, 35T or 38A point mutations. Methods that employ the reagent mix and kits for performing the same are also provided.

Abstract: A composition for reducing the inhibitory effects of contaminants on nucleic acid amplification is provided. The composition includes a plurality of zirconium oxide particles, a non-ionic surfactant, and an organic iron-chelating reagent. The organic iron-chelating reagent has a first affinity constant greater than or equal to 104.2 with respect to ferric iron and a second affinity constant less than 103.8 with respect to magnesium, wherein the first affinity constant and the second affinity constant are determined in deionized water at pH 8.45 and 20° C. Optionally, the composition includes polyvinylpyrrolidone. Optionally, the composition comprises water. The composition has a pH of about 8.45 to 8.85. Methods of using the composition to prepare a sample for nucleic acid amplification are also provided.

Abstract: For use with a cellular communication network having a base station transmitting downlink signals received by mobile device/s: a downlink signal reception enhancement system including partial repeater apparatus enhancing quality of reception of at least a portion of downlink signal/s by mobile device/s, the partial repeater apparatus including a downlink receiver receiving at least a portion of downlink signal/s arriving from the base station; a controller including a critical region selector, selecting only a portion of at least one individual downlink signal; and a partial transmitter generating signal/s by regenerating, according to characteristic/s of at least one of a downlink signal and the mobile device, at least the portion selected by the critical region selector, and to transmit a signal including at least the regenerated portion plus less than all of the individual downlink signal.

Abstract: Panels of biomarkers, methods and systems are disclosed for determining gene expression, and diagnosing and treating melanoma.

Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, a method for determining the nucleic acid make-up of a sample is provided.

Abstract: Diagnostic assays for discriminating Waldenstrom's Macroglobulinemia from IgM monoclonal gammopathy of undetermined significance are provided. The method comprises obtaining a biological sample from a subject in need thereof, performing an allele-specific polymerase chain reaction assay to determine in the biological sample a level of a transcript comprising a mutation at position 38182641 in chromosome 3p22.2, and providing a report indicating whether delta CT value of the biological sample is less than a reference value, wherein the subject has Waldenstrom's Macroglobulinemia if the delta CT value is less than the reference value.

Abstract: A method for extracting differentiated cells from a cell population comprising undifferentiated cells after induction of the differentiation of pluripotent stem cells. A method for extracting differentiated cells from a cell population, comprising the following steps: (1) a step of introducing, into a cell population, mRNA comprising a marker gene operably linked to the target sequence of miRNA specifically expressed in pluripotent stem cells; and (2) a step of extracting cells in which the marker gene has been translated.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: Provided herein are methods and kits for isothermal nucleic acid amplifications that use a target nucleic acid template; a reaction mixture comprising a DNA polymerase having a strand displacement activity, a deoxyribonucleoside triphosphate (dNTP) mixture, a primer with a 3? end and a 5? end, a molecular crowding reagent, and a buffer solution for amplifying the target nucleic acid template. The buffer solution maintains a low salt concentration of the reaction mixture, and wherein the salt concentration results in a melting temperature (Tm) of the primer at least 10° C. below the reaction temperature. The amplification is effected under isothermal condition.

Abstract: The invention is directed to a non-naturally occurring microbial organism comprising a first attenuation of a succinyl-CoA synthetase or transferase and at least a second attenuation of a succinyl-CoA converting enzyme or a gene encoding a succinate producing enzyme within a multi-step pathway having a net conversion of succinyl-CoA to succinate.

Abstract: Methods of prognosing the outcome of cancer and/or cancer treatment are provided. The methods involve quantitating the level of methylation at a site that regulates expression of the mda-9/Syntenin gene, site cg17197774. High levels of methylation indicate a good prognosis whereas low levels of methylation indicate a poor prognosis and determination of these levels permits risk stratification of patients with cancer.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.

Abstract: Provided herein are chelator constructs (e.g., nucleic acid, peptide, peptide nucleic acid, etc.) that sequester metal ions (e.g., Mg2+) under a first set of conditions and fail to sequester or release sequestered metal ions under a second set of conditions. In particular, nucleic acid constructs are provided that sequester metal ions (e.g., Mg2+) under conditions that favor secondary and tertiary structure formation and release or fail to sequester metal ions under conditions that disfavor the formation of such structures.

Abstract: The invention comprises methods and compositions for enriching for a target nucleic acid with a single primer extension and low-bias limited amplification.