Abstract: Assays and methods including mobile tagged single stranded nucleic acid reagents pre-loaded on an analysis device, which are preferably tagged, but not labeled and are complementary to a strand (preferably the anti-sense strand in double stranded DNA targets) of the target nucleic acid. The assay also includes a running buffer that includes a dye or other detectable label that nonspecifically binds only to double stranded nucleic acids. In addition, the analysis device includes a detection zone including one or more test zones that have an immobilized tag that binds to the tag on the mobile nucleic acid reagent.

Abstract: The invention provides a recombinant nucleotide sequence, including the sequence of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3 or SEQ ID No. 4, wherein the recombinant nucleotide sequence encodes an anti-polyethylene glycol recombinant single chain membrane antibody.

Abstract: This invention relates generally to methods for detecting cell damage as a consequence of pathophysiological or traumatic insults such as in a nuclear accident, bioterror attack, tumorigenesis, infections or in individuals with cardiovascular disease.

Abstract: Techniques for atomic force microscope manipulation of living cells include functionalizing a nanoscale tip of a microscale cantilever with a first ligand for a first receptor associated with a surface of a first type of cell. The method further comprises, controlling the cantilever to cause the first ligand on the nanoscale tip to contact the first receptor on a surface of a living cell of the first type in a particular temporal pattern to induce a target response by the living cell. Other techniques for controlling an atomic force microscope comprising a nanoscale tip include controlling the cantilever to cause the nanoscale tip to contact a living cardiomyocyte at a predetermined pressure. The cantilever is also controlled to turn off vertical deflection feedback after contacting the cardiomyocyte and collecting deflection data that indicates a time series of nanoscale vertical deflections of the microscale cantilever caused by the living cardiomyocyte.

Abstract: The present invention discloses new nanoassembled complexes consisting of a central nucleus formed by a high-affinity interaction from nucleic acids and avidin, wherein said nucleus is stabilized in aqueous solutions, even saline, and protected from further unspecific unwanted interactions by means of suitable polymeric agents capable to mask totally or partially the nucleus itself. The nanocomplexes obtained have been shown to be stable in aqueous solutions and to have nanoparticle features. In addition, the nano-complexes have shown characteristics useful for use in biotechnological field and in nanomedicine.

Abstract: A microfluidic-based flow assay and methods of manufacturing the same are provided. Specifically, the microfluidic flow assay includes a micropatterned surface that induces clot formation and an array of microfluidic channels though which blood flows. The micropatterned surface contains two clotting stimuli, one for inducing platelet adhesion and another for inducing the coagulation cascade.

Abstract: The present invention relates to methods of assessing damage to cellular DNA including the type, frequency and/or distribution of the DNA damage in the genome. The invention further provides methods of evaluating DNA damage in a cell caused by an agent and/or event as well as methods of determining a subject's prior exposure to an agent and/or event that is known or suspected to cause DNA damage. Further provided are methods of determining whether a subject is at an increased risk for a disease or disorder as a result of cellular DNA damage.

Abstract: The present invention provides a method and kit for detection of two or more target molecules in a single tissue sample, such as for gene and protein dual detection in a single tissue sample. Methods comprise treating a tissue sample with a first binding moiety that specifically binds a first target molecule. Methods further comprise treating the tissue sample with a solution containing a soluble electron-rich aromatic compound prior to or concomitantly with contacting the tissue sample with a hapten-labeled binding moiety and detecting a second target molecule. In one example, the first target molecule is a protein and the second is a nucleic acid sequence, the first target molecule being detected by immunohistochemistry and the second by in situ hybridization. The disclosed method reduces background due to non-specific binding of the hapten-labeled specific binding moiety to an insoluble electron rich compound deposited near the first target molecule.

Abstract: The present invention provides isolated, non-viable bacterial cells comprising a plurality of nucleic acid crosslinks, methods for making said cells, and methods for using said cells to isolate DNA-protein complexes. In particular, the nucleic acids of the cells are crosslinked by contacting the cells with a furocoumarin compound and ultraviolet light.

Abstract: Provided are methods for determining the amount of thyroglobulin in a sample using various purification steps followed by mass spectrometry. The methods generally involve purifying thyroglobulin in a test sample, digesting thyroglobulin to form peptide T129, purifying peptide T129, ionizing peptide T129, detecting the amount of peptide T129 ion generated, and relating the amount of peptide T129 ion to the amount of thyroglobulin originally present in the sample.

Abstract: The gene associated and causative of classical late infantile neuronal ceroid lipofuscinosis (LINCL), CLN2, has been identified and characterized. The translation product of this gene is a novel protease and a deficiency in this activity results in LINCL. Identification of CLN2 will not only aid in the prevention of LINCL through genetic counseling but provides strategies and test systems for therapeutic intervention. In addition, further characterization of this previously unknown lysosomal enzyme may provide useful insights into other more common human neurodegenerative disorders. Finally, the utility of a general approach for determining the molecular bases for lysosomal disorders of unknown etiology has been demonstrated.

Abstract: Provided are a biosensor, an apparatus and a method for detecting a biomolecule using the biosensor. The biosensor may include a supporting substrate, a semiconductor layer spaced apart from a top surface of the supporting substrate by supporting patterns, and a nano-motor array formed on a top surface of the semiconductor layer. The nano-motor array may include a plurality of nano-metal rods configured to exhibit an autonomous propulsion in a fluid.

Abstract: In some aspects, the present invention provides compositions and methods relating at least in part to modulation of the Cohesin-Mediator interaction. The invention provides compositions and methods useful for modulating Cohesin-Mediator function. The invention further provides compositions and methods useful for identifying compounds that modulate Cohesin-Mediator function. In some aspects, the invention provides compositions and methods useful for treating a disorder involving altered Cohesin-Mediator function.

Abstract: Methods and compositions are provided for detecting small target RNAs where the target RNA may be single-stranded or double-stranded and may be contained in a mixture of RNAs of different types and sizes. The methods and compositions utilize a p19 fusion protein that is capable of binding double-stranded RNA in a size-specific but sequence-independent manner and is further capable of binding to a matrix such as beads or plastic microwell plates. By labeling the p19 fusion protein or the target RNA in a polynucleotide duplex either directly or indirectly, low levels of target RNA including microRNAs can be detected from cells. This can be applied to diagnosis of pathological conditions.

Abstract: Alkynyl-derivatized cap analogs, alkynyl-modified capped RNA, 1,4-disubstituted triazole-derivatized capped RNA, methods of preparation, methods of isolation, and uses thereof are provided. The “click” modification facilitates detection and isolation of capped RNAs and the 1,4-disubstituted triazole derivatives formed by the “click” reaction are useful for producing RNA transcripts and encoded protein.

Abstract: Methods and compositions for detecting the sub-cellular localization of a molecule are provided. Aspects of the invention include detecting translocation of a cell-surface receptor to a sub-cellular compartment, e.g., the endosome, using a reduced affinity enzyme complementation reporter system. Also provided are systems and kits for use in practicing embodiments of the methods.

Abstract: Provided herein are antibodies and antigen-binding antibody fragments that bind to human soluble Growth Stimulation-Expressed Gene 2 (ST2) protein, kits containing these antibodies and antibody fragments, and methods of using these antibodies and antibody fragments.

Abstract: A reusable nanowire field effect transistor for detecting biomolecular interactions. The field effect transistor contains nanowire covalently linked to a docking molecule, which is capable of binding to an anchor molecule in a reversible manner, i.e., at an association constant of 105 to 109 M?1.

Abstract: Embodiments of the invention relate generally to methods of diagnosing diseases and measuring homeostatic states. In particular, the methods described here are used to characterize RNA from vesicles for expression of disease related markers. Embodiments of the invention also relate generally to the characterization of RNA by using sensitive techniques such as PCR to internally sample organ health using whole blood.

Abstract: A method of diagnosing and treating a glioma or a breast cancer is disclosed. The method of diagnosing comprises analyzing an amount or activity of heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) in a brain or breast cell sample of the subject, wherein an up-regulation in an amount or activity of hnRNP A2/B1 beyond a predetermined threshold with respect to a control cell sample is indicative of the breast cancer or glioma. The method may also be used for staging the cancer and for predicting patient's prognosis of survival. The method of treating glioblastoma and metastatic breast cancer includes inhibiting the expression and/or activity of hnRNP A2/B1.

Abstract: Embodiments of the invention relate generally to methods of characterizing kidney function. In particular, several embodiments quantify kidney-associated marker RNA isolated from vesicles contained in patient urine samples.

Abstract: A kit for dot immunogold directed filtration assay including a dot immunogold directed filtration card, a detection probe labeled by nano colloidal gold or latex beads, a negative standard, a positive standard, and a cleaning solution.

Abstract: A method of sex sorting sperm is disclosed. The sperm may be stained with a DNA selective fluorescent dye, which fluoresces when excited, a dead quenching dye, which selectively quenches fluorescence emitted by the DNA selective fluorescent dye within the membrane of compromised sperm, and a split enhancing dye. The stained sperm may then sorted into one or more gender enriched subpopulations of viable sperm.

Abstract: The present invention relates to the use of proteins that are differentially expressed in tumor associated stromal cells, as compared to normal stromal, as biomolecular targets for tumor treatment therapies. The present invention also provides compounds and pharmaceutically acceptable compositions for administration in the methods of the invention.

Abstract: Methods for identifying agents capable of disrupting a salt bridge in an influenza A virus nucleoprotein corresponding to the E339 . . . R416 salt bridge in SEQ ID NO:1, and thus the trimerization of the NP protein; and uses of such agents, e.g., small molecules and peptides, for inhibiting influenza virus replication and treating infection caused by influenza virus.

Abstract: Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.

Abstract: The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising of the steps of: (a) compartmentalising genetic elements into microcapsules; (b) expressing the genetic elements to produce their respective gene products within the microcapsules; (c) sorting the genetic elements which produce the gene product having a desired activity. The invention enables the in vitro evolution of nucleic acids by repeated mutagenesis and iterative applications of the method of the invention.

Abstract: Methods, materials, apparatus and systems are described for performing capillary flow assay. In one aspect, a system includes a sample collection unit to collect a sample liquid and a sample testing and storing unit to interface with the sample collection unit to test and store the collected sample liquid. The sample testing and storing unit includes a sample inlet shaped to receive the collected sample from the sample collection unit, and a sample well positioned below the sample inlet to retain at least a portion of the sample liquid. The sample testing and storing unit includes a sample housing unit to store a remainder of the sample liquid not retained in the sample well, and an analyte testing unit housing shaped to receive an analyte detecting unit to test a presence of a target analyte in the sample liquid.

Abstract: The present invention relates to a method for identifying a specific type and/or state of a mammalian cell in a sample obtained from a mammal, comprising a) analyzing the relative amount of accessible chromatin in regions that are specific for a cell-type and/or cellular state in the genome of said cell, b) comparing said relative amount of accessible chromatin said in regions with the relative amount of accessible chromatin in regions in the genome of said cell that are unspecific for a cell-type and/or cellular state, and c) deducing the specific type and/or state of said mammalian cell in said sample based on said comparison. Preferably, said identifying further comprises a relative quantification of said specific cell type and/or state based on said comparison. The method can further comprise a diagnosis of a predisposition to a disease or a disease based on said identification. Kits and certain markers in regions of accessible chromatin in the genome are described, too.

Abstract: The present invention provides assays and devices for detection of substances in liquid samples. The assays and devices utilize passive diffusion between a porous material and a porous membrane containing a specific binding pair member to enable detection of the substance of interest.

Abstract: The invention encompasses microfluidic microarray assemblies (MMA) and subassemblies and methods for their manufacture and use. In one embodiment, first and second channel plates are provided and are sealingly connected to a test chip in consecutive steps. Each plate includes microfluidic channels configured in a predetermined reagent distribution pattern. The test chip comprises a plurality of discrete test positions, each test position being located at the intersection between a first predetermined reagent pattern and a second predetermined reagent pattern, wherein at least one of said patterns is non-linear. The first channel plate allows the distribution of a first reagent on said test chip, wherein said first reagent is immobilized at said test positions. The second channel plate allows the distribution of a second reagent on said test chip, wherein said second reagent comprises a plurality of different test samples.

Abstract: The present invention relates to the method of determining the risk of acute kidney injury comprising determining the amount of a marker selected from VCAN, NRP1, CCL2, CCL19, COL3A1, GZMM or any combination thereof in a sample.

Abstract: This invention pertains to the discovery that an amplification of the CYP24 gene or an increase in CYP24 activity is a marker for the presence of, progression of, or predisposition to, a cancer (e.g., breast cancer). Using this information, this invention provides methods of detecting a predisposition to cancer in an animal. The methods involve (i) providing a biological sample from an animal (e.g. a human patient); (ii) detecting the level of CYP24 within the biological sample; and (iii) comparing the level of CYP24 with a level of CYP24 in a control sample taken from a normal, cancer-free tissue where an increased level of CYP24 in the biological sample compared to the level of CYP24 in the control sample indicates the presence of said cancer in said animal.

Abstract: The invention is directed to enhanced methods for detecting an analyte of interest in situ, by immunoassay, or by hybridization comprising binding an enzyme-labeled conjugate molecule to an analyte of interest in the presence of a redox-inactive reductive species and a soluble metal ion. The enzyme catalyzes the conversion of the inactive reductive species to an active reducing agent, which in turn reduces the metal ion to a metal atom thereby providing an enhanced means of detecting the analyte via metal deposition.

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: To gain a better understanding of brain tumor angiogenesis, new techniques for isolating brain endothelial cells (ECs) and evaluating gene expression patterns were developed. When transcripts from brain ECs derived from normal and malignant colorectal tissues were compared with transcripts from non-endothelial cells, genes predominantly expressed in the endothelium were identified. Comparison between normal- and tumor-derived endothelium revealed genes that were specifically elevated in tumor-associated brain endothelium. These results confirm that neoplastic and normal endothelium in human brains are distinct at the molecular level, and have significant implications for the development of anti-angiogenic therapies in the future.

Abstract: The present invention concerns oxocarbonamide peptide nucleic acids (OxoPNAs). OxoPNAs provide increased stability, sensitivity, and specificity as compared to their natural DNA and RNA counterparts. The OxoPNA molecules of the present invention may be employed in a wide range of applications, particularly in applications involving hybridization. For example, OxoPNA probes may be employed for the detection and functional analysis of nucleic acid molecules, including miRNAs and other non-coding RNAs.

Abstract: We describe examples using aptamers for capturing and reporting the presence of a target, such as a pathogen. Examples described here include a set of aptamers that are specific to F. tularensisis. Other examples described here include an Aptamer-Linked Immobilized Sorbent Assay (ALISA) and dot blot assay. An example of a method provided here comprises: providing a set of DNA sequences that exhibit high binding affinity to target antigen, placing the DNA sequences in a sandwich aptamer-linked immobilized sorbent assay (ALISA), contacting the DNA sequences with a sample, and detecting whether the target is present in the sample. Some alternative implementations may include dot blots and different reporters. Quantum dot sandwich assays and quantum dot de-quenching reporters can be used.

Abstract: This invention provides promoter sequences that are useful for modulating transcription of a desired polynucleotide and/or in the construction of recombinant genes for plant transformation to enable expression of foreign or endogenous coding sequences in plants. The promoters are functional in a both monocotyledonous and dicotyledonous plant species and are active in a wide range of vegetative or generative plant organs. The invention also provides a polynucleotide construct comprising a promoter of the invention operably linked to a foreign or endogenous polynucleotide encoding a protein of interest or a transcript capable of modulating expression of a target gene. The invention is further concerned with transformed plant cells, as well as differentiated plants, plant parts, plant tissues or plant seeds containing the construct.

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: The technology relates in part to multimer conjugates comprising a scaffold linked to two or more polypeptides that specifically interact with a nucleic acid containing beta-D-glucosyl-hydroxymethylcytosine or beta-D-glucosyl-hydroxymethyluracil. The scaffold can be chosen from an antibody, an antibody fragment, a multimerized binding partner that interacts with a binding partner counterpart in each of the polypeptides, a polymer, and a polyfunctional molecule. The polypeptides can be from a kinetoplastid flagellate organism and may comprise a full-length native or modified protein or a fragment thereof that specifically interacts with the beta-D-glucosyl-hydroxymethylcytosine and/or the beta-D-glucosyl-hydroxymethyluracil in the nucleic acid. The conjugates provided herein can be used to detect the presence, absence or amount of beta-D-glucosyl-hydroxymethylcytosine and/or beta-D-glucosyl-hydroxymethyluracil-containing nucleic acid in a sample.

Abstract: The present invention provides simple and inexpensive assays for the detection of virtually any analyte in any sample that is in liquid form or that can be solubilized. The assays utilize the fluid dynamics of drop evaporation whereby soluble materials, including analytes and particles binding thereto, are drawn to the edge of the drop and ultimately form a concentrated residual ring. The presence or absence of certain reagents can then be detected through a number of different approaches.

Abstract: Generally, aspects of the present disclosure are directed to conjugate systems, self-illuminating quantum dot conjugates, methods of detecting a target in a host, methods of treating a disease in a host, and the like.

Abstract: Carriers or holders for holding microfluidic devices are provided. Some of the carriers that are provided include a hydration control device and/or a source of controlled fluid pressure to facilitate use of the carrier in conducting various types of analyses.

Abstract: 5-bromo-2?-deoxy-uridine (BrdU) labeled nucleotide triphosphates and nucleic acid probes are described herein. The BrdU labeled nucleotide triphosphates include a linker between the nucleotide triphosphate and the BrdU moiety. The linker can be cleavable or non-cleavable. The nucleotide triphosphates can be a ribonucleotide triphosphates, 2?-deoxyribonucleotide triphosphates or 2?,3?-dideoxyribonucleotide triphosphates. The nucleic acid probes can be used for in situ hybridization.

Abstract: Methods for probing multiple targets in a biological sample are provided. The methods include the steps of providing a sample containing multiple targets, binding at least one probe having a binder coupled to an enzyme to one or more target present in the sample, and reacting the bound probe with an enzyme substrate coupled to a fluorescent signal generator. The methods include the steps of observing a signal from the fluorescent signal generator and applying to the sample a solution containing an oxidizing agent that substantially inactivates both the fluorescent signal generator and the enzyme. The methods further include the steps of binding at least one probe having a binder coupled to an enzyme to one or more target present in the sample of step, reacting the bound probe with an enzyme substrate coupled to a fluorescent signal generator; and observing a signal from the fluorescent signal generator.

Abstract: Disclosed are a method and apparatus that use an electric field for improved biological assays. The electric field is applied across a device having wells, which receive reactants, which carry a charge. The device thus uses a controllable voltage source between the first and second electrodes, which is controllable to provide a positive charge and a negative charge to a given electrode. By controlled use of the electric field charged species in a fluid in a fluid channel are directed into or out of the well by an electric field between the electrodes. The present method involves the transport of fluids, as in a microfluidic device, and the electric field-induced movement of reactive species according to various assay procedures, such as DNA sequencing, synthesis or the like.

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: It is an object of the preset invention to provide an activity measurement molecule necessary for measuring biological reactions or changes in in vivo conditions, and a method for measuring activity using the above activity measurement molecule. It is intended to provide an activity measurement molecule used for simultaneously analyzing multiple biological reactions and/or changes in in vivo conditions, which is characterized in that one or more fluorescent molecule-labeled and/or —unlabeled biomolecules used as targets of the biological reactions or changes in in vivo conditions bind onto a quantum dot, and a method for simultaneously analyzing multiple biological reactions and/or changes in in vivo conditions using the above activity measurement molecule.

Abstract: The invention relates to pharmaceutical compositions comprising trophic factors, methods to decrease the degeneration of a retina, methods of treating ocular degenerative diseases and methods to select cells for transplantation.