Abstract: The invention provides methods and materials related to a gene expression-based survival predictor for DLBCL patients.

Abstract: Systems, methods, and apparatuses are provided for detecting nucleic acid sequence variants. Other embodiments are directed to systems and computer readable media associated with methods described herein.

Abstract: The present invention describes methods for performing higher multiplexed PCR for detection and quantitation of target nucleic acids using tagged hydrolysis probes.

Abstract: Ion sensor based on differential measurement comprising an ISFTET-REFET pair wherein the REFET is defined by a structure composed of an ISFET covered by a microreservoir where an internal reference solution is contained. The sensor comprises a first and a second ion-selective field effect transistor, an electrode, a substrate on the surface whereof are integrated the two transistors, connection tracks and the electrode and a structure adhered on the first ion-selective field effect transistor which creates a microreservoir on the gate of said first transistor, with the microreservoir having a microchannel which connects the microreservoir with the exterior and the microreservoir being filled with the reference solution.

Abstract: The invention relates to the soybean variety designated 01073304. Provided by the invention are the seeds, plants and derivatives of the soybean variety 01073304. Also provided by the invention are tissue cultures of the soybean variety 01073304 and the plants regenerated therefrom. Still further provided by the invention are methods for producing soybean plants by crossing the soybean variety 01073304 with itself or another soybean variety and plants produced by such methods.

Abstract: A unit structure-type pharmaceutical composition includes a single nucleic acid, such as an antisense nucleic acid, electrostatically bound to a single block copolymer having a cationic polyamino acid segment and a hydrophilic polymer chain segment. The negative charges of the nucleic acid are counterbalanced, at least substantially, by the positive charges of the cationic polyamino acid segment such that the pharmaceutical composition is electrically neutral or nearly electrically neutral. Further, the nucleic acid is covered with the hydrophilic polymer chain segment. The block copolymer thereby improves the blood retention capability of the nucleic acids.

Abstract: A method of ligating DNA molecules, wherein the DNA molecules are in a hybrid with an RNA molecule, including the steps of providing DNA molecules that are in a RNA:DNA hybrid with an RNA molecule, and ligating the DNA molecules to each other with a double strand specific ligase.

Abstract: Craftwork tools are described. The craftworks tools may include a stamp and a jig with matching alignment patterns. Methods of using same are also described. The method may include placing the jig on a stamp platform, aligning the stamp with the jig, placing cardstock or another substrate on the jig, inking the stamp, and closing the lid of the stamp platform to mark the cardstock with the stamp. The cardstock and the jig may then be rotated clockwise or counterclockwise on the stamp platform without rotating the stamp on the lid, the stamp may be re-inked and then the lid may be closed again to mark the cardstock with the stamp. Methods of using embossing tools are also described.

Abstract: A method is provided for use in a plant breeding program to generate a population having one or more desired traits. The method includes removing a tissue sample from each of one or more seeds using an automated seed sampler while preserving germination viability of the sampled seeds; analyzing the tissue samples for the presence or absence of a genetic sequence associated with at least one desired trait; based on the analysis of the tissue samples, cultivating plants from the sampled seeds that either possess or lack the genetic sequence associated with the at least one desired trait; creating a parental cross using at least one of the cultivated plants; and selecting seeds from the parental cross and cultivating offspring of the parental cross using the selected seeds.

Abstract: A method, comprising amplifying a nucleic acid sequence of interest in a sample comprising genomic DNA of a subject; amplifying a reference nucleic acid sequence in the sample; quantifying the amplified sequence of interest relative to the amplified reference sequence; and determining a copy number of the sequence of interest from the relative quantified amplified sequence of interest. The reference sequence may have at least 80% sequence identity to at least one of SEQ ID NO:1-38, such as SEQ ID NO:1-13. Also disclosed are kits and compositions, each comprising a first probe which specifically hybridizes to at least a portion of at least one reference sequence. Also disclosed is a system configured to perform the above method.

Abstract: Provided is a method for modifying a ssRNA at the 3? end, the method including contacting the strand with a ssRNA 2?-O-methyltransferase in the presence of a co-factor, under conditions which allow for the transfer by the ssRNA 2?-O-methyltransferase of a part of the co-factor onto the 3? end of the ssRNA to form a modified ssRNA, wherein the ssRNA bears 2?-OH group at 3? terminal nucleotide and wherein the part of the co-factor transferred includes a reporter group or a functional group.

Abstract: A multiple molecular diagnosis chip structure according to one embodiment of the present invention comprises: a reaction pad; a channel pad; and a transfer pad.

Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.

Abstract: The present disclosure provides, among other things, methods for colorectal cancer detection (e.g., screening) and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include analysis of methylation status of one or more methylation biomarkers, and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer detection (e.g., screening) that include detecting (e.g., screening) methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include detecting (e.g., screening) methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA, using MSRE-qPCR.

Abstract: The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“ChIP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation.

Abstract: The present invention provides devices and methods for detecting and capturing molecular biomarkers from a subject in situ. Specifically, the devices contain an array of microneedles to which are attached probes specific for one or more biomarkers of interest. The devices can be used directly on a subject (e.g., via skin piercing) in detecting the biomarkers in the body of the subject (e.g., tissues, blood stream).

Abstract: The present invention provides methods of amplifying a target nucleic acid utilizing a clamp oligonucleotide comprising a first target-binding region on the 3?-terminus and a second target-binding region on the 5?-terminus and tether region in between. The tether region may comprise a variety of user-defined sequences or elements that allow for further manipulation of the target nucleic acid. Such as, for example, capture followed by amplification, identification and/or sequencing. The target-binding regions bind to the target nucleic acid, the 3?-terminus functions as a primer to initiate extension across the target nucleic acid sequence and ligation of the gap results in formation of a circularized nucleic acid. This circular template can be used in a variety of processes, including amplification and sequencing.

Abstract: Disclosed aspects manage a shared pool of configurable computing resources. A resource demand value is identified for a target host. Resource supply values of dynamically-assigned resources are computed for donor hosts. Using the resource demand value and the resource supply values, dynamically-assigned resources are reclaimed from the donor hosts and distributed to the target host.

Abstract: A method of forming an enhanced super-resolution image is provided. The method includes: preparing a substrate comprising a glass substrate, a metal layer on the glass substrate, and a biolayer on the metal layer; placing a biological specimen on the substrate, the biological specimen being in contact with the biolayer and being attached to the metal layer through the biolayer, in which the biological specimen is labeled by a plurality of spontaneous blinking elements therein; irradiating a light beam to the metal layer via the glass substrate; receiving fluorescence signals emitted from the spontaneous blinking elements within a time period; fitting a plurality of functions respectively to each of the fluorescence signals; pinpointing peak positions of the functions; and reconstructing the peak positions to derive the enhanced super-resolution image of an underlying structure of the biological specimen in proximity to the metal layer.

Abstract: Pre-coated analysis substrates, and methods of making the substrates and using them to analyze animal tissue, are described. The pre-coated analysis substrates can be made by forming a matrix surface on an analysis substrate; adding a protease to the matrix surface to form a pre-coated analysis substrate; and placing an animal tissue specimen on the matrix surface. The animal tissue can then be analyzed by allowing the protease to partially digest the animal tissue specimen; and analyzing the partially digested animal tissue specimen by mass spectrometry.

Abstract: Nanopore-based molecular analysis systems including a disposable well array, methods of analysis of biomolecules using nanopore molecular analysis systems, and methods of fabricating disposable well arrays are provided.

Abstract: A retrotransposable element based multiplexed qPCR assay to robustly quantitate and distinguish cell free DNA integrity and concentration in blood plasma and serum is described. The multiplexed system for characterizing cancer in humans includes a sample of serum, plasma, urine, or other biological fluid, the sample comprising cell free DNA, the cell free DNA comprising long and short retrotransposable element targets and an added internal positive control, the long and short targets being independent of each other, a distinctly labeled TaqMan probe corresponding to each target, a forward primer and a reverse primer corresponding to each target, a DNA standard for generating standard curves, a qPCR system for amplifying the targets and a qPCR data analysis system.

Abstract: The invention relates to a detective molecule, and more particularly to a detective molecule and a kit for detecting a target molecule, a method for predicting fragrance production in an orchid, and a method for breeding a scented orchid.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: Disclosed herein are codon-optimized nucleic acids encoding a reduced-size ATP7A protein. Also disclosed are vectors and recombinant viruses (such as recombinant adeno-associated viruses) including the codon-optimized nucleic acids encoding the reduced-size ATP7A protein and compositions including the disclosed vectors and viruses. Further disclosed herein are methods of treating copper transport disorders, for example by administering a disclosed nucleic acid, vector, or recombinant virus to a subject with a copper transport disorder, such as Menkes disease, occipital horn syndrome, or ATP7A-related distal motor neuropathy.

Abstract: The present invention relates to methods of using cell-free DNA analysis for guiding treatment of advanced prostate cancer. In particular, liquid biopsies are collected from urine and/or plasma of patients for measuring copy number variation in cell-free DNA associated with metastatic prostate cancer. In particular, urine genomic abnormality (UGA) and plasma genomic abnormality (PGA) values are contemplated for use in predicting treatment responses in advanced prostate cancer patients and for use in making decisions related to androgen deprivation therapy (ADT) treatment outcomes in hormone sensitive stage and for starting or changing chemotherapy treatments in castrate resistant advanced cancer stage.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: The invention concerns a method for detecting isothermal loop-mediated (LAMP) amplification of a target nucleic acid sequence which is based on the fluorescence resonance energy transfer (FRET) mechanism. The invention also concerns a set of oligonucleotides and a kit adapted for carrying out the LAMP-FRET method of the invention.

Abstract: This application relates to the use of measurements of cell-free DNA, protein, and/or metabolite found in biofluid (e.g., urine) for identifying and treating organ injury. The application includes methods and compositions for monitoring, detecting, quantifying, and treating kidney injury in subjects suffering from or suspected of having an altered renal status by measuring amounts of cfDNA and one or more other markers, such as inflammation markers, apoptosis markers, protein, and DNA methylation.

Abstract: A high-density micro-chamber array has a translucent flat substrate, a hydrophobic layer in which a plurality of micro-chambers are provided, and a lipid bilayer membrane formed in each of the openings of the micro-chambers, wherein an electrode is provided in each of the micro-chambers, and when the side of the substrate on which the hydrophobic layer is provided is directed upward, the micro-chamber array is configured such that with at least one of the following A) and B) being met, light entering the substrate from below is transmitted through the substrate and penetrates into the micro-chambers' interiors, and light entering the substrate from the micro-chambers' interiors is transmitted through the substrate and escapes toward below the substrate. A) The electrode is provided on an inner side surface of each of the micro-chambers. B) The electrode is transparent and provided on a bottom surface of each of the micro-chambers.

Abstract: The present disclosure relates to devices and methods for the detection and/or sorting of nucleic acids. Further disclosed are methods for device fabrication.

Abstract: The present application relates to a method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications. A substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene can be used for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives.

Abstract: Disclosed herein are targeted chimeric polypeptides, compositions thereof, expression vectors, and methods of use thereof, for the generation of transgenic cells, tissues, plants, and animals. The compositions, vectors, and methods of the present invention are also useful in gene therapy and cell therapy techniques. The chimeric polypeptide includes a CRISPR-Cas domain and a recombinase domain.

Abstract: The invention relates to polynucleotide agents, e.g., antisense polunucleotide agents, targeting the ALAS1 gene, and methods of using such agents to alter (e.g., inhibit) expression of ALAS1 and to treat ALAS1 associated diseases, e.g., porphyria.

Abstract: Systems, methods, and compositions for monitoring and analyzing nucleic acid hybridization state using L-DNA probes are described. The methods include adding L-DNA probes that can be fluorescently detected to a system including D-DNA. The L-DNA probes include primer, target, and antisense nucleotide sequences, and fluorescent dye compounds. The L-DNA probes are particularly useful for monitoring and analyzing various parameters during DNA amplification using the polymerase chain reaction.

Abstract: A bioelectrochemical sensor utilizing a nanoporous gold electrode. The bioelectrochemical sensor is suitable for measuring redox in biologic media while having increased resistance to biofouling as compared to conventional electrodes such as planar gold electrodes, due to greater exposed surface area of the three-dimensional ligature structure defining the nanopores. The nanopores have a pore size of 5-100 nm, preferably with an average pore size of less than 50 nm, and more preferably with an average pore size of less than 20 nm.

Abstract: A methodology for assays and diagnostics utilizes a nanoporous or corrugated metal-containing surface, fiber or particle which enhances or suppresses the optical detectability of a label. The resulting optical, electromagnetic, or imaging signal signals the presence of a pathogen or analyte of interest. Preferred embodiments pertain to label-free, in situ monitoring of individual DNA hybridization in microfluidics using molecular sentinel probes immobilized on nanoporous gold disks. By immobilizing molecular sentinel probes on nanoporous gold disks, single-molecule sensitivity is demonstrated via surface-enhanced Raman scattering which provides robust signals. The described methodology is generally applicable to most amplification independent assays and molecular diagnostics.

Abstract: Chimeric proteins comprising an N-terminal domain derived from an N-terminal nucleotide binding domain of TDP-43 and a C-terminal domain derived from a splicing repressor are described. These proteins may be administered to a subject to treat or prevent disease manifesting TDP-43 proteinopathy such as inclusion body myocytosis, amyotrophic lateral sclerosis (ALS), or frontotemporal dementia (FTD).

Abstract: The disclosed methods for preparing cytological samples may include placing a cytological sample in a concave filter in a filtration system, applying a negative pressure to an outer side of the concave filter with a vacuum device to withdraw a liquid from the cytological sample, applying a sectionable matrix material over the filtered cellular material within the concave filter, and removing an assembly including the filtered cellular material and the sectionable matrix material from the filtration system. Various other related methods, systems, and materials are also disclosed.

Abstract: A bottleneck in the Next Generation Sequencing (NGS) workflow is the quantification of libraries for accurate pooling and loading of the sequencing instrument flow cell or chip. Disclosed herein are methods that improve performance and reduce time compared to existing methods.

Abstract: A system and method for sample droplet processing, the system including a substrate, an electrode array network coupled to the substrate and configured to provide a pattern of controlled electric fields for manipulation of the set of sample droplets; a first layer in communication with the electrode array network, the first layer separating the electrode array network from fluid of the set of sample droplets; and a second layer opposing the first layer and displaced from the first layer to define a region wherein droplets of the set of sample droplets can reside. In some variations, the system can additionally include an electronics subsystem coupled to at least one of the substrate and the electrode array network, and a control module in communication with the electronics subsystem, wherein the control module generates and manipulates the pattern of controlled electric fields.

Abstract: A kit having instructions for use for performing uterine lavage in a female patient includes a uterine lavage catheter configured for insertion into a woman's uterus to remove viable blastocysts from the uterus, and one or more first containers having a sufficient dosage amount of a GnRH antagonist to cause desynchronization of the endometrium of the patient prior to, during and/or following recovery of viable blastocysts from the uterus.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with psoriasis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, including groups of nucleic acid molecules that may be used as a signature marker set, such as a haplotype, a diplotype, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: A sensing device includes a first substrate having a plurality of TSVs extending therethrough, and a second substrate positioned adjacent the first substrate, with the TSVs being electrically connected to the second substrate. At least one carbon nanotube sensor is positioned on the first substrate. Each of a plurality of contact pads is positioned on the first substrate and on one of the carbon nanotube sensors such that each contact pad is electrically connected to one of the TSVs and the one of the carbon nanotube sensors, and such that an end of the one of the carbon nanotube sensors is embedded in the contact pad.

Abstract: A system identifies ancestral birth locations or surnames estimated to be associated with an individual's ancestors using an individual's genetic sample. The system identifies users who are genetic matches to the individual and determines whether and how often a birth location or surname appears in the pedigrees of those users. Birth locations or surnames that appear frequently throughout the pedigrees of genetically matching users may represent birth locations or surnames that are affiliated with the individual's ancestors. The system determines whether the frequency of appearance of a birth location or surname is statistically significant to eliminate biases for certain birth locations or surnames that appear more frequently than others. The birth location or surname may be provided to the individual based on an also-determined enrichment score.

Abstract: The present invention relates to methods for simultaneously determining the presence or absence of mutations, deletions, duplications and single nucleotide polymorphisms in a cystic fibrosis transmembrane regulator (CFTR) nucleic acid. Oligonucleotide primers and kits used to amplify regions of a CFTR nucleic acid for high throughput, massively parallel sequencing and methods of determining an individual's cystic fibrosis status are also disclosed.

Abstract: A biopolymer (e.g. DNA) sequencing system comprises a biopolymer capture element for capturing a biopolymer from a sample disposed on a substrate for receiving the sample which capture element is preferably provided by a helicase which further acts as a size exclusion molecular motor for delivering a biopolymer such as DNA to a discrete detection means associated with the capture element and the substrate. The detection means may detect signals or variances in a signal associated with the biomolecule and, in particular, components of the biomolecule (e.g. nucleotides or bases). The biomolecule may be returned to the sample. Highly efficient, high speed, low cost sequencing of biopolymers such DNA are thereby achievable.

Abstract: An apparatus to detect more than one analyte in a solution comprising at least one electrode in contact with the solution, at least two dyes including a first dye and a second dye, and an electrochemically active agent, where the solution has a pH, the electrode is configured to modulate the pH of the solution by oxidizing or reducing the electrochemically active agent, the first dye and the second dye fluoresce at different pH levels, fluorescence of the first dye is used to indicate the presence of a first analyte, and fluorescence of the second dye is used to indicate the presence of a second analyte. Methods of detecting multiple analytes in a solution are also provided.

Abstract: An additive composition used in a loop mediated isothermal amplification (LAMP) reaction for reducing a threshold time for a positive sample includes but not limited to EDTA, EGTA, BSA, DMSO, nonionic surfactants, and polymers, and the additive composition used in LAMP reactions includes at least one of the above mentioned additives and may be any combination use of the additives.

Abstract: Methods and nucleic acid molecules for detecting chromosomal abnormalities such as aneuploidy. Methods for selecting nucleic acid molecules for use in the methods of the disclosure.