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Небесная энциклопедия

Космические корабли и станции, автоматические КА и методы их проектирования, бортовые комплексы управления, системы и средства жизнеобеспечения, особенности технологии производства ракетно-космических систем

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Мониторинг СМИ

Мониторинг СМИ и социальных сетей. Сканирование интернета, новостных сайтов, специализированных контентных площадок на базе мессенджеров. Гибкие настройки фильтров и первоначальных источников.

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Поддерживает ввод нескольких поисковых фраз (по одной на строку). При поиске обеспечивает поддержку морфологии русского и английского языка
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Применить Всего найдено 20732. Отображено 100.
12-01-2012 дата публикации

Thermoelectric method of sequencing nucleic acids

Номер: US20120009568A1
Автор: Eric J. Guilbeau
Принадлежит: Individual

The present invention relates to a novel thermoelectric method for determining the sequence of nucleotides on a nucleic acid molecule through use of a thermopile and/or sequencing reagents flowing under the conditions of laminar flow. The methods disclosed herein involve the measurement of the heat generated by a deoxynucleotide incorporation event that can be accomplished without the need to control the temperature of any of a thermopile's junctions.

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Номер записи: 1
26-01-2012 дата публикации

Materials and methods for isothermal nucleic acid amplification

Номер: US20120021460A1
Автор: Anna K. Fulbright, Brian Lowe
Принадлежит: Qiagen Gaithersburg LLC

A method for isothermal amplification of a target nucleic acid sequence is disclosed. The target nucleic acid is amplified by an enzyme with helicase activity and an enzyme with reverse transcriptase activity and DNA-dependant DNA polymerase activity. Also disclosed is a kit for isothermal amplification of a target nucleic acid sequence, including HPV nucleic acids. The kit comprises a first enzyme with helicase activity and a second enzyme having both reverse transcriptase activity and DNA-dependant DNA polymerase activity.

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Номер записи: 2
16-02-2012 дата публикации

Primers, probes and methods for nucleic acid amplification

Номер: US20120040352A1
Автор: Arthur Reis, Cristina Hartshorn, J. Aquiles Sanchez, Jesse Salk, John Rice, Kenneth Pierce, Lawrence J. Wangh
Принадлежит: BRANDEIS UNIVERSITY

Homogenous detection during or following PCR amplification, preferably LATE-PCR, utilizing fluorescent DNA dye and indirectly excitable labeled primers and probes, improves reproducibility and quantification. Low-temperature homogeneous detection during or following non-symmetric PCR amplification, preferably LATE-PCR, utilizing fluorescent DNA dye and indirectly excitable labeled mismatch-tolerant probes permits analysis of complex targets. Sequencing sample preparation methods following LATE-PCR amplifications reduce complexity and permit “single-tube” processing.

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Номер записи: 3
01-03-2012 дата публикации

Compositions, Kits, and Methods for Predicting Anti-Cancer Response to Anthracyclines

Номер: US20120052079A1
Автор: Andrea L. Richardson, Zhigang C. Wang
Принадлежит: Dana Farber Cancer Institute Inc

The present invention is based, in part, on the discovery that amplification of human chromosome 8q22-23 regions and over-expression of 8q22-23 genes (e.g., LAPTM4B and YWHAZ) is associated with and predictive of resistance to anthracycline-type chemotherapy. Accordingly, the invention relates to compositions, kits, and methods for predicting the response of cancer cells, e.g., breast, prostate, lung, ovarian, pancreatic, liver, and colon malignancies to anthracyclines.

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Номер записи: 4
29-03-2012 дата публикации

Method for Detecting and Quantitating Multiple-Subcellular Components

Номер: US20120075453A1
Автор: Michael Kilpatrick, Triantafyllos Tafas
Принадлежит: Ikonisys Inc

A method for detecting and quantitating multiple and unique fluorescent signals from a cell sample is provided. The method combines immunohistochemistry and a fluorescent-labeled in situ hybridization techniques. The method is useful for identifying specific subcellular components of cells such as chromosomes and proteins.

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Номер записи: 5
05-04-2012 дата публикации

Cell Analysis On Microfluidic Chips

Номер: US20120082978A1
Автор: Carina Debes-Marun, Christopher Backhouse, Govind Kaigala, Linda Pilarski, Patrick Pilarski, Vincent Sieben
Принадлежит: University of Alberta

The present invention provides for a method of implementing fluorescent in situ hybridization (FISH) or other cellular analysis processes using intact cells within a microfluidic, chip-based, apparatus. The invention further provides for a method of cellular immobilization within a microfluidic device. Also provided is a method for automated analysis of FISH or other cellular analysis using discrete colormetric probes.

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Номер записи: 6
03-05-2012 дата публикации

Encapsulated reagents and methods of use

Номер: US20120107834A1
Автор: Lee H. Angros
Принадлежит: Individual

The present invention contemplates use of encapsulated aqueous and non-aqueous reagents, solutions and solvents and their use in laboratory procedures. These encapsulated aqueous or non-aqueous reagents, solutions and solvents can be completely contained or encapsulated in microcapsules or nanocapsules that can be added to an aqueous or non-aqueous carrier solution or liquid required for medical and research laboratory testing of biological or non-biological specimens.

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Номер записи: 7
03-05-2012 дата публикации

Dual polarity analysis of nucleic acids

Номер: US20120108443A9
Автор: Elazar Rabbani, James J. Donegan
Принадлежит: Enzo Life Sciences Inc

This invention provides methods for characterizing the amounts of nucleic acids, including plus/minus determinations, the use of different constructs, the use of a library and a reference library. Expression may also be compared in two or more samples using the methods of this invention. Also provided are heterophasic arrays comprising labeled positive copies of nucleic acids hybridized to the array and labeled negative copies of nucleic acids hybridized to the array, in which the labeled positive copies are separately quantifiable from the labeled negative copies.

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Номер записи: 8
03-05-2012 дата публикации

Methods and apparatus for nanoparticle-assisted nucleic acid hybridization and microarray analysis

Номер: US20120108451A1
Автор: Lin Wang, Paul Chi Hang Li
Принадлежит: SIMON FRASER UNIVERSITY

The invention provides nucleic acid hybridization methods for detecting target nucleic acid sequences wherein complexes comprising nanoparticles non-covalently associated with single-stranded tartlet nucleic acid molecules are incubated with immobilized probe nucleic acid molecules. Because the nanoparticles function as competitors in the hybridization reaction between the target nucleic acid molecules and the probe nucleic acid molecules. The methods provide a high degree of discrimination between a perfectly matched target sequence and a sequence having at least a single-base-pair mismatch, even when the hybridization reaction is performed at room temperature. The invention also provides microarray methods and apparatus which incorporate the nanoparticle-assisted hybridization methods.

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Номер записи: 9
10-05-2012 дата публикации

Method of analyzing genetically abnormal cells

Номер: US20120115146A1
Автор: Kiyohiko Hatake, Takashi Abe, Yuji Mishima
Принадлежит: JAPANESE FOUNDATION FOR CANCER RESEARCH, Olympus Corp

The present invention relates to a method for analyzing genetically abnormal cells including (a) preparing a cell sample containing eukaryotic cells, (b) conducting an antigen-antibody reaction to cells contained in the cell sample using antibodies which specifically bind to a molecule existing on the cell surface of eukaryotic cells after (a), (c) subjecting the cells contained in the cell sample to a permeation treatment after (b), (d) subjecting the cells contained in the cell sample to an immobilization treatment after (b), (e) conducting FISH to the cells contained in the cell sample using nucleic acid probes after (d), (f) analyzing fluorescence signals from the nucleic acid probes in the cells contained in the cell sample using a three-dimensional image analysis method after (e), and (g) determining whether the cells contained in the cell sample are genetically abnormal cells or not based on the results of (b) and (f).

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Номер записи: 10
14-06-2012 дата публикации

Methods of evaluating cells and cell cultures

Номер: US20120149013A1
Автор: Stephen J. Duguay, Stephen M. Rapko
Принадлежит: Genzyme Corp

Methods of evaluating the composition of a cell culture (e.g., to distinguish chondrocytes from fibroblasts) and methods for evaluating the phenotype of an individual cell (e.g., as a chondrocyte) are disclosed. The methods may be used, for example, for assessing chondrocyte cultures used for treatment of cartilage defects. In some embodiments, the invention involves identifying cell culture composition or the identity of a cell based on expression level of a fibroblast marker. In other embodiments, the invention involves comparing expression levels of at least one chondrocyte marker and at least one fibroblast marker in a cell culture sample or in an individual cell. In illustrative embodiments, the chondrocyte marker is hyaluronan and proteoglycan link protein 1 (HAPLN1), and the fibroblast marker is microfibrillar associated protein 5 (MFAP5).

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Номер записи: 11
28-06-2012 дата публикации

Methods and compositions for detection of small rnas

Номер: US20120164651A1
Автор: Brian H. Johnston, Pavan Kumar, Sergei A. Kazakov
Принадлежит: Individual

Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5′-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences. Our invention also reduces number of steps and reagents while increasing sensitivity and accuracy of detection of small RNAs with both 2′OH and 2′-OMe at their 3′ ends. Our invention increase sensitivity and specificity of detection of microRNAs and other small RNAs with both 2′OH and 2′-OMe at their 3′ ends while allowing us to distinguish these two forms from each other.

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Номер записи: 12
05-07-2012 дата публикации

Systems and devices for isothermal biochemical reactions and/or analysis

Номер: US20120171756A1
Автор: Ali Nadim, Anna Hickerson, Christopher Cooney, II Robert W. Doebler, James D. Sterling
Принадлежит: Individual

An isothermal reaction and analysis system may include a receiver to receive sample holders, a thermal control subsystem to control a temperature of the receiver, an excitation subsystem, a detection subsystem and an analysis subsystem. Excitation sources and/or detectors are positioned to enhance data collection. Sample holders may include filters, selectively blocking and passing wavelengths or bands of electromagnetic radiation.

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Номер записи: 13
26-07-2012 дата публикации

Generic Matrix for Control Nucleic Acids

Номер: US20120190010A1
Автор: Andreas Woelfelschneider, Dirk Zimmermann, Eberhard Russmann, Meike Eickhoff
Принадлежит: Roche Molecular Systems Inc

The present invention belongs to the field of in-vitro diagnostics. Within this field, it particularly concerns the amplification of at least a first target nucleic acid that may be present in at least one fluid sample using an internal control nucleic acid for qualitative and/or quantitative purposes and at least one external control nucleic acid in an aqueous buffer. It further provides an analytical system comprising an internal control nucleic acid for qualitative and/or quantitative purposes and at least one external control nucleic acid in an aqueous buffer.

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Номер записи: 14
30-08-2012 дата публикации

Presence of ERG Gene Rearrangements and Protein Over-expression in Low Grade PIN (LG-PIN) in Prostate Biopsies

Номер: US20120220672A1
Автор: Alexandra Dea Nagy, Connie CORTEZ, Gary Pestano, Karl Garsha, Ray NAGLE, Ryan DITTAMORE, Ubaradka SATHYANARAYANA
Принадлежит: Ventana Medical Systems Inc

The present disclosure relates to methods for the early detection of ERG over-expression, gene rearrangements, and diagnosis and/or prognosis of prostate cancer using a combined ERG IHC-FISH assay.

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Номер записи: 15
27-09-2012 дата публикации

GENE EXPRESSION ANALYSIS METHOD USING TWO DIMENSIONAL cDNA LIBRARY

Номер: US20120245053A1
Автор: Hideki Kambara, Kiyomi Taniguchi, Masataka Shirai
Принадлежит: HITACHI LTD

The present invention provides a method and/or means for collecting and analyzing an individual cell in a tissue, and at the same time, quantitatively monitoring the expression levels of various genes while keeping two-dimensional information in the tissue. Specifically, the present invention provides a method comprising preparing a cDNA library from mRNA while keeping two-dimensional cellular distribution information and obtaining the gene expression levels at any site or all sites at a level of single cell. More specifically, the present invention provides a method comprising preparing a cDNA library in a sheet-form from mRNA while keeping two-dimensional cellular distribution information and repeatedly using the cDNA library in the detection of the gene expression, thereby allowing measurement of the expression distribution for a number of genes at a high accuracy.

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Номер записи: 16
04-10-2012 дата публикации

Methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction

Номер: US20120252686A1
Автор: Gregory Porreca, Mark Umbarger
Принадлежит: Good Start Genetics Inc

The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a solution including a template nucleic acid, introducing an identifier nucleic acid to the solution, incorporating the same barcode sequence into the template and the identifier nucleic acids, and sequencing the template and the identifier nucleic acids.

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Номер записи: 17
18-10-2012 дата публикации

Solutions, methods and kits for deactivating nucleic acids

Номер: US20120260951A1
Автор: Daniel L. Kacian, James Russell, Kenneth A. Browne, Lizhong Dai, Margarita B. Kaminsky, Mark E. Filipowsky, Norman C. Nelson
Принадлежит: Gen Probe Inc

The present invention relates to reagents for use in deactivating nucleic acids and methods of making and using the same.

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Номер записи: 18
01-11-2012 дата публикации

Kit for detection of microorganism

Номер: US20120277121A1
Автор: Shinichi Yoshida, Takashi Soejima
Принадлежит: Morinaga Milk Industry Co Ltd

A kit for use in a method for detecting live cells, injured cells and dead cells of a microorganism in a test sample by a nucleic acid amplification method is disclosed. The kit includes a cross-linker capable of cross-linking DNA by irradiation with light having a wavelength of 350 nm to 700 nm, medium, and a primer (s) for amplifying a DNA target region in the microorganism by a nucleic acid amplification method. The nucleic acid amplification method may be a PCR, LAMP, SDA, LCR or DNA microarray method. A cross-linker may be included in the kit such as ethidium monoazide, ethidium diazide, psoralen, 4,5′,8-trimethyl psoralen, or 8-methoxy psoralen.

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Номер записи: 19
15-11-2012 дата публикации

Cartridge for conducting a chemical reaction

Номер: US20120288924A1
Автор: Douglas B. Dority, Farzad Pourahmadi, Kurt E. Peterson, Ronald Chang, William A. McMillan
Принадлежит: Cepheid

A cartridge for conducting a chemical reaction includes a body having at least one flow path formed therein. The cartridge also includes a reaction vessel extending from the body for holding a reaction mixture for chemical reaction and optical detection. The vessel comprises a rigid frame defining the side walls of a reaction chamber. The frame includes at least one channel connecting the flow path to the chamber. The vessel also includes flexible films or sheets attached to opposite sides of the rigid frame to form opposing major walls of the chamber. In addition, at least two of the side walls are optically transmissive and angularly offset from each to permit real-time optical detection of analyte in the reaction chamber.

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Номер записи: 20
06-12-2012 дата публикации

Microchip for nucleic acid amplification reaction and a method of manufacturing the same

Номер: US20120309084A1
Автор: Hidetoshi Watanabe, Tasuku Yotoriyama, Tomoteru Abe
Принадлежит: Sony Corp

To provide a microchip for a nucleic acid amplification reaction which allows high-precision analysis by a simple method. There is provided a microchip A for a nucleic acid amplification reaction including an entrance through which a liquid enters from the outside, a plurality of wells configured to function as reaction sites of nucleic acid amplification reaction, and flow channels through which the liquid entered from the entrance is fed into each of the wells, in which a plurality of reagents needed for the reaction are laminated and anchored in a prescribed order in each well.

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Номер записи: 21
06-12-2012 дата публикации

Oligonucleotide sequence formula for labeling oligonucleotide probes and proteins for in-situ analysis

Номер: US20120309951A1
Автор: John F. Connaughton, Joseph G. Utermohlen
Принадлежит: Ventana Medical Systems Inc

The present invention provides oligonucleotide probes and oligonucleotide probe collections for detecting or localizing a plurality nucleic acid target genes within a cell or tissue sample. Specifically, the invention provides collections of oligonucleotide probes for use in in situ hybridization analyses in which each probe has a label-domain with the sequence formulas of (CTATTTT) n CT, (AAAATAG) n or (TTTTATC) n or (GATAAAA) n in which all cases “n” would equal 1 or greater. The present invention also provides collections or “cocktails” of oligonucleotide probes for detecting or localizing specific nucleic acid target genes within a cell or tissue sample.

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Номер записи: 22
20-12-2012 дата публикации

Development of Novel Detergents for Use in PCR Systems

Номер: US20120322066A1
Автор: Jonathan Wang, Parul Angrish, Zhiwei Yang
Принадлежит: Life Technologies Corp

This disclosure relates to novel detergents for use in various procedures including, for example, nucleic acid amplification reactions such as polymerase chain reaction (PCR). Methods for preparing the modified detergents are also described.

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Номер записи: 23
31-01-2013 дата публикации

Methods and uses involving genetic abnormalities at chromosome 12

Номер: US20130029337A1
Автор: Annamari Ranki, Kai Krohn, Leena Karenko, Markku Helle, Paivi Peltomaki, Sonja Hahtola, Wael Hassan
Принадлежит: UNIVERSITY OF HELSINKI

The present invention relates to the fields of genetics and oncology and provides methods for predicting and identifying tumors of epithelial origin. Specifically, the present invention relates to a novel method of predicting tumor initiation, tumor progression and/or carcinomas, the method comprising detecting genetic abnormality associated with tumors of epithelial origin. The present invention further relates to a novel method of identifying an individual with potential for developing carcinoma, the method comprising detection of genetic abnormalities. The present invention also relates to a method of predicting the progression of carcinomas and the transformation thereof to an aggressive variant, the method comprising detection of genetic abnormalities, which indicate the probability to develop carcinoma. The present invention also relates to a use of specific chromosomal region, a gene or a fragment thereof, and/or genetic markers for predicting tumor initiation, tumor progression and/or carcinoma. The present invention also relates to a use of specific chromosomal region or a gene or a fragment thereof in therapy, for the development of therapy, and for the preparation of a medicament for treating tumors of epithelial origin.

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Номер записи: 24
07-02-2013 дата публикации

Chamber free nanoreactor system

Номер: US20130034880A1
Автор: Mark F. Oldham
Принадлежит: Individual

Aspects of the invention include methods for improving the accuracy and read length of sequencing reactions by utilizing unlabeled unincorporable nucleotides, or by rephasing colony based sequencing reactions. Other aspects include systems and devices for improved measurement of biological reactions associated with bead which may be removed, utilizing current measurement methods through the counter ions associated with said beads due to the presence of reactants bound or associated with said bead, wherein electrodes for generating and measuring said current may be within the Debye length of said bead. Other aspects of the invention include methods for determining concentrations of input samples, means for reuse of an array, methods and apparatus for separating beads with different charge levels from each other.

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Номер записи: 25
21-02-2013 дата публикации

Methods of Polynucleotide Detection

Номер: US20130045166A1
Автор: Allen T. Christian, G. David Grothaus, Jianping Xu, Larry A. Gilbertson, Mingqi Deng, R. Douglas Sammons, Ryan K. Bartlett, Sonya J. Franklin
Принадлежит: MONSANTO TECHNOLOGY LLC

The present invention provides methods of detecting for the presence of a polynucleotide in vivo. These methods are particularly useful for performing identification and/or analysis of samples or specimens in which it is impossible, impractical, or undesirable to move or remove them from their current environment. Methods of practicing the present invention for the purpose of identifying and/or analyzing transgenic plant tissue or cells, in addition to animal tissue or cells and bacterial cells are also provided.

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Номер записи: 26
07-03-2013 дата публикации

Translocation and mutant ros kinase in human non-small cell lung carcinoma

Номер: US20130059305A1
Автор: Ailan Guo, Anthony Possemato
Принадлежит: Cell Signaling Technology Inc

In accordance with the invention, a novel gene translocation, (4p15, 6q22), in human non-small cell lung carcinoma (NSCLC) that results in a fusion proteins combining part of Sodium-dependent Phosphate Transporter Isoform NaPi-3b protein (SLC34A2) with Proto-oncogene Tyrosine Protein Kinase ROS Precursor (ROS) kinase has now been identified. The SLC34A2-ROS fusion protein is anticipated to drive the proliferation and survival of a subgroup of NSCLC tumors. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ROS kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides. The disclosed identification of the new fusion protein enables new methods for determining the presence of these mutant ROS kinase polypeptides in a biological sample, methods for screening for compounds that inhibit the proteins, and methods for inhibiting the progression of a cancer characterized by the mutant polynucleotides or polypeptides, which are also provided by the invention.

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Номер записи: 27
14-03-2013 дата публикации

METHODS FOR SCREENING Th2 INFLAMMATORY DISEASES

Номер: US20130065972A1
Автор: Dent Alexander L., Sawant Deepali
Принадлежит: INDIANA UNIVERSITY RESEARCH AND TECHNOLOGY CORPORATION

The present invention provides a method for screening for a Th2 inflammatory disease in a subject comprising the steps of: assaying a miR-21 expression level in a biological sample from the subject, and comparing the miR-21 expression level in the biological sample from the subject to the miR-21 expression level in a control, wherein an increase in the miR-21 expression level in the biological sample from the subject compared to the miR-21 expression level in the control indicates the presence of Th2 inflammatory disease in the subject. 1. A method of screening for a Th2 inflammatory disease in a subject , the method comprising the steps of:assaying miR-21 expression level in a biological sample from the subject by at least one of quantitative PCR, a microarray, or in situ hybridization; andcomparing miR-21 expression level in the biological sample from the subject to miR-21 expression level in a control; anddetermining the subject has a Th2 inflammatory disease if there is an increase in miR-21 expression level in the biological sample from the subject compared to miR-21 expression level in the control.2. The method of claim 1 , further comprising the step of developing a treatment plan if the increase in miR-21 expression level in the biological sample from the subject is at least 5-fold compared to miR-21 expression level in the control.3. The method of claim 1 , wherein the biological sample is selected from the group consisting of blood claim 1 , serum claim 1 , a biopsy sample claim 1 , a tissue sample claim 1 , a cell suspension claim 1 , saliva claim 1 , oral fluid claim 1 , cerebrospinal fluid claim 1 , lymph claim 1 , urine claim 1 , gastric fluid claim 1 , synovial fluid claim 1 , mucus claim 1 , sputum claim 1 , and mixtures thereof.4. The method of claim 1 , wherein the disease is selected from the group consisting of allergic asthma claim 1 , eosinophilic esophagitis claim 1 , allergic rhinitis claim 1 , atopic dermatitis claim 1 , and combinations ...

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Номер записи: 28
21-03-2013 дата публикации

METHODS, PROBE SETS, AND KITS FOR DETECTION OF DELETION OF TUMOR SUPPRESSOR GENES BY FLUORESCENCE IN SITU HYBRIDIZATION

Номер: US20130071843A1
Автор: Squire Jeremy A., Yoshimoto Maisa
Принадлежит:

Methods, probe sets, kits, and compositions for gene deletion assays are disclosed. In some embodiments, the methods relate to preparing probes for a deletion assay, performing a deletion assay, or optimizing a deletion assay. In some embodiments, the methods and probe sets can provide reduced artifactual deletion frequency, for example, when analyzing samples subject to truncation artifacts. In some embodiments, the methods and probe sets can distinguish between small and large deletions. 1. A method of preparing a probe set for a FISH-based tumor suppressor deletion assay , the method comprising:(a) identifying at least one boundary zone on a chromosome, said chromosome comprising a tumor suppressor gene, wherein the at least one boundary zone comprises a first boundary zone centromeric to the tumor suppressor gene;(b) providing at least a first flanking probe that hybridizes to a nucleic acid sequence within the first boundary zone or to a nucleic acid sequence distal to the tumor suppressor gene relative to the first boundary zone;(c) providing at least a second flanking probe that hybridizes to a nucleic acid sequence telomeric to the tumor suppressor gene; and(d) providing at least one target probe that hybridizes to a nucleic acid sequence in the tumor suppressor gene between the boundary zones.2. A method of conducting a FISH-based assay for deletion of a tumor suppressor gene comprising:(a) performing FISH with a probe set on a cellular sample comprising a plurality of cells,wherein the probe set comprises at least a first flanking probe that hybridizes to a position centromeric to the tumor suppressor gene, at least a second flanking probe that hybridizes to a position telomeric to the tumor suppressor gene, and at least one target probe that hybridizes to the tumor suppressor gene;(b) enumerating FISH signals from the at least first and at least second flanking probes and the at least one target probe in the plurality of cells;(c) providing at least one ...

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Номер записи: 29
21-03-2013 дата публикации

Compositions, Kits, and Methods for Identification, Assessment, Prevention, and Therapy of Cancer

Номер: US20130072392A1
Автор: Cameron Brennan, Giovanni Tonon, John D. Shaughnessy, JR., Kenneth C. Anderson, Lynda Chin, Ronald A. DePinho, Ruben D. Carrasco
Принадлежит: Dana Farber Cancer Institute Inc, University of Arkansas

The invention relates to compositions, kits, and methods for detecting, characterizing, preventing, and treating human cancer. A variety of chromosomal regions (MCRs) and markers corresponding thereto, are provided, wherein alterations in the copy number of one or more of the MCRs and/or alterations in the amount, structure, and/or activity of one or more of the markers is correlated with the presence of cancer.

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Номер записи: 30
28-03-2013 дата публикации

Biomarkers for Ulcerative Colitis and Crohn's Disease

Номер: US20130079245A1
Автор: Alsobrook John, Davis Lisa, Harris Cole
Принадлежит: Exagen Diagnostics, Inc.

The present invention provides compositions and their use in diagnosing ulcerative colitis, Crohn's Disease, and inflammatory bowel disease. 1. A biomarker consisting of between 2 and 35 different nucleic acid probe sets , including:(a) a first probe set that selectively hybridizes under high stringency conditions to a nucleic acid target selected from the group consisting of IGH (SEQ ID NO:11, 12, 13, 14, 15, and/or 16), MMD (SEQ ID NO:2), PDLIM1 (SEQ ID NO:3), PDIA6 (SEQ ID NO:4), CD4 (SEQ ID NO:5), DNAJA1 (SEQ ID NO:6), HBA2 (SEQ ID NO:7), RBM4 (SEQ ID NO:8), QARS (SEQ ID NO:9), WIPF1 (SEQ ID NO:10), or full complements thereof; and(b) a second probe set that selectively hybridizes under high stringency conditions to a nucleic acid target selected from the group consisting of IGH (SEQ ID NO:11, 12, 13, 14, 15, and/or 16), MMD (SEQ ID NO:2), PDLIM1 (SEQ ID NO:3), PDIA6 (SEQ ID NO:4), CD4 (SEQ ID NO:5), DNAJA1 (SEQ ID NO:6), HBA2 (SEQ ID NO:7), RBM4 (SEQ ID NO:8), QARS (SEQ ID NO:9), WIPF1 (SEQ ID NO:10), or full complements thereof,wherein the first probe set and the second probe set do not selectively hybridize to the same nucleic acid target.2. The biomarker of claim 1 , including a third probe set that selectively hybridizes under high stringency conditions to a nucleic acid target selected from the group consisting of IGH (SEQ ID NO:11 claim 1 , 12 claim 1 , 13 claim 1 , 14 claim 1 , 15 claim 1 , and/or 16) claim 1 , MMD (SEQ ID NO:2) claim 1 , PDLIM1 (SEQ ID NO:3) claim 1 , PDIA6 (SEQ ID NO:4) claim 1 , CD4 (SEQ ID NO:5) claim 1 , DNAJA1 (SEQ ID NO:6) claim 1 , HBA2 (SEQ ID NO:7) claim 1 , RBM4 (SEQ ID NO:8) claim 1 , QARS (SEQ ID NO:9) claim 1 , WIPF1 (SEQ ID NO:10) claim 1 , or full complements thereof claim 1 ,wherein none of the first probe set, the second probe set, and the third probe set selectively hybridize to the same nucleic acid target.3. The biomarker of claim 2 , including a fourth probe set that selectively hybridizes under high stringency ...

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Номер записи: 31
04-04-2013 дата публикации

Nucleic Acid Analysis Reaction Cell and Nucleic Acid Analyzer

Номер: US20130084629A1
Автор: Inaba Ryoji, Nagaoka Yoshihiro, Nakazawa Taro, Narahara Masatoshi, Togashi Shigenori
Принадлежит: HITACHI HIGH-TECHNOLOGIES CORPORATION

A nucleic acid analysis reaction cell and a nucleic acid analyzer are provided, in which a uniform flow rate is realised, so that a portion where a flow rate is low is removed and washing time for reagent removal is shortened. 1. A nucleic acid analysis reaction cell comprising:a flow path including a detection area for detecting sequence information of a nucleic acid fragment and detection outer areas disposed at both ends of the detection area, whereinan inflow port is provided in one of the detection outer areas and an outflow port is provided in the other of the detection outer areas,the detection outer areas disposed at both the ends of the detection area are areas whose widths become narrow toward ends, andbranch members for branching a liquid are provided in at least the detection outer area in which the inflow port is provided.2. A nucleic acid analysis reaction cell comprising:a flow path including a detection area for detecting sequence information of a nucleic acid fragment and detection outer areas disposed at both ends of the detection area, whereinan outflow port is provided in one of the detection outer areas and an inflow port is provided in the other of the detection outer areas,the detection outer areas disposed at both the ends of the detection area are areas whose widths become narrow toward ends, anda liquid is branched in the detection outer area in which the inflow port is provided.3. The nucleic acid analysis reaction cell according to claim 1 , wherein flow rates of respective flow paths divided by the branch members are made almost uniform.4. The nucleic acid analysis reaction cell according to claim 1 , wherein the branch members are disposed at specified intervals in a direction perpendicular to a direction directed from the inflow port to the outflow port.5. The nucleic acid analysis reaction cell according to claim 1 , wherein the branch members are disposed at equal intervals in a direction perpendicular to a direction directed from ...

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Номер записи: 32
11-04-2013 дата публикации

Microfluidic flow cell

Номер: US20130089920A1
Автор: Bruce K. Gale, Carl T. Wittner, Scott O. Sundberg
Принадлежит: University of Utah Research Foundation UURF

A microfluidic flow cell having a body with a fluid transport channel disposed therein, the fluid transport channel having a proximal end and a distal end defining a fluid flow path, a fluid inlet port disposed at the proximal end of the fluid transport channel at a central portion of the body and an outlet port disposed at the distal end of the fluid transport channel at an outer portion of the body, and a plurality sample wells disposed in the fluid transport channel substantially perpendicular to the fluid flow path in the fluid transport channel. The microfluidic flow cell may have hundreds or thousands of individual, sub-microliter sample wells. The microfluidic flow cell can be filled by applying a flowable liquid to the inlet port and spinning the flow cell to cause fluid to flow into fluid transport channel.

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Номер записи: 33
18-04-2013 дата публикации

Self-sustained fluidic droplet cassette and system for biochemical assays

Номер: US20130096035A1
Автор: Samuel Yang, Seungkyung Park, Tza-Huei Wang, Yi Zhang
Принадлежит: JOHNS HOPKINS UNIVERSITY

A fluidic cartridge for biochemical assays includes a cartridge body defining a first droplet region and a second droplet region with a droplet restraining barrier therebetween. The droplet restraining barrier has a gap between the first and the second droplet regions. The fluidic cartridge also includes a first droplet dispensed in the first droplet region. The first droplet includes a plurality of magnetic particles dispersed therein. The fluidic cartridge also includes a second droplet disposed in the second droplet region. The plurality of magnetic particles are sufficiently small to be drawn through the gap between the first and second droplet regions when compelled by an applied magnetic field, and the first droplet is restrained by the restraining barrier while the plurality of magnetic particles are drawn through the gap. A biochemical assay system includes a stage adapted to receive a fluidic cartridge, and a magnetic control assembly that includes a magnet. The magnet of the magnetic control assembly is movable to direct motion of magnetic particles contained within the fluidic cartridge.

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Номер записи: 34
25-04-2013 дата публикации

CROSSLINKED POLYNUCLEOTIDE STRUCTURE

Номер: US20130101512A1
Автор: Cutler Joshua I., Giljohann David A., Mirkin Chad A., Thaxton C. Shad
Принадлежит:

The present invention provides structures formed from crosslinked polynucleotides, where a subset of the polynucleotides binds to a target under physiological conditions, where the signal group detectably changes upon binding. 1. A structure formed from crosslinked polynucleotides , comprising:a plurality of crosslinkable polynucleotides that are crosslinked; where a subset of the crosslinkable polynucleotides are binding polynucleotides that are sufficiently complementary to a target to allow them to hybridize under physiological conditions;a plurality of signaling moieties hybridized to at least some of the binding polynucleotides in the structure, where each signaling moiety comprise either a quencher or a signal group attached to a signal polynucleotide which is sufficiently complementary to the binding polynucleotide to allow it to hybridize under physiological conditions,when the signaling moiety comprises the quencher, then the signal group is bound to the structure, or when the signaling moiety comprises the signal group, then the quencher is bound to the structure;where lack of hybridization leads to a detectably change in the signal.2. The structure of claim 1 , which is metal free.3. The structure of claim 1 , which is hollow.4. The structure of claim 1 , further comprising a spacer claim 1 , wherein the crosslinkable polynucleotides are crosslinked through the spacer.5. The structure of claim 1 , where the quencher is bound to the structure.6. The structure of claim 1 , where the signal is bound to the structure.7. The structure of claim 1 , wherein the crosslinkable polynucleotides are crosslinked via amine claim 1 , amide claim 1 , alcohol claim 1 , ester claim 1 , aldehyde claim 1 , ketone claim 1 , thiol claim 1 , disulfide claim 1 , carboxylic acid claim 1 , phenol claim 1 , imidazole claim 1 , hydrazine claim 1 , hydrazone claim 1 , azide claim 1 , or alkyne groups.8. The structure of claim 7 , wherein the crosslinkable polynucleotides are ...

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Номер записи: 35
16-05-2013 дата публикации

RNA Interactome Analysis

Номер: US20130123123A1
Автор: Ci Chu, Howard Yuan-Hao Chang
Принадлежит: Leland Stanford Junior University

A method of sample analysis is provided. In certain cases, the method comprises: a) cross-linking the contents of a cell using a heat stable crosslinking agent to produce cross-linked ribonucleotide complexes; b) fragmenting the cross-linked ribonucleotide complexes to produce complexes comprising protein, RNA fragments and, optionally, genomic DNA fragments; c) contacting the complexes with a plurality of non-overlapping oligonucleotides comprise an affinity tag and that are complementary to a specific target RNA of the cell under high stringency conditions that include high temperature; d) isolating complexes that contain the oligonucleotides using the affinity tag to produce isolated complexes; e) enzymatically releasing the protein, RNA fragments and/or the genomic DNA fragments from the isolated complexes to produce a released component, without reversing the crosslinking; and f) analyzing the released component.

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Номер записи: 36
30-05-2013 дата публикации

Methods for nucleic acid manipulation

Номер: US20130137145A1
Автор: Frank Salinas, Stephen J Benkovic
Принадлежит: PENN STATE RESEARCH FOUNDATION

A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.

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Номер записи: 37
30-05-2013 дата публикации

SYSTEMS AND METHODS FOR PERFORMING AMPLICON RESCUE MULTIPLEX POLYMERASE CHAIN REACTION (PCR)

Номер: US20130137594A1
Автор: Bertrand Jeff, Han Jian
Принадлежит:

Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data. The control element is further configured to analyze the test data received from the reader and to produce an output indicative of a comparison of the test data to predefined data. 1. A system , comprising:a self-contained cassette containing a nucleic acid sample and having a movable pipette; anda processor configured to receive and manipulate the cassette for performing polymerase chain reaction (PCR) on the nucleic acid sample, the processor configured to move the pipette and to heat the nucleic acid sample during the PCR.2. The system of claim 1 , wherein the cassette comprises a cam bar connected to the pipette claim 1 , wherein the processor has a cam bar shaft engaged with the cam bar claim 1 , wherein rotation of the cam bar shaft rotates the cam bar causing the pipette to move.3. The system of claim 1 , wherein the processor causes the cassette to deposit nucleic acids on a microarray within the cassette.4. The system of claim 1 , wherein the cassette is associated with an identifier claim 1 , wherein the processor ...

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Номер записи: 38
06-06-2013 дата публикации

Oligonucleotide Trapping

Номер: US20130143208A1
Автор: Beliveau Brian, Wu Chao-Ting
Принадлежит: President and Fellows of Harvard College

Novel methods and compositions for identifying one or more factors associated with a nucleic acid sequence (e.g., DNA and/or RNA) of interest are provided. 1. A method for identifying one or more factors associated with a nucleic acid sequence of interest comprising the steps of:providing a biological sample including a nucleic acid sequence of interest;contacting the biological sample with a plurality of oligonucleotide paints, wherein the oligonucleotide paints include a targeting moiety, and wherein substantially all of the oligonucleotide paints have a unique nucleotide sequence relative to one another;allowing the oligonucleotide paints to bind to the nucleic acid sequence of interest;allowing the targeting moiety to bind to the one or more factors; andidentifying the one or more factors bound to the targeting moieties of the oligonucleotide paints.2. The method of claim 1 , wherein the one or more factors are selected from the group consisting of a protein claim 1 , a peptide claim 1 , a carbohydrate claim 1 , a lipid claim 1 , a chemical moiety and any combination of these.3. The method of claim 1 , wherein the oligonucleotide paints are between about 20 and about 32 base pairs in length.4. The method of claim 1 , wherein the oligonucleotide paints are between about 32 and about 40 base pairs in length.5. The method of claim 1 , further comprising the step of retrieving the oligonucleotide paint prior to the step of identifying.6. The method of claim 5 , wherein the oligonucleotide paint further includes a retrievable moiety.7. The method of claim 6 , wherein the retrievable moiety is one component of a binding pair.8. The method of claim 6 , wherein the retrievable moiety is biotin.9. The method of claim 6 , wherein the oligonucleotide paint is retrieved by binding the retrievable moiety.10. The method of claim 1 , wherein the targeting moiety is inert until activation.11. The method of claim 10 , wherein activation is selected from the group consisting of ...

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Номер записи: 39
06-06-2013 дата публикации

Methods and compositions for high yield, specific amplification

Номер: US20130143219A1
Автор: Aoy Tomita Mitchell, Mats Hidestrand, Michael Mitchell
Принадлежит: MEDICAL COLLEGE OF WISCONSIN

The present invention is directed to methods and compositions for amplifying nucleic acids. Included in the present invention are methods and compositions that amplify nucleic acids with high yield with the formation of unstable target extension products, preferably with minimal or no introduction of allelic bias. Also included in the present invention are high yield, instability primers for use in amplification methods, as multiplexed amplification methods.

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Номер записи: 40
06-06-2013 дата публикации

METHODS FOR MULTIPLEXING AMPLIFICATION REACTIONS

Номер: US20130143754A1
Автор: Best Elaine, Gerdes John C., Marmaro Jeffery M.
Принадлежит: APPLIED BIOSYSTEMS, LLC

A two-step multiplex amplification reaction includes a first step which truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid. In particular, nucleic acid sequences that uniquely identify were identified using the multiplex amplification method. 1. A method for simultaneously amplifying multiple nucleic acid sequence targets contained in a sample of nucleic acids by an amplification method comprising:(a) contacting the sample with at least two primer pairs that target different nucleic acid sequences;(b) pre-amplifying the sample wherein the reaction plateau is not reached;(c) dividing said pre-amplified sample into at least two distinct chambers(d) amplifying said divided pre-amplified sample with at least one of said primer pairs;(e) detecting at least one target sequence in the divided pre-amplified sample.2. The method of claim 1 , wherein said sample is DNA.3. The method of claim 1 , wherein said sample is RNA.4. The method of claim 1 , wherein said pre-amplifying step is accomplished using polymerase chain reaction.5. The method of claim 1 , wherein said amplifying step is accomplished using polymerase chain reaction.6. The method of claim 1 , wherein said pre-amplifying step is accomplished using isothermal methodology.7. The method of claim 1 , wherein said amplifying step is accomplished using isothermal methodology.8. The method of claim 1 , wherein said pre-amplifying step is accomplished using nucleic acid sequence based amplification.9. The method of claim 1 , wherein said amplifying step is accomplished using nucleic acid sequence based amplification ...

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Номер записи: 41
13-06-2013 дата публикации

METHODS AND KITS FOR ROOM TEMPERATURE IN SITU DETECTION OF A TARGET NUCLEIC ACID IN A BIOLOGICAL SAMPLE

Номер: US20130149705A1
Автор: Aurich-Costa Joan
Принадлежит: CELLAY, INC.

The present invention relates to in situ hybridization methods for detecting a target nucleic acid in a biological sample comprising performing one or more method steps (e.g., pretreatment, denaturation, hybridization, washes) at room temperature. The invention further relates to kits for performing such methods. 1. A method for detecting a target nucleic acid in a biological sample , comprising the steps of:a) pretreating a biological sample comprising the target nucleic acid with a solution comprising a protease at a temperature in the range of about 19 degrees Celsius to about 25 degrees Celsius;b) denaturing the sample;c) hybridizing at least one probe to the target nucleic acid in the sample, wherein the probe comprises a nucleotide sequence that is substantially complementary to a nucleotide sequence in the target nucleic acid and at least one detectable label;d) washing the sample to remove probes that have not hybridized to the target nucleic acid; ande) detecting the at least one detectable label on the oligonucleotide probe following hybridization to the target nucleic acid, thereby detecting the target nucleic acid in the sample.2. The method of claim 1 , wherein the solution in a) comprises about 0.1 to about 0.3% pepsin.3. The method of claim 2 , wherein the solution in a) has an acidic pH.4. The method of claim 3 , wherein the solution in a) comprises 0.01N HCl.5. A method for detecting a target nucleic acid in a biological sample claim 3 , comprising the steps of: 1) is present in a hybridization buffer comprising about 1-10 mM base and having a pH in the range of about 10 to about 13, and', '2) comprises a nucleotide sequence that is substantially complementary to a nucleotide sequence in the target nucleic acid and at least one detectable label;, 'a) hybridizing at least one probe to the target nucleic acid in the sample at a temperature in the range of about 19 degrees Celsius to about 25 degrees Celsius, wherein the probeb) washing the sample to ...

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Номер записи: 42
13-06-2013 дата публикации

SOLID GEL AMPLIFICATION METHOD AND APPARATUS FOR GENOTYPING AND PATHOGEN DETECTION

Номер: US20130149709A1
Автор: Acker Jason, Atrazhev Alexey
Принадлежит: THE GOVERNORS OF THE UNIVERSITY OF ALBERTA

The present invention provides for a novel system and method for amplification and detection of nucleic acids within a miniaturized device. 1. A method for detecting a nucleic acid molecule within a hydrogel post array comprisinga) providing a hydrogel post array of 2×1 or greater containing a cell-free, enzymatic, nucleic-acid amplification system;b) applying to at least one of said hydrogel posts nucleic acid molecules of, at least one of which may comprise a template for said amplification system;c) incubating said hydrogel posts under conditions promoting the synthesis of an amplified nucleic acid product by said amplification system from said at least one template;wherein said amplification system comprises at least two non-immobilized nucleic acids, capable of promoting synthesis of amplified nucleic acid product from said template.2. The method of wherein the hydrogel posts contain a marker claim 1 , wherein said marker has different properties claim 1 , capable of being measured claim 1 , when interacting with double-stranded nucleic acids than with single-stranded nucleic acids.3. The method of wherein said measurement is in real-time and the fluorescent marker is selected from the group comprising LC Green claim 2 , SYBR Green or SYTO 62.4. The method of wherein said hydrogel post is comprised of polyacrylamide of 2.0-12% weight per unit volume claim 3 , and photopolyrnerized in the absence of APS.5. The method of wherein said template is included in said hydrogel posts.6. The method of wherein said template is provided externally to said hydrogel posts.7. The method of wherein the template is between 3 claim 1 ,800 and 250 claim 1 ,000 claim 1 ,000 base pairs in size.8. A method for detecting a nucleic acid molecule within a hydrogel post array comprisinga) providing a hydrogel post array of 2×1 or greater containing a cell-free, enzymatic, nucleic-acid amplification system;b) including nucleic acid molecules in at least one of said hydrogel posts, at ...

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Номер записи: 43
13-06-2013 дата публикации

Reagents and methods for direct labeling of nucleotides

Номер: US20130150254A1
Автор: Jiang Ying, Link-Cole Ryan, Naleway John J.
Принадлежит:

The present invention provides systems and methods for production of activatable diazo-derivatives for use in labeling nucleotides. Labeling nucleotides is accomplished by contacting a stable hydrazide derivative of a detectable moiety with an activating polymer reagent which is used to directly label the nucleotide sample. Labeling occurs on the phosphate backbone of the nucleotide which does not perturb hybridization of the labeled nucleotide with its anti-sense strand. Since the method involves direct labeling, all types of nucleotides can be labeled without prior amplification or alteration. 2. The method of claim 1 , wherein the analyte is selected from the group consisting of phosphate claim 1 , carboxylic acid claim 1 , boronate claim 1 , nucleotide claim 1 , deoxynucleotide claim 1 , oligonucleotide and oligodeoxynucleotide.3. The method of claim 2 , wherein said nucleotide claim 2 , deoxynucleotide claim 2 , oligonucleotide or oligodeoxynucleotide comprises a nucleotide base selected from the group consisting of adenine claim 2 , thymidine claim 2 , cytosine claim 2 , guanine claim 2 , uridine claim 2 , purine and pyrimidine.4. The method of claim 2 , wherein said nucleotide is a constituent of a DNA or RNA polynucleotide.5. The method of claim 1 , wherein said detectable moiety is selected from the group consisting of a dye claim 1 , a fluorochrome claim 1 , an enzyme claim 1 , a chemiluminescent compound claim 1 , biotin claim 1 , digoxigenin claim 1 , avidin claim 1 , streptavidin claim 1 , an antibody and a lectin.6. The method of claim 1 , wherein said linking group comprises less than twenty carbon atoms.7. The method of claim 6 , wherein the carbon atoms of the linking group (L) are non-branched.8. The method of claim 1 , wherein said linking group comprises four carbon atoms and one heteroatom.9. The method of claim 8 , wherein the heteroatom is selected from the group consisting of oxygen and nitrogen.10. The method of claim 1 , wherein said ...

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Номер записи: 44
20-06-2013 дата публикации

Self-Contained Biological Analysis

Номер: US20130157349A1
Автор: David E. Jones, Gary Clark Kessler, Kirk M. Ririe, Mark Aaron Poritz, Michael R. Newswander, Randy P. Rasmussen, Stewart Benjamin Smith
Принадлежит: Biofire Diagnostics Inc

Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include nucleic acid amplification and detection and immuno-PCR.

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Номер записи: 45
04-07-2013 дата публикации

Sequence Specific Real-Time Monitoring of Loop-Mediated Isothermal Amplification (LAMP)

Номер: US20130171643A1
Автор: Jenkins Daniel M., Kubota Ryo
Принадлежит: UNIVERSITY OF HAWAII

Gene-based diagnostics capable of rapidly discriminating selected strains of a selected pathogen from other populations within the same species are disclosed. Sequence-specific, real-time monitoring of LAMP of DNA may be accomplished through the use of oglionucleotide probes, referred to as “assimilating probes.” The assimilating probes include two oglionucleotide strands, one which includes a quencher (referred to as the quenching probe) and another which includes a fluorophore (referred to as the fluorescent probe). A fluorescent signal results when the two strands are displaced from one another during the LAMP reaction. By monitoring the emitted fluorescence, sequence specific amplification may be detected. 1. A method of monitoring LOOP-mediated isothermal amplification (LAMP) of a target DNA , comprising:contacting an assimilating probe and a DNA polymerase with a LAMP reaction mixture,wherein the LAMP reaction mixture comprises the target DNA and one or more LAMP primers that hybridize with the target DNA,wherein the assimilating probe comprises a first and second oligonucleotide strands, wherein the first oligonucleotide strand comprises a quencher probe at a 3′ end and wherein the second oligonucleotide strand of the assimilating probe comprises a fluorophore at a 5′ end;wherein the ratio of the amount of the second oligonucleotide strand to the amount of the first oligonucleotide strand is less than 1:1;andmeasuring fluorescence emitted by the LAMP reaction mixture that has been contacted with the assimilating probe and the DNA polymerase.2. The method of claim 1 , wherein the quencher comprises DABCYL claim 1 , TAMRA claim 1 , or a Black Hole Quencher.3. The method of claim 1 , wherein the fluorophore comprises fluorescein claim 1 , cy3 claim 1 , cy5 claim 1 , or one or more quantum dots.4. The method of claim 1 , wherein the first oligonucleotide strand and the second oligonucleotide strand are not hybridized with each other.5. The method of claim 1 , ...

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Номер записи: 46
11-07-2013 дата публикации

SAMPLE PREPARATION FOR IN SITU NUCLEIC ACID ANALYSIS, METHODS AND COMPOSITIONS THEREFOR

Номер: US20130177905A1
Автор: Fekete Richard A., NGUYEN ANNALEE
Принадлежит: APPLIED BIOSYSTEMS, LLC

Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms. 154.-. (canceled)55. A kit for preparing a sample containing RNA for in situ analysis of RNA or a surrogate thereof , the kit comprising lysis mixture components ,wherein the lysis mixture components comprise a polypeptide having deoxyribonuclease activity and a surfactant that substantially lacks fluorescence between 300 nm and 750 nm when in use for in situ analysis of RNA or a surrogate thereof,wherein the lysis mixture components are substantially free of a cation chelator, wherein the cation chelator is EDTA.56. The kit of further comprising reagents for reverse transcription.57. The kit of further comprising a ribonuclease inhibitor.58. A process for preparing a sample containing nucleic acid for in situ analysis of nucleic acid or a surrogate thereof claim 55 , the process comprising:contacting the sample containing nucleic acid with a lysis mixture under conditions and for a time to produce a lysate,admixing the lysate with a stop mixture at substantially the same temperature as the contacting step to form a stopped mixture compatible with nucleic acid polymerase reaction conditions, andcontacting the stopped mixture with reagents for nucleic acid polymerization to form a first amplification reaction.59. The process of wherein the sample contains RNA and the nucleic acid polymerase is a reverse transcriptase.60. The process of wherein the sample contains DNA and the nucleic acid polymerase is a DNA polymerase.61. The process of wherein contacting the sample with a lysis mixture is for a time of 2 minutes to 30 minutes ...

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Номер записи: 47
18-07-2013 дата публикации

LABELED REACTANTS AND THEIR USES

Номер: US20130183663A1
Автор: Korlach Jonas, Wegener Jeffrey
Принадлежит: Pacific Biosciences of California, Inc.

Labeled reactant compositions, and particularly labeled nucleic acid reaction compositions, that include structural components that maintain potentially damaging labeling components sufficiently distal from the reactant portion of the molecule such that damaging effects of the label group on other reaction components, such as enzymes, are reduced, minimized and/or eliminated. 1. A method of monitoring an enzyme reaction , comprising:providing a reaction mixture comprising the enzyme and at least a first reactant composition, the reactant composition comprising a compound having (i) a reactant component comprising a nucleotide, (ii) a fluorescent label component, and (iii) a linker component joining the reactant component to the label component, wherein the linker component is coupled to the reactant component through a phosphate group on the nucleotide, and the linker component maintains the label component at a functional distance away from the reactant component such that a reduction in the activity of the enzyme is reduced by at least 20%;illuminating the reaction mixture to excite the fluorescent label component; anddetecting a fluorescent signal from the reaction mixture characteristic of the enzyme reaction.2. The method of claim 1 , wherein a reduction in the activity of the enzyme is reduced by at least 50%;3. The method of claim 1 , wherein a reduction in the activity of the enzyme is reduced by at least 90%;4. The method of claim 1 , wherein a reduction in the activity of the enzyme is a photo induced decrease in enzyme activity.5. The method of claim 1 , wherein the linker component maintains the label component at. a functional distance of at least 2 nm from the reactant component.6. The method of claim 1 , wherein the linker component maintains the label component at a functional distance of at least 5 nm from the reactant component.7. The method of claim 1 , wherein the linker component maintains the label component at a functional distance of at least ...

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Номер записи: 48
25-07-2013 дата публикации

In Situ Cloning From Pathological Tissue Specimens

Номер: US20130189698A1
Автор: Eberwine James H., Kelz Max B.
Принадлежит: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA

The present invention pertains to methods related to cloning nucleic acids from biological samples, particularly pathological tissue samples. This method includes hybridizing a population of oligonucleotide sequence probes comprising degenerate sequence tags to a fixed tissue, isolating the hybridized oligonucleotide sequence probes and amplifying the sequence tags in the hybridized oligonucleotide sequence probes. This method can be utilized to identify genes associated with disease and to quantitate the expression of disease-related transcripts. The method can also be used to identify truncated mRNAs. 1. A method of cloning a nucleic acid from a biological sample comprising:(a) providing a population of oligonucleotide sequence probes, wherein each of said oligonucleotide sequence probe comprises a sequence tag flanked by a 5′-end extension sequence and a 3′-end extension sequence, wherein said sequence tag is a degenerate sequence and wherein at least one of said 5′-end extension sequence and said 3′-end extension sequence comprises a detection sequence;(b) hybridizing said population of oligonucleotide sequence probes with said nucleic acid in said biological specimen, thereby forming a population of hybridized oligonucleotide sequences probes and a population of unhybridized oligonucleotide sequence probes;(c) washing away said population of unhybridized oligonucleotide sequence probes; and(d) isolating said population of hybridized oligonucleotide sequence probes thereby forming an isolated population of hybridized oligonucleotide sequence probes, thereby cloning said nucleic acid from said biological sample.2. The method of claim 1 , further comprising the step of:(e) amplifying said isolated population of hybridized oligonucleotide sequence probes to produce a population of amplified fragments comprising sequence tags.3. A method of Obtaining a cell or tissue of interest from a biological specimen claim 1 , said method comprising:(a) providing a population ...

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Номер записи: 49
08-08-2013 дата публикации

METHODS AND KITS FOR IN SITU DETECTION OF NUCLEOTIDE SEQUENCES

Номер: US20130203055A1
Автор: Aurich-Costa Joan
Принадлежит:

The present invention relates to in situ hybridization methods comprising a room temperature hybridization step for detecting a target nucleic acid in a biological sample. The invention further relates to kits for performing such methods. 1. A method for determining whether a target nucleic acid is present in a biological sample , comprising the steps of:a) contacting the sample with a solution comprising a base and about 50% to about 80% alcohol;b) incubating at least one single-stranded oligonucleotide probe with the sample at a temperature in the range of about 19 degrees Celsius to about 25 degrees Celsius, wherein the oligonucleotide probe comprises a nucleotide sequence that is substantially complementary to a nucleotide sequence in the target nucleic acid and at least one detectable label; andc) determining whether the target nucleic acid is present in the sample by detecting one or more oligonucleotide probes that have hybridized to the target nucleic acid in the sample.2. The method of claim 1 , wherein the base is present in the solution of step a) at a concentration of about 0.03N to about 0.17N.3. The method of claim 2 , wherein the base is sodium hydroxide.4. The method of claim 3 , wherein step a) is performed at a temperature of about 19 degrees Celsius to about 25 degrees Celsius.5. The method of claim 3 , wherein step a) is performed at a temperature of about 21 degrees Celsius.6. The method of claim 4 , wherein the sample is contacted with the solution for about 3 to about 20 minutes in step a).7. The method of claim 4 , wherein the sample is contacted with the solution for about 11 to about 17 minutes in step a).8. The method of claim 4 , wherein the sample is contacted with the solution for about 13 to about 15 minutes in step a).9. The method of claim 8 , wherein the solution in step a) comprises about 0.07M sodium hydroxide.10. The method of claim 9 , wherein the solution in step a) comprises about 70% ethanol.11. The method of claim 10 , ...

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Номер записи: 50
08-08-2013 дата публикации

SET OF OLIGONUCLEOTIDE PROBES AS WELL AS METHODS AND USES THERETO

Номер: US20130203628A1
Автор: Bergmann Frank, Eberle Walter, Fischer Thomas, von der Eltz Herbert
Принадлежит: ROCHE DIAGNOSTICS OPERATIONS, INC.

The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further, the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component. 1. A set of oligonucleotide probes for detecting a genomic target of interest , the set comprising at least 100 oligonucleotide probes , the oligonucleotide probes each comprising a different nucleotide sequence directed to a different subsequence of the genomic target sequence of interest , each oligonucleotide probe comprising at least one label attached to one of a base , a sugar , and a phosphate moiety of a nucleotide.2. The set of claim 1 , wherein the set comprises one of at least 200 claim 1 , 300 claim 1 , 400 claim 1 , 500 claim 1 , and 1 claim 1 ,000 different oligonucleotide probes.3. The set of claim 1 , wherein the oligonucleotide probes each comprise a length of at least 20 to not greater than 200 nucleotides claim 1 , and wherein each oligonucleotide probe comprises at least two labels.4. (canceled)5. The set of claim 3 , wherein the at least two labels of each of the oligonucleotide probes are disposed at about equally spaced positions.6. The set of claim 5 , wherein the at least two labels of each of the oligonucleotide probes are positioned at locations separated by between 10 to 20 nucleotides.7. (canceled)8. The set of claim 1 , wherein the label is attached to the one of the base claim 1 , the sugar claim 1 , and the phosphate moiety of the nucleotide indirectly via a linker.9. (canceled)10. The set of claim 1 , wherein the label is detectable by one of a chromogenic reaction and a metallographic reaction.11. The set of claim 1 , wherein ...

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Номер записи: 51
15-08-2013 дата публикации

HELICASE DEPENDENT ISOTHERMAL AMPLIFICATION USING NICKING ENZYMES

Номер: US20130210019A1
Автор: Grosshauser Gerd, Himmelreich Ralf, Korfhage Christian, Rothmann Thomas
Принадлежит: QIAGEN GmbH

The present invention relates to a method for amplifying a template nucleic acid, wherein the method comprises amplifying said template nucleic acid using the helicase dependent amplification (HDA) reaction in the presence of a nicking endonuclease, and wherein said template nucleic acid comprises a sequence recognized by said nicking endonuclease or a sequence recognized by said nicking endonuclease is introduced into the template nucleic acid during the HDA reaction. The invention further pertains to a kit for amplifying a nucleic acid, comprising a nicking endonuclease, a helicase and a DNA polymerase. 1. A method for amplifying a template nucleic acid ,Wherein the method comprises amplifying said template nucleic acid using the helicase dependent amplification (HAD) reaction in the presence of a nicking endonuclease, andWherein said template nucleic acid comprises a sequence recognized by said nicking endonuclease or a sequence recognized by said nicking endonuclease is introduced into the template nucleic acid during the HAD reaction, wherein the HAD reaction is a thermophilic HAD (tHDA), wherein the sequence recognized by a nicking endonuclease is introduced into the template nucleic acid using an oligonucleotide primer comprising the sequence recognized by a nicking endonuclease and wherein the amplified sequence or sequences are shorter than 400 bp.2. The method according to claim 1 , wherein said primer comprising the sequence recognized by a nicking endonuclease comprises a 5′ tag sequence that does not hybridize to the template nucleic acid and the sequence recognized by a nicking endonuclease is in said tag sequence.3. The method according to claim 1 , wherein the template nucleic acid is a double-stranded template nucleic acid claim 1 , preferably a DNA.4. The method according to claim 1 , wherein the helicase is selected from the group consisting of superfamily I helicases such as dda claim 1 , perA claim 1 , F-plasmid traI protein helicase and UvrD ...

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Номер записи: 52
22-08-2013 дата публикации

Production of closed linear dna using a palindromic sequence

Номер: US20130216562A1
Автор: Angus Knight, Karen Oliver, Kinga KARBOWNICZEK, Lisa Caproni, Neil Porter
Принадлежит: Touchlight Genetics Ltd

A primer for the amplification of a DNA template comprising a protelomerase target sequence, particularly for production of closed linear DNA, which primer is capable of specifically binding to a palindromic sequence within a protelomerase target sequence and priming amplification in both directions.

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Номер записи: 53
22-08-2013 дата публикации

EXTERNAL FILES FOR DISTRIBUTION OF MOLECULAR DIAGNOSTIC TESTS AND DETERMINATION OF COMPATIBILITY BETWEEN TESTS

Номер: US20130217013A1
Автор: Larsen Mark, Steel Adam, Wojeck Thomas, Young Mike
Принадлежит: BECTON, DICKINSON AND COMPANY

Embodiments disclosed herein relate to methods and systems for performing an automated assay, and particularly to performing an assay on a plurality of samples on an automated instrument. 1. A method of performing an automated assay on a plurality of samples , said method comprising:providing an automated instrument comprising a first workstation and a second workstation, each of said first and second workstations configured to receive and processes a plurality of samples according to a plurality of different automated assay workflows, wherein each different automated assay workflow has an associated unique assay definition or user-defined protocol file;determining whether two discrete assay workflows are compatible or incompatible with each other for concurrent processing on the automated instrument; andperforming said discrete assay workflows concurrently on said instrument when said assays are compatible.2. The method of claim 1 , wherein said assay definition or user defined protocol file comprises a first level compatibility index value claim 1 , and wherein said determining step comprises:(a) selecting a first assay from among a first list of available assays; and(b) evaluating which of a plurality of other available assays have an assay definition file comprising the same first level compatibility index value as said first assay, wherein the same first level compatibility index value is indicative of first-level compatibility.3. The method of claim 2 , wherein said evaluating step comprises:(b1) identifying any assays which have first level compatibility index values different from the first compatibility index value of said first assay; and(b2) providing a second list of second assays, wherein said second list excludes any assay having a first level compatibility index value different from the first compatibility index value of said first assay.4. The method of claim 2 , wherein each assay definition file comprises a second level compatibility index value ...

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Номер записи: 54
22-08-2013 дата публикации

MICROFLUIDIC CARTRIDGE

Номер: US20130217026A1
Автор: Bienvenue Joan, Egan Michael, Hayes Jason, Kinnon Paul, LANDERS James, Root Brian, Saul David, SCOTT Orion N., Solomon Matthew, SOUTH Douglas J., SPRINGER Matthew, Tsuei An-Chi, van Ruijven Peter
Принадлежит:

A microfluidic cartridge can include at least one nucleic acid analysis portion. Each nucleic acid analysis portion can include a fluidic network being configured for micro-liter volumes or less, a sample input at the beginning of the fluidic network, a plurality of vent ports and fluidic channels in the fluidic network configured to effectuate hydrodynamic movement within the fluidic network, an extraction mixture reservoir in the fluidic network, a mixing chamber in the fluidic network, an amplification chamber in the fluidic network, and a separation channel in the fluidic network. A nucleic acid analyzer can be capable of performing nucleic acid analysis using the microfluidic cartridge. A nucleic acid analysis method can be performed using the microfluidic cartridge. 1. A microfluidic cartridge , comprising:at least one nucleic acid analysis portion, each nucleic acid analysis portion including:a fluidic network defined within the nucleic acid analysis portion, the fluidic network being configured for micro-liter volumes or less;a sample input at a beginning of the fluidic network, the sample input having a fitting that is configured to be mated to a complementary fitting of a sample acceptor to form a fluid-tight seal;a plurality of vent ports and fluidic channels in the fluidic network configured to effectuate hydrodynamic movement within the fluidic network;an extraction mixture reservoir in the fluidic network, the extraction mixture reservoir being configured to hold an enzymatic mixture for performing nucleic acid extraction on a sample provided by the sample acceptor;a mixing chamber in the fluidic network, the mixing chamber being configured to mix amplification reagents and a portion of an extracted nucleic acid mixture; andan amplification chamber in the fluidic network, the amplification chamber being configured to hold an amplification mixture during nucleic acid amplification.2. The microfluidic cartridge of claim 1 , wherein at least a major ...

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Номер записи: 55
22-08-2013 дата публикации

Methods and compositions for performing nucleic acid amplification reactions

Номер: US20130217071A1
Автор: Luz Montesclaros, Paul Wyatt
Принадлежит: Bio Rad Laboratories Inc

The present disclosure provides methods and compositions for performing nucleic acid reactions, such as the reverse transcriptase-polymerase chain reaction (RT-PCR).

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Номер записи: 56
29-08-2013 дата публикации

METHOD FOR ISOTHERMAL AMPLIFICATION OF NUCLEIC ACIDS

Номер: US20130224799A1
Автор: Korfhage Christian
Принадлежит: QIAGEN GmbH

A method is disclosed for improved isothermal amplification of nucleic acids comprising the step of release of an essential component from a matrix under predetermined conditions. Furthermore, the invention relates to a kit comprising mesophilic enzyme and a matrix with embedded essential components for isothermal amplification. A composition comprising a matrix and a mesophilic enzyme and a method for embedding a mesophilic enzyme are disclosed as well. 1. A method for isothermal amplification of nucleic acids comprising the steps of: a) a mesophilic enzyme for amplifying nucleic acids under isothermal conditions;', 'b) one or more primer for amplifying a target nucleic acid;', 'c) dNTPs and/or NTPs;', 'd) essential co-factors and/or reagents of the enzyme for amplifying nucleic acids under isothermal conditions;', 'e) at least one target nucleic acid;', 'wherein at least one of the reaction components a) to e) is embedded in a matrix, wherein said matrix disintegrates at temperatures of 60° C. or more, preferably 65° C. or more;, 'i) providing at least the following reaction componentsii) incubating the reaction components under conditions which result in the disintegration of said matrix in order to obtain the reaction mixture;iii) incubating the reaction mixture under conditions suited for the isothermal amplification reaction;wherein the incubation temperature under step ii) is 1° C. to 50° C. higher than the incubation temperature of step iii), preferably 5° C. to 25 ° C. higher, more preferably 10° C. to 20° C. higher.2. The method according to claim 1 , wherein the mesophilic enzyme for amplifying nucleic acids has an optimum temperature of 20° C. to 70° C. claim 1 , preferably 30° C. to 65° C. claim 1 , more preferably 37° C. to 60° C.3. The method according to claim 1 , wherein the matrix forms a hydrogel.4. The method according to claim 1 , wherein the matrix is selected from the group comprising polysaccharides (agarose claim 1 , low-melting agarose ...

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Номер записи: 57
12-09-2013 дата публикации

Phage Phi 29 DNA Polymerase Chimera

Номер: US20130236886A1
Автор: Jose M. Lazaro Bolos, Luis Blanco Davila, Margarita Salas Falgueras, Mario Mencia Caballero, Miguel DE VEGA JOSÉ
Принадлежит: Consejo Superior de Investigaciones Cientificas CSIC

A DNA polymerase chimera comprising an amino-terminal (N-terminal) region encoding a φ29 type DNA polymerase and a carboxyl-terminal (C-terminal) region comprising at least one HhH domain which are bound by a connecting amino acid sequence is disclosed along with and the use thereof for replicating, amplifying or sequencing a template DNA. Also disclosed is a method for replicating, amplifying or sequencing a deoxyribonucleic acid with a DNA polymerase chimera and kits for carrying out the methods.

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Номер записи: 58
03-10-2013 дата публикации

Method for detecting the presence of a dna minor contributor in a dna mixture

Номер: US20130260380A1
Автор: Diana Hall, Vincent Castella
Принадлежит: Centre Hospitalier Universitaire Vaudois CHUV

The present invention concerns a method of detecting the presence of a DNA minor contributor in a DNA mixture by determining several haplotypes present in said one or more DNA samples.

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Номер записи: 59
03-10-2013 дата публикации

Thermal cycler and control method of thermal cycler

Номер: US20130260421A1
Автор: Akemi Yamaguchi, Hiroshi Koeda
Принадлежит: Seiko Epson Corp

An attachment unit for attachment of a reaction container including a channel filled with a reaction solution and a liquid having a specific gravity different from that of the reaction solution and being immiscible with the reaction solution, the reaction solution moving close to opposed inner walls, a first heating unit that heats a first region of the channel and a second heating unit that heats a second region of the channel when the reaction container is attached to the attachment unit, a drive mechanism that switches arrangement of the attachment unit, the first heating unit, and the second heating unit between a first arrangement and a second arrangement in which a lowermost position of the channel is located within a first region and a second region, respectively, and a control unit that controls the drive mechanism, the first heating unit, and the second heating unit are provided.

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Номер записи: 60
17-10-2013 дата публикации

METHOD FOR CHROMOGENIC DETECTION OF TWO OR MORE TARGET MOLECULES IN A SINGLE SAMPLE

Номер: US20130273540A1
Автор: Bieniarz Christopher A., Farrell Michael, Gaire Fabien, Gniewek Richard, Grogan Thomas, Kelly Brian Daniel, Kosmeder Jerome II W., Lehrkamp Megan, Nitta Hiro, Padilla Mary
Принадлежит:

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. 3. The method of claim 2 , wherein the electron-rich aromatic compound comprises naphthol.4. The method of claim 3 , where the naphthol concentration is effective to allow dual nucleic acid and protein detection in a single sample and ranges from 1 milligrams per milliliter to 30 milligrams per milliliter.5. The method of claim 3 , where the naphthol concentration is effective to allow dual nucleic acid and protein detection in a single sample and ranges from 1 milligrams per milliliter to 7 milligrams per milliliter.6. The method of claim 3 , where the naphthol concentration ranges from about 0.3 milligrams per milliliter to about 1 milligram per milliliter.7. The method of claim 1 , where the hapten of the hapten-labeled nucleic acid probe is a nitroaryl compound.8. The method of claim 7 , where the nitroaryl compound is dinitrophenol.9. The method of claim 8 , where the concentration of the dinitrophenol nucleic acid-labeled probe is at least 5 μg/ml.10. The method of claim 9 , where the concentration of the ...

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Номер записи: 61
17-10-2013 дата публикации

NUCLEIC ACID AMPLIFICATION REACTION STATION FOR DISPOSABLE TEST DEVICES

Номер: US20130273644A1
Автор: Barnes Bryan W., Catazariti Luigi, Colin Bruno, Cotter Christopher, Dachaud Jacque, Gennari Fabio, Graziano Louis, Guy Michel, McKinley Geoff A., Paris Cecile
Принадлежит: bioMerieux, Inc.

An instrument for conducting nucleic acid amplification reactions in a disposable test device is provided. The test device includes a first reaction chamber containing a first nucleic acid amplification reagent (e.g., primers and nucleotides) and a second reaction chamber either containing, or in fluid communication, with a second nucleic acid amplification reagent (e.g., an amplification enzyme such as RT). The instrument includes a support structure receiving the test device. A temperature control system maintains the first reaction chamber at a first elevated temperature but simultaneously maintains the second nucleic acid amplification reagent at a second temperature lower than the first temperature so as to preserve the second nucleic acid amplification reagent. An actuator operates on a fluid conduit in the test device to place the first and second reaction chambers in fluid communication with each other after a reaction has occurred in the first reaction chamber at the first temperature. A pneumatic system is also provided that assists in fluid transfer of a reaction solution from the first chamber to the second chamber. 120-. (canceled)21. A disposable nucleic acid amplification test device for insertion into an amplification station conducting an amplification reaction using the test device , the test device comprising:a body defining a first chamber for receiving a sample and a second chamber for conducting a nucleic acid amplification reaction therein, wherein the sample is transferred from the first chamber to the second chamber;a valve controlling the transfer of the sample from the first chamber to the second chamber; anda barrier between the environment and the sample after addition of the sample to the first chamber;wherein the portion of the body of the test device defining the second chamber has an external configuration sized and shaped so as to place the second chamber into thermal contact with controlled heating elements provided in the ...

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Номер записи: 62
24-10-2013 дата публикации

METHOD, DEVICE AND TEST KIT FOR MOLECULAR-BIOLOGICAL REACTIONS

Номер: US20130280695A1
Автор: Daskalow Katjana, Graser Elmara, Hillebrand Timo
Принадлежит: AJ INNUSCREEN GMBH

The invention relates to a device, method and test kit for carrying out molecular-biological reactions, wherein the different components for the molecular-biological reactions are located on a solid carrier in different, spatially separated compartments prior to the start of the reaction. The carrier is preferably a porous filter disk made of polyethylene. Fields of application are the amplification of nucleic acids, for example PCR or RealTime PCR, the reverse transcription of RNA in DNA enzyme-substrate interactions or antigen-antibody interactions, or protein synthesis. 1. A device for performing a molecular-biological reaction , comprising:individual reaction components; anda solid support material;wherein individual reaction components needed for a reaction are present at the same reaction site, but before the reaction are spatially separated from one another on said solid support material, so that an unwanted interaction of the individual reaction components before the reaction start is impossible.2. The device according to claim 1 , wherein the molecular-biological reactions are:a) amplification of nucleic acids, e.g. PCR or real-time PCR, orb) reverse transcription of RNA into DNA, orc) enzyme-substrate interactions, ord) antigen-antibody reactions, ore) protein syntheses.3. The device according to claim 1 , wherein the solid support material is a porous support material.4. The device according to claim 1 , wherein the solid support material has a surface on which the individual reaction components are applied in spatially separated manner.5. The device according to claim 1 , wherein the support comprises of polyethylene.6. The device according to claim 5 , whereinf) primer and enzyme, org) primer, enzyme and probe orh) primer, enzyme, probe and dNTPs, ori) primer, enzyme, probe, dNTPs and buffer orj) enzyme and coenzyme ork) two or more different antibodiesare present on the support in different spatially separated compartments.7. The device according to ...

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Номер записи: 63
31-10-2013 дата публикации

Modified rnase h enzymes and their uses

Номер: US20130288245A1
Автор: Joseph Alan Walder, Joseph Dobosy, Mark Aaron Behlke, Scott D. Rose, Susan Marie Rupp
Принадлежит: Integrated DNA Technologies Inc

The invention provides a provides improvements to assays that employ RNase H cleavage for biological applications related to nucleic acid amplification and detection, where the RNase H has been reversibly inactivated.

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Номер записи: 64
31-10-2013 дата публикации

INSTRUMENTS FOR MIXING THE CONTENTS OF A DETECTION CHAMBER

Номер: US20130288348A1
Автор: Breidenthal Scott S., Fan Sara H., Lee Richard S., NELSON Norman C., Scott Matthew J., Taylor Jason A.
Принадлежит:

A receptacle having a plurality of interconnected chambers arranged to permit multiple process steps or processes to be performed independently or simultaneously. The receptacles are manufactured to separate liquid from dried reagents and to maintain the stability of the dried reagents. An immiscible liquid is included to control loading of process materials, facilitate mixing and reconstitution of dried reagents, limit evaporation, control heating of reaction materials, concentrate solid support materials to prevent clogging of fluid connections, provide minimum volumes for fluid transfers, and to prevent process materials from sticking to chamber surfaces. The receptacles can be adapted for use in systems having a processing instrument that includes an actuator system for selectively moving fluid substances between chambers and a detector. The actuator system can be arranged to concentrate an analyte in a sample. The detector can be used to detect an optical signal emitted by the contents of the receptacle. 1. An instrument for processing a sample in a receptacle having a plurality of interconnected chambers , the instrument comprising:a receptacle-receiving area for receiving the receptacle;a detector having components positioned to detect a light signal from the contents of a detection chamber of the receptacle when the receptacle is placed in an operative position in said receptacle-receiving area, said components comprising a light source and a signal detecting element disposed on the same side of the receptacle-receiving area;at least one movable compression element disposed to be adjacent the detection chamber and situated between the receptacle and said light source and said signal detecting element of said detector when the receptacle is placed in the operative position in said receptacle-receiving area,wherein said compression element is configured to transmit light from said light source to said detection chamber and to transmit light signals from said ...

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Номер записи: 65
14-11-2013 дата публикации

Encapsulated reagents and methods of use

Номер: US20130302803A1
Автор: Lee H. Angros
Принадлежит: Individual

The present invention contemplates use of encapsulated aqueous and non-aqueous reagents, solutions and solvents and their use in laboratory procedures. These encapsulated aqueous or non-aqueous reagents, solutions and solvents can be completely contained or encapsulated in microcapsules or nanocapsules that can be added to an aqueous or non-aqueous carrier solution or liquid required for medical and research laboratory testing of biological or non-biological specimens.

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Номер записи: 66
21-11-2013 дата публикации

METHODS AND COMPOSITIONS FOR NUCLEIC ACID AMPLIFICATION

Номер: US20130309673A1
Автор: ARNOLD, BECKER Michael M., BRENTANO Steven T., CARLSON James D., JR. Lyle J., LYAKHOV Dmitry, NELSON Norman C.
Принадлежит: GEN-PROBE INCORPORATED

Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products. 1. A composition comprising:a TSU promoter oligonucleotide that includes a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to a target sequence contained in a target nucleic acid, wherein the TSU promoter oligonucleotide is a TSU promoter primer that has a 3′ terminus that is capable of being extended by a polymerase, or is a TSU promoter provider oligonucleotide that has a blocked 3′ terminus that is incapable of being extended by a polymerase,a TSU non-promoter primer oligonucleotide made up of a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1, anda means for directly or indirectly joining the TSU promoter oligonucleotide to the TSU non-promoter primer oligonucleotide, thereby forming a target specific universal (TSU) primer complex.2. The composition of claim 1 , wherein the means for directly joining the TSU promoter oligonucleotide to the TSU non-promoter primer oligonucleotide is a covalent linkage.3. The composition of claim 2 , wherein the covalent linkage is formed via a polynucleotide linker sequence.4. The composition of claim 2 , wherein the covalent linkage is formed via a non- ...

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Номер записи: 67
05-12-2013 дата публикации

AMPLIFICATION SYSTEM WITH SPATIAL SEPARATION

Номер: US20130323741A1
Автор: Bernet Roland, Gisler Andreas, Kaeppeli Marcel, Ochsenbein Raymond, Schlaubitz Thomas
Принадлежит: ROCHE MOLECULAR SYSTEMS, INC.

An automated nucleic acid analysis method and analytical system are described comprising separate modules, wherein the air flow of any one of said modules is controlled and wherein at least the air flow between the module for isolation and purification of the analyte and the module for analysis of the analyte are separated. 113-. (canceled)14. A method for isolating and analyzing an analyte present in a fluid sample in an automated analyzer , the method comprising the automated steps of:a) transferring a fluid sample from a sample vessel to a multiwell plate in a sample cell;b) combining together a solid support material and said fluid sample in a well of said multiwell plate for a period of time under conditions sufficient to permit said analyte to be immobilized on the solid support material;c) isolating the solid support material from other material present in the fluid sample of said well in a separation station;d) purifying the analyte in the separation station by washing the solid support material one or more times with a wash buffer and separating the analyte from the solid support material isolated from step c); ande) analyzing said analyte in an amplification cell,wherein steps b) to d) are performed in a process cell of said automated analyzer, and step e) is performed in said amplification cell, wherein said process cell of said automated analyzer comprises a first air flow and said amplification cell comprises a second air flow, the first air flow and the second air flow are separated, and wherein said sample cell has an air flow which is separate from said first air flow of said process cell and said second air flow of said amplification cell, and wherein said sample cell comprises an air pressure that is the same as the air pressure of said process cell.15. The method of claim 14 , wherein said amplification cell comprises an air pressure that is lower than said air pressure of said sample cell and said air pressure of said process cell.16. The method ...

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Номер записи: 68
05-12-2013 дата публикации

Methods for nucleic acid manipulation

Номер: US20130323792A2
Автор: Frank Salinas, Stephen J Benkovic
Принадлежит: PENN STATE RESEARCH FOUNDATION

A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.

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Номер записи: 69
05-12-2013 дата публикации

AMPLIFICATION SYSTEM WITH SPATIAL SEPARATION

Номер: US20130323826A1
Автор: Bernet Roland, Gisler Andreas, Kaeppeli Marcel, Ochsenbein Raymond, Schlaubitz Thomas
Принадлежит: ROCHE MOLECULAR SYSTEMS, INC.

An automated nucleic acid analysis method and analytical system are described comprising separate modules, wherein the air flow of any one of said modules is controlled and wherein at least the air flow between the module for isolation and purification of the analyte and the module for analysis of the analyte are separated. 113-. (canceled)14. An automated analytical apparatus for processing an analyte , comprisinga processing module comprising a separation device for isolating and purifying said analyte, wherein said processing module has a first air flow;a sample module for transferring samples from a sample vessel to a processing vessel;an analytical module for analyzing said analyte contained in said reaction vessel, wherein said analytical module has a second air flow;a transfer system for transferring said reaction vessel comprising said analyte from the processing module to the analytical module;wherein the first air flow and the second air flow are separated, and wherein said sample module has an air flow which is separate from said first air flow of said processing module and said second air flow of said analytical module, and wherein said sample module comprises an air pressure that is the same as the air pressure of said processing module.15. The automated analytical apparatus of claim 14 , wherein said analytical module comprises a second air pressure that is lower than said air pressure of said sample module and said processing module.16. The automated analytical apparatus of claim 14 , wherein an air-lock is located between said processing module and said analytical module.17. The automated analytical apparatus of claim 14 , wherein said apparatus comprises separation walls located between said modules.18. The automated analytical apparatus of claim 14 , wherein said sample module comprises a filter for filtration of air flowing in said sample module.19. The automated analytical apparatus of claim 14 , additionally comprising gaskets in an upper ...

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Номер записи: 70
12-12-2013 дата публикации

METHODS AND COMPOSITIONS FOR DETERMINATION OF VECTOR BACKBONE IN A NUCLEIC ACID SAMPLE

Номер: US20130330733A1
Автор: Fan Chunyang, He Chengkun, Ke John, Russell Doug, Zhong Heng
Принадлежит:

The invention provides methods and compositions for detecting and/or quantifying vector backbone in a nucleic acid preparation comprising a polynucleotide of interest using amplification assays that amplify a junction located between the polynucleotide of interest and the vector backbone, under conditions whereby amplification can occur, wherein the junction comprises a recognition site for a nuclease, and detecting the absence of an amplification product, whereby the absence of the amplification product indicates low or no vector backbone and/or quantifying the amount of amplification product to determine the amount of vector backbone in the nucleic acid preparation. 1. A method of detecting vector backbone in a nucleic acid preparation comprising a polynucleotide of interest (POI) , the method comprising:performing an amplification reaction to amplify a junction located between the POI and a vector backbone, under conditions whereby amplification can occur, wherein the junction comprises a recognition site for a nuclease; anddetecting the absence of an amplification product, whereby the absence of the amplification product indicates low or no vector backbone in said nucleic acid preparation.2. The method of claim 1 , wherein the junction comprises said recognition site linked at one end to a synthetic polynucleotide (SN) claim 1 , and the junction is linked at one end to the POI via the SN and at the other end to the vector backbone via the recognition site and the amplification product comprises the recognition site and at least a portion of the SN.3. The method of claim 2 , wherein the amplifying comprises hybridizing a first oligonucleotide primer to the SN of the junction and hybridizing a second oligonucleotide primer to the vector backbone and the amplification product comprises the recognition site claim 2 , at least a portion of the SN claim 2 , and a portion of the vector backbone.4. The method of claim 1 , wherein the junction comprises said recognition ...

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Номер записи: 71
12-12-2013 дата публикации

UNIVERSAL RANDOM ACCESS DETECTION OF NUCLEIC ACIDS

Номер: US20130331286A1
Автор: Sappenfield Christopher C.
Принадлежит: IBIS BIOSCIENCES, INC.

Provided herein is technology relating to detecting nucleic acids in a sample and particularly, but not exclusively, to systems and methods related to random access primer pair libraries that are used to configure or customize assays for nucleic acid detection. 1. A system for identifying a nucleic acid , the system comprising:a) a random access primer component configured to provide a primer;b) a nucleic acid amplification component configured to amplify a nucleic acid using the primer to generate an amplicon; andc) an amplicon detection component configured to detect a property of the amplicon.2. The system of further comprising an expert system.3. The system of further comprising a conveyance component configured to convey the primer from the random access primer component to the amplification component and/or configured to convey the amplicon from the nucleic acid amplification component to the amplicon detection component.4. The system of further comprising a controller operably connected to one or more of the random access primer component claim 3 , the nucleic acid amplification component claim 3 , the amplicon detection component claim 3 , and/or the conveyance component and configured to effect one or more of conveying the primers from the random access primer component to the nucleic acid amplification component claim 3 , conveying the amplicon from the nucleic acid amplification component to the amplicon detection component claim 3 , amplifying the nucleic acid with the nucleic acid amplification component claim 3 , and/or detecting a property of the amplicon with the amplicon detection component.5. The system of wherein the random access primer component comprises a random access primer library and/or an oligonucleotide synthesis component.6. The system of wherein the nucleic acid amplification component comprises a thermocycler component.7. The system of wherein the amplicon detection component comprises a mass spectrometer component claim 1 , a ...

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Номер записи: 72
12-12-2013 дата публикации

Analyzer and disposable cartridge for molecular in vitro diagnostics

Номер: US20130331298A1
Автор: Larry Rea
Принадлежит: Great Basin Scientific

An in vitro diagnostics analyzer and assay cartridge for carrying out biochemical assays is disclosed. The analyzer includes a tilted clamp assembly for holding an assay cartridge, upper and lower motor assemblies for manipulating the assay cartridge, and an optical reader. The cartridge includes an injection port for receiving a biological sample, a central channel through which the sample passes, one or more processing chambers, one or more reagent containers, a detection chamber, and optionally a waste chamber. The analyzer and cartridge may be used for detection of a variety of analytes, including pathogens for medical diagnostics.

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Номер записи: 73
26-12-2013 дата публикации

Microfluidic Devices

Номер: US20130344475A1
Автор: Blaga Iuliu Ioan, Boronkay Allen, Jovanovich Stevan Bogdan
Принадлежит: INTEGENX INC.

Methods and devices for the interfacing of microchips to various types of modules are disclosed. The technology disclosed can be used as sample preparation and analysis systems for various applications, such as DNA sequencing and genotyping, proteomics, pathogen detection, diagnostics and biodefense. 1. A modular system , comprising:a first module comprising means for capturing and purifying a target analyte and means for introducing said target analyte into a microfluidic device, anda second module comprising said microfluidic device, wherein said microfluidic device is suitable for detecting or analyzing said target analyte.2. The system of claim 1 , wherein said target analyte is selected from the group consisting of a bacterium claim 1 , a virus claim 1 , a spore claim 1 , a eukaryotic cell claim 1 , or a nucleic acid.3. The system of claim 1 , wherein said target analyte is DNA.4. The system of claim 3 , wherein said analyzing comprises sequencing said DNA.5. The system of claim 3 , wherein said analyzing comprises amplifying said DNA.69.-. (canceled)10. A method of lysing or disrupting a target analyte claim 3 , comprising: [ 'flowthrough tube; and', 'a rotating pole piece;'}, 'a magnetic fixed piece,', 'wherein said rotating pole piece, said tube and said fixed pole piece are arranged in a manner and comprise materials suitable for producing a traveling magnetic wave in said flowthrough tube upon rotation of said pole piece; and, 'a) introducing a target analyte and a magnetic bead into the flowthrough tube of the traveling magnetic wave device comprisingb) rotating the pole piece of said device at a frequency suitable for accelerating said magnetic bead in one or more directions within said tube, whereby said bead lyses or disrupts said target analyte.11. The method of claim 10 , wherein said target analyte is selected from the group consisting of a bacterium claim 10 , a spore claim 10 , a virus claim 10 , a eukaryotic cell claim 10 , and a nucleic acid.12. ...

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Номер записи: 74
16-01-2014 дата публикации

METHOD AND KIT FOR DETECTING TARGET NUCLEIC ACID

Номер: US20140017692A1
Автор: KOMIYA Ken
Принадлежит:

[Problem] To provide a method for detecting a nucleic acid (such as DNA and RNA) under isothermal conditions, in particular a method by which a short-chain nucleic acid can be directly detected. [Solution] A method for detecting a target nucleic acid in a sample of the present invention comprises: (a) a step of preparing a first oligonucleotide which comprises, in the direction from 5′ to 3′, a first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence complementary to the target nucleic acid; (b) a step of carrying out a nucleic acid amplification reaction using the target nucleic acid contained in the sample as a primer in the presence of an endonuclease which recognizes the endonuclease recognition site that is used in a nicking reaction; and (c) a step of detecting an oligonucleotide which is obtained by the nucleic acid amplification reaction and comprises a sequence complementary to the first arbitrary sequence. 116-. (canceled)17. A method for detecting a target nucleic acid in a sample , the method comprising:(a) preparing a first oligonucleotide including, in the direction from 5′ to 3′, a first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence complementary to the target nucleic acid; and a second oligonucleotide including, in the direction from 5′ to 3′, a second arbitrary sequence having a sequence substantially homologous to the first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence substantially homologous to the first arbitrary sequence;(b) performing a nucleic acid amplification reaction at a temperature of about 35° C. using the target nucleic acid contained in the sample as a primer in the presence of an endonuclease; and(c) detecting an oligonucleotide obtained by the nucleic acid amplification reaction and having a sequence complementary to the second arbitrary sequence.18. The method ...

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Номер записи: 75
23-01-2014 дата публикации

Methods of detecting dna, rna and protein in biological samples

Номер: US20140024024A1
Автор: Antti Eljas Seppo, Anup Sood, Elizabeth Mary COLLINS, Fiona Mary Ginty, Michael John Gerdes, Wei Gao
Принадлежит: General Electric Co

Novel methods of probing multiple targets in a biological sample are provide whereby the targets are DNA, RNA and protein. The method comprises subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe that binds an RNA target, observing a signal, and optionally removing the signal. The method further comprises an antigen retrieval protocol, observing a signal, removing the signal, and optionally applying a protease treatment to access the sample's DNA targets by subjecting the sample to an in situ hybridization reaction using a labeled nucleic acid probe, observing a signal from the labeled DNA targets, and optionally removing the signal.

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Номер записи: 76
23-01-2014 дата публикации

Method For Determining DNA Fragmentation In Microorganisms

Номер: US20140024031A1
Автор: German Bau Arevalo, Jaime Gosalvez Berenguer, Jose Luis Fernandez Garcia, Lourdes Muriel Rios, Monica Cartelle Gestal, Vicente Goyanes Villaescusa
Принадлежит: Universidad Autonoma de Madrid

The present invention relates to a process for determining the DNA integrity in microorganisms and a kit for evaluating the DNA integrity therein. Due to the fact that cell death means DNA fragmentation, with the present process the DNA fragmentation levels in microorganisms can be clearly discriminated in a simple, quick and accurate manner.

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Номер записи: 77
23-01-2014 дата публикации

Method for Detecting Chromosome Structure and Gene Expression Simultaneously in Single Cells

Номер: US20140024032A1
Автор: Levesque Marshall J., Raj Arjun
Принадлежит: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA

The present invention relates to systems and methods for measuring chromosome structure and gene expression. In one embodiment, the present invention includes an assay for determining the spatial organization of gene expression in the nucleus. The present invention also includes a method based on fluorescence in situ hybridization (FISH) that simultaneously yields information on the physical position and expression of individual genes. By lighting up a large number of targets on a particular chromosome using a bar-coding scheme, the large scale structure of an entire chromosome can be determined. 1. A method for determining the structural conformation of a chromosome in a cell , comprising hybridizing a plurality of target sequences of RNA in the cell with members of at least one set of fluorescently labeled oligonucleotide probes , wherein the plurality of targeted sequences of RNA are transcribed from portions of at least one chromosome , and wherein the pattern of fluorescently labeled probes hybridized to the target sequences of RNA is indicative of the structural conformation of the chromosome.2. The method of claim 1 , wherein the location of the hybridized probes is simultaneously indicative of the chromosomal location of gene expression for the transcribed RNA.3. The method of claim 2 , wherein the number claim 2 , the intensity claim 2 , or both claim 2 , of fluorescing probes is indicative of the level of gene expression at the chromosomal location.4. The method of claim 1 , wherein each set of fluorescently labeled oligonucleotide probe sets are labeled with a different fluorophore resulting in a different and distinguishable color when measurably fluorescent.5. The method of claim of claim 1 , further comprising counting fluorescent spots corresponding to single molecules of target RNA to obtain a gene expression profile corresponding to the simultaneously determined claim 1 , associated chromosomal conformation.6. The method of claim 1 , wherein the ...

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Номер записи: 78
23-01-2014 дата публикации

COMPREHENSIVE FMR1 GENOTYPING

Номер: US20140024035A1
Автор: Choudhary Ashish, Latham Gary, Sah Sachin
Принадлежит: ASURAGEN, INC

Disclosed herein are methods for the automated reconstruction of a genotype of a gene, fragment, or genomic region using exhaustive enumeration. The methods can be used to reconstruct the genotype of any GC-rich sequence, such as the CGG repeat region in the 5′ UTR of FMR1 or the CCG repeat region in the 5′ UTR of FMR2. Also disclosed is an apparatus for use in conducting automated genotype reconstruction, as well as methods of diagnosis and treatment using exhaustive enumeration methods to reconstruct and identify genotypes associated with a disease or disorder. 1. A method of automated reconstruction of a genotype , comprisinga. providing a sample from a patient, wherein the sample comprises a nucleic acid having at least one repeat or GC-rich region;b. determining parameter information for the nucleic acid; andc. using an apparatus to conduct automated exhaustive enumeration on the parameter information to generate a reconstructed genotype.2. The method of claim 1 , wherein determining the parameter information comprises determining a total length of the at least one repeat or GC-rich region claim 1 , a distance in the forward direction to any interruptions in the region claim 1 , and a distance in the reverse direction to any interruptions in the region.3. The method of claim 1 , wherein the parameter information is determined by polymerase chain reaction.4. The method of claim 1 , wherein exhaustive enumeration comprisesa. using the total length of the at least one repeat or GC-rich region and either the distance in the forward direction to any interruptions in the region or the distance in the reverse direction to any interruptions in the region to generate a set of potential genotypes comprising all possible arrangements of the interruptions in the region; andb. evaluating the set of potential genotypes to determine a solution genotype that satisfies all the parameter information.5. The methods of claim 1 , wherein the apparatus comprises a processor and a ...

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Номер записи: 79
30-01-2014 дата публикации

METHOD FOR ENHANCING EFFICIENCY AND SENSITIVITY IN NUCLEIC ACID AMPLIFICATION FROM BIOLOGICAL MATERIALS USING IONIC LIQUIDS

Номер: US20140030719A1
Автор: Chi Sung-min, HWANG Kyu-youn, JUNG Sun-ok, JUNG Sung-ouk, JUNG Won-jong, KIM Joon-ho, KWON Sung-hong
Принадлежит:

A method for amplifying a nucleic acid amplification in the presence of an ionic liquid that suppresses an inhibitor of nucleic acid amplification, particularly when in a biological material, and a composition useful for performing the method. 1. A method for amplifying a nucleic acid , the method comprising: amplifying a nucleic acid in the presence of an ionic liquid.2. The method of claim 1 , comprising amplifying the nucleic acid in the presence of an ionic liquid and a nucleic acid amplification inhibitor claim 1 , and the ionic liquid suppresses the inhibitory effect of the nucleic acid amplification inhibitor.3. The method of claim 1 , wherein the nucleic acid is in a biological material comprising a nucleic acid amplification inhibitor.4. The method of claim 1 , further comprisingadding an ionic liquid to at least one of a biological material comprising a nucleic acid for amplification or a nucleic acid amplification mixture;combining the biological material and the nucleic acid amplification mixture to provide a reaction mixture for nucleic acid amplification; andamplifying the nucleic acid,wherein biological material comprises a nucleic acid amplification inhibitor and the ionic liquid suppresses a nucleic acid amplification inhibitor.6. The method of claim 3 , wherein the biological material comprises a body fluid or tissue claim 3 , which is claim 3 , optionally claim 3 , diluted or dissolved claim 3 , preserved claim 3 , washed claim 3 , or freeze-dried.7. The method of claim 6 , wherein the biological material comprises feces claim 6 , urine claim 6 , blood claim 6 , mucus claim 6 , saliva claim 6 , or sweat claim 6 , body fluid claim 6 , and tissue.8. The method of claim 1 , wherein the concentration of the ionic liquid is about 0.001% (v/v) to about 50% (v/v).9. The method of claim 2 , wherein the nucleic acid amplification inhibitor comprises bile acid claim 2 , bile salts claim 2 , polysaccharides claim 2 , bilirubin claim 2 , heparin claim 2 , ...

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Номер записи: 80
30-01-2014 дата публикации

DUAL REFERENCE CALIBRATION METHOD AND SYSTEM FOR QUANTIFYING POLYNUCLEOTIDES

Номер: US20140030720A1
Автор: CARRICK James M., GILLY Michael J., VIJAYSRI NAIR Sangeetha, Wang Xianqun, YAMAGATA Susan K.
Принадлежит: GEN-PROBE INCORPORATED

Method and system for quantifying target nucleic acids using real-time amplification and internal calibration adjustment. The invention employs dual reference calibration curves for approximating a complete calibration curve from only a single adjustment calibrator amplified on the instrument that is to be calibrated. 1. A method of establishing an adjusted calibration curve for an assay that quantifies an analyte polynucleotide using a local instrument that amplifies nucleic acids and monitors synthesis of amplification products as amplification is occurring , said method comprising the steps of: wherein each of the first and second calibration curves relates normalized indicia of amplification for analyte polynucleotide standards to indicia of amplification for a fixed amount of an internal calibrator polynucleotide that co-amplified therewith as a function of starting amounts of the analyte polynucleotide in amplification reactions of the assay, and', 'wherein each of the calibration curves is different from the other;, '(a) obtaining first and second equations respectively defining first and second calibration curves specific for the assay,'}(b) obtaining an adjustment calibrator comprising an amount of the analyte polynucleotide and said fixed amount of the internal calibrator polynucleotide;(c) co-amplifying, in a nucleic acid amplification reaction carried out with the local instrument, the analyte polynucleotide and the internal calibrator polynucleotide of the adjustment calibrator;(d) determining indicia of amplification for each of the analyte polynucleotide and the internal calibrator polynucleotide of the adjustment calibrator that co-amplified in the nucleic acid amplification reaction;(e) normalizing the determined indicia of amplification for the analyte polynucleotide to the determined indicia of amplification for the internal calibrator polynucleotide of the adjustment calibrator; the difference between the normalized value determined for the ...

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Номер записи: 81
30-01-2014 дата публикации

Exonuclease Enabled Proximity Extension Assays

Номер: US20140030721A1
Автор: Eriksson Anna, Fredriksson Simon, Lundberg Martin, Rennel-Dickens Emma
Принадлежит: OLINK AB

The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a component comprising 3′ exonuclease activity, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) contacting said sample with a component comprising 3′ exonuclease activity; (d) extending the 3′ end of at least one nucleic acid domain of said duplex to generate an extension product, wherein the step may occur contemporaneously with or after step (c); and (e) amplifying and detecting the extension product. 1. A method for detecting an analyte in a sample , comprising:(a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte;(b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex;(c) contacting said sample with a component comprising 3′ exonuclease activity;(d) extending the 3′ end of at least one nucleic acid domain of said duplex to generate an extension product, wherein the step may occur contemporaneously with or after step (c); and(e) amplifying and detecting the extension product.2. The method of claim 1 , wherein said detecting in ...

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Номер записи: 82
30-01-2014 дата публикации

Multiplex detection of molecular species in cells by super-resolution imaging and combinatorial labeling

Номер: US20140031243A1
Автор: Eric Lubeck, Long Cai
Принадлежит: California Institute of Technology CalTech

Methods and systems are provided for creating molecular barcodes or indicia for cellular constituents within single cells and for resolving such barcodes or indicia with super-resolution technologies such as super-resolution microscopy. By this approach, numerous molecular species that can be measured simultaneously in single cells. It has been demonstrated that multiple mRNA transcripts can be labeled with a spatially ordered sequence of fluorophores, and that barcodes can be resolved. In addition, alternative splicing events can be characterized by identifying and quantifying mRNA isoforms in an individual cell.

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Номер записи: 83
06-02-2014 дата публикации

METHOD OF DETERMINING HOMOZYGOTE AND HETEROZYGOTE

Номер: US20140038189A1
Автор: Igata Eishi
Принадлежит: CANON KABUSHIKI KAISHA

In order to accurately determine a homozygote and a heterozygote in a melting curve analysis, provided is an apparatus for detecting a signal from a specimen, the apparatus including a fluidic device including: a fluid path through which the specimen is passable; a reaction unit provided in the fluid path; a heater configured to elevate a temperature of the specimen in the reaction unit so as to perform the melting curve analysis; and a heater driving unit configured to drive the heater. The heater driving unit is configured to drive the heater at a first temperature elevation rate that is equal to or higher than 1° C./s and a second temperature elevation rate that is different from the first temperature elevation rate so that the fluidic device performs multiple times of the melting curve analysis for specimens including the same component. 1. A fluidic device , comprising:a fluid path through which a specimen is passable;at least one reaction unit provided in the fluid path;a heater configured to elevate a temperature of the specimen in the reaction unit; anda heater driving unit,wherein the heater driving unit is configured to drive the heater at a first temperature elevation rate that is equal to or higher than 1° C./s and a second temperature elevation rate that is different from the first temperature elevation rate so that the fluidic device performs multiple times of a melting curve analysis for specimens including the same component.2. The fluidic device according to claim 1 , wherein the specimen comprises a nucleic acid.3. The fluidic device according to claim 2 , wherein the fluidic device is configured to detect a heterozygote through driving of the heater at the first temperature elevation rate.4. The fluidic device according to claim 2 , wherein:the second temperature elevation rate is lower than 1° C./s; andthe fluidic device is configured to detect a homozygote through driving of the heater at the second temperature elevation rate.5. The fluidic ...

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Номер записи: 84
06-02-2014 дата публикации

MICROCHIP FOR NUCLIEIC ACID AMPLIFICATION REACTION

Номер: US20140038280A1
Автор: Kato Yoshiaki, MACHIDA KENZO, Nakamura Tomohiko, Ohnishi Michihiro, Sato Masaki, Watanabe Toshio
Принадлежит: SONY CORPORATION

There is provided a microchip for a nucleic acid amplification reaction including a reagent accommodation region including a solid-phase reagent and a particle, the solid-phase reagent containing a substance necessary for a nucleic acid amplification reaction. 1. A microchip for a nucleic acid amplification reaction comprisinga reagent accommodation region including a solid-phase reagent and a particle, the solid-phase reagent containing a substance necessary for a nucleic acid amplification reaction.2. The microchip for a nucleic acid amplification reaction according to claim 1 ,wherein a particle accommodation section allowing the particle to be accommodated therein is provided in the reagent accommodation region at a predetermined position.3. The microchip for a nucleic acid amplification reaction according to claim 2 ,wherein the particle has a higher specific gravity than a sample to be introduced into the reagent accommodation region.4. The microchip for a nucleic acid amplification reaction according to claim 3 ,wherein the particle accommodation section is a recessed portion of a bottom surface of the reagent accommodation region.5. The microchip for a nucleic acid amplification reaction according to claim 4 ,wherein the bottom surface of the reagent accommodation region is formed as a curved surface bulging toward a surface facing the bottom surface.6. The microchip for a nucleic acid amplification reaction according to claim 2 ,wherein the particle has a lower specific gravity than a sample to be introduced into the reagent accommodation region.7. The microchip for a nucleic acid amplification reaction according to claim 6 ,wherein the particle accommodation section is a recessed portion of a surface facing a bottom surface of the reagent accommodation region.8. The microchip for a nucleic acid amplification reaction according to claim 7 ,wherein the surface facing the bottom surface of the reagent accommodation region is formed as a curved surface bulging ...

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Номер записи: 85
13-02-2014 дата публикации

COMPOSITION FOR BIOSAMPLE TREATMENT AND METHOD FOR NUCLEIC ACID AMPLIFICATION USING THE SAME

Номер: US20140045220A1
Автор: Chen Yi-Chang, TSAI Jane S-C
Принадлежит: INDUSTRIAL TECHNOLOGY RESEARCH INSTITUTE

A composition for a biosample treatment and method for nucleic acid amplification using the same are provided. The composition for biosample treatment includes at least one halocarbon, at least one polyether and at least one surfactant. The composition contains 1˜70% by weight of the halocarbon based on the total weight of the composition. Accordingly, a biosample can be lysed and homogenized in a single tube at one step. Furthermore, reagents for use in nucleic acid amplification can be directly added in the same tube for nucleic acid amplification at the next step. The process, operation periods and risks of contamination can be therefore reduced and a result of nucleic acid amplification with less background noises can be therefore obtained as well. 1. A composition for a biosample treatment , comprising:at least one halocarbon,at least one polyether, andat least one surfactant;wherein the composition contains 1˜70% by weight of the halocarbon based on the total weight of the composition.2. The composition as claimed in claim 1 , wherein the halocarbon comprises perfluorocarbons.3. The composition as claimed in claim 2 , wherein the perfluorocarbon comprises tetrafluoromethane claim 2 , hexafluoroethane claim 2 , perfluropropane claim 2 , perfluorobutane claim 2 , perfluoropentane claim 2 , perfluorohexane claim 2 , perfluoroheptane or perfluorooctane.4. The composition as claimed in claim 1 , wherein the polyether comprises paraformaldehyde claim 1 , polyoxymethylene claim 1 , polyacetal claim 1 , polyethylene glycol claim 1 , polyethylene oxide claim 1 , polyoxyethylene claim 1 , polypropylene glycol claim 1 , polypropylene oxide claim 1 , polyoxypropylene claim 1 , polytetramethylene glycol claim 1 , polytetramethylene ether glycol claim 1 , polytetrahydrofuran or a combination thereof.5. The composition as claimed in claim 1 ,wherein the surfactant comprises odium lauryl sulfate claim 1 , lithium dodecyl sulfate claim 1 , polysorbate claim 1 , polyethylene ...

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Номер записи: 86
06-03-2014 дата публикации

MULTIPHASE NUCLEIC ACID AMPLIFICATION

Номер: US20140066326A1
Автор: ARNOLD, CHELLISERRY Jijumon, DAI Lizhong, JR. Lyle J., NELSON Norman C., PHELPS Steven
Принадлежит: GEN-PROBE INCORPORATED

Improved methods for use in nucleic acid amplification, including multiplex amplification, where the amplification is carried out in two or more distinct phases are disclosed. The first phase amplification reaction preferably lacks one or more components required for exponential amplification. The lacking component is subsequently provided in a second, third or further phase(s) of amplification, resulting in a rapid exponential amplification reaction. The multiphase protocol results in faster and more sensitive detection and lower variability at low analyte concentrations. Compositions for carrying out the claimed methods are also disclosed. 1. A method of quantifying a target nucleic acid sequence in a sample , comprising the steps of:(a) contacting the sample with a first amplification oligonucleotide, specific for a first portion of the target nucleic acid sequence, under conditions allowing hybridization of the first amplification oligonucleotide to the first portion of the target nucleic acid sequence, thereby generating a pre-amplification hybrid that comprises the first amplification oligonucleotide and the target nucleic acid sequence;(b) isolating the pre-amplification hybrid by target capture onto a solid support followed by washing to remove any of the first amplification oligonucleotide that did not hybridize to the first portion of the target nucleic acid sequence in step (a); wherein the first phase amplification reaction mixture comprises a second amplification oligonucleotide, the second amplification oligonucleotide being complementary to a portion of an extension product of the first amplification oligonucleotide, and', 'wherein the first amplification product is not a template for nucleic acid synthesis during the first phase, substantially isothermal, transcription-associated amplification reaction;, '(c) amplifying, in a first phase amplification reaction mixture, at least a portion of the target nucleic acid sequence of the pre-amplification ...

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Номер записи: 87
13-03-2014 дата публикации

Nicking and Extension Amplification Reaction for the Exponential Amplification of Nucleic Acids

Номер: US20140072978A1
Автор: Andrew P. Miller, Brian K Maples, Jarrod Provins, Jeffrey Mandell, Rebecca C. Holmberg, Richard Roth
Принадлежит: Ionian Technologies LLC

The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.

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Номер записи: 88
13-03-2014 дата публикации

IMAGING CHROMOSOME STRUCTURES BY SUPER-RESOLUTION FISH WITH SINGLE-DYE LABELED OLIGONUCLEOTIDES

Номер: US20140073520A1
Автор: CAI LONG, ZHIYENTAYEV Timur
Принадлежит: California Institute of Technology

Methods and systems are provided for creating molecular barcodes for DNA sequences of interest in chromosomes within single cells and for resolving such barcodes using super-resolution technologies. The invention additionally teaches creating molecular barcodes for mRNA sequences that can be visualized at the same time as the aforementioned DNA sequences. The inventive approach allows for the detection of multiple loci on the chromosomes of tumor biopsy sample cells, and can accomplish all of the current applications of DNA FISH in cancer diagnostics, with the additional benefit of being highly multiplexable. 1. A method , comprising: (a) providing a plurality of probe-pairs that are each specific to a DNA sequence of interest, wherein each probe-pair comprises an activator fluorophore and a reporter fluorophore;', '(b) hybridizing, within said cell, a quantity of said one or more DNA sequences of interest with a plurality of said probe-pairs, wherein when the probe-pairs hybridize with said DNA sequences of interest, the reporter fluorophore and activator fluorophore of each probe-pair are in sufficiently close proximity to form a functional dye pair; and wherein each of the DNA sequences of interest that is hybridized with said plurality of probe-pairs emits two or more distinct signals, so as to create the molecular barcode; and, '(i) creating a molecular barcode for one or more DNA sequences of interest in a chromosome of a cell by a method comprising(ii) resolving said molecular barcode by resolving said signals emitted from said plurality of probe-pairs associated with each of said DNA sequences of interest, wherein each emitted signal is a component of the barcode associated with each of said DNA sequences of interest and wherein each DNA sequence of interest is associated with a distinct barcode, so as to detect one or more DNA sequences of interest in a chromosome of a single cell.2. The method of claim 1 , wherein the barcode is resolved using super ...

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Номер записи: 89
27-03-2014 дата публикации

Enclosed unit for rapid detection of a target nucleic acid amplification product

Номер: US20140087373A1
Автор: Gu Jiayong, HU Lin, YOU Qimin, Yu Qinhao
Принадлежит:

The invention relates to a method for rapid detection of a target nucleic acid amplification product while preventing cross-contamination between target nucleic acid amplification products and avoiding false positives, comprising the steps of: a) leaving the reaction tube unopened after the amplification reaction is finished, so as to prevent the target nucleic acid amplification product from leaking out and resulting in contamination; b) placing the unopened reaction tube inside an enclosed unit, making the target nucleic acid amplification product be transferred to a test strip from the reaction tube in a physically enclosed environment; c) performing detection in a visual read-out manner, and determining the result; d) discarding the enclosed unit in a safety place as a whole without opening it after the detection. The invention also relates to a totally enclosed unit for detecting a target nucleic acid amplification product, and still relates to applications of the totally enclosed rapid detection unit in detection of infectious pathogens, food industry, agriculture, livestock husbandry, customs quarantine control, and determination of DNA. 111.-. (canceled)12. A method of detecting a target nucleic acid amplification product which is retained in a detection device thereby avoiding contamination of a proximate space comprising the steps of:a) placing the sealed container containing a target nucleic acid amplification product into the detection device;b) closing the detection device such that the sealed container is punctured and the fluid containing the target nucleic amplification product is transferred to a sterile visual detection strip within the device such that the fluid is retained within the detection device; andc) detecting the target nucleic acid amplification product.13. The method of claim 12 , wherein the detection device cannot be reopened once it is closed thereby preventing the fluid from leaking out of the detection device.14. A method of ...

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Номер записи: 90
27-03-2014 дата публикации

METHOD, PROBE AND KIT FOR DNA IN SITU HYBRIDATION AND USE THEREOF

Номер: US20140087378A1
Автор: Chatre Laurent Arnaud, Ricchetti Miria
Принадлежит:

The invention relates to a method for the detection of the occurrence of initiation of replication events in genomic DNA in a eukaryotic cell, involving contacting said eukaryotic cell comprising said genomic DNA with a first nucleotide probe, under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said DNA genome and detecting said first nucleotide probe hybridized to said DNA. Further detection of at least one RNA molecule can be achieved. The invention also relates to a nucleic acid molecule suitable for use as a probe, hybridizing with a target region in a eukaryotic genomic DNA, and comprising a nucleic acid sequence which has no identified corresponding annealing RNA in the metabolically active cell containing said eukaryotic genomic DNA and therefore remains RNA-free during transcription and replication of said DNA genome. The invention also encompasses kit(s) for carrying out in situ hybridization and use of the method(s), nucleic acid molecule(s) or kit(s) of the invention in the detection of mitochondrial disease(s), neoplasic diseases(s) or cancer(s), or in the testing of the cytotoxicity of organic or chemical compounds, especially drugs, on eukaryotic cells. 127.-. (canceled)28. A method for the detection of the occurrence of initiation of replication events in genomic DNA in a eukaryotic cell , comprising the steps of:contacting said eukaryotic cell comprising said genomic DNA with a first nucleotide probe, under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and thereby ...

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Номер записи: 91
03-04-2014 дата публикации

Method and Apparatus for Generating Thermal Melting Curves in a Microfluidic Device

Номер: US20140093879A1
Автор: Aaron Rulison, Allen Boronkay, Andrew Fabans, Deborah John Boles, Edward Donlon, Ivor T. Knight, Michael Slater, Robert Moti, Wesley B. Dong
Принадлежит: Canon US Life Sciences Inc

The present invention provides novel methods and devices that employ microfluidic technology to generate molecular melt curves. In particular, the devices and methods in accordance with the invention are useful in providing for the analysis of PCR amplification products.

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Номер записи: 92
03-04-2014 дата публикации

Nicking and Extension Amplification Reaction for the Exponential Amplification of Nucleic Acids

Номер: US20140093883A1
Автор: Andrew P. Miller, Brian K. Maples, Jarrod Provins, Jeffrey Mandell, Rebecca C. Holmberg, Richard Roth
Принадлежит: Ionian Technologies LLC

The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.

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Номер записи: 93
03-04-2014 дата публикации

Method of Removing Nucleic Acid Contamination in Reverse Transcription and Amplification Reactions

Номер: US20140093938A1
Автор: Dag Rune Gjellesvik, Morten Elde, Olav Lanes
Принадлежит: BIOTEC PHARMACON ASA

The invention provides methods of removing nucleic acid contamination from reverse transcription reactions and hot-start PCR, wherein said hot-start PCR is a barrier hot-start PCR set up and/or involves a hot-start DNA polymerase, which methods comprise use of a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA. The invention further provides a DNase that is substantially irreversibly inactivated by heating at a temperature of about 50° C. for 5 minutes, and that is substantially specific for double stranded DNA, nucleic acids encoding said DNase and kits or compositions comprising said DNase or said nucleic acid.

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Номер записи: 94
10-04-2014 дата публикации

APPARATUS AND METHOD FOR PROCESSING BIOLOGICAL SAMPLES AND A RESERVOIR THEREFOR

Номер: US20140099631A1
Автор: FELDBALLE Ole, MATTHIESEN Steen Hauge, POULSEN Tim Svenstrup, TESTA Gregory A., Winther Lars
Принадлежит:

An apparatus for processing at least one biological sample accommodated on at least one carrier member () in a chamber includes, at least one reservoir () able to accommodate a fluid on a surface inside the chamber adjacent to and/or facing a substantial part of the at least one biological sample. The apparatus may comprise a bottom member () arranged to support at least one carrier member () carrying at least one biological sample and a lid () including at least one fluid reservoir (). The reservoir filled with water provides humidity to the chamber and impedes drying out of the sample. 1139-. (canceled)140. An automatic stainer for staining biological samples , wherein at least one biological sample is arranged on at least one carrier member in a chamber , said stainer comprising:a bottom member supporting said at least one carrier member;a hydrophilic porous solid reservoir configured to sorb and desorb water and water vapor;a lid for the chamber, detachable from the bottom member, the lid and the bottom member forming a closed chamber when the lid is positioned atop the bottom member, wherein the lid is configured to position the reservoir inside the closed chamber directly above the at least one biological sample such that the reservoir does not touch said at least one biological sample, when said lid is positioned atop the bottom member to form the closed chamber; anda sample temperature controlling device below said at least one carrier member controlling the temperature of said at least one carrier member and said at least one biological sample, wherein said reservoir either sorbs or desorbs water and water vapor so as to control relative humidity within said chamber at above 85% relative humidity, when said lid is positioned atop the bottom member to form the closed chamber.141. The stainer of claim 140 , wherein the stainer is carousel type.142. The stainer of claim 140 , wherein the stainer is robotic and configured to move reagents and slides.143. The ...

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Номер записи: 95
10-04-2014 дата публикации

NOVEL COMPOSITIONS, METHODS AND KITS FOR REAL TIME POLYMERASE CHAIN REACTION (PCR)

Номер: US20140099644A1
Автор: BORNARTH Carole, Lau Michael, Stevens Junko
Принадлежит:

The present disclosure is directed to compositions, methods and kits for amplifying target nucleic acids while reducing non-specific amplification and undesired amplification products using a dual hot start reaction mixture that comprise at least two different hot start mechanisms. 1. A composition comprising:a) a nucleic acid polymerase; andb) a dual hot start reaction mixture.2. The composition of claim 1 , wherein the nucleic acid polymerase is a DNA-dependent DNA polymerase or an RNA-dependent DNA polymerase.3. The composition of claim 1 , wherein the nucleic acid polymerase is thermostable.4. The composition of claim 1 , wherein the nucleic acid polymerase is selected from the group consisting of Taq DNA polymerase claim 1 , Tfl DNA polymerase claim 1 , Tfi DNA polymerase claim 1 , Pfu DNA polymerase claim 1 , and Vent™ DNA polymerase.5. The composition of claim 1 , wherein the dual hot start reaction mixture comprises at least two different hot start mechanisms.6. The composition of claim 5 , wherein the at least two different hot start mechanisms are selected from the group consisting of antibodies or combinations of antibodies that block DNA polymerase activity at lower temperatures claim 5 , oligonucleotides that block DNA polymerase activity at lower temperatures claim 5 , reversible chemical modifications of the DNA polymerase that dissociate at elevated temperatures claim 5 , amino acid modifications of the DNA polymerase that provide reduced activity at lower temperatures claim 5 , fusion proteins that include hyperstable DNA binding domains and topoisomerase claim 5 , temperature dependent ligands that inhibit the DNA polymerase claim 5 , single stranded binding proteins that sequester primers at lower temperatures claim 5 , modified primers claim 5 , or modified dNTPs.7. A composition comprising:a) a thermostable nucleic acid polymerase; andb) a dual hot start reaction mixture that substantially inhibits the polymerase activity of the polymerase at a ...

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Номер записи: 96
06-01-2022 дата публикации

SPATIALLY DISTINGUISHED, MULTIPLEX NUCLEIC ACID ANALYSIS OF BIOLOGICAL SPECIMENS

Номер: US20220002791A1
Автор: Aravanis Alex, Bazargan Leila, Cann Gordon M., Frisen Jonas, Lundeberg Joakim, Ståhl Patrik
Принадлежит:

A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen. 1. A method for determining the spatial location of target nucleic acids in a biological specimen , comprising:(a) providing a solid support comprising a population of nucleic acids randomly located across a population of features of said solid support, wherein the nucleic acids comprise a spatial tag sequence and a primer binding sequence, and wherein the spatial tag sequence differs from spatial tag sequences of other nucleic acids in the population;(b) performing a sequencing reaction to determine the spatial tag sequences, or complements thereof, of the nucleic acids located across the population of features on the solid support, thereby determining the positions of the spatial tag sequences on the solid support;(c) contacting a biological specimen with the solid support;(d) hybridizing the target nucleic acids from the biological specimen to capture sequences on the randomly located nucleic acids that are proximal to the target nucleic acids;(e) extending the capture sequences, wherein the extended ...

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Номер записи: 97
07-01-2016 дата публикации

Nanotubes as Carriers of Nucleic Acids into Cells

Номер: US20160002669A1
Автор: Hicham Fenniri, Thomas J. Webster, Usha Devi Hemraz, Yupeng Chen
Принадлежит: Hicham Fenniri, Thomas J. Webster, Usha Devi Hemraz, Yupeng Chen

The present invention is directed to transfection complexes of rosette nanotubes and one or more nucleic acids.

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Номер записи: 98
07-01-2016 дата публикации

MUTLIPLEXED IN SITU MOLECULAR ANALYSES AND PROGRAMMABLE MOLECULAR PROBES FOR REGULATED AMPLIFICATION

Номер: US20160002704A1
Автор: DIEHL Michael, DUOSE Dzifa Y., SAMSON Edward B., SCHWELLER Ryan, ZIMAK Jan
Принадлежит: William Marsh Rice University

The present invention generally relates to methods for detecting a target in a sample; methods for modulating the reporting intensity of a labeled target in a sample of fixed cells or tissues; methods for detecting the location of at least two targets in a sample; and related compositions. 13-. (canceled)4. A method for detecting a target in a sample , the method comprising:complexing a target-recognition agent to the target, wherein the target-recognition agent comprises a polynucleotide, to form a polynucleotide-target complex;reacting the polynucleotide-target complex via strand displacement with a branched or dendridic dynamic DNA complex to create a dynamic DNA-target complex;reacting the dynamic DNA-target complex via strand displacement with at least one branched or dendridic structure dynamic DNA complex to form a multi-generation dynamic DNA-target complex;reacting the multi-generation dynamic DNA-target complex via strand displacement with a first probe comprising at least one dye and a polynucleotide to form a labeling complex.5. The method of claim 4 , wherein at least one dye is a fluorescent dye.6. The method of claim 4 , where at least one probe comprises at least two dye molecules.7. The method of claim 6 , wherein the at least two dye molecules are the same dye.8. The method of claim 6 , wherein the at least two dye molecules are different dyes.9. The method of claim 4 , further comprising reacting the multi-generation dynamic DNA-target complex via strand displacement with a second probe comprising at least one dye and a polynucleotide claim 4 , wherein the first probe and the second probe comprise different dyes.10. The method of claim 4 , wherein at least one polynucleotide is at least one selected from a group consisting of DNA and RNA.11. The method of claim 4 , wherein the target-recognition agent comprises at least one antibody claim 4 , peptide claim 4 , aptamer claim 4 , enzyme claim 4 , or self-assembling protein.12. (canceled)13. A method ...

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Номер записи: 99
07-01-2016 дата публикации

METHODS OF MULTIPLEXING DNA SENSORS AND LOCALIZING DNA SENSOR

Номер: US20160002713A1
Автор: Krishnan Yamuna, Modi Souvik, Surana Sunaina
Принадлежит:

The present disclosure relates to a method of multiplexing DNA sensors and optionally measuring pH in cell, a method of localizing DNA sensor in Golgi Network of scFv-Furin expressing cell and a method of identifying optimal location of fluorophore pair on the DNA sensor for multiplexing DNA sensors. The DNA sensors of the present disclosure follow independent cellular pathways and do not interact with or compromise functionality of another DNA sensor. 1. A method of multiplexing DNA sensors and optionally measuring pH in cell , wherein said DNA sensor comprises Nucleic Acid Assembly and fluorophore , optionally along with protein , said method comprising acts of:a) adding the DNA sensors to the cell in labelling media for cellular uptake, to obtain a cell with the DNA sensors;b) incubating the cell obtained in step a) in the labelling media for multiplexing the DNA sensors, wherein the DNA sensors are engineered to follow specific cellular pathways within the cell; andc) mapping the multiplexed DNA sensors within the cell at time intervals, optionally determining D/A ratio and obtaining calibration curve for measuring pH in the cell.2. The method as claimed in claim 1 , wherein the cellular pathways followed by the DNA sensors are independent; and wherein each of the DNA sensors does not interact with or compromise functionality of another DNA sensor.3. The method as claimed in claim 1 , wherein the cellular pathways are selected from group comprising endocytic pathway and non-endocytic pathway claim 1 , preferably secretory pathway claim 1 , transcytosis claim 1 , nuclear translocation claim 1 , cell-cell fusion claim 1 , intracellular fission and fusion phenomena.4. The method as claimed in claim 1 , wherein the adding of the DNA sensors to the cell is sequentially or simultaneously; and wherein the cell is selected from group comprising eukaryotic cell claim 1 , prokaryotic cell and recombinant cell.5. The method as claimed in claim 4 , wherein the recombinant ...

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Номер записи: 100