Detecting Nucleic Acid By Specific Antibody, Protein Or Ligand-receptor Binding Assay Patents (Class 435/6.19)
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Patent number: 9470651Abstract: According to one aspect, the disclosure is directed to an example embodiment in which a circuit-based arrangement includes a circuit-based substrate securing a channel, with an effective width that is not limited by the Debye screening length, along a surface of the substrate. A pair of reservoirs are included in or on the substrate and configured for containing and presenting a sample having bio-molecules for delivery in the channel. A pair of electrodes electrically couple a charge in the sample to enhance ionic current flow therein (e.g., to overcome the electrolyte screening), and a sense electrode is located along the channel for sensing a characteristic of the biological sample by using the electrostatic interaction between the enhanced ionic current flow of the sample and the sense electrode. Actual detection occurs by using a charge-signal processing circuit to process the sensed charge signal and, therefrom, provide an output indicative of a signature for the bio-molecules delivered in the channel.Type: GrantFiled: October 15, 2015Date of Patent: October 18, 2016Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Yang Liu, Robert W. Dutton, Roger T. Howe
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Patent number: 9459186Abstract: The device has a fluid inlet; a filtering compartment, connected to the fluid inlet and accommodating a filtering matrix in presence of adsorption agents; a fluidic circuit connected downstream of the filtering compartment and including a discharge circuit and a loading circuit; a discharge chamber, connected downstream of the discharge circuit; a preparation outlet, connected downstream of the loading circuit; and suction pumps, connected to the fluidic circuit and configured so as to fluidically connect the filtering compartment alternatively to the discharge circuit or to the loading circuit.Type: GrantFiled: April 8, 2013Date of Patent: October 4, 2016Assignee: STMicroelectronics S.r.l.Inventors: Ubaldo Mastromatteo, Flavio Francesco Villa, Gabriele Barlocchi
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Patent number: 9442125Abstract: A method of characterizing the coagulation or sedimentation dynamics of a fluid such as whole blood, a blood fraction, or blood plasma, the method including: illuminating a sample of the fluid with a beam of coherent light; acquiring a time series of images of a speckle pattern generated by interaction between the sample and the spatially coherent light beam; and processing the time series of images; wherein the processing step includes calculating a function representative of the variation in the speckle pattern between two or more images of the series. The invention also provides a device for implementing such a method.Type: GrantFiled: October 28, 2015Date of Patent: September 13, 2016Assignee: Commissariat a L'Energie et aux Energies AlternativesInventors: Patrick Pouteau, Magalie Faivre, Philippe Peltie, Anne Planat-Chretien
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Patent number: 9399826Abstract: A thin film deposition apparatus and a thin film deposition method using an electric field are provided. The thin film deposition apparatus includes: a first substrate; a plurality of electrodes in a 2D arrangement on the first substrate; and a solution provided on the plurality of electrodes and in which charged nanoparticles are distributed, wherein the charged nanoparticles are selectively deposited on at least a part of the plurality of electrodes by independently applying a voltage to each of the plurality of electrodes.Type: GrantFiled: May 15, 2014Date of Patent: July 26, 2016Assignees: SAMSUNG ELECTRONICS CO., LTD., The Regents of The University of CaliforniaInventors: Jin S. Heo, Hwi-yeol Park, Kyung-hoon Cho, Kyoung-hwan Choi, Se-jung Kim, Michael J. Heller, Young-jun Song
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Patent number: 9322063Abstract: A technique is disclosed for recapturing and recycling biomolecule reagents. The technique may be applied in a range of settings, including biopolymer synthesis, sequencing, and so forth. Biomolecule reagents such as nucleotides and oligonucleotides used to process nucleic acids, which may be marked with fluorescent tags, carry blocking agents, and so forth, are introduced to samples in a sample container. After the desired reaction occurs with some of the biomolecule reagents, such as some of the nucleotides or oligonucleotides, the effluent stream is processed to recapture unreacted biomolecule reagents. These may be separated from other reaction components, and recycled into the same or a different sample container. The recaptured biomolecule reagents may be mixed with additional biomolecule reagents prior to reintroduction to the same or different samples.Type: GrantFiled: January 25, 2008Date of Patent: April 26, 2016Assignee: ILLUMINA, INC.Inventor: Chanfeng Zhao
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Patent number: 9309558Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: November 20, 2013Date of Patent: April 12, 2016Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Jennifer O'Neil, Rachel Kasinskas, Shiaw-Min Chen, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Patent number: 9310326Abstract: Provided is a device for determining a monomer molecule sequence of a polymer including different electrodes, and a method of efficiently determining a monomer molecule sequence of a polymer.Type: GrantFiled: June 14, 2013Date of Patent: April 12, 2016Assignee: SAMSUNG ELECTRONICS CO., LTD.Inventors: Heejeong Jeong, Jeo-young Shim, Kun-sun Eom, Dong-ho Lee, Tae-han Jeon
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Patent number: 9313558Abstract: Provided herein, among other things, is an assembly comprising a pin or a piece of jewelry and a transponder affixed thereto. The transponder can be a very small, light-triggered transponder (“MTP”).Type: GrantFiled: September 22, 2011Date of Patent: April 12, 2016Assignee: Pharmaseq Inc.Inventors: Wlodek Mandecki, Ziye Qian, Richard Morris, Garry Thomas Jolley-Rogers, David Keith Yeates, Philip John Suter, James Reginald Croft, Edith Margaret Cawsey, Jeffrey Michael Webb
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Patent number: 9289436Abstract: Methods are directed to the treatment of subjects with prostate cancer, in particular those with castration resistant prostate cancer, with glucocorticoid receptor antagonists. The prostate cancer may be one that has become resistant to androgen deprivation therapy, for example, by increase in glucocorticoid receptor expression and/or activity.Type: GrantFiled: February 21, 2013Date of Patent: March 22, 2016Assignee: The University of ChicagoInventors: Russell Z. Szmulewitz, Suzanne D. Conzen
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Patent number: 9175335Abstract: The present patent application describes a cantilever for atomic force microscopy (AFM), which includes a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.Type: GrantFiled: March 17, 2014Date of Patent: November 3, 2015Assignees: POSCO, POSTECH FOUNDATIONInventors: Joon Won Park, Yu Jin Jung, Bong Jin Hong, Saul Tendler, Stephanie Allen
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Patent number: 9157116Abstract: High throughput methods are used that combine the features of using a matrix-type microfluidic device, labeled nucleic acid probes, and homogenous assays to detect and/or quantify nucleic acid analytes. The high throughput methods are capable of detecting nucleic acid analyes with high PCR and probe specificity, producing a low fluorescence background and therefore, a high signal to noise ratio. Additionally, the high throughput methods are capable of detecting low copy number nucleic acid analyte per cell.Type: GrantFiled: February 9, 2009Date of Patent: October 13, 2015Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Marc Unger
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Patent number: 9157885Abstract: The present invention provides a method for electrochemically detecting a target substance and a method for electrochemically detecting an analyte using a probe holding substrate with a probe for trapping a target substance or an analyte held on the substrate body as well as a test chip and a detection set using the above detection methods.Type: GrantFiled: September 24, 2011Date of Patent: October 13, 2015Assignee: SYSMEX CORPORATIONInventors: Shigeki Iwanaga, Hiroya Kirimura
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Patent number: 9121849Abstract: 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.Type: GrantFiled: March 8, 2013Date of Patent: September 1, 2015Assignee: Rapid Pathogen Screening, Inc.Inventors: Uma Mahesh Babu, Robert P. Sambursky, Robert W. VanDine
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Patent number: 9116128Abstract: Micro-cavity resonant sensors have outer surfaces that are functionalized using click chemistry, e.g., involving a cycloaddition reaction of an alkyne functional group and an azide functional group. A first polymer linking element binds to an outer surface of the micro-cavity and has an azide functional group, which bonds to an alkyne functional group of a second polymer linking element as a result of a cycloaddition reaction. A functionalization element such as an antibody, antigen or protein for sensing a target molecule is bound to the second linking element.Type: GrantFiled: January 9, 2012Date of Patent: August 25, 2015Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGYInventors: Andrea M. Armani, Akinleye C. Alabi, Mark E. Davis, Richard C. Flagan, Scott E. Fraser
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Patent number: 9102977Abstract: Disclosed is a fast and simple method for quantification of nucleic acid of biological cells as 2-step protocol. In the first step cells are treated with an acidic solution containing a non-ionic detergent and a fluorescent DNA specific label. In the second step the sample may be neutralized. Determining of the content of nucleic can be performed by fluorescence microscopy. The method may also be used for obtaining information of cell cycle analysis, ploidy determination, measurements of nucleotide incorporation and assays for proliferation, health, stress level, apoptosis, necrosis, or other state of conditions of cells. The invention also relates to a kit of parts comprising an acidic agent, a detergent, a labelling agent and optionally a neutralization agent.Type: GrantFiled: February 10, 2011Date of Patent: August 11, 2015Assignee: ChemoMetec A/SInventors: Søren Kjaerulff, Martin Glensbjerg
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Publication number: 20150141274Abstract: Disclosed herein are methods, compositions, and kits for isolating actively translated mRNA from heterogeneous cell populations. Also disclosed herein are methods, compositions, and kits for identifying cell types that respond to stimuli in heterogeneous cell populations.Type: ApplicationFiled: May 9, 2013Publication date: May 21, 2015Inventors: Jeffrey M. Friedman, Zachary A. Knight, Keith Tan, Kivan Birsoy
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Publication number: 20150132755Abstract: An assembly for processing a sample is provided. The assembly comprises a first body having a plurality of spaced-apart conduits and a second body having a plurality of chambers wherein each conduit is fluidically connected to a separate chamber. The assembly forms a plurality of liquid flow paths, each flow path comprising a conduit and a chamber. An analyte capture element is detachably attached to a conduit and is in fluidic communication with the liquid flow path of the conduit. Optionally, the assembly further may comprise a third body comprising a plurality of reservoirs. The assembly can be used to process a liquid sample for detecting an analyte.Type: ApplicationFiled: May 24, 2013Publication date: May 14, 2015Applicant: 3M INNOVATIVE PROPERTIES COMPANYInventors: Jon A. Kirschhoffer, Andrew H. Tilstra, Wensheng Xia
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Publication number: 20150119333Abstract: The invention provides Galectin-3 binding protein (Gal-3BP, BTBD17B) polypeptide sequences and compositions that include Gal-3BP polypeptide sequences, and methods of using Gal-3BP polypeptide sequences, including modified forms and wild type (native) forms of Gal-3BP polypeptide, such as in treatment, diagnostic, detection and prognostic methods.Type: ApplicationFiled: September 18, 2013Publication date: April 30, 2015Applicant: La Jolla Institute for Allergy and ImmunologyInventors: Klaus LEY, Christian GLEISSNER
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Publication number: 20150111217Abstract: Improved assays incorporating single-cell based image analyses that enable quantitation of expression of individual cellular proteins and heterogeneity in terms of individual cellular protein molecule numbers per cell at the single cell level and mapped across sections of clinical tissue samples are disclosed.Type: ApplicationFiled: June 20, 2013Publication date: April 23, 2015Inventors: Bart S. Hendriks, Elena Geretti, Arthur J. Kudla, Matthew David Onsum, Violette Paragas, Sharon Moulis
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Publication number: 20150111761Abstract: The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).Type: ApplicationFiled: October 24, 2014Publication date: April 23, 2015Inventors: Richard A. Young, Warren Whyte, Denes Hnisz, Jakob Loven, Heather Hoke, David Orlando, Charles Y. Lin, Tony Lee
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Publication number: 20150099269Abstract: The present invention discloses a transcription activator-like effector-based strategy, termed “TALEColor”, for labeling specific repetitive DNA sequences in human chromosomes. TALEs were custom designed for human telomeric repeats and fused with any of numerous fluorescent proteins (FPs). TALE-telomere-FP fusion proteins were used to detect telomeric sequence in both living cells and fixed cells. Using human cells with different average telomere lengths, TALEColor signals correlated positively with telomere length. TALEs were also designed to detect centromeric sequences unique to specific chromosomes, enabling localization of these specific human chromosomes in live cells. These methods may have significant potential both for basic chromosome and genome research as well as in clinical applications.Type: ApplicationFiled: October 3, 2014Publication date: April 9, 2015Inventor: Hanhui Ma
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Patent number: 8993243Abstract: Methods of isolating weakly interacting molecules in a fluidic sample using an immiscible phase filtration technique are disclosed. A complex is formed between a solid phase substrate, a molecule immobilized on the solid phase substrate, and at least one target molecule present in the fluidic sample. The complex is transferred into an immiscible phase by applying an external force to the solid phase substrate. The methods eliminate the need for complex and time consuming washing steps.Type: GrantFiled: January 10, 2011Date of Patent: March 31, 2015Assignee: Wisconsin Alumni Research FoundationInventors: David Beebe, Richard Burgess, Lindsay Strotman, Scott Berry
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Patent number: 8993260Abstract: The invention relates to a method of detecting viable cells in a cell sample, using a membrane permeable fluorescent label that permeates both viable and non-viable cells and a membrane impermeant quencher that selectively permeates non-viable cells.Type: GrantFiled: May 2, 2013Date of Patent: March 31, 2015Assignee: Charles River Laboratories, Inc.Inventor: Eric Stimpson
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Patent number: 8993259Abstract: The invention relates to a method of detecting viable cells in a cell sample, using a membrane permeable fluorescent label that permeates both viable and non-viable cells and a membrane impermeant quencher that selectively permeates non-viable cells.Type: GrantFiled: May 2, 2013Date of Patent: March 31, 2015Assignee: Charles River Laboratories, Inc.Inventor: Eric Stimpson
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Publication number: 20150079603Abstract: Compositions, devices, systems and methods for reducing and/or preventing photo-induced damage of one or more reactants in an illuminated analytical reaction by addition of one or more photoprotective compounds to the reaction mixture and allowing the reaction to proceed for a period that is less than a photo-induced damage threshold period.Type: ApplicationFiled: August 11, 2014Publication date: March 19, 2015Inventors: Stephen Yue, Robert Weber, Xiangxu Kong, Andrei Fedorov, John Lyle
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Publication number: 20150079602Abstract: The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.Type: ApplicationFiled: January 13, 2014Publication date: March 19, 2015Inventors: Ulla Bonas, Jens Boch, Sebastian Schornack, Thomas Lahaye
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Patent number: 8980638Abstract: Provided herein are methods and compositions for the prognostic evaluation of a patient suspected of having, or having, cancer by assessing the expression of IMP3 in a biological sample of a patient. Methods can be used at the time of initial diagnosis of malignant tumors to identify a group of patients with a high potential to develop progression or metastasis later. Therefore, methods not only are able to provide very useful prognostic information for patients but also can help clinicians to select a candidate patient likely to benefit from early and aggressive cancer therapy. Methods and compositions for the treatment of cancer associated with expression of IMP3 are also provided.Type: GrantFiled: December 18, 2012Date of Patent: March 17, 2015Assignee: University of MassachusettsInventor: Zhong Jiang
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Publication number: 20150072352Abstract: Methods, assays, and products for the detection of small molecules are provided. In one aspect, for example, a method of detecting a small molecule in a sample can include reacting together a first half of a DNA split aptamer having a first reactive group coupled thereto, a second half of a DNA split aptamer having a second reactive group coupled thereto, where the DNA split aptamer is selective for the small molecule, and a sample containing the small molecule. The first half and the second half bind to the small molecule and the first reactive group and the second reactive group react to form an aptamer ligation product of the first half and the second half. The method can also include assaying for the aptamer ligation product in order to detect the small molecule presence in the sample.Type: ApplicationFiled: May 27, 2014Publication date: March 12, 2015Applicant: University of Utah Research FoundationInventor: Jennifer M. Heemstra
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Publication number: 20150065373Abstract: A novel method that enables prostate cancer testing that is noninvasive and more accurate than conventional methods is disclosed. The present inventors intensively analyzed urine samples from prostate cancer patients, and non-cancer subjects, who are free of prostate cancer, and, as a result, newly discovered urinary peptides that can be used as indicators in prostate cancer testing. Use of these urinary peptides as indicators enables various prostate cancer-related tests including detection of prostate cancer, discrimination between prostate cancer and benign prostatic hyperplasia, monitoring of a therapeutic effect of prostate cancer therapy and monitoring of postoperative recurrence.Type: ApplicationFiled: March 28, 2013Publication date: March 5, 2015Applicant: KYOTO UNIVERSITYInventors: Kenji Nakayama, Kazuharu Shimizu, Jun Utsumi, Takahiro Inoue, Osamu Ogawa
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Patent number: 8969008Abstract: The present invention relates to methods for detecting for the presence of an agent that putatively causes or potentiates DNA damage comprising subjecting a cell (containing a DNA sequence encoding a reporter protein operatively linked to a human GADD45? gene promoter and a human GADD45? gene regulatory element arranged to activate expression of the DNA sequence in response to DNA damage) to an agent; and monitoring the expression of the reporter protein from the cell. The invention also concerns expression cassettes, vectors and cells which may be used according to such a method and also modified media that may be employed in fluorescence assays and in preferred embodiments of the method of the invention.Type: GrantFiled: April 10, 2013Date of Patent: March 3, 2015Assignee: Gentronix LimitedInventors: Paul Hastwell, Richard Walmsley
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Publication number: 20150056629Abstract: Provided are compositions, systems, and methods that employ one or more fusion protein pairs, wherein each fusion protein within a fusion protein pair comprises a sequence-specific nucleic acid binding protein, such as sequence-specific Cas9 protein (e.g., a CRISPR), a sequence specific transcription activator-like enhancer (“TALE”) protein, a sequence specific homing endonuclease (“HE”; a/k/a meganuclease), a three prime exonuclease (“TREX”), and/or a sequence specific zinc finger (“ZF”) protein, which sequence-specific nucleic acid binding protein is operably linked to one half of a split-reporter molecule, such as a split-fluorescent reporter molecule, a split-luminescent reporter molecule, a Förster resonance energy transfer (FRET) reporter molecule, or a Bioluminescence Resonance Energy Transfer (BRET) reporter molecule.Type: ApplicationFiled: April 14, 2014Publication date: February 26, 2015Inventor: Katriona Guthrie-Honea
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Publication number: 20150056630Abstract: An object of the present invention is to provide DNA which regulates the expression of miR-140, a reporter vector which contains the DNA, cells and animals into which the reporter vector is introduced and a screening system for drugs which control the expression of miR-140 and is also to contribute in the development of new therapeutic agents for cartilage diseases such as osteoarthritis and intervertebral disk degeneration using the screening system. The DNA sequence according to the present invention is able to express any gene in a site where miR-140 is expressed and, in addition, it is also able to be utilized for screening a drug which regulates the expression of miR-140. Moreover, the drug that is selected by the screening system of the present invention is expected as a therapeutic agent for cartilage diseases accompanied by abnormality of cartilage.Type: ApplicationFiled: April 2, 2013Publication date: February 26, 2015Inventors: Hiroshi Asahara, Satoshi Yamashita, Mitsuru Naiki, Kentaro Abe
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Patent number: 8951736Abstract: 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.Type: GrantFiled: April 25, 2012Date of Patent: February 10, 2015Assignee: Sequenom, Inc.Inventor: Karsten Schmidt
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Patent number: 8951484Abstract: Candidate cells, such as circulating tumor cells (CTCs), present with blood are captured using a multiple stage device, having successive stages configured to deviate candidate cells out of the blood while slowing down the flow rates of the deviated resultant for easier capture of CTCs through progressive stages. The devices can include separation channel and deviation channels formed of micro-post patterns dimensioned to deviate different desired candidate cells for analysis.Type: GrantFiled: January 31, 2013Date of Patent: February 10, 2015Assignee: The Regents of The University of MichiganInventors: Tommaso F. Bersano-Begey, Daniel F. Hayes
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Publication number: 20150037809Abstract: The present invention relates to polypeptides and more particularly to Transcription Activator-Like Effector derived proteins that allow to efficiently target and/or process nucleic acids. Particularly, the present invention reports the characterization of TALE derived proteins that can efficiently target methylated DNA. The present invention more specifically relates to TALE derived proteins that allow activation of methylated promoters responsible for gene silencing.Type: ApplicationFiled: March 15, 2013Publication date: February 5, 2015Inventors: Philippe Duchateau, Julien Valton
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Publication number: 20150037808Abstract: A system and method for ultrasonic sample preparation, includes a vessel having a wall defining an inner volume. An ultrasonic probe is disposed in the inner volume of the vessel. A microplate having a plurality of sample wells is also disposed in the inner volume of the vessel. An actuator is connected to the microplate and is configured to move the microplate relative to the ultrasonic probe in the inner volume to facilitate uniform distribution of ultrasonic energy.Type: ApplicationFiled: August 1, 2013Publication date: February 5, 2015Inventor: Michael Donaty
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Publication number: 20150031749Abstract: A method of determining the Crohn's disease status of a subject comprising the steps of determining the level of miR-29 in a sample from said subject; and comparing the level of miR-29 determined in step (a) with one or more reference values.Type: ApplicationFiled: March 12, 2013Publication date: January 29, 2015Applicant: Isis Innovation LimitedInventor: Alison Simmons
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Publication number: 20150030602Abstract: A novel monoclonal antibody and like antigen-binding molecules against transmembrane protein with EGF-like and two follistatin-like domains 2 (TMEFE2) are provided with unique immunological and biological properties useful in the therapy of affective disorders such as depression and bipolar disorders as well as anxiety disorders. In addition, pharmaceutical compositions and kits comprising such antibody and derivatives thereof are described.Type: ApplicationFiled: January 2, 2013Publication date: January 29, 2015Applicant: PHENOQUEST AGInventors: Ingeborg Sillaber, Marcelo Paez-Pereda
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Publication number: 20150017655Abstract: A label-free sequencing method for a single molecular nucleic acid is provided. The primer is paired with the nucleic acid template to be assembled to a polymerase. When the nucleotides are added, the electrical conductance signal is measured by the polymerase being connected to the protein transistor to determine the sequences of the nucleic acid template. The trajectory of the measured electrical conductance signal contains plateaux with obvious spikes, which is used to identify four types of the nucleotides and their bases. Furthermore, the sequencing method is suitable for sequencing of complex nucleic acids.Type: ApplicationFiled: April 29, 2014Publication date: January 15, 2015Applicant: NATIONAL CHIAO TUNG UNIVERSITYInventors: GUE-WHA HUANG, MENG-YEN HUNG, YU-SHIUN CHEN
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Patent number: 8932819Abstract: Methods, compositions and kits are disclosed for assays to determine the binding affinity of DNA-binding proteins or RNA-binding proteins for their corresponding recognition site(s). In particular, assays are disclosed for measuring binding affinities when either the binding protein, or the recognition sequence of the recognition site, or cofactor proteins, contain one or more mutations. The disclosed assays can thus be utilized to measure the effect on transcription factor binding caused by mutations within the recognition site, or mutations within the binding domain of the protein, and to provide binding affinity information that can be correlated with altered gene regulation and expression. The disclosed assays can be personalized to a specific person or organism, with the measured binding affinities based upon an individual's specific binding proteins and recognition sites.Type: GrantFiled: July 6, 2012Date of Patent: January 13, 2015Assignee: Affymetrix, Inc.Inventor: Philip Dickinson
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Patent number: 8927218Abstract: The invention provides methods, compositions and kits for segregating a target nucleic acid from a mixed nucleic acid sample. The methods, compositions and kits comprise a non-processive endonuclease (e.g., a restriction enzyme) or an antibody that binds the target nucleic acid (e.g., has methylation specificity). The mixed nucleic acid sample can comprise prokaryotic and eukaryotic nucleic acid and/or nucleic acid from more than one prokaryotic or eukaryotic organisms.Type: GrantFiled: June 26, 2012Date of Patent: January 6, 2015Assignee: Flir Systems, Inc.Inventor: Roger Allyn Forsyth
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Publication number: 20140369934Abstract: The invention provides methods of identifying metakaryotic stem cells, as well as methods of identifying agents that selectively modulate the growth, migration, replication, and/or survival of these cells by detecting an intermediate dsRNA/DNA duplex genome. Also provided are diagnostic, prognostic, and treatment methods for disorders, such as atherosclerosis, restenosis, and benign or malignant tumors.Type: ApplicationFiled: June 1, 2012Publication date: December 18, 2014Inventors: William G. Thilly, Elena V. Gostjeva, B. David Stollar
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Publication number: 20140349303Abstract: The present disclosure relates to biological material identification systems and methods. DNA oligomers may be used to encode for specific characteristics of biological materials. Encoding may be done by depositing suitable amounts of DNA oligomers onto a portion of a biological material. To identify the biological materials, the encoded portions of the biological materials may be extracted and immersed in buffer solutions. Then, lateral flow tests may be used to decode the DNA for interpretation, creating a readable barcode that may be compared with a database to determine if the biological material may be approved.Type: ApplicationFiled: May 24, 2013Publication date: November 27, 2014Applicant: Sunpower Technologies LLCInventor: Travis Jennings
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Publication number: 20140349304Abstract: Assay methods and apparatus for the analysis of biopolymers are disclosed. The assays employ nicking endonucleases to enable the generation of flaps on target biomolecules which are detected in nanopore or fluidic channel devices. Identification of flap locations enables a map of the target biomolecule to be derived.Type: ApplicationFiled: March 6, 2014Publication date: November 27, 2014Applicant: NABsys, Inc.Inventor: John S. Oliver
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Publication number: 20140329700Abstract: The invention relates to compositions and methods to isolate nucleic acids, and the identification of polyadenylation sites in a gene of interest. In one aspect, the invention provides an oligonucleotide comprising at least one nucleic acid and an affinity moiety, wherein said nucleic acid is 30-60 nucleotides in length and said nucleic acid comprises 1-25 uracil and 5-50 thymine nucleotides.Type: ApplicationFiled: August 23, 2012Publication date: November 6, 2014Applicant: RUTGERS, THE STATE UNIVERSITY OF NEW JERSEYInventors: Bin Tian, Wenting Luo, Zhe Ji, Mainul Hoque
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Patent number: 8877446Abstract: The present invention relates to a method for detecting protein-protein interactions in living cells, and more particularly, to a method for providing cells comprising a first construct and a second construct, wherein the first construct comprises a polynucleotide encoding a first fusion protein which comprises a bait protein, a first fluorescent protein and a CBD (cellulose-binding domain) protein, and wherein the second construct comprises a polynucleotide encoding a second fusion protein which comprises a prey protein and a second fluorescent protein so as to allow formation of inclusion bodies, and detecting interactions between the bait protein and the prey protein that are displayed by inclusion bodies, a method for isolating the prey protein bound to the bait protein using the cells comprising the constructs, the cells, and a kit for detecting protein-protein interactions, comprising the constructs.Type: GrantFiled: June 15, 2012Date of Patent: November 4, 2014Assignee: Korea Research Institute of Bioscience and BiotechnologyInventors: Seung Goo Lee, Su-Lim Choi, Jong Sik Gam, Jae Jun Song, Sang Jun Lee
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Publication number: 20140322719Abstract: The invention relates to a method for detecting and measuring the presence of nucleosome-protein adducts and the use of such measurements for the detection and diagnosis of disease. The invention also relates to a method of identifying nucleosome adduct biomarkers for the detection and diagnosis of disease and to biomarkers identified by said method.Type: ApplicationFiled: December 7, 2012Publication date: October 30, 2014Inventors: Jacob Vincent Micallef, Mark Edward Eccleston, Marielle Herzog
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Publication number: 20140296218Abstract: The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).Type: ApplicationFiled: October 25, 2013Publication date: October 2, 2014Applicant: Whitehead Institute for Biomedical ResearchInventors: Richard A. Young, Warren Whyte, Denes Hnisz, Jakob Loven, Heather Hoke, David Orlando, Charles Y. Lin, Tony Lee
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Patent number: 8835360Abstract: A method for selecting combinations of drugs for treatment of diseases that arise from deranged signaling pathways is disclosed. The method involves measuring the activity states for signaling proteins in a diseased cell and determining whether the activity states are different from the activity states observed for a reference cell such as a normal cell. Based on the observed differences, combinations of two or more drugs are selected to reduce these differences. Treatment of a subject with the combinations restores the activity states of the signaling proteins of the deranged disease-associated signaling pathways toward the activity states observed in the reference cell. Since the diseased cell and the reference cell can both be obtained from the same subject, combinations of drugs that specifically target patient-specific signaling derangements is possible.Type: GrantFiled: April 24, 2012Date of Patent: September 16, 2014Assignee: The United States of America as represented by the Secretary of the Department of HHSInventors: Arpita I. Mehta, Lance A. Liotta, Emanuel F. Petricoin
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Publication number: 20140255949Abstract: An assay kit for determination of thymidine kinase (TK) activity in a biological sample, such as blood, serum, plasma, Cerebral Spinal Fluid (CSF), pleural fluid, ascites, tissues, cells and extracts thereof, is described. The assay kit can used in a method that comprises contacting, in a buffer, a Basic Reaction Mixture comprising: solid surface-attached primer and/or template, a modified deoxy nucleoside, such as BromodeoxyUridine, IododeoxyUridine, FluorodeoxyUridine or VinyldexoyThymidine as a kinase enzyme substrate, a phosphate donor, a nucleotide polymerizing enzyme, and a kinase enzyme source devoid of TK activity, such as a yeast extract, with the biological sample. After incubation the amount of modified deoxy nucleoside that has been incorporated into the solid surface-attached primer and/or template, is determined and the TK activity present in the biological sample is directly proportional to the amount of incorporated modified deoxy nucleoside.Type: ApplicationFiled: May 23, 2014Publication date: September 11, 2014Applicant: BIOVICA INTERNATIONAL ABInventor: J. Simon GRONOWITZ