Настройки

Укажите год
-

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

Подробнее
-

Мониторинг СМИ

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

Подробнее

Форма поиска

Поддерживает ввод нескольких поисковых фраз (по одной на строку). При поиске обеспечивает поддержку морфологии русского и английского языка
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Ведите корректный номера.
Укажите год
Укажите год
Применить Всего найдено 11221. Отображено 100.
05-01-2012 дата публикации

Identification of nucleic acid delivery vehicles using dna display

Номер: US20120004137A1
Автор: Richard W. Wagner, Steven Mark SHAMAH, Yan Chen
Принадлежит: X Body Inc

The present invention features methods and compositions for the identification of molecules that facilitate the intracellular delivery of a, e.g., nucleic acid molecule. The methods and compositions of the invention utilize any display methodology wherein a library (e.g., a small molecule or protein library) is coupled to a nucleic acid (e.g., RNA or DNA) that encodes each library member.

Подробнее
Номер записи: 1
19-01-2012 дата публикации

Methods of forming and using a solid-phase support

Номер: US20120012250A1
Автор: Aaron Jones, Brett Ellman, David Heiner, Michal Lebl, Steve Fambro
Принадлежит: Illumina Inc

Disclosed herein are methods of method of making a substrate for performing a chemical synthesis reaction.

Подробнее
Номер записи: 2
01-03-2012 дата публикации

Method and Device for Microparticle Assay Fluorescence Intensity Reference Intraplex

Номер: US20120053085A1
Автор: Brian P. Hanley
Принадлежит: Individual

A method for making suspended microarray readings from a single sample more reliably accurate. It can be applied to any assay system that uses discrete particles coupled with an assay. Most of these are fluidic systems that read the assay result using flow cytometry. However, other methods such as the distribution of tiny assay devices coupled with miniature transponders, where the sampling is of the environment, can also make use of this method. This invention combines a reference set of signal levels on particles with separately identified assays of one sample. By elimination of outliers, averaging, taking ratios of averages, and then taking ratios of assay signal levels against the reference set this method makes possible highly reliable diagnostics. When used standalone, the method uses different signal intensities to better calibrate an instrument. This method compensates for multiple sources of errors that can occur in this type of assay system.

Подробнее
Номер записи: 3
01-03-2012 дата публикации

Methods of creating and screening dna-encoded libraries

Номер: US20120053091A1
Автор: Richard W. Wagner
Принадлежит: X Chem Inc

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Подробнее
Номер записи: 4
22-03-2012 дата публикации

Single column immunological test elements

Номер: US20120071345A1
Автор: Mark Sawczuk, Raymond F. Jakubowicz
Принадлежит: Ortho Clinical Diagnostics Inc

A plurality of individual single column test elements are provided for use in a clinical testing apparatus. Each test element is defined by a single test column that includes a quantity of a test material, such as gel material or a bead matrix, including a cover strip used to access the contents of the test column. Individual test elements can be stored, retained and dispensed for testing patient samples.

Подробнее
Номер записи: 5
19-04-2012 дата публикации

Compositions and Methods for Determining Immune Status

Номер: US20120094861A1
Автор: Alex Tikhonov, Barry Schweitzer, Gengxin Chen, James Meegan, Robert G. Ulrich
Принадлежит: Invitrogen Inc, US Army Medical Research and Materiel Command USAMRMC

The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals.

Подробнее
Номер записи: 6
03-05-2012 дата публикации

Apparatus for synthesizing oligonucleotides and methods of use

Номер: US20120107181A1
Автор: Francis J. Ring, Isaiah E. Cedillo, Max N. Moore
Принадлежит: ISIS PHARMACEUTICALS INC

The present invention relates to apparatus and methods for synthesizing oligonucleotides wherein a reaction zone has a variable volume based on the position of a piston, and the piston is adjusted to control the amount of headspace above solid support in the reaction zone. Methods and apparatus that limit the size or existence of the headspace are described.

Подробнее
Номер записи: 7
17-05-2012 дата публикации

Differential multiplexing with pattern recognition

Номер: US20120122704A1
Автор: Craig T. Narasaki, Daniel H. Atchley, John R. Hickman
Принадлежит: US Air Force

This novel form of multiplexing allows the user to probe for multiple targets and simultaneously identify a specific target. An example of solutions provided here comprises: providing one or more assay mixes for a number of targets (the number of assay mixes is less than the number of targets); providing a number of reference patterns (each of the reference patterns is associated with one of the targets); contacting each of a number of aliquots with one of the assay mixes; generating a result pattern, based on positive or negative results; and selecting the reference pattern most similar to the result pattern, to thereby detect the target. Solutions provided here, which we term differential multiplexing with pattern recognition, may involve molecular or immunological techniques to identify one of many indicators of drug use, illness, disease, or medical condition. For example, we provide a simple method for identifying targets using combinations of real-time PCR reagent mixes and only one reporter. This is an effective and inexpensive method that can be used to identify targets with minimal reagents and supplies.

Подробнее
Номер записи: 8
24-05-2012 дата публикации

Polymer microfluidic biochip fabrication

Номер: US20120128548A1
Автор: Jason A.A. West, Jesse Thompson
Принадлежит: Arcxis Biotechnologies Inc

Provided are microfluidic devices and methods for fabricating and bonding such devices. Also provided are kits for analyzing analyte-containing samples and for lysing cells.

Подробнее
Номер записи: 9
24-05-2012 дата публикации

Gb1 peptidic libraries and methods of screening the same

Номер: US20120129715A1
Автор: Maruti Uppalapati, Sachdev S. Sidhu
Принадлежит: University of Toronto

GB1 peptidic libraries and methods of screening the same for specific binding to a target protein are provided. Libraries of polynucleotides that encode GB1 peptidic compounds are provided. These libraries find use in a variety of applications in which specific binding to target molecules, e.g., target proteins is desired. Also provided are methods of screening the libraries for binding to a target.

Подробнее
Номер записи: 10
24-05-2012 дата публикации

Method for screening new drug candidate inhibiting target protein-protein interaction for development of first-in-class drug

Номер: US20120129722A1
Автор: So Youn Kim
Принадлежит: Industry Academic Cooperation Foundation of Dongguk University

The present invention relates to a method for screening a substance inhibiting protein-protein interactions, and more particularly to a method for screening a substance inhibiting protein-protein interactions, the method comprising using a protein chip having immobilized thereon spots comprising a mixture of a sol-gel material and a protein. According to the invention, a protein chip can be easily manufactured in a 96-well plate using a sol-gel material, whereby an inhibitor that inhibits protein-protein interactions can be easily screened from a library of natural substances.

Подробнее
Номер записи: 11
14-06-2012 дата публикации

Protein fragment complementation assays for high-throughput and high-content screening

Номер: US20120149597A1
Автор: Helen Yu, Ingrid Remy, Jane Lamerdin, John K. Westwick, Marnie MacDonald, Stephen William Watson Michnick
Принадлежит: Odyssey Pharmaceuticals Inc

The present invention provides protein fragment complementation assays for drug discovery, in particular to identify compounds that activate or inhibit cellular pathways. Based on the selection of an interacting protein pair combined with an appropriate PCA reporter, the assays may be run in high-throughput or high-content mode and may be used in automated screening of libraries of compounds. The interacting pair may be selected by cDNA library screening; by gene-by-gene interaction mapping; or by prior knowledge of a pathway. Fluorescent and luminescent assays can be constructed using the methods provided herein. The selection of suitable PCA reporters for high-throughput or high-content (high-context) assay formats is described for a diversity of reporters, with particular detail provided for examples of monomeric enzymes and fluorescent proteins. Methods are described for constructing such assays for one or more steps in a biochemical pathway; testing the effects of compounds from combinatorial, natural product, peptide, antibody, nucleic acid or other diverse libraries on the protein or pathway(s) of interest; and using the results of the screening to identify specific compounds that activate or inhibit the protein or pathway(s) of interest. Single-color and multi-color assays are disclosed. Further disclosed are universal expression vectors with cassettes that allow the rapid construction of assays for a large and diverse number of gene/reporter combinations. The development of such assays is shown to be straightforward, providing for a broad, flexible and biologically relevant platform for drug discovery.

Подробнее
Номер записи: 12
05-07-2012 дата публикации

Multi-well rotary synthesizer

Номер: US20120171088A1
Автор: Daniel W. Hugens, Gary R. McLuen, Richard J. Hanney
Принадлежит: McLuen Design Inc

An apparatus for synthesizing polymer chains includes a controller, a plurality of precision fit vials circularly arranged in multiple banks on a cartridge, a drain corresponding to each bank of vials, a chamber bowl, a plurality of valves for delivering reagents to selective vials, and a waste tube system for purging material from the vials. A purging operation can be selectively performed on one or more of the banks of vials. The plurality of vials are stored in the cartridge and are divided among individual banks wherein each bank of vials has a corresponding drain. There is at least one waste tube system for expelling the reagent solution from vials within a particular bank of vials when the waste tube system is coupled to the corresponding drain. The cartridge holding the plurality of vials rotates relative to the stationary banks of valves and the waste tube system.

Подробнее
Номер записи: 13
19-07-2012 дата публикации

Methods for screening and arraying microrganisms such as viruses using subtractive contact printing background

Номер: US20120184458A1
Автор: Daniel J. Solis, Emmanuel Delamarche, Sean R. Coyer
Принадлежит: International Business Machines Corp

Methods for screening and arranging microorganisms such as viruses in an array using subtractive contact printing are provided. In one embodiment, a method for forming an array of receptors for microorganisms comprises: patterning an array of structures on a first substrate to form a template on a surface of the first substrate; applying a receptor material to a face of a second substrate; and contacting the face of the second substrate with the template to remove a portion of the receptor material from the second substrate, thereby forming an array of receptors on the second substrate.

Подробнее
Номер записи: 14
16-08-2012 дата публикации

Microchemical reactor

Номер: US20120208222A1
Автор: Andrew Mark Hecht, Paul Martin Baca
Принадлежит: Individual

Microchemical reactors embedded in absorbant materials are described that allow operators to perform chemical reactions and chemical cascades using multiple microencapsulated reagents, which release stoichiometric amounts of reagents in a predetermined time sequence with a predetermined logic.

Подробнее
Номер записи: 15
23-08-2012 дата публикации

Isolating biological modulators from biodiverse gene fragment libraries

Номер: US20120214709A1
Автор: Paul M. Watt, Wayne R. Thomas
Принадлежит: Phylogica Ltd

The present invention provides a method for identifying a modulator or mediator of a biological activity, which activity includes antigenicity and or immunogenicity, said method comprising the step of: (i) producing a gene fragment expression library derived from defined nucleotide sequence fragments; and (ii) assaying the expression library for at least an amino acid sequence derived from step (i) for a biological activity wherein that activity is different from any activity the amino acid sequence may have in its native environment.

Подробнее
Номер записи: 16
30-08-2012 дата публикации

Arrays of microparticles and methods of preparation thereof

Номер: US20120220495A1
Автор: Chiu Wo Chau, Hui Huang, Jiacheng Yang, Michael Seul, Sukanta Banerjee, Ye Hong
Принадлежит: Bioarray Solutions Ltd

This invention provides high unit density arrays of microparticles and methods of assembling such arrays. The microparticles in the arrays may be functionalized with chemical or biological entities specific to a given target analyte. The high unit density arrays of this invention are formed on chips which may be combined to form multichip arrays according to the methods described herein. The chips and/or multichip arrays of this invention are useful for chemical and biological assays.

Подробнее
Номер записи: 17
06-09-2012 дата публикации

Apparatus and method for separation of liquid phases of different density and for fluorous phase organic syntheses

Номер: US20120223025A1
Автор: Michal Lebl
Принадлежит: Illumina Inc

A simple, efficient apparatus and method for separating layers of immiscible or partially miscible liquids useful in methods of high-throughput combinatorial organic synthesis or parallel extraction of large libraries or megaarrays of organic compounds is disclosed. The apparatus and method are useful, whether as part of an automated, robotic or manual system for combinatorial organic synthesis or purification (extraction). In a preferred embodiment, an apparatus and method for separating layers of immiscible or partially miscible liquids compatible with microtiter plate type array(s) of reaction vessels is disclosed. Another application of centrifugation based liquid removal was found for washing the plates in biological assays or synthesis on modified substrates.

Подробнее
Номер записи: 18
06-09-2012 дата публикации

Method for conducting multiple reactions in a single reaction tube

Номер: US20120225456A1
Автор: Johnson Kian Kok Ng, Lars Thomsen
Принадлежит: Biochip Devises Pte Ltd

There is disclosed a method for conducting at least two reactions in a reaction tube, said method comprising the steps of providing at least two reaction phases within said reaction tube for allowing said reactions to occur therein, providing a separation phase that is immiscible with said two reaction phases and which is disposed therebetween, providing at least one particle capable of being coupled to a chemical species, wherein said particle is movable between said reaction phases to introduce said chemical species thereto.

Подробнее
Номер записи: 19
13-09-2012 дата публикации

CH2 Domain Template Molecules Derived From Rational Grafting Of Donor Loops Onto CH2 Scaffolds

Номер: US20120230981A1
Автор: David Bramhill, Gopalan Raghunathan
Принадлежит: Research Corp Technologies Inc

Novel CH2 domain template molecules wherein donor loops from a database of domains are transferred to a CH2 domain scaffold. At least one or up to three loops from a donor are transferred to the CH2 domain. The donor loops may be chosen based on length, e.g., the donor loop may have a length that is similar to that of a structural loop in the CH2 domain scaffold.

Подробнее
Номер записи: 20
13-09-2012 дата публикации

Protein arrays and uses thereof

Номер: US20120231969A1
Автор: Donghui Ma, Wei-Wu He, Youmin Shu, Zairen Sun
Принадлежит: Origene Technologies Inc

Illustrative embodiments herein disclosed relate to protein arrays, methods for making the arrays and methods for using them, among others. In some embodiments known proteins representing at least 50% of the loci in the human genome are arrayed in known positions on a support. In some embodiments arrays are made of proteins purified from cell lysates by affinity binding to the support. In some embodiments protein arrays are used to decode the binding specificity of antibodies. In some embodiments protein arrays are used to diagnose auto-immune disorders. Many other embodiments and general features are disclosed.

Подробнее
Номер записи: 21
27-09-2012 дата публикации

Method for Assembly of Analyte Filter Arrays Using Biomolecules

Номер: US20120245055A1
Автор: Daniel R. Mitchell, George L. Murphy, Jeremy J. John, Steve M. Savoy
Принадлежит: Nanohmics Inc

Analyte filter arrays and methods for making an analyte filter array are provided. The arrays are formed using a dispersion of filter particles having selected moieties attached to the surface of the particles and a microarray having complementary moieties formed in an array on a substrate, such that each filter particle is attached to a selected region of the microarray. The moiety on the substrate may be RNA or DNA or other molecule. The substrate may be a surface of a detector array, a membrane that may be placed in registration with the detector array or a stamp used to transfer the filter array to a detector array.

Подробнее
Номер записи: 22
27-09-2012 дата публикации

Whole proteome tiling microarrays

Номер: US20120245057A1
Автор: Jochen Buhler, Klaus-Peter Stengele, Matthew Rodesch, Todd Richmond, TOM Albert
Принадлежит: NimbleGen Systems GmbH, Roche Nimblegen Inc

The present invention relates to a microarray comprising at least 50,000 oligopeptide features per cm 2 where the oligopeptide features represent at least 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100% of the proteome of a virus or an organism. The present invention further relates to methods for the synthesis of such microarrays and methods of using microarrays comprising at least 50,000 oligopeptide features per cm 2 . In an embodiment of the invention, the oligopeptide features represent proteins expressed in the same species, wherein the oligopeptide features are presented in a tiling pattern representing at least about 5,000 to-at least about 25,000 proteins expressed in a species. In some embodiments, the oligopeptide microarray features represent proteins expressed in the same species, wherein the microarray features are present in a tiling pattern that represents at least about 5,000 to at least about 50,000 expressed proteins.

Подробнее
Номер записи: 23
11-10-2012 дата публикации

Methods, Compositions, and Kits for Making Targeted Nucleic Acid Libraries

Номер: US20120258892A1
Автор: Yan Wang
Принадлежит: Individual

The present invention provides a method and a kit for selecting and enriching target sequences specific for a genomic region of interest or a subset of a transcriptome using a target-capturing sequence library. The target-capturing sequence library comprises random DNA fragments generated from a target sequence template encompassing all the target sequences. The present invention provides an efficient and cost-effective method of target selection for targeted genome resequencing.

Подробнее
Номер записи: 24
18-10-2012 дата публикации

Agents for enhanced charge transport across microbial membranes

Номер: US20120264649A1
Автор: Guillermo C. Bazan, James J. Sumner, Logan E. GARNER
Принадлежит: UNIVERSITY OF CALIFORNIA

The invention provides molecules useful for enhancing charge transport across membranes, such as electron transport across membranes, and methods of using such molecules, for example in improving the performance of a microbial fuel cell or in staining microbes for observation. The amphiphilic molecule comprises a conjugated core with hydrophilic groups on either end. The amphiphilic molecule inserts into the membrane of a microbe and facilitates charge transfer across the membrane of the microbe.

Подробнее
Номер записи: 25
25-10-2012 дата публикации

High affinity adaptor molecules for redirecting antibody specifity

Номер: US20120271033A1
Автор: Albert Collinson, Anders Vahlne, Gregor Schurmann, Matti Sallberg, Peter Wagner, Robert Kamen
Принадлежит: OPSONIC THERAPEUTICS Inc

Disclosed are methods for identifying high affinity adaptor molecules that bind to both a circulating antibody and a target molecule and redirect the specificity of the circulating antibody to the target molecule. Exemplary high affinity adaptor molecules are also provided.

Подробнее
Номер записи: 26
13-12-2012 дата публикации

Methods and compositions for nucleic acid analysis

Номер: US20120316074A1
Автор: Serge Saxonov
Принадлежит: Bio Rad Laboratories Inc

Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes.

Подробнее
Номер записи: 27
03-01-2013 дата публикации

Photonic Crystal MicroArray Layouts for Enhanced Sensitivity and Specificity of Label-Free Multiple Analyte Sensing, Biosensing and Diagnostic Assay

Номер: US20130005605A1
Автор: Ray T. Chen, Swapnajit Chakravarty
Принадлежит: Omega Optical Inc

Methods and systems for label-free multiple analyte sensing, biosensing and diagnostic assay chips consisting of an array of photonic crystal microcavities along a single photonic crystal waveguide are disclosed. The invention comprises an on-chip integrated microarray device that enables detection and identification of multiple species to be performed simultaneously using optical techniques leading to a high throughput device for chemical sensing, biosensing and medical diagnostics. Other embodiments are described and claimed.

Подробнее
Номер записи: 28
21-02-2013 дата публикации

Library characterization by digital assay

Номер: US20130045875A1
Автор: Benjamin J. Hindson, Michael Y. Lucero, Ryan T. Koehler, Serge Saxonov, Svilen S. Tzonev
Принадлежит: Bio Rad Laboratories Inc

Methods of characterizing a nucleic acid library by digital assay.

Подробнее
Номер записи: 29
28-02-2013 дата публикации

Biochip stamping device and stamping method thereof

Номер: US20130047399A1
Автор: Bo Sung Ku, Hee Ju Son, Sang Youl JEON
Принадлежит: Samsung Electro Mechanics Co Ltd

There is provided a biochip stamping device. The biochip stamping device includes a stamping jig in which a first biochip is aligned; an inverting mechanism vertically inverting a second biochip; and a movement mechanism transferring the vertically inverted second biochip on the stamping jig to combine the first biochip and the second biochip.

Подробнее
Номер записи: 30
28-03-2013 дата публикации

Compound Arrays for Sample Profiling

Номер: US20130079250A1
Автор: Phillip Stafford, Stephen Albert Johnston
Принадлежит: Arizona Board of Regents of ASU

The invention provides arrays of compound for use in profiling samples. The arrays include compounds bind to components of the samples at relatively low affinities. The avidity of compounds binding to components of the samples can be increased by forming arrays such that multivalent components of the samples (e.g., antibodies or cells) can bind to more than one molecule of a compound at the same time. When a sample is applied to an array under such conditions, the compounds of the array bind to component(s) of the sample with significantly different avidities generating a profile characteristic of the sample.

Подробнее
Номер записи: 31
11-04-2013 дата публикации

Multiplexed Assay Using Spectrally-Encoded Solid Support Matrices

Номер: US20130090260A1
Автор: Nova Michael P., Senyei Andrew E.
Принадлежит: IRORI TECHNOLOGIES, INC.

In a multiplexed assay, each molecule of a plurality of molecules is attached to a support matrix particle with a substrate adapted for attachment and/or synthesis of molecules. A spectrally-encoded identifier embodied in a photochemical medium is embedded or encased within the substrate to uniquely identify the molecule attached to the substrate. The molecules are exposed to one or more processing conditions, and then placed within the path of an optical detector adapted to read the spectrally-encoded identifier and measure biochemical activity on each support matrix particle. The measured biochemical activity is associated with the unique identity of the support matrix particle and, hence, with the molecule attached to the particle. 1. A multiplexed assay , comprising:attaching each molecule of a plurality of molecules to a separate support matrix particle, each support matrix particle comprising a substrate adapted for attachment of a molecule and a spectrally-encoded identifier embodied in a photochemically-active medium incorporated into the substrate, the spectrally-encoded identifier adapted to uniquely identify the molecule attached to the substrate;exposing the plurality of molecules and their corresponding support matrix particles to one or more processing conditions in suspension to produce a plurality of processed molecules;placing the plurality of support matrix particles into a vessel feeding into an optically-transparent tube disposed within the detection path of each of an optical detector and an analytical instrument, wherein the optical detector comprises a light source emitting at a wavelength adapted to induce activity in the photochemically-active medium for reading the spectrally-encoded identifier and wherein the analytical instrument is adapted to measure biochemical activity on each support matrix particle; andassociating the measured biochemical activity with the spectrally-encoded identifier for the corresponding support matrix particle ...

Подробнее
Номер записи: 32
18-04-2013 дата публикации

METHODS FOR MANUFACTURING MOLECULAR ARRAYS

Номер: US20130096033A1
Автор: Routenberg David A.
Принадлежит: PROGNOSYS BIOSCIENCES, INC.

The methods of the present invention provide methods for manufacturing a master substrate and methods for manufacturing replica arrays from the master substrate. The methods may be used, for example, directly to manufacture or “print” peptide arrays from a DNA array; however, the methods are applicable to a wide range of manufacturing applications for use any time multiple copies of an array needs to be printed. 1. A method of manufacturing an array of products on a replica array comprising:providing a master substrate having partitioned reaction volumes;generating products by one or more enzymatic processes in the partitioned reaction volumes; andimmobilizing the products from the partitioned reaction volumes from the master substrate on capture moieties disposed on a replica array that is in contact with the partitioned reaction volumes; wherein partitioning of the reaction volumes prevents diffusion of products between them.2. The method of claim 1 , wherein the reaction volumes are partitioned by surface energetic barriers on the master substrate.3. The method of claim 1 , wherein the master substrate is a template array.4. The method of claim 1 , wherein there are at least 100 partitioned reaction volumes per square centimeter on the master substrate.5. The method of claim 4 , wherein there are at least 10 claim 4 ,000 partitioned reaction volumes per square centimeter on the master substrate.6. The method of claim 1 , wherein at least 1000 different products from separate partitioned reaction volumes on the master substrate are arrayed on the replica array at a density of at least 1000 different products per square centimeter.7. The method of claim 1 , wherein at least a portion of each product from substantially all partitioned reaction volumes are arrayed on the replica array.8. The method of claim 1 , further comprising after the immobilizing step claim 1 , the steps of removing the replica array; sequentially furnishing one or more replica arrays ...

Подробнее
Номер записи: 33
18-04-2013 дата публикации

MICROFABRICATION METHODS FOR THE OPTIMAL PATTERNING OF SUBSTRATES

Номер: US20130096034A1
Автор: Barker David L., Heiner David L., Lebl Michal, Zhao Chanfeng
Принадлежит: Illumina, Inc.

A method of fabricating a microarray including the steps of: (a) contacting a substrate having wells with a reagent reactive with said substrate to produce a surface modification within said wells and a surface modification surrounding said wells; (b) polishing said substrate to produce a polished surface modification surrounding said wells, wherein said surface modification surrounding said wells is removed and said surface modification within said wells is retained, and (c) depositing a biopolymer onto said substrate, wherein different affinities of said surface modification within said wells and said polished surface facilitate localization of said biopolymer within said wells. 1. A method of fabricating a microarray , comprising:(a) contacting a substrate having wells with a reagent reactive with said substrate to produce a surface modification within said wells and a surface modification surrounding said wells;(b) polishing said substrate to produce a polished surface surrounding said wells, whereby said surface modification surrounding said wells is removed and said surface modification within said wells is retained, and(c) depositing a biopolymer onto said substrate, wherein higher affinity of said surface modification within said wells compared to said polished surface facilitates localization of said biopolymer within said wells.2. The method of claim 1 , wherein said polishing comprises removing a first portion of a layer to expose a second portion of the layer.3. The method of claim 1 , wherein said substrate comprises a first layer and a second layer.4. The method of claim 3 , wherein said first layer comprises an inner layer of said substrate corresponding to the bottoms of said wells.5. The method of claim 4 , wherein said second layer comprises an outer layer of said substrate corresponding to at least a portion of the sides of said wells.6. The method of claim 3 , wherein said first layer comprises silicon.7. The method of claim 3 , wherein said ...

Подробнее
Номер записи: 34
25-04-2013 дата публикации

Microarray Comprising Immobilisation Particles

Номер: US20130102500A1
Автор: Daub Martina, RUPP Jochen, Stumber Michael
Принадлежит: ROBERT BOSCH GMBH

A microarray comprises a carrier substrate and a plurality of immobilization particles configured to immobilize capture molecules. Each immobilization particle comprises a first sub-section bonded to the carrier substrate and a second sub-section which is exposed. 1. A microarray , comprising:a carrier substrate; anda plurality of immobilization particles configured to immobilize catcher molecules of a plurality of catch molecules, each immobilization particle of the plurality of immobilization particles including a first sub-section bonded to the carrier substrate and a second sub-section,wherein the second sub-section is exposed.2. The microarray as claimed in claim 1 , wherein the first sub-section is bound into the carrier substrate.3. The microarray as claimed in claim 1 , wherein the second sub-section projects from the carrier substrate.4. The microarray as claimed in claim 1 , wherein:the carrier substrate is formed from a plastic and each immobilization particle of the plurality of immobilization particles includes a particle core composed of glass or plastic, orthe carrier substrate is formed from glass and each immobilization particle of the plurality of immobilization particles includes a particle core comprised of plastic.5. The microarray as claimed in claim 4 , wherein:the surface of the particle cores is functionalized for immobilizing catcher molecules of the plurality of catcher molecules, and/orthe particle cores each comprise an immobilization coating for immobilizing catcher molecules of the plurality of catcher molecules.6. The microarray as claimed in claim 1 , wherein catcher molecules of the plurality of catcher molecules are immobilized on the second sub-section.7. A device for producing a microarray claim 1 , having a carrier substrate and a plurality of immobilization particles claim 1 , comprising:a carrier substrate holder for holding the carrier substrate, andat least one movable pin for receiving at least one immobilization particle ...

Подробнее
Номер записи: 35
02-05-2013 дата публикации

HIGH EFFICIENCY, SMALL VOLUME NUCLEIC ACID SYNTHESIS

Номер: US20130109596A1
Автор: PETERSON Todd C., POEHMERER Thomas, TREFZER Axel C.
Принадлежит: LIFE TECHNOLOGIES CORPORATION

The disclosure generally relates to compositions and methods for the production of nucleic acid molecules. In some aspects, the invention allows for the microscale generation of nucleic acid molecules, optionally followed by assembly of these nucleic acid molecules into larger molecules. In some aspects, the invention allows for efficient production of nucleic acid molecules (e.g., large nucleic acid molecules such as genomes). 1. A multiwell plate for non-template directed synthesis of nucleic acid molecules , the plate comprising:(a) a magnetic bead located in each of a plurality of wells of the plate, and(b) an electrochemically generated acid being present in one or more well, wherein the bead is between 1.0 μm and 100 μm in diameter.2. The multiwell plate of claim 1 , wherein the number of wells in the plate is between 10 and 50 claim 1 ,000.3. The multiwell plate of claim 1 , wherein the total volume of each well is between 0.1 μl and 50 μl.4. The multiwell plate of claim 1 , wherein each well is operably connected to a pair of electrodes.5. The multiwell plate of claim 1 , wherein the wells of the plate are connected to microfluidic channels for the introduction and removal of reagents.6. A method for the generation of an assembled nucleic acid molecule claim 1 , the method comprising:(a) synthesizing a plurality of nucleic acid molecules, wherein each nucleic acid molecule is prepared in a well of a plate in an average amount of from about 0.001 nanomoles to about 1,000 nanomoles;(b) combining the nucleic acid molecules generated in (a) to produce a pool;(c) oining some or all of the nucleic acid molecules present in the pool formed in (b) to form a plurality of larger nucleic acid molecules;(d) eliminating nucleic acid molecules which contain sequence errors from the plurality of larger nucleic acid molecules formed in (c) to produce an error corrected nucleic acid molecule pool; and(e) assembling the nucleic acid molecules in the error corrected nucleic ...

Подробнее
Номер записи: 36
09-05-2013 дата публикации

Peptide Microarray and Method of Use

Номер: US20130116146A1
Автор: Wang Wei, Xu Zheng
Принадлежит: The Regents of the University of California

A peptide microarray comprising a plurality of predicted unique binding peptides being selected by computational prediction of interaction with a protein of interest or a domain thereof. The selected unique binding peptides are pre-synthesized and then printed and/or immobilized onto a solid support surface via N-terminus with a linker. Methods of using the invention peptide microarray for quantitative determination of protein-peptide interaction, epitope mapping, and drug screening are also provided. 1. A peptide microarray comprising a solid support surface and a plurality of predicted unique binding peptides being pre-synthesized and immobilized onto the solid support surface by a linker , wherein the predicted unique binding peptides have been selected for the microarray by computational prediction of interaction with a protein of interest or a domain thereof.2. The peptide microarray of claim 1 , wherein between 100-1000 predicted unique binding peptides are immobilized on the solid support surface.3. The peptide microarray of claim 1 , wherein the linker is aminohexanoic acid (Ahx) or polyethylene glycol (PEG).4. The peptide microarray of claim 1 , wherein at least one predicted unique binding peptide is methylated or acetylated.5. The peptide microarray of claim 1 , wherein said predicted unique binding peptides are capped with Alanine at each terminus.6. The peptide microarray of claim 1 , wherein said computational predictions comprises a combination of at least three analytical approaches selected from the group consisting of structural information claim 1 , energetic pattern of said peptide-protein interactions claim 1 , molecular dynamics simulation claim 1 , conservation during evolution claim 1 , mutation claim 1 , subcellular location claim 1 , functional filtering processes claim 1 , proteome scan claim 1 , and mass spectra evidence.7. A method of identifying one or more binding peptides interacting with a protein of interest or a domain thereof ...

Подробнее
Номер записи: 37
09-05-2013 дата публикации

MICROARRAY FABRICATION SYSTEM AND METHOD

Номер: US20130116153A1
Автор: Beierle John M., Berti Lorenzo, Bowen M. Shane, Gunderson Kevin L., Lin Shengrong, Park Sang Ryul, Rogert Bacigalupo Maria Candelaria, Tsay James, Venkatesan Bala Murali, Vijayan Kandaswamy, Wu Yir-Shyuan
Принадлежит: Illumina, Inc.

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites. 1. A method for preparing a biological microarray , comprising:providing an array of base pads at predetermined sites on a substrate, wherein individual base pads are configured to capture a nucleic acid molecule; andcontacting the array of base pads with a mixture of different nucleic acid molecules under conditions wherein a nucleic acid molecule is captured at each base pad,wherein a porous attachment layer is disposed over the base pads and the porous attachment layer is configured to attach amplified copies of the nucleic acid molecules comprising nucleotides or nucleotide-like components.2. The method of claim 1 , wherein individual base pads are configured to capture no more than one nucleic acid molecule.3. The method of claim 2 , wherein a single nucleic acid molecule is captured by each and every base pad in the array.4. The method of claim 2 , wherein a single nucleic acid molecule is captured by fewer than all of the base pads in the array.5. The method of claim 1 , wherein the nucleic acid molecules comprise nucleotides or nucleotide-like components.6. The method of claim 1 , further comprising amplifying the single nucleic acid molecule at each base pad to obtain at each base pad a region comprising copies of the nucleic acid molecule claim 1 , wherein the copies of the nucleic acid molecule are attached to the porous attachment layer.7. The method of claim 1 , wherein the substrate comprises a glass.8. The method of claim 1 , wherein the base pads comprise gold.9. The method of claim 1 , wherein the base pads are formed by an ...

Подробнее
Номер записи: 38
16-05-2013 дата публикации

METHOD OF MAKING A MICROBEAD ARRAY WITH ATTACHED BIOMOLECULES

Номер: US20130123146A1
Автор: Seul Michael
Принадлежит: BioArray Solutions, Ltd.

A method and apparatus for the manipulation of colloidal particulates and biomolecules at the interface between an insulating electrode such as silicon oxide and an electrolyte solution. Light-controlled electrokinetic assembly of particles near surfaces relies on the combination of three functional elements: the AC electric field-induced assembly of planar aggregates; the patterning of the electrolyte/silicon oxide/silicon interface to exert spatial control over the assembly process; and the real-time control of the assembly process via external illumination. The present invention provides a set of fundamental operations enabling interactive control over the creation and placement of planar arrays of several types of particles and biomolecules and the manipulation of array shape and size. The present invention enables sample preparation and handling for diagnostic assays and biochemical analysis in an array format, and the functional integration of these operations. In addition, the present invention provides a procedure for the creation of material surfaces with desired properties and for the fabrication of surface-mounted optical components. 1. A method of making a bead array comprising: a) contacting a substrate having a planar surface with a suspension comprising populations of several differently-encoded beads having diameters of up to 10 microns , wherein each population of differently-encoded beads has a different biomolecule attached thereto; and b) applying energy to said substrate or said suspension , or both , such that the populations of differently-encoded beads form an ordered array on the planar surface and the beads are at pre-determined distances from each other.2. The method according to wherein the biomolecule is a protein or an oligonucleotide.3. The method according to wherein the beads are immobilized to the substrate following step b).4. The method according to wherein the beads are immobilized by anchoring to the substrate.5. The method ...

Подробнее
Номер записи: 39
23-05-2013 дата публикации

METHODS FOR IDENTIFYING POLYPEPTIDE TARGETS AND USES THEREOF FOR TREATING IMMUNOLOGICAL DISEASES

Номер: US20130129748A1
Автор: Kaykas Ajamete, Smith Craig A., Wiley Steven
Принадлежит: Viral Logic Systems Technology Corp.

The present invention provides methods for identifying viral virulence factors and for identifying cellular polypeptides to which the viral polypeptides bind. The cellular polypeptide is useful as a therapeutic target or as a therapeutic agent for treating diseases and disorders, including immunological diseases or disorders. 1. A method of identifying a cellular polypeptide to which a viral polypeptide binds comprising:(a) contacting a cell, or a fraction or a supernatant of the cell, and a fusion protein comprising a viral polypeptide fused to an affinity tag comprising a polypeptide tag, under conditions and for a time sufficient that permit a viral polypeptide moiety of the fusion protein to interact with a polypeptide associated with the cell, or the fraction or the supernatant of the cell, to provide a fusion protein:cellular polypeptide complex, wherein the viral polypeptide exhibits at least one virulence trait;(b) isolating the fusion protein:cellular polypeptide complex; and(c) determining the amino acid sequence of the cellular polypeptide or of at least one cellular polypeptide fragment comprising at least eight amino acids, and thereby identifying a cellular polypeptide to which a viral polypeptide binds.2. The method of further comprising prior to step (a) claim 1 , (i) identifying in the genome of a virus claim 1 , a polynucleotide sequence that encodes a viral polypeptide claim 1 , which viral polypeptide comprises at least 40 amino acids; and (ii) producing a fusion protein comprising the viral polypeptide fused to an affinity tag sequence.3. The method of claim 2 , wherein the at least one virulence trait is selected from (a) the trait that expression of a mutant viral polypeptide in a cell infected by the virus correlates with a decrease in virulence of the virus; (b) the trait that absence of expression of the viral polypeptide in a cell infected by the virus correlates with a decrease in virulence of the virus; (c) the trait that the viral ...

Подробнее
Номер записи: 40
23-05-2013 дата публикации

OLIGONUCLEOTIDE LIBRARY ENCODING RANDOMISED PEPTIDES

Номер: US20130130938A1
Автор: Ashraf Mohammed, Hine Anna Victoria, Hughes Marcus Daniel
Принадлежит:

The invention relates to a method of producing an oligonucleotide library comprising a plurality of oligonucleotides, each oligonucleotide in the library having at least one predetermined position, a randomisation codon selected from a defined group of codons, the codons within said defined group coding for different amino acids. Vector, host cells containing such libraries and kits for the production of such libraries are also provided. 120.-. (canceled)21. A kit for producing an oligonucleotide library by a method , said method comprising a plurality of oligonucleotides , each oligonucleotide in the library having at least one predetermined position , a randomisation codon selected from a defined group of codons , the codons within said defined group coding for different amino acids , said method comprising the steps of:(a) Providing one or more double-stranded starter oligonucleotides, wherein the starter oligonucleotides have one or more blunt ends; (i) a coding strand, the coding strand comprising a randomisation codon; and', '(ii) a substantially complementary non-coding strand, wherein each double stranded randomisation oligonucleotide comprises a nucleotide sequence coding for a restriction endonuclease recognition site capable of being recognised by a restriction endonuclease, the restriction endonuclease capable of cleaving the randomisation oligonucleotide upstream or downstream of the endonuclease recognition site at a predetermined cleavage site to create a blunt ended cut;, '(b) Providing a plurality of different double stranded randomisation oligonucleotides comprising(c) Ligating each double-stranded starter oligonucleotide to a double-stranded randomisation oligonucleotide to form ligated oligonucleotides;(d) Amplifying the ligated oligonucleotides;(e) Digesting the ligated oligonucleotide with the restriction endonuclease to form a plurality of randomised double-stranded oligonucleotides, each of which comprise, at one end, a randomisation codon; ...

Подробнее
Номер записи: 41
30-05-2013 дата публикации

SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS

Номер: US20130137605A1
Автор: Hiatt Joseph, Patwardhan Rupali, Shendure Jay, Turner Emily
Принадлежит: UNIVERSITY OF WASHINGTON

The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. 1. A method for generating sequence assemblies from short sequencing reads , comprising:a) fragmenting at least one member of an input library to produce a plurality of linear DNA fragments having a first fragment end and a second fragment end proximal to a fragmentation breakpoint,b) attaching a common nucleic acid adaptor to the first and second linear DNA fragment ends proximal to a fragmentation breakpoint, wherein the common adaptor comprise the same unique sequence tag, i) sequence complementary to at least the unique sequence tag of an adaptor, and', 'ii) sequence complementary to at least a portion of a member of the input library,, 'c) optionally amplifying the plurality of linear DNA fragments to produce a sequencing library comprising a plurality of amplified DNA fragments, wherein at least one of the plurality of amplified DNA fragments comprisesd) sequencing at least a portion of the DNA fragments, wherein the presence of a unique adaptor sequence tag in a plurality of fragment sequences thereby associates the fragment sequences having ends that were proximal to the same fragmentation breakpoint, ande) assembling the plurality of breakpoint tag-associated fragment sequences, or subassembly sequences comprising breakpoint-associated sequences, to generate longer subassembly sequences of the input library.2. The method of claim 1 , wherein prior to step a) at least one of a plurality of nucleic acid end adaptors is attached to one or both ends of at least one member of a target library comprising a plurality of nucleic acid molecules claim 1 , wherein the plurality of nucleic acid end adaptors comprise a first defined sequence.3. The method of claim 2 , wherein the plurality of nucleic ...

Подробнее
Номер записи: 42
06-06-2013 дата публикации

METHOD AND DEVICE FOR THE DECONTAMINATION OF PLASTIC FLAKES

Номер: US20130142699A1
Автор: Friedlaender Thomas, Marx Frank, Rieckmann Thomas
Принадлежит: KRONES AG

A method for preparing contaminated plastics ground into flakes, such as RPET or such polymers, having at least decontamination and SSP treatment steps, with at least one reactor, with heating to the process temperature taking place essentially outside the reactor. Also, a device for carrying out the method, and having at least one decontamination reactor and at least one SSP reactor, a device for heating plastic flakes to the process temperature being arranged upstream of the decontamination reactor. Also an SSP reactor having at least two individual reactors, and preferably between 3 and 7 individual reactors. 1. Device for carrying out a method for preparing contaminated plastics ground into flakes , such as , for example , RPET or similar polymers , comprising at least decontamination and SSP treatment steps , the two steps of decontamination and SSP treatment taking place in at least one reactor , and carrying out a heating to the process temperature substantially outside of the at least one reactor , the device comprising:at least one decontamination reactor and the at least one SSP reactor for the preparation of the plastic flakes, and a device for heating plastic flakes to the process temperature connected in front of the at least one decontamination reactor.2. Device according to claim 1 , wherein the device for heating the flakes to the process temperature is formed from one of a heating screw or a vibrating helical conveyor.3. Device according to claim 1 , wherein the at least one decontamination reactor presents a conical shape claim 1 , which broadens in the direction of gravity.4. Device according to claim 1 , wherein two decontamination reactors are provided.5. Device according to claim 1 , wherein the at least one decontamination reactor presents a gas through-flow device claim 1 , which removes the contaminants from the reactor.6. Device according to claim 1 , and a device for further heating flakes to heat the flakes a higher temperature than the ...

Подробнее
Номер записи: 43
06-06-2013 дата публикации

METHOD FOR DETECTING GENE REGION FEATURES BASED ON INTER-ALU POLYMERASE CHAIN REACTION

Номер: US20130143746A1
Автор: Mei Lingling, Xue Hong
Принадлежит: PHARMACOGENETICS LTD.

An array of inter-Alu gene-enriched amplicons produced by a polymerase chain reaction (“PCR”) process. The PCR process comprises combining one or a plurality of Head-type/Tail-type Alu- or AluY- or any other Alu-subfamily-consensus sequence-based primer; a genomic DNA template isolated from cells; and a PCR-extension mix. The combination of primers, DNA template; and PCR extension mix comprises an inter-Alu-PCR-mixture. After making the inter-Alu-PCR mixture, an inter-Alu PCR cycle program is used in connection with a PCR machine for a period of time to produce the array of inter-Alu gene-enriched amplicons that are sequenced by massively parallel sequencing to allow genome wide scanning of sequence and structure variations in the human genome. 1. An array of inter-Alu gene-enriched amplicons produced by a polymerase chain reaction (“PCR”) process comprising: i. a plurality of Alu consensus sequence-based primers', 'ii. a genomic DNA template isolated from cells; and', a set of free deoxynucleotide triphosphate A,G,T and C bases;', 'a thermostable DNA polymerase; and', 'a buffer solution;, 'iii. a PCR-extension mix comprising, 'to give an inter-Alu-PCR-mixture,, '(a) combining(b) completing an inter-Alu PCR cycle program with the inter-Alu-PCR-mixture in a PCR machine for a period of time to produce the array of inter-Alu gene-enriched amplicons.2. The PCR process of claim 1 , further comprising a step of selecting the plurality of Alu consensus sequence-based primers to be AluY consensus sequence based primers from the AluY subfamily of Alu elements.3. The PCR process of claim 1 , further comprising a step of selecting the plurality of Alu consensus sequence-based primers to be: a Head-type AluY consensus sequence-based primer; a First Tail type AluY consensus sequence based primer; and a Second tail type AluY consensus sequence based primer.4. The PCR process of claim 3 , further comprising the step of selecting SEQ ID No.: 2 (5′ TGGTCTCGAT CTCCTGACCT C-3) as the ...

Подробнее
Номер записи: 44
06-06-2013 дата публикации

HIGH-SPEED MATURATION METHOD FOR AN OLIGONUCLEOTIDE LIBRARY FOR THE PURPOSE OF PREPARING A PROTEIN LIBRARY

Номер: US20130143773A1
Автор: Kanamori Takashi, Katoh Shizue, Kojoh Kanehisa, Miyakoshi Akira, UEDA Takuya
Принадлежит:

The present invention provides a method of producing a maturated oligonucleotide library, including a step of obtaining a terminal-modified product of a maturation target oligonucleotide library, including adding a tag sequence to the 5′ terminus of the maturation target oligonucleotide library and an arrest sequence, which stalls translation elongation on a ribosome, to the 3′ terminus of the maturation target oligonucleotide library, a step of transcribing the terminal-modified sequence product to give a transcript, and a step of in vitro translation for translating the transcript in vitro, wherein the maturation target oligonucleotide library is a random oligonucleotide library. 1. A method of producing a maturated oligonucleotide library , comprisinga step of obtaining a terminal-modified product of a maturation target oligonucleotide library, comprising adding a tag sequence to the 5′ terminus of said maturation target oligonucleotide library and an arrest sequence, which stalls translation elongation on a ribosome, to the 3′ terminus of said maturation target oligonucleotide library,a step of transcribing said terminal-modified sequence product to give a transcript, anda step of in vitro translation for translating said transcript in vitro,wherein said maturation target oligonucleotide library is a random oligonucleotide library.2. The method of claim 1 , wherein said random oligonucleotide library is an oligonucleotide library containing NNK sequence claim 1 , NNS sequence or NNY sequence.3. The method of claim 1 , wherein said arrest sequence is SecM sequence.4. The method of claim 1 , wherein said tag sequence is FLAG sequence.5. The method of claim 1 , wherein said in vitro translation step is a step of translating said transcript in vitro using a cell-free translation system.6Escherichia coli. The method of claim 1 , wherein said in vitro translation step is a step of translating said transcript in vitro using an cell-free translation system.7. The method ...

Подробнее
Номер записи: 45
06-06-2013 дата публикации

Aromatics Production Process and Apparatus

Номер: US20130144097A1
Автор: Bender Timothy P., Go Anthony, Iaccino Larry L., Porter John R., Rebeck John W., Vebeliunas Rimas V., WOOD GLENN C.
Принадлежит: ExxonMobil Chemical Patents Inc.

In a process for producing para-xylene, a naphtha feed is reformed under conditions effective to convert at least 50 wt % of the naphthenes in the naphtha feed to aromatics, but to convert no more than 25 wt % of the paraffins in the naphtha feed, and thereby produce a reforming effluent. A first stream containing benzene and/or toluene is removed from the reforming effluent and is fed to a xylene production unit under conditions effective to convert benzene and/or toluene to xylenes. In addition, a second stream containing C8 aromatics is removed from the reforming effluent and is fed, together with at least part of the xylenes produced in the xylene production unit, to a para-xylene recovery unit to recover a para-xylene product stream and leave a para-xylene-depleted C8 stream. At least part of para-xylene-depleted C8 stream is then fed to a xylene isomerization unit effective to isomerize xylenes in para-xylene-depleted stream back towards an equilibrium mixture of xylenes and thereby produce an isomerization effluent. The isomerization effluent is then recycled to the para-xylene extraction unit. 1. A process for producing para-xylene , the process comprising:(a) reforming a naphtha feed under reforming conditions effective to convert at least 50 wt % of the naphthenes in the naphtha feed to aromatics, but to convert no more than 25 wt % of the paraffins in the naphtha feed, and thereby produce a reforming effluent;(b) removing at least a first stream containing benzene and/or toluene and a second stream containing C8 aromatics from the reforming effluent;(c) feeding at least part of the benzene and/or toluene from the first stream to a xylene production unit under conditions effective to convert benzene and/or toluene to xylenes;(d) feeding at least part of the C8 aromatics from the second stream and at least part of the xylenes produced in (c) to a para-xylene recovery unit to recover a para-xylene product stream and leave a para-xylene-depleted C8 stream;(e) ...

Подробнее
Номер записи: 46
13-06-2013 дата публикации

Systems and methods for high speed array printing and hybridization

Номер: US20130150266A1
Автор: Holger Eickhoff, Thomas C. Tisone
Принадлежит: Biodot Inc

Novel and improved systems and methods for high speed arraying, hybridization, quantitative development and/or assaying are provided. Some embodiments provide a web based arraying format. Some other embodiments provide a sheet based arraying format. Some embodiments use a drop on drop assaying or hybridization mode. In some embodiments, a substantially inert substrate is utilized. In some other embodiments, an interactive substrate is utilized.

Подробнее
Номер записи: 47
20-06-2013 дата публикации

STRUCTURE-ACTIVITY RELATIONSHIPS

Номер: US20130157900A1
Автор: Davis Simon Christopher, Grate John H., Huisman Gjalt W., Krebber Anke, Mundorff Emily
Принадлежит: CODEXIS, INC.

The present disclosure relates to compositions and methods for screening a plurality of polypeptide variants. 1. A kit for identifying at least one polypeptide having a desired activity , comprising:(i) at least one plurality of addressable polypeptides, wherein each member of each plurality reacts with at least one ligand to produce a detectable signal, and wherein at least two members of each plurality are related to a parent polypeptide and react with different ligands; and(ii) instructions for use.2. The kit of claim 1 , wherein said at least one ligand is placed on a surface.3. The kit of claim 2 , wherein said surface is selected from plastic claim 2 , glass claim 2 , silica claim 2 , metal claim 2 , microparticles claim 2 , microchips claim 2 , and beads.4. The kit of claim 3 , wherein said at least one ligand is immobilized on said surface.5. The kit of claim 3 , wherein said plastic comprises the wells of a microtiter plate.6. The kit of claim 5 , wherein the wells of said microtiter plate contain at least one ligand.7. The kit of claim 6 , wherein the wells of said microtiter plate contain different ligands.8. The kit of claim 7 , wherein said at least one ligand is immobilized in at least one well of said microtiter plate.9. The kit of claim 6 , wherein said at least one ligand is in solution in said wells of said microtiter plate.10. The kit of claim 1 , wherein said at plurality of addressable polypeptides is placed on a surface.11. The kit of claim 10 , wherein said surface is selected from plastic claim 10 , glass claim 10 , silica claim 10 , metal claim 10 , microparticles claim 10 , microchips claim 10 , and beads.12. The kit of claim 10 , wherein at least one member of said plurality of addressable polypeptides is immobilized on said surface.13. The kit of claim 11 , wherein said plastic comprises the wells of a microtiter plate.14. The kit of claim 13 , wherein the wells of said microtiter plate contain at least one member of said plurality of ...

Подробнее
Номер записи: 48
27-06-2013 дата публикации

SYNTHESIS OF OLIGOMERS IN ARRAYS

Номер: US20130165349A1
Автор: Butler John
Принадлежит: LIFE TECHNOLOGIES CORPORATION

Systems, including apparatus and methods, for synthesis of oligomers in arrays. 1. A device comprising:an array portion comprising a plurality of porous islands and a spacer separating said islands, said plurality of porous islands being more hydrophilic than said spacer, each island defining at least one pore configured to permit fluid communication between opposing surfaces of said array portion.2. The device of claim 1 , wherein said device further comprises a reaction surface.3. The device of claim 2 , wherein said reaction surface is integral to at least one porous island.4. The device of claim 2 , wherein said reaction surface is integral to at least one pore.5. The device of claim 2 , wherein said reaction surface is contained within or attached to said porous island.6. The device of claim 1 , wherein at least one island comprises a plurality of pores.7. The device of claim 1 , wherein each island comprises a plurality of pores.8. The device of claim 1 , wherein said plurality of porous islands defines an array.9. The device of claim 1 , further comprising a least one channel comprising a first and a second end claim 1 , wherein said first end of said channel is in fluid communication with at least one porous island and wherein said channel is configured to permit fluid flowthrough.10. The device of claim 9 , wherein said channel is configured to receive reagents at said first end of said channel and is configured to release at least a portion of said reagents at said second end of said channel.11. The device of claim 9 , wherein said at least one of said channels further comprises a reaction surface.12. The device of claim 11 , wherein said reaction surface is integral to said channel.13. The device of claim 11 , wherein said reaction surface is a structure contained within or attached to said channel.14. A method of placing reagents in reaction compartments of an array comprising:dispensing a first reagent to one or more porous islands in an array of porous ...

Подробнее
Номер записи: 49
04-07-2013 дата публикации

Arrays and Methods of Use

Номер: US20130172216A1
Автор: Mir Kalim
Принадлежит:

Methods are provided for producing a molecular array comprising a plurality of molecules immoblised to a solid substrate at a density which allows individual immobilised molecules to be individually resolved, wherein each individual molecule in the array is spatially addressable and the identity of each molecule is known or determined prior to immobilisation. The use of spatially addressable low density molecular arrays in single molecule detection and analysis techniques is also provided. Novel assays and methods are also provided. 13-. (canceled)4. A method for producing a molecular array wherein molecules on the array can be individually resolved which method comprises:(i) providing a molecular array comprising a plurality of functional molecules of known identity immobilised to a solid phase; and(ii) labeling only a portion the density of functional immobilised molecules in the array such that remaining labeled individual functional immobilised molecules are spatially addressable and capable of being individually resolved by optical methods.516-. (canceled)16. The method according to wherein the label can be read by optical methods.17. The method according to wherein the label is a single fluorescent molecule claim 16 , nanoparticle or nanorod claim 16 , or one of a plurality of fluorescent molecules claim 16 , nanoparticles or nanorods.1819-. (canceled)20. The method according to wherein the molecules are selected from defined chemical entities claim 4 , oligonucleotides claim 4 , polynucleotides claim 4 , peptides claim 4 , polypeptides claim 4 , conjugated polymers claim 4 , small organic molecules or analogues claim 4 , mimetics or conjugates thereof.21. The method according to wherein the molecules are cDNA and/or genomic DNA.2223-. (canceled)25. The method according to wherein each of the labeled immobilised molecules in step (ii) are immobilised onto a single electrode.26. The method according to wherein the electrode transduces a signal when a target ...

Подробнее
Номер записи: 50
11-07-2013 дата публикации

USING POPULATIONS OF BEADS FOR THE FABRICATION OF ARRAYS ON SURFACES

Номер: US20130178397A1
Автор: Boutell Jonathan Mark, Rigatti Roberto, Smith Geoffrey Paul
Принадлежит: ILLUMINA CAMBRIDGE LIMITED

The present invention provides a method of creating an array of features. The method can include steps of (a) providing a plurality of beads, wherein each bead in the plurality of beads includes probe content; (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface; and (c) transferring the probe content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature includes probe content from a bead in the plurality of beads. 1. A method of creating an array of features , comprising(a) providing a plurality of beads, wherein each bead in the plurality of beads comprises probe content;(b) contacting the plurality of beads with a surface to produce a layer of beads on the surface; and(c) transferring the probe content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature comprises probe content from a bead in the plurality of beads.2. The method of claim 1 , wherein the transferring of the probe content comprises physically transferring a probe from each of the beads to attach the probe to a feature on the surface.3. The method of claim 1 , wherein the transferring comprises covalently attaching the probe content from the beads to each of the spatially discrete features on the surface.4. The method of claim 1 , wherein the transferring comprises non-covalently attaching the probe content from the beads to each of the spatially discrete features on the surface.5. The method of claim 1 , wherein a single probe molecule is transferred from each of the beads to each of the spatially discrete features.6. The method of claim 1 , wherein several copies of a single probe species are transferred from each of the beads to each of the spatially discrete features.7. The method of claim 1 , wherein the probe content comprises proteins.8. The method of claim 1 , wherein the probe content ...

Подробнее
Номер записи: 51
18-07-2013 дата публикации

GENOTYPING BY NEXT-GENERATION SEQUENCING

Номер: US20130184165A1
Автор: Liu Sanzhen, Schnable Patrick S., Wu Wei
Принадлежит: Data2Bio

Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing. 1. A method for genotyping by sequencing , the method comprising:1) digesting a nucleic acid with a restriction enzyme to produce a fragment;2) ligating a single-stranded barcode oligonucleotide to the fragment to produce a template;3) amplifying the template to produce an amplicon; and4) sequencing the amplicon to produce a sequence read.2. The method of wherein a template pool is produced by mixing a plurality of templates.3. The method of wherein a template pool is produced by mixing a plurality of templates from a plurality of individuals.4. The method of further comprising parsing the sequence read claim 1 , mapping the sequence read claim 1 , and assigning a genotype.5. The method of wherein the nucleic acid is digested with two different restriction enzymes.6. The method of wherein the nucleic acid is digested with NspI and BfuCI.7. The method of wherein the single-stranded barcode oligonucleotide identifies a subject that was the source of the nucleic acid.8. The method of wherein the amplifying comprises the use of a target specific primer.9. The method of wherein the amplifying selects an amplicon for sequencing.10. A method for genotyping by sequencing claim 1 , the method comprising:1) providing a first plurality of nucleic acids from a first subject;2) providing a second plurality of nucleic acids from a second subject;3) digesting the first plurality of nucleic acids with a restriction enzyme to produce a first plurality of fragments;4) digesting the second plurality of nucleic acids with the restriction enzyme to produce a second plurality of fragments;5) ligating a first single-stranded barcode oligonucleotide to each fragment of the first plurality of fragments to produce a first plurality of templates;6) ligating a second single-stranded barcode oligonucleotide to each fragment of the ...

Подробнее
Номер записи: 52
18-07-2013 дата публикации

MULTIPLEXED AMPLIFICATION OF SHORT NUCLEIC ACIDS

Номер: US20130184171A1
Автор: Lao Kai Qin, Livak Kenneth J., Straus Neil A.
Принадлежит: LIFE TECHNOLOGIES CORPORATION

The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR-based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein. 1. A method of quantitating at least 300 different short target nucleic acids , wherein each short target nucleic acid is 18-30 nucleotides in length , said method comprising;contacting the at least 300 different short target nucleic acids with at least 300 different target-specific stem-loop reverse transcription primers, wherein each of the at least 300 stem-loop reverse transcription primers comprises a unique 3′ target-specific portion, a unique zip-coded stem, and a loop;extending the at least 300 stem-loop reverse transcription primers in a reverse transcription reaction to form a collection of reverse transcription products;performing a PCR-based pre-amplification on the collection of reverse transcription products to form a collection of PCR-based pre-amplification products, wherein the PCR-based pre-amplification comprises at least 300 different forward primers and at least one reverse primer, wherein the sequence of the reverse primer comprises substantially the same sequence as the loop of the at least one stem-loop reverse transcription primer, and a Tm-enhancing tail;wherein each of the at least 300 different forward primers comprises i) a 3′ target-specific portion that is complementary to the 5′ end of a particular reverse ...

Подробнее
Номер записи: 53
01-08-2013 дата публикации

PATTERNED DEVICES AND METHODS FOR DETECTING ANALYTES

Номер: US20130196880A1
Автор: Lewis Heather, Ni Hong, Pang Lizhen, Stanislaw Stacey, Tang Lei
Принадлежит: Ventana Medical Systems, Inc.

Disclosed herein are devices for the detection of target molecules and methods for their use and production. The disclosed devices may include optically decipherable patterns that facilitate an understanding of binding events between a target molecule and a detection molecule. In one example, a device includes a macroscopic pattern constructed using microscopic elements that can be chromogenically developed to memorialize a binding event. In another example, a device includes characters that can be chromogenically developed using an automated slide staining instrument to memorialize a binding event. 1. A device comprisinga substrate with at least one substrate surface anda plurality of immobilized detection molecules bound to the substrate surface,wherein the plurality of immobilized detection molecules are patterned on the substrate surface to form at least one optically decipherable pattern.2. The device of claim 1 , wherein the detection molecules are oligonucleotides or peptides.3. The device of claim 1 , wherein the optically decipherable pattern includes a shape pattern and/or a positional pattern.4. The device of claim 1 , wherein the at least one optically decipherable pattern is a glyph rendered from a character selected from the Universal Character Set claim 1 , defined by the International Standard ISO/IEC 10646.5. The device of claim 3 , wherein the glyph is associated with a typeface claim 3 , the typeface having a typographic size of between about 1 and about 216 points or between about 3 and about 96 points claim 3 , wherein one point is 1/72 of inch.6. The device of claim 1 , wherein the plurality of detection molecules includes a first immobilized detection molecule that is specific to a first target molecule and a second immobilized detection molecule that is specific to a first control molecule.7. The device of claim 6 , wherein the first immobilized detection molecule is patterned on the substrate surface to form a first character and the second ...

Подробнее
Номер записи: 54
01-08-2013 дата публикации

Parallel Preparation of High Fidelity Probes in an Array Format

Номер: US20130197208A1
Автор: Kuimelis Robert G., McGall Glenn H.
Принадлежит: Affymetrix, Inc.

The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 10to about 10different sequences, generally between 25-160 bases in length). 138-. (canceled)44. The method of wherein the oligonucleotide is released from the substrate.45. The method of wherein the oligonucleotide released from the substrate has authentic 3′ hydroxyl termini.49. The method of wherein the first reactive site claim 39 , second reactive site claim 39 , third reactive site or reactive site is an oxygen atom.50. The method of wherein the B of the structure is G claim 47 , A claim 47 , T claim 47 , or C.51. The method of wherein the oligonucleotide is between about 80 to about 160 nucleotides. The present invention relates generally to the fabrication of oligonucleotides such as probes and primers using oligonucleotide array technology. The present invention relates to massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides.PCR techniques are well-established and widely used across various segments of life-science research, diagnostics, etc. An increasingly important trend in the application of PCR is the ability to multiplex the reaction, which requires, in addition to the usual thermal cycling equipment and enzyme, sets of carefully designed oligonucleotide primers (or probes). Oligonucleotide primers are traditionally prepared by the solid-supported phosphoranidite approach, either on controlled-pore glass, polymeric support or membrane support.Following oligonucleotide assembly, the support is typically treated with a deprotection reagent to remove protecting groups and to cleave the oligonucleotide from the support in a single step. Due to the high stepwise efficiency of the solid-supported phosphoramidite approach, it is often not necessary to rigorously ...

Подробнее
Номер записи: 55
08-08-2013 дата публикации

Method of Preparing a Nucleic Acid Library

Номер: US20130203606A1
Автор: Eckhardt Allen E., Pollack Michael G, Rouse Jeremy, Thwar Prasanna
Принадлежит: ADVANCED LIQUID LOGIC INC

A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; (b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments; coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and (d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments. 1. A method of preparing a nucleic acid library in droplets in contact with oil , comprising:(a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments;(b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments;(c) coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and(d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments.2. A method of preparing a nucleic acid library in droplets in contact with oil , comprising:(a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments;(b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments;(c) coupling nucleic acid adapters to the blunt ended nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments.3. The method of wherein recovery of adapter-ligated nucleic acid fragments from step 1.d is at least 5% on a molar basis of nucleic acid fragments input into step 1.a.4. The method of wherein ...

Подробнее
Номер записи: 56
08-08-2013 дата публикации

LIBRARY-BASED METHODS AND COMPOSITIONS FOR INTRODUCING MOLECULAR SWITCH FUNCTIONALITY INTO PROTEIN AFFINITY REAGENTS

Номер: US20130203609A1
Автор: Horn James R.
Принадлежит: BOARD OF TRUSTEES OF NORTHERN ILLINOIS UNIVERSITY

Methods and compositions are disclosed for introducing molecular switch functionality into a protein affinity reagent to render its binding to a target molecule sensitive to an environmental trigger, such as pH, while maintaining binding affinity to the target molecule. Combinatorial libraries created by the method are also disclosed. 1. A method for introducing molecular switch functionality into a wild type protein affinity reagent that binds a target molecule via a target binding interface , the method comprising:(a) obtaining an ionizable residue-scanning protein display library of the protein affinity reagent, the library comprising all possible combinations of amino acid residues of the target binding interface wherein each residue position was modified as an ionizable amino acid residue, and the remaining positions maintain residues in an existing protein affinity reagent;(b) selecting a target binding population of reagents from the library based on their ability to bind the target molecule;(c) selecting a target binding subpopulation from the target binding population that exhibits binding to the target molecule sensitive to the environmental trigger; and(d) identifying a modified target binding reagent from the subpopulation with molecular switch functionality sensitive to the environmental trigger while maintaining binding affinity to the target molecule.2. The method of claim 1 , wherein the protein affinity reagent is an antibody.3. The method of wherein the protein affinity reagent is a heavy chain variable domain antibody (VHH).4. The method of claim 1 , wherein the target molecule is selected from a group consisting of a protein claim 1 , DNA claim 1 , RNA claim 1 , low molecular weight haptens claim 1 , and carbohydrates.5. The method of claim 1 , wherein the target binding interface includes about 10 to 35 amino acid residues.6. The method of claim 1 , wherein the modification of the amino acids is done by substitution claim 1 , insertion claim 1 , ...

Подробнее
Номер записи: 57
08-08-2013 дата публикации

Plant Chimeric Binding Polypeptides For Universal Molecular Recognition

Номер: US20130203633A1
Автор: Jones Jennifer
Принадлежит: MONSANTO TECHNOLOGY LLC

Libraries of nucleic acids encoding chimeric binding polypeptides based on plant scaffold polypeptide sequences. Also described are methods for generating the libraries. 1. (canceled)2. A library of nucleic acids encoding at least ten different polypeptides , the amino acid sequence of each polypeptide comprising:{'sub': 1', '1', '2', '2', '3', '3', '4, 'C-X-C-X-C-X-C, wherein'}{'sub': 1', '2', '3', '4', '1', '4, 'figref': [{'@idref': 'DRAWINGS', 'FIG. 2'}, {'@idref': 'DRAWINGS', 'FIG. 4'}, {'@idref': 'DRAWINGS', 'FIG. 2'}, {'@idref': 'DRAWINGS', 'FIG. 4'}, {'@idref': 'DRAWINGS', 'FIG. 2'}, {'@idref': 'DRAWINGS', 'FIG. 4'}, {'@idref': 'DRAWINGS', 'FIG. 2'}, {'@idref': 'DRAWINGS', 'FIG. 4'}], '(i) subsequence Cis selected from or , subsequence Cis selected from or , subsequence Cis selected from or ; subsequence Cis selected from or , and each of C-Ccomprise up to 10 single amino acid substitutions, deletions, insertions, or additions to the selected subsequence;'}{'sub': 1', '4, '(ii) C-Care homogeneous across a plurality of the encoded polypeptides;'}{'sub': 1', '3, '(iii) each of X-Xis an independently variable subsequence consisting of 2-20 amino acids; and'}{'sub': 1', '3, '(iv) each of X-Xare heterogeneous across a plurality of the encoded polypeptides.'}3. A library of nucleic acids encoding at least ten different polypeptides , the amino acid sequence of each polypeptide comprising:{'sub': 1', '1', '2', '2', '3', '3', '4, 'C-X-C-X-C-X-C, wherein'}{'sub': 1', '2', '3', '4', '1', '4, 'figref': [{'@idref': 'DRAWINGS', 'FIG. 3'}, {'@idref': 'DRAWINGS', 'FIG. 5'}, {'@idref': 'DRAWINGS', 'FIG. 3'}, {'@idref': 'DRAWINGS', 'FIG. 5'}, {'@idref': 'DRAWINGS', 'FIG. 3'}, {'@idref': 'DRAWINGS', 'FIG. 5'}, {'@idref': 'DRAWINGS', 'FIG. 3'}], '(i) subsequence Cis selected from or , subsequence Cis selected from or , subsequence Cis selected from or ; subsequence Cis selected from XX, and each of C-Ccomprise up to 30 single amino acid substitutions, deletions, insertions, or ...

Подробнее
Номер записи: 58
15-08-2013 дата публикации

MICROFLUIDIC DEVICES

Номер: US20130210639A1
Автор: Link Darren R., Marran David, Rothberg Jonathan M., Weiner Michael
Принадлежит:

The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids. 174-. (canceled)75. A sample preparation method , the method comprising:obtaining nucleic acid;attaching an adapter to the nucleic acid; andforming a flowing droplet comprising the nucleic acid.76. The method according to claim 75 , further comprising conducting an amplification reaction in the droplet.77. The method according to claim 76 , wherein the amplification reaction is selected from the group of PCR claim 76 , QPCR claim 76 , and rolling circle amplification.78. The method according to claim 76 , wherein the amplification reaction comprises:introducing primer pairs into the droplet, wherein the primer pairs hybridizes to the adapters on the nucleic acids; andconducting a PCR reaction.79. The method according to claim 77 , further comprising releasing the nucleic acid from the droplet.80. The method according to claim 79 , further comprising sequencing the released nucleic acid.81. The method according to claim 81 , wherein the nucleic acid is attached to a solid support.82. The method according to claim 75 , wherein the droplet is flowing through a channel.83. The method according to claim 82 , wherein the droplet is surrounded by an immiscible carrier fluid.84. The method according to claim 83 , wherein the immiscible carrier fluid is an oil.85. The method according to claim 84 , wherein the oil comprises a surfactant.86. The method according to claim 85 , wherein the surfactant is a fluorosurfactant.87. A method for amplifying nucleic acid claim 85 , the method comprising:forming a flowing droplet comprising a nucleic acid template, wherein an adapter is attached to the template; andconducting an amplification reaction ...

Подробнее
Номер записи: 59
15-08-2013 дата публикации

SYSTEMS AND METHODS FOR AMPLIFICATION AND PHAGE DISPLAY

Номер: US20130210680A1
Автор: Derda Ratmir, Tang Sindy K.Y., Whitesides George M.
Принадлежит: President and Fellows of Harvard College

The present invention generally relates to amplification of biological entities, for example, for phage display. In one aspect, members of a library of biological entities are encapsulated in separate compartments (e.g., in separate microfluidic droplets) and amplified. As a specific example, by putting members of a phage display library into microfluidic droplets such that no droplet contains more than one member of the library, the library can be amplified without any substantial changes in growth rates or population distributions, or other artifacts created due to differences in growth rates or amplification between different members of the library. In some cases, the volume of the compartments can be used to control the copy number of a biological entity during amplification. In certain cases, biological entities with different amplification rates can be amplified independently of each other. In some embodiments, the ratio of a rapidly amplifying biological entity to a slowly amplifying biological entity can be controlled. This can be advantageous, for example, in preserving diversity within a library by preventing rapidly amplifying biological entities from outcompeting slowly amplifying biological entities. For example, certain methods and systems of the invention can be useful in situations where preferential amplification of library members can present a problem. 2. The method of claim 1 , wherein the replicable genetic package is a virus claim 1 , a eukaryotic cell claim 1 , a spore claim 1 , a yeast cell claim 1 , a bacterial cell claim 1 , a nucleic acid sequence claim 1 , or a recombinant thereof.3. The method of claim 1 , wherein the replicable genetic package is a virus claim 1 , and wherein substantially each of the individual compartments further comprises at least one host cell capable of supporting replication of the replicable genetic package claim 1 , wherein the number of host cells within each of the individual compartments is substantially the ...

Подробнее
Номер записи: 60
22-08-2013 дата публикации

IN VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS

Номер: US20130217601A1
Автор: Ahn Keunho, Bibette Jérôme, Griffiths Andrew David, Link Darren Roy, Weitz David
Принадлежит:

The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention. 1107-. (canceled)108. A method of producing a library of entities , comprising the steps of:producing a plurality of microcapsules, each microcapsule comprising at least one entity of a species; andpooling the microcapsules into one or more common compartments, thereby providing a library of encapsulated entities,wherein at least one step of the method is performed under microfluidic control.109. The method of claim 108 , wherein the entities are nucleic acids claim 108 , proteins claim 108 , or cells.110. The method of claim 109 , wherein the nucleic acids are primers for a polymerase chain reaction (PCR).111. The method of claim 108 , wherein the entities are labeled.112. The method of claim 111 , wherein the entities are optically labeled.113. The method of claim 111 , wherein the entities are fluorescently labeled antibodies.114. The method of claim 111 , wherein the entities are chemically labeled antibodies.115. The method of claim 108 , wherein the plurality of microcapsules are unable to fuse or coalesce due to the presence of a surfactant.116. The method of claim 108 , wherein the surfactant is a fluorinated surfactant.117. The method of claim 108 , wherein producing comprises forming the microcapsules in carrier fluid.118. The method of claim 117 , wherein the carrier fluid comprises an oil.119. The method of claim 118 , wherein the oil is a fluorinated or perfluorinated oil.120. The method of claim 108 , wherein the microcapsules are ...

Подробнее
Номер записи: 61
29-08-2013 дата публикации

Method of Ligating a Nucleic Acid

Номер: US20130225450A1
Автор: Eckhardt Allen E., Pollack Michael G., Rouse Jeremy, Thwar Prasanna
Принадлежит: ADVANCED LIQUID LOGIC INC

A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; 1. A method of ligating a nucleic acid to a blunt-ended nucleic acid fragment in a droplet in contact with oil , comprising merging a sample droplet comprising bunt-ended nucleic acid fragments with one or more reagent droplets comprising the nucleic acid and ligation reagents to yield a product droplet comprising ligated nucleic acid fragments.2. The method of further comprising merging the product droplet with a bead droplet comprising solid phase reversible immobilization beads to capture the ligated nucleic acid fragments.3. The method of further comprising washing the solid phase reversible immobilization beads using a droplet-based merge-and-split wash protocol using wash buffer droplets to yield a droplet comprising washed beads comprising the ligated nucleic acid fragments claim 2 , wherein the wash buffer droplets consist essentially of an aqueous buffer.4. The method of further comprising merging a droplet comprising washed beads with an elution buffer droplet to yield an elution droplet comprising eluted ligated nucleic acid fragments.5. The method of further comprising separating the A-tailed nucleic acid fragments from the solid phase reversible immobilization beads to yield a droplet comprising the ligated nucleic acid fragments in the oil.6. A method of making A-tailed nucleic acid fragments in a droplet in contact with oil claim 4 , comprising merging in the oil a sample droplet comprising nucleic acid fragments with one or more reagent droplets comprising A-tailing reagents to yield a product droplet comprising A-tailed nucleic acid fragments.7. The method of further comprising merging the product droplet with a bead droplet comprising solid phase reversible immobilization beads to capture the A-tailed nucleic acid fragments.8. The method of further ...

Подробнее
Номер записи: 62
05-09-2013 дата публикации

COMPOSITIONS AND METHODS FOR TARGETED NUCLEIC ACID SEQUENCE ENRICHMENT AND HIGH EFFICIENCY LIBRARY REGENERATION

Номер: US20130231253A1
Автор: Amorese Doug, Armour Chris, Kurn Nurith
Принадлежит:

The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.

Подробнее
Номер записи: 63
12-09-2013 дата публикации

PROTEIN OR PEPTIDE PRINTING METHOD, PROTEIN ARRAY OR PEPTIDE ARRAY AND FUNCTIONAL PROTEIN OR FUNCTIONAL PEPTIDE IDENTIFICATION METHOD

Номер: US20130237430A1
Автор: Biyani Manish, ICHIKI Takanori, SHIONO Hirofumi
Принадлежит: THE UNIVERSITY OF TOKYO

The present invention relates to a protein or peptide printing method, comprising (a) a step for preparing nucleic acids and a cell-free protein synthesis system in an engraved plate composed of microscopic grooves having a specific opening shape, (b) a step for superimposing a substrate on the engraved plate so as to contact a protein or peptide to be synthesized in the microscopic grooves, and (c) a step for synthesizing the protein or peptide from the nucleic acids using the cell-free protein synthesis system in the microscopic grooves, and immobilizing the protein or peptide on the substrate along the specific opening shapes of the microscopic grooves. 1. A protein or peptide printing method , comprising:(a) preparing nucleic acids and a cell-free protein synthesis system in an engraved plate composed of microscopic grooves having a specific opening shape,(b) superimposing a substrate on the engraved plate so as to contact a protein or peptide to be synthesized in the microscopic grooves, and(c) synthesizing the protein or peptide from the nucleic acids using the cell-free protein synthesis system in the microscopic grooves, and immobilizing the protein or peptide on the substrate along the specific opening shapes of the microscopic grooves.2. The protein or peptide printing method according to claim 1 , wherein the protein or peptide includes an amino acid sequence as a solid-phase binding site claim 1 , and the substrate has a solid-phase binding site recognition site having affinity for the amino acid sequence.3. The protein or peptide printing method according to claim 2 , wherein the solid-phase binding site recognition site is nickel ion or cobalt ion.4. The protein or peptide printing method according to claim 2 , wherein the amino acid sequence is polyhistidine.5. A protein or peptide printing method according to claim 1 , whereina biotinylated puromycin derivative is further provided in the microscopic grooves in the (a), andan avidin-labeled substrate ...

Подробнее
Номер записи: 64
12-09-2013 дата публикации

SPOTTING PLATE AND PROCESS FOR ITS PRODUCTION

Номер: US20130237443A1
Автор: Eickhoff Holger, KNEBEL Guenther
Принадлежит:

A process for the production of a reaction chamber assembly, wherein a flat substrate and bottomless reaction chambers are provided, the substrate is first loaded with a biological agent and then the bottomless reaction chambers are bonded glue-free to the substrate, in particular through laser bonding, and liquid-tight reaction chambers, for instance individual wells, individually connected wells, such as strips, or wells in the form of a microtiter plate, are obtained. The present invention further provides a kit comprising a substrate suitable for being loaded with at least one biological agent and at least one bottomless reaction chamber, wherein the kit is suitable for glue-free bonding of the bottomless reaction chamber to the substrate. 1. A process for the production of a reaction chamber assembly , which process comprises the following process steps in the following order:a) providing a polymeric flat substrate having a reaction surface and a bottom surface and at least one polymeric bottomless reaction chamber, subsequentlyb) loading at least one biological agent onto the reaction surface of the substrate, subsequentlyc) glue-free bonding the at least one bottomless reaction chamber to the reaction surface of the substrate and subsequentlyd) obtaining a reaction chamber assembly comprising at least one liquid-tight reaction chamber.2. The process according to claim 1 , wherein the glue-free bonding is laser bonding claim 1 , thermal bonding or ultrasonic-bonding.3. The process according to claim 1 , wherein the substrate has a thickness from 10 to 2000 m.4. The process according to claim 1 , wherein in step b) the at least one biological agent is spotted onto the reaction surface of the substrate providing a geometrical pattern of spots corresponding to inner dimensions of the bottomless reaction chamber.5. The process according to claim 1 , wherein in step b) the at least one biological agent is loaded onto the reaction surface of the substrate by means ...

Подробнее
Номер записи: 65
12-09-2013 дата публикации

Template directed split and mix synthesis of small molecule libraries

Номер: US20130237459A1
Автор: Peter Birk Rasmussen
Принадлежит: Individual

The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).

Подробнее
Номер записи: 66
19-09-2013 дата публикации

Molecular Display Method

Номер: US20130244883A1
Автор: Gakhal Amandeep, Moffat Jason, Patel Nish, Persson Helena, Sidhu Sachdev, Sundararajan Saravanan, YE Wei
Принадлежит: THE GOVERNING COUNCIL OF THE UNIVERSITY OF TORONTO

There is provided herein a method for identifying and/or recovering at least one genetically encoded affinity reagent specific for a target molecule by screening using molecular display in conjunction with the sequencing of positive and negative selection pools from the screen. 1. A method for identifying and/or recovering at least one genetically encoded affinity reagent specific for a target molecule , the method comprising:(a) providing a molecular display system which displays a library of potential genetically encoded affinity reagents;(b) screening the library against the target molecule to produce positive and negative selection pools, preferably with multiple rounds of selection;(c) sequencing genetically encoded affinity reagents in each of the positive and negative selection pools;(d) identifying at least one sequence that is more abundant in the positive selection pool as compared to the negative selection pool; and(e) recovering at least one clone corresponding to the sequence.2. The method of claim 1 , wherein the display system is selected from the group consisting of phage display claim 1 , bacterial display claim 1 , yeast display claim 1 , ribosome display and mRNA display.3. The method of claim 2 , wherein the display system is phage display.4. The method of claim 1 , wherein the sequencing comprises deep/high-throughput sequencing.5. The method of claim 4 , wherein the deep sequencing comprises Illumina sequencing.6. The method of claim 4 , wherein the deep sequencing comprises Ion semiconductor sequencing.7. The method of claim 1 , wherein each of the affinity reagents in the library contain unique sequence tags and the sequencing identifies the unique sequence tags.8. The method of claim 7 , wherein the at least one clone is recovered by annealing primers specific for the unique sequence tags.9. The method of claim 1 , wherein the affinity reagents are selected from the group consisting of nucleic acid molecules and polypeptides.10. The method ...

Подробнее
Номер записи: 67
19-09-2013 дата публикации

APTZAYME CAPABLE OF SELECTIVE SILENCING OF TARGET miRNA BY RELEASING AN ANTISENSE SEQUENCE IN HEPATITIS C VIRUS-INFECTED CELLS AND USE THEREOF

Номер: US20130245094A1
Автор: Lee Chang-Ho, LEE Seong-Wook
Принадлежит: INDUSTRY-ACADEMIC COOPERATION FOUNDATION DANKOOK UNIVERSITY

The present invention relates to an aptazyme comprising an aptamer for hepatitis C virus (HCV) RNA-encoding component; a hammerhead ribozyme comprising an antisense sequence to microRNA at the site released by self-cleavage; and a communication module sequence that connects the aptamer and hammerhead ribozyme and triggers a self-cleavage activity of the hammerhead ribozyme upon binding of the aptamer with the HCV RNA-encoding component. The present aptazyme inhibits microRNA activity specifically in HCV proliferating cells and thus a composition of the present invention comprising the aptazyme can be effectively used for treatment of HCV-related diseases. 1. An aptazyme capable of releasing an antisense sequence to microRNA specifically in HCV-infected cells , comprising an aptamer for hepatitis C virus (HCV) RNA-encoding component; a hammerhead ribozyme comprising an antisense sequence to microRNA at the site released by self-cleavage; and a communication module sequence that connects the aptamer and hammerhead ribozyme and induces self-cleavage activity of hammerhead ribozyme upon binding of the aptamer with the HCV RNA-encoding component.2. The aptazyme according to having the hammerhead ribozyme that comprises a sequence shown in claim 1 , wherein 5′-NCNNNNNNGN-3′ part of stem II in hammerhead ribozyme of is substituted with 5′ communication module sequence—aptamer sequence—3′ communication module sequence.3. The aptazyme according to claim 2 , wherein (NNN)n part (N representing A claim 2 , C claim 2 , G or U claim 2 , and n representing natural number) of stem I in the hammerhead ribozyme having the sequence disclosed in is substituted with an antisense sequence to microRNA.4. The aptazyme according to claim 1 , wherein the aptamer is an aptamer for NS5B protein.5. The aptazyme according to claim 4 , wherein the aptamer is a sequence selected from the group consisting of SEQ ID Nos. 1 to 4.6. The aptazyme according to any one of to claim 4 , wherein the ...

Подробнее
Номер записи: 68
26-09-2013 дата публикации

cDNA SYNTHESIS USING NON-RANDOM PRIMERS

Номер: US20130252823A1
Автор: Armour Christopher, Castle John, Raymond Christopher
Принадлежит: LIFE TECHNOLOGIES CORPORATION

The present invention provides methods for selectively amplifying a target population of nucleic acid molecules in a population of RNA template molecules (e.g., all mRNA molecules expressed in a cell type except for the most highly expressed mRNA species). The invention also provides a method of generating a population of oligonucleotide primers for transcriptome profiling of total RNA from a subject of interest. 1. A method of generating a cDNA library representative of the transcriptome profile contained in total RNA in a subject of interest , comprising:(a) synthesizing a population of single-stranded primer extension products from a target population of nucleic acid molecules within total RNA obtained from a subject of interest using reverse transcriptase enzyme and a first population of oligonucleotide primers comprising a hybridizing portion consisting of 6 to 9 nucleotides, a first PCR primer binding site located 5′ to the hybridizing portion, and a spacer portion consisting of from 2 to 10 nucleotides located between the hybridizing region and the PCR primer binding site, wherein the hybridizing portion is selected from all possible oligonucleotides having a length of from 6 to 9 nucleotides that hybridize under defined conditions to non-redundant target population of nucleic acid molecules, and do not hybridize under defined conditions to the non-target redundant population of nucleic acid molecules in the sample; and(b) synthesizing double-stranded cDNA from the population of single-stranded primer extension products generated according to step (a) using a DNA polymerase and a second population of oligonucleotide primers comprising a hybridizing portion consisting of from 6 to 9 nucleotides, a second PCR primer binding site located 5′ to the hybridizing portion, and a spacer portion consisting of from 2 to 10 nucleotides located between the hybridizing portion and the PCR primer binding region, to generate a cDNA library representative of the transcriptome ...

Подробнее
Номер записи: 69
26-09-2013 дата публикации

METHOD OF MAKING A PAIRED TAG LIBRARY FOR NUCLEIC ACID SEQUENCING

Номер: US20130252851A1
Автор: Li Bin, RANADE Swati, WANG Yangzhou, Xi Lei
Принадлежит: APPLIED BIOSYSTEMS, LLC

The present disclosure relates to methods and compositions for making paired tags and paired tag libraries. 191-. (canceled)92. A plurality of circular nucleic acid molecules , the individual circular molecules in the plurality comprising:(a) a universal sequence region common to the plurality of circular nucleic acid molecules and having two nicks; and(b) a target sequence region that differs between different molecules of the plurality of circular molecules.93. The molecules of claim 92 , wherein the universal sequence region comprises a double-stranded nucleic acid.94. The molecules of claim 92 , wherein the universal sequence further comprises a binding moiety.95. The molecule of claim 94 , wherein the binding moiety comprises biotin.96. The molecules of claim 94 , further comprising a purifying moiety.97. The molecules of wherein the purifying moiety comprises streptavidin.98. The molecule of claim 92 , further comprising a nick translating enzyme.99. The molecule of claim 98 , wherein the nick translating enzyme comprises DNA polymerase I.100. A plurality of circular nucleic acid molecules claim 98 , the individual circular molecules in the plurality comprising:(a) a universal sequence region common to the plurality of circular nucleic acid molecules, the universal sequence region having a first end and a second end;(b) a target sequence region that differs between different molecules of the plurality of circular molecules, the target sequence region having a first end and a second end;(c) a first nick between the first end of the universal sequence region and the first end of the target sequence region; and(d) a second nick between the second end of the universal sequence region and the second end of the target sequence region. This application is a continuation of U.S. Nonprovisional application Ser. No. 12/350,837, filed Jan. 8, 2009, which claims priority to U.S. Provisional Applications Ser. No. 61/109,638, filed Oct. 30, 2008 and 61/020,114, filed Jan. 9 ...

Подробнее
Номер записи: 70
26-09-2013 дата публикации

Oligonucleotides Related to Lipid Membrane Attachment

Номер: US20130252852A1
Автор: Höök Fredrick, Pfeiffer Indriati
Принадлежит: Bio-Rad Laboratories Inc.

A method of forming a lipid membrane attached linker comprises contacting a lipid membrane with an oligonucleotide having a first strand and a second strand of nucleic acid and two or more hydrophobic anchoring moieties located in its terminal ends. The two strands are hybridized to each other in a duplex section in a manner that the first strand terminal end is not a part of the duplex section and free from a hydrophobic anchoring moiety and the two or more hydrophobic anchoring moieties are covalently attached to the adjacent terminal ends of the first strand and the second strand of said oligonucleotide, thereby accomplishing a direct attachment of the oligonucleotide by the moieties on the same membrane. 1. A method of forming a lipid membrane attached linker , comprising contacting a lipid membrane with an oligonucleotide having a first strand and a second strand of nucleic acid and two or more hydrophobic anchoring moieties located in its terminal ends , said two strands being hybridized to each other in a duplex section in a manner that the first strand terminal end is not a part of said duplex section and free from a hydrophobic anchoring moiety and wherein said two or more hydrophobic anchoring moieties are covalently attached to the adjacent terminal ends of said first and second strands of said oligonucleotide , thereby accomplishing a direct attachment of said oligonucleotide by said moieties on the same membrane.2. A method according to claim 1 , wherein said membrane forms a lipid vesicle.3. A method according to claim 1 , wherein said membrane is a bilayer membrane.4. A method according to claim 1 , wherein said attachment is irreversible.5. A method according to claim 1 , wherein the first strand terminal end not being part of the duplex section is free to hybridize with a third strand.6. A method according to claim 5 , wherein the first strand has hydrophobic anchoring moieties in both terminal ends.7. A method according to claim 5 , wherein the ...

Подробнее
Номер записи: 71
03-10-2013 дата публикации

NUCLEIC ACID ADAPTORS AND USES THEREOF

Номер: US20130261027A1
Автор: Biorac Tanya, CHEN Zhoutao, Li Bin, Wei Melvin
Принадлежит: LIFE TECHNOLOGIES CORPORATION

Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest. 1. A method for joining a first and a second nucleic acid , comprising:a) providing a first nucleic acid overhang having a first nucleic acid sequence and a second nucleic acid overhang having a second nucleic acid sequence, the first and second nucleic acid sequences being at least partially complementary to each other, wherein the first overhang is hybridized to a first blocking oligonucleotide over at least a portion of its length and the second overhang is hybridized to a second blocking oligonucleotide over at least a portion of its length;b) separating the first and the second blocking oligonucleotides from the first and the second nucleic acid overhangs; andc) hybridizing the first nucleic acid sequence with the second nucleic acid sequence, thereby joining together the first and the second nucleic acid overhangs.2. The method of claim 1 , wherein the first nucleic acid overhang comprises a first double-stranded nucleic acid adaptor.3. The method of claim 1 , wherein the second nucleic acid overhang comprises a second double-stranded nucleic acid ...

Подробнее
Номер записи: 72
03-10-2013 дата публикации

VARIABLE PITCH ARRAY SPOTTER

Номер: US20130261029A1
Автор: Aoki Hiroshi, Ikeda Takashi, Tao Hiroaki, TORIMURA Masaki
Принадлежит: NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY

A spotter that includes a plurality of spotting heads, each of the plurality of spotting heads having a discharging portion at a tip portion, the plurality of spotting heads form an m×n array (m, n>1) with m spotting heads arranged lengthwise and n spotting heads arranged crosswise; and a pitch varying mechanism configured to vary an array pitch of the plurality of spotting heads arrayed in a lengthwise direction and an array pitch of the plurality of spotting heads arrayed in a crosswise direction. 1. A spotter comprising:a plurality of spotting heads, each of the plurality of spotting heads being flexible and having a discharging portion at a tip portion, the plurality of spotting heads form an m×n array (m, n≧1) with m spotting heads arranged lengthwise and n spotting heads arranged crosswise; anda pitch varying mechanism configured to vary an array pitch of the plurality of spotting heads in a lengthwise direction and an array pitch of the plurality of spotting heads in a crosswise direction,the pitch varying mechanism comprising:n first guiding members arranged in the crosswise direction, each of the n first guiding members has a first guiding hole, the m spotting heads arranged in the lengthwise direction being inserted into the first guiding hole, respectively, the first guiding hole extending in the lengthwise direction; andm second guiding members arranged in the lengthwise direction, each of the m second guiding members has a second guiding hole, the n spotting heads arranged in the crosswise direction being inserted into the second guiding hole, respectively, the second guiding hole extending in the crosswise direction;whereineach of the n first guiding members guides the m spotting heads in the lengthwise direction;each of the m second guiding members guides the n spotting heads in the crosswise direction;the n first guiding members movably held in the crosswise direction, respectively;the m second guiding members movably held in the length wise ...

Подробнее
Номер записи: 73
10-10-2013 дата публикации

Method of tagging using a split DBR

Номер: US20130267424A1
Автор: Brenner Sydney, Casbon James, Claas Andreas, Lichtenstein Conrad, Osborne Robert
Принадлежит:

Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications. 124-. (canceled)25. A method of sequencing , comprising:a) appending a degenerate base region (DBR) sequence to both ends of a plurality of target nucleic acid molecules in a genomic sample, wherein said DBR sequence comprises at least one nucleotide base selected from: R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof and wherein said appending produces a population of asymmetrically tagged nucleic acid molecules that each comprise: (i) a target polynucleotide, (ii) a first DBR sequence at the 5′ end of the target polynucleotide and (iii) a second DBR sequence at the 3′ end of the target polynucleotide, wherein:in each of said asymmetrically tagged nucleic acid molecules the first DBR sequence is different from the second DBR sequence; andthe different asymmetrically tagged nucleic acid molecules in said population have different first DBR sequences and different second DBR sequences, relative to one another;b) amplifying at least some of said asymmetrically tagged nucleic acid molecules, thereby producing a population of amplified asymmetrically tagged nucleic acid molecules; andc) ...

Подробнее
Номер записи: 74
17-10-2013 дата публикации

Method for analyzing proteins contributing to autoimmune diseases, and method for testing for said diseases

Номер: US20130273579A1
Автор: Ichiro Aoki, Tatsuya Sawasaki, Tomoaki Ishigami, Yaeta Endo
Принадлежит: Ehime University NUC, YOKOHAMA CITY UNIVERSITY

Provided are a detection method for a myriad of proteins involved in an autoimmune disease with high sensitivity and high efficiency, and an analysis method for data resulting from the detection method. In order to construct the detection method and analysis method, there is provided means for comprehensively analyzing the proteins involved in an autoimmune disease by bringing a mammal-derived protein expressed in a cell-free protein synthesis system into contact with a sample derived from a patient with an autoimmune disease to detect autoantibody production, and subjecting the detected data to statistical analysis processing, and further, gene ontology analysis and/or pathway analysis.

Подробнее
Номер записи: 75
17-10-2013 дата публикации

High-Throughput Single Cell Barcoding

Номер: US20130274117A1
Автор: Church George M., VIGNEAULT Francois
Принадлежит: President and Fellows of Harvard College

Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery. 120-. (canceled)21. A bead , comprisinga first bar code and a second bar code, wherein the second bar code is an amplified product of the first bar code.22. The bead of claim 21 , further comprising one or more target polynucleotides from an isolated single cell.23. The bead of claim 22 , wherein the one or more target polynucleotides comprise a heavy chain mRNA and a light chain mRNA.24. A method of bar coding one or more target polynucleotides claim 22 , comprising performing a reverse transcription reaction on the bead of .25. The method of claim 24 , wherein the bead is isolated with the single cell.26. The method of claim 25 , wherein the bead and the single cell are isolated in an oil and water emulsion.27. The method of claim 26 , wherein the single cell is lysed.28. The method of claim 25 , wherein the isolated single cell is a B-cell.29. The bead of claim 21 , wherein the first bar code is comprised in a first polynucleotide claim 21 , comprising: a first sequencing primer region claim 21 , the first barcode claim 21 , and a first annealing primer region.30. The bead of claim 29 , further comprising a third bar code identical to the first bar code claim 29 , and the third bar code is comprised in a second polynucleotide comprising: a second sequencing primer region claim 29 , the third bar code claim 29 , and a second annealing primer region that is not identical to the first annealing primer region.31. The method of claim 24 , further comprising claim 24 , amplifying the one or more bar coded target polynucleotides.32. The method of claim 31 , further comprising sequencing two or more of the amplified claim 31 , bar coded target polynucleotides.33. The method of claim 32 , further comprising correlating one of the two ...

Подробнее
Номер записи: 76
24-10-2013 дата публикации

Methods for sorting nucleic acids and preparative in vitro cloning

Номер: US20130281308A1
Автор: Joseph Jacobson, Li-Yun A. Kung
Принадлежит: Gen9 Inc

Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.

Подробнее
Номер записи: 77
24-10-2013 дата публикации

Bi-functinal complexes and methods for making and using such complexes

Номер: US20130281324A1
Автор: Alex Haahr Gouliaev, Kim Birkebaek Jensen, Michael Anders Godskesen, Thomas Franch
Принадлежит: Nuevolution AS

The present invention is directed to a method for the synthesis of a bi-functional complex comprising a molecule part and an identifier oligonucleotide part identifying the molecule part. A part of the synthesis method according to the present invention is preferably conducted in one or more organic solvents when a nascent bi-functional complex comprising an optionally protected tag or oligonucleotide identifier is linked to a solid support, and another part of the synthesis method is preferably conducted under conditions suitable for enzymatic addition of an oligonucleotide tag to a nascent bi-functional complex in solution.

Подробнее
Номер записи: 78
31-10-2013 дата публикации

Method for Making an Enriched Library

Номер: US20130288929A1
Автор: Allan Beck Christensen, Frank Abildgaard SLØK, Johan Holmkvist, Judith Rasmussen-Dietvorst, Lars Kolster Petersen, Leif Kongskov Larsen, Nils Jakob Vest Hansen, Peter Blakskjaer, Tara Heitner Hansen
Принадлежит: VIPERGEN APS

A method for making an enriched library comprising specific nucleic acid sequence information allowing to identifying at least one binding entity that binds to at least one target wherein the specific binding entity has been present in an in vitro display library.

Подробнее
Номер записи: 79
31-10-2013 дата публикации

EFFICIENT METHOD FOR DISPLAYING PROTEIN MULTIMER

Номер: US20130288930A1
Автор: Kanamori Takashi, Katoh Shizue, Kojoh Kanehisa, Tsuihiji Kumiko
Принадлежит:

The invention provides a method of producing a protein multimer-nucleic acid complex comprising a protein multimer and any one target component of the protein multimer. A nucleic acid encoding the target component is subjected to in vitro translation to provide a translation product containing a target component-nucleic acid complex of the target component and the nucleic acid encoding the target component. A nucleic acid encoding a non-target component constituting the protein multimer together with the target component is translated into the non-target component by adding the nucleic acid encoding the non-target component to the previously provided translation product to provide the non-target component. The non-target component then is associated with the target component contained in the target component-nucleic acid complex to form a protein multimer, thus affording the protein multimer-nucleic acid complex of the protein multimer and the nucleic acid encoding the target component. 1. A method of producing a protein multimer-nucleic acid complex comprising the protein multimer and a nucleic acid encoding any one target component of the protein multimer , which comprises the following steps:i) translating a nucleic acid encoding the target component into the target component by an in vitro translation system to give a translation product containing a target component-nucleic acid complex containing the target component and the nucleic acid encoding the target component, andii) translating a nucleic acid encoding a non-target component constituting the protein multimer together with the target component into the non-target component by adding the nucleic acid encoding the non-target component to the translation product obtained in i) to give the non-target component, associating the non-target component with the target component in the target component-nucleic acid complex to form the protein multimer, thus affording the protein multimer-nucleic acid complex ...

Подробнее
Номер записи: 80
07-11-2013 дата публикации

Methods and Devices for Nucleic Acid Synthesis

Номер: US20130296194A1
Автор: Hudson Mike, Jacobson Joseph, Kung Li-Yun A., RAMU Senthil, Schindler Daniel, Wilson Andrew Kirk
Принадлежит: Gen9, Inc.

Methods and apparatus relate to the synthesis of polynucleotides having a predefined sequence on a support. Assembly methods include primer extension to generate overlapping construction oligonucleotides and assembly of the polynucleotides of interest onto an anchor support-bound oligonucleotides. Methods and apparatus for selection of polynucleotides having the predefined sequence and/or length are disclosed. 1. A method for producing at least one polynucleotide having a predefined sequence , the method comprising:a. providing at least a first and a second pluralities of support-bound single-stranded oligonucleotides, wherein each first and second pluralities of oligonucleotides has a predefined sequence and is bound to a discrete feature of the support, each first plurality of oligonucleotides comprising a sequence region at its 3′ end complementary to a sequence region of a 3′ end of the second plurality of oligonucleotides;b. generating at least a first and a second pluralities of construction oligonucleotides complementary to the first and second pluralities of support-bound oligonucleotides in a chain extension reaction;c. providing a plurality support-bound anchor single-stranded oligonucleotides at a selected feature, wherein the 5′ end of the plurality of a first anchor oligonucleotide is the same as a sequence region of the first plurality of support-bound oligonucleotides;d. hybridizing the at least first and second pluralities of construction oligonucleotides to the of anchor oligonucleotides; ande. ligating the at least first and second pluralities of construction oligonucleotides, thereby generating the at least one polynucleotide.2. The method of wherein the at least first and second pluralities of construction oligonucleotides are dissociated from the at least first and second plurality of support-bound oligonucleotides.3. The method of further comprising transferring the first plurality of construction oligonucleotides from a first feature to a ...

Подробнее
Номер записи: 81
14-11-2013 дата публикации

ANTIGEN-BINDING MOLECULE CAPABLE OF BINDING TO TWO OR MORE ANTIGEN MOLECULES REPEATEDLY

Номер: US20130303396A1
Автор: Igawa Tomoyuki, ISHII Shinya, Maeda Atsuhiko, Nakai Takashi
Принадлежит:

The present inventors discovered that antibodies having weaker antigen-binding activity at the early endosomal pH in comparison with that at the pH of plasma are capable of binding to multiple antigen molecules with a single antibody molecule, have long half-lives in plasma, and have improved durations of time in which they can bind to antigen. 150-. (canceled)51. A method for producing a pharmaceutical composition comprising an antibody , the method comprising:(a) determining the antigen-binding activity of an antibody at pH 6.7 to pH 10.0(b) determining the antigen-binding activity of the antibody at pH 4.0 to pH 6.5;(c) determining that the antigen-binding activity of the antibody at pH 6.7 to pH 10.0 is greater than that at pH 4.0 to pH 6.5;(d) obtaining nucleic acid comprising a coding sequence encoding the antibody of (c);(e) producing the antibody using the nucleic acid obtained in (d); and(f) formulating the antibody produced in (e) in a pharmaceutical composition.52. The method of claim 51 , comprising mutating the nucleic acid to substitute at least one codon of the coding sequence with a histidine codon claim 51 , or to insert at least one histidine codon into the coding sequence claim 51 , and producing a mutant antibody using the mutated nucleic acid.53. The method of claim 51 , comprising assaying the mean retention time in plasma in vivo of the antibody produced in step (e).54. The method of claim 51 , comprising assaying the time required for the antibody produced in step (e) to eliminate an antigen from plasma in vivo.55. The method of claim 51 , wherein the antibody is a chimeric antibody.56. The method of claim 51 , wherein the antibody is a humanized antibody.57. The method of claim 51 , wherein the antibody is a bispecific antibody.58. The method of claim 51 , wherein the antibody comprises a constant region.59. The method of claim 51 , wherein the antibody comprises an FcRn-binding region.60. The method of claim 51 , wherein the antibody is a ...

Подробнее
Номер записи: 82
14-11-2013 дата публикации

COMPOSITIONS AND METHODS FOR PROCESSING AND AMPLIFICATION OF DNA, INCLUDING USING MULTIPLE ENZYMES IN A SINGLE REACTION

Номер: US20130303407A1
Автор: Kamberov Emmanuel, MAKAROV Vladimir L., Tarrier Brendan J.
Принадлежит:

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome. 1. A method of preparing a nucleic acid molecule , comprising:providing a double stranded nucleic acid DNA molecule; andattaching one strand of a stem-loop oligonucleotide comprising an inverted repeat and a loop to the double stranded nucleic acid molecule to produce an oligonucleotide-attached nucleic acid molecule, wherein the stem-loop oligonucleotide comprises at least one deoxy-uridine.2. (canceled)3. The method of claim 1 , wherein the attaching is further defined as attaching the oligonucleotide to the double stranded nucleic acid molecule under conditions to produce a non-covalent junction in the oligonucleotide-attached nucleic acid molecule.4. The method of claim 3 , wherein the non-covalent junction comprises a nick claim 3 , a gap claim 3 , or a 5′ flap structure.5. The method of claim 1 , wherein the attaching is further defined as ligating.6. The method of claim 1 , further comprising displacing one strand of the oligonucleotide from the oligonucleotide-attached nucleic acid molecule by strand displacement or by nick translation polymerization.7. The method of claim 1 , wherein at least part of the oligonucleotide-attached nucleic acid molecule is amplified.8. The method of claim 7 , wherein the amplification comprises polymerase chain reaction.9. The method of claim 7 , wherein the amplification comprises RNA transcription.10. The method of claim 7 , wherein the amplification comprises strand displacement.11. The method of claim 1 , further comprising amplifying ...

Подробнее
Номер записи: 83
21-11-2013 дата публикации

Antibody preparation method, and antibody and antibody library thus prepared

Номер: US20130310274A1
Автор: Guoxing Wang, Xiaoqing Wang, Xun Meng, Zeyong CHEN
Принадлежит: Individual

Provided is a method for preparing antibodies against a protein of interest, through which highly specific antibodies against all proteins can be effectively and rapidly prepared with low cost, and the epitope to which the antibody is directed can be determined, so that a library covering epitopes on the surface of the proteins of interest and a library of antibodies against all the epitopes can be established. The antibodies are proved to be useful in detection, protein function investigation and antibody pharmaceuticals.

Подробнее
Номер записи: 84
21-11-2013 дата публикации

ANTIDIABETIC ENOLIC GLUCOSIDE OF PHENYLPYRUVIC ACID

Номер: US20130310331A1
Автор: FEY Stephen John, JOUBERT Elizabeth, LOUW Johan, TYAGI Rahul, ULVEN Trond
Принадлежит: Zadec ApS

There is provided an antidiabetic enolic glucoside of phenylpyruvic acid and derivatives thereof for use as medicaments, especially normoglycemic agents, i.e. for lowering blood glucose levels to normal levels in mammals that are obese, pre-diabetic or have diabetes, obesity and/or syndrome X. Hence the compounds of the present invention help to manage blood sugar levels, i.e. helping the body by balancing the blood sugar levels; helping to keep balanced blood glucose levels, particularly in humans with diabetes; aiding by enhancing the glucose uptake by the cells and by reducing sugar levels, thus improving or restoring the glucose tolerance; optimizing the glycemic response; normalizing the glucose tolerance. 134.-. (canceled)37. Compound according to claim 35 , wherein Xis —OH or —C(O)R.38. Compound according to claim 35 , wherein A is —COOH.39. Compound according to claim 35 , wherein R claim 35 , R claim 35 , R claim 35 , and Rare independently selected from the group consisting of hydrogen claim 35 , fluorine claim 35 , chlorine claim 35 , bromine claim 35 , iodine claim 35 , hydroxy claim 35 , cyano claim 35 , and nitro claim 35 , preferably hydrogen.40. Compound according to claim 35 , wherein Rand Rare hydrogen.41. Compound according to claim 35 , wherein Ris hydrogen.42. Compound according to for use as a medicament.43. Compound according to for use as a medicament for the treatment of a metabolic disease claim 35 , including diabetes claim 35 , obesity and/or syndrome X.44. A method for the treatment of T1D claim 35 , non-autoimmune T2D claim 35 , obesity and/or syndrome X in animals including humans claim 35 , said method comprising the step of administering an effective dose of a compound of the formula I as defined in to animals including humans which are in need thereof.47. Compound according to claim 45 , wherein A is —COOH.48. Compound according to claim 45 , wherein R claim 45 , R claim 45 , R claim 45 , and Rare independently selected from the ...

Подробнее
Номер записи: 85
21-11-2013 дата публикации

Natural Gas to Liquid Fuels

Номер: US20130310468A1
Автор: Greer F. Conrad
Принадлежит: GREENWAY INNOVATIVE ENERGY, INC.

A method and apparatus for converting natural gas from a source, such as a wellhead, pipeline, or a storage facility, into hydrocarbon liquid stable at room temperature, comprising a skid or trailer mounted portable gas to liquids reactor. The reactor includes a preprocessor which desulfurizes and dehydrates the natural gas, a first stage reactor which transforms the preprocessed natural gas into synthesis gas, and a liquid production unit using a Fischer-Tropsch or similar polymerization process. The hydrocarbon liquid may be stored in a portable tank for later transportation or further processed on site. 1. A mobile or portable apparatus , comprising:a hydrogenation unit having an input configured to receive natural gas;a Fischer-Tropsch reactor having an input coupled to an output of the hydrogenation unit, the Fischer-Tropsch reactor comprising a plurality of catalyst-filled pipes wrapped around a center cooling pipe; anda fractionation tower having an input coupled to an output of the Fischer-Tropsch reactor, the fractionation tower having one or more outputs for liquid hydrocarbons.2. The apparatus of claim 1 , further comprising:a natural gas powered electric generator.3. The apparatus of claim 1 , further comprising:a desulfurization unit having an input adapted to receive natural gas, the desulfurization unit configured to remove sulfur from the natural gas, the desulfurization unit having an output coupled to the input of the hydrogenation unit.4. The apparatus of claim 1 , wherein the hydrogenation unit is selected from the group consisting of:a hydrogen generator;a steam methane reformer;an auto thermal reformer; anda hydrogen tank.5. A mobile or portable apparatus claim 1 , comprising:a hydrogenation unit having an input configured to receive natural gas, the hydrogenation unit comprising a plurality of catalyst-filled pipes wrapped around a center cooling pipe;a Fischer-Tropsch reactor having an input coupled to an output of the hydrogenation unit; ...

Подробнее
Номер записи: 86
28-11-2013 дата публикации

Cell-Free Polypeptide Synthesis

Номер: US20130316397A1
Автор: Isoken Airen, James Robert Swartz
Принадлежит: Leland Stanford Junior University

Methods, microbial strains and reaction mixtures for cell-free synthesis of polypeptides are provided. The methods of the invention utilize a reaction mixture comprising microbial cell extracts that are modified in the protein component relative to an extract from a native cell. The modification may be one or both of (i) increased levels of proteins that increase synthetic yield; and (ii) decreased levels of proteins that decrease synthetic yield. The modification may result from a genetic modification of the microbial cell, or from ex vivo supplementation or depletion of an extract.

Подробнее
Номер записи: 87
28-11-2013 дата публикации

Isolation of CpG Islands by Thermal Segregation and Enzymatic Selection-Amplification Method

Номер: US20130316913A1
Автор: Kamberov Emmanuel, MAKAROV Vladimir L., Tarrier Brendan J.
Принадлежит: Rubicon Genomics, Inc.

The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example. 1. A method of amplifying a plurality of amplifiable DNA molecules , comprising:providing a plurality of DNA molecules, said plurality haying molecules comprising one or more regions that are GC-poor and having molecules comprising one or more regions that are GC-rich;subjecting the plurality to a first temperature such that the GC-poor regions are substantially denatured and such that the GC-rich regions are undenatured or are denatured only in part;subjecting plurality to a second temperature such that at least part of the GC-poor regions incompletely renature and such that at least part of the GC-rich regions substantially completely renature, thereby producing renatured amplifiable GC-rich molecules;ligating an adaptor onto the end of at least some of the renatured GC-rich molecules to produce adaptor-ligated molecules, wherein the adaptor is further defined as a stem-loop oligonucleotide comprising an inverted repeat and a loop.2. The method of claim 1 , wherein the conditions to denature GC-poor regions but not to denature GC-rich regions comprise temperature sufficient to denature GC-poor regions but not to denature GC-rich regions claim 1 , pressure sufficient to denature GC-poor regions but not to denature GC-rich regions ...

Подробнее
Номер записи: 88
28-11-2013 дата публикации

GLYCOPEPTIDE ARRAY

Номер: US20130316932A1
Автор: Abe Hiroki, Abe Midori, Fukushima Masao, Igarashi Kohta, Matsushita Takahiko, Nishimura Shin-Ichiro, Shimaoka Hideyuki, Takada Wataru
Принадлежит:

The present invention provides: a glycopeptide array which is useful for the detection of the binding between a substance to be detected and a glycopeptide; and an array which can inhibit the non-specific adsorption or binding of a substance to be detected without the need of coating any adsorption-inhibiting agent and which has the glycopeptide immobilized thereon. In the present invention, it was found that a glycopeptide that has a molecule having a carbonyl group bound to a peptide moiety thereof can be immobilized on a substrate that is coated with a polymer compound containing a unit having a primary amino group with high efficiency through the carbonyl group. Particularly, it was found by the present inventors that a glycopeptide can be immobilized on a substrate with high efficiency and the non-specific adsorption or binding of a substance to be detected can be inhibited effectively when a substrate that is coated with a polymer compound containing a unit having a primary amino group, a unit for retaining hydrophilicity and a unit having a hydrophobic group is used as the substrate for the glycopeptide. 1. A glycopeptide array in which a glycopeptide is immobilized on a substrate , wherein:the glycopeptide comprises a molecule comprising a carbonyl group bound to a peptide moiety thereof;the substrate is coated with a polymer compound comprising a unit having a primary amino group; andthe glycopeptide is immobilized on the substrate by binding between the carbonyl group and the primary amino group.2. The array according to claim 1 , wherein the polymer compound on the substrate further comprises a unit having a phosphorylcholine group and a unit having a hydrophobic group.5. The array according to claim 2 , wherein the primary amino group in the polymer compound comprises an oxylamino group claim 2 , a hydrazide group claim 2 , or both.6. The array according to claim 5 , wherein a content of the unit having a primary amino group in the polymer compound is ...

Подробнее
Номер записи: 89
12-12-2013 дата публикации

NOVEL PEPTIDES AND USES THEREOF

Номер: US20130331297A1
Автор: Fan Xiaomin
Принадлежит: AVANTGEN, INC.

The present disclosure relates to novel peptides and their uses including, proline-rich peptides that are useful for displaying a protein of interest at the surfaces of a host cell such as a yeast. Polynucleotides, proteins, vectors and host cells that comprise or encode the novel proline-rich peptides, including libraries comprising such polynucleotides, proteins, vectors and/or host cells that comprise or encode novel proline-rich peptides are provided. Methods and materials for display and expression of proteins of interest are provided. Methods and materials are also provided by the present disclosure for isolating peptides capable of displaying a protein of interest (e.g., a marker protein), for generating libraries to display and/or express proteins of interest (e.g., antibodies such as humanized antibodies), for generating secretion vectors for such proteins of interest, and for generating proteins of interest (e.g., antibodies). 1. A library of host cells displaying on their surface proteins of interest associated with a proline-rich peptide.2. The library of host cells of claim 1 , wherein the host cells are yeast.3. The library of host cells of claim 1 , wherein the protein of interest is an antibody or fragment thereof.4. (canceled)5. The library of host cells of claim 1 , wherein the proline-rich peptide is an amino acid sequence comprising any of the amino acid sequences depicted in SEQ ID NOS: 1-116.612-. (canceled)13. A library of host cells comprising polynucleotides coding for a protein of interest and a proline-rich peptide.14. The library of host cells of claim 13 , wherein the host cells are yeast15. The library of host cells of claim 13 , wherein the protein of interest is an antibody or binding fragment thereof.16. (canceled)17. The library of host cells of claim 13 , wherein the proline-rich peptide is an amino acid sequence comprising PPP or any of the amino acid sequences depicted in SEQ ID NOS: 1-116.1827-. (canceled)28. A nucleic acid ...

Подробнее
Номер записи: 90
19-12-2013 дата публикации

METHOD AND SUBSTANCES FOR ISOLATING MIRNAS

Номер: US20130338011A1
Автор: DAWSON Elliott P., WOMBLE Kristie E.
Принадлежит: BIOVENTURES, INC.

A capture probe suitable for use with a method for isolating miRNAs. A method for isolating an miRNA of interest from a sample comprising the miRNA of interest comprising providing the capture probe. A method for identifying an miRNA of interest. 1. A method for isolating a microRNA of interest comprising a 3′ end and a 5′ end from a sample comprising the microRNA of interest according to through ; the method comprising:a) providing a sample comprising the microRNA of interest; i) a first adapter segment having a first adapter segment sequence, the first adapter segment comprising a 3′ end and a 5′ end;', 'ii) a second adapter segment having a second adapter segment sequence, the second adapter segment comprising a 3′ end and a 5′ end; and', 'iii) a microRNA binding segment having a microRNA binding segment sequence, the microRNA binding segment comprising a 3′ end and a 5′ end;, 'b) providing a capture probe comprisingwhere the microRNA binding segment is substantially complementary to, and capable of hybridizing to, one or more than one microRNA of interest by Watson-Crick base pairing;where the 5′ end of the first adapter segment is connected to the 3′ end of the microRNA binding segment; andwhere the 3′ end of the second adapter segment is connected to the 5′ end of the microRNA binding segment;c) providing a first linker comprising between 6 and 50 residues, where the first linker has a first linker sequence, comprises a 3′ end and a 5′ end, and is substantially complementary to, and capable of hybridizing to, the first adapter segment of the capture probe;d) providing a second linker comprising between 6 and 50 residues, where the second linker has a second linker sequence, comprises a 3′ end and a 5′ end, and is substantially complementary to, and capable of hybridizing to the second adapter segment of the capture probe;e) combining the sample, the capture probe, the first linker and the second linker in a solution;f) allowing the first linker to hybridize ...

Подробнее
Номер записи: 91
19-12-2013 дата публикации

KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES

Номер: US20130338042A1
Автор: Boutell Jonathan Mark, Bowen M. Shane, Gunderson Kevin, Ronaghi Mostafa, Shen Min-Jui Richard, Stephens Kathryn M., Venkatesan Bala Murali, Vijayan Kandaswamy
Принадлежит: Illumina, Inc.

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. 1. A method for amplifying nucleic acids , comprising (i) an array of amplification sites, and', '(ii) a solution comprising a plurality of different target nucleic acids,', 'wherein the number of the different target nucleic acids in the solution exceeds the number of amplification sites in the array,', 'wherein the different target nucleic acids have fluidic access to the plurality of amplification sites, and', 'wherein each of the amplification sites comprises a capacity for several nucleic acids in the plurality of different nucleic acids; and, '(a) providing an amplification reagent comprising'}(b) reacting the amplification reagent to produce a plurality of amplification sites that each comprise a clonal population of amplicons from an individual target nucleic acid from the solution,wherein the reacting comprises simultaneously (i) transporting the different target nucleic acids to the amplification sites at an average transport rate, and (ii) amplifying the target nucleic acids that are at the amplification sites at an average amplification rate, ...

Подробнее
Номер записи: 92
26-12-2013 дата публикации

Reaction Device

Номер: US20130341322A1
Автор: Katsuyoshi Tabuse, Minoru ONCHI
Принадлежит: SUNNY ENGINEERING Co Ltd

A reaction device including a microwave oscillation means for generating microwaves; holding containers for individually holding multiple samples collected from collection targets (e.g., human targets, etc.); a microwave irradiation container on which each of the holding containers can be individually loaded; a temperature sensor for detecting the temperature of a sample held in a holding container or of the interior of the microwave irradiation container; and a microwave control means for varying the microwaves generated by the microwave oscillation means on the basis of the temperature detected by the temperature sensor. The microwave irradiation container includes: a microwave introduction port for introducing the microwaves generated by the microwave oscillation means into the microwave irradiation container; and ring-shaped patterns for irradiating each of the holding containers with the microwaves introduced from the microwave introduction port.

Подробнее
Номер записи: 93
26-12-2013 дата публикации

ELECTROCHEMICAL DEBLOCKING SOLUTION FOR ELECTROCHEMICAL OLIGOMER SYNTHESIS ON AN ELECTRODE ARRAY

Номер: US20130341561A1
Автор: Cooper, JR. John J., Maurer Karl, Strathmann Michael
Принадлежит: CustomArray, Inc.

There is disclosed an electrochemical deblocking solution for use on an electrode microarray. There is further disclosed a method for electrochemical synthesis on an electrode array using the electrochemical deblocking solution. The solution and method are for removing acid-labile protecting groups for synthesis of oligonucleotides, peptides, small molecules, or polymers on a microarray of electrodes while substantially improving isolation of deblocking to active electrodes. The method comprises applying a voltage or a current to at least one electrode of an array of electrodes. The array of electrodes is covered by the electrochemical deblocking solution. 1. An electrochemical organic deblocking solution for use on an electrode microarray comprising an acid-source reducible solvent , an organic salt , and N ,N-diisopropylethylamine , where the N ,N-diisopropylethylamine provides basicity to quench the acid-source reducible solvent.2. The electrochemical organic deblocking solution of claim 1 , where the acid-source reducible solvent is selected from the group consisting of methylene chloride claim 1 , 1 claim 1 ,1 claim 1 ,1-trichloroethane claim 1 , 1 claim 1 ,1 claim 1 ,2-trichloro-1 claim 1 ,2-difluoroethane claim 1 , 1 claim 1 ,1 claim 1 ,2-trichloroethane claim 1 , 1 claim 1 ,4-dichlorobenzene claim 1 , 1-butanol claim 1 , 1-hexene claim 1 , 1-propanol claim 1 , 2-(2-butoxyethoxy)ethyl acetate claim 1 , 2-butoxyethanol acetate claim 1 , 2-butoxyethyl acetate claim 1 , 2-ethoxyethanol acetate claim 1 , 2-ethoxyethanol claim 1 , 2-methoxyethanol acetate claim 1 , 2-methoxyethanol claim 1 , 2-methylhexane claim 1 , 2-nitropropane claim 1 , acetone alcohol claim 1 , acetone claim 1 , acetonitrile claim 1 , allyl alcohol claim 1 , benzene claim 1 , benzotrifluoride claim 1 , benzyl chloride claim 1 , biphenyl claim 1 , carbon disulfide claim 1 , chlorobenzene claim 1 , chlorobromomethane claim 1 , cyclodecane claim 1 , cycloheptane claim 1 , cyclohexane claim 1 , ...

Подробнее
Номер записи: 94
02-01-2014 дата публикации

METHOD AND SYSTEM FOR THE ANALYSIS OF HIGH DENSITY CELLS SAMPLES

Номер: US20140005060A1
Автор: "OFarrell Brendan", Baunoch David, Moore Mathew, Reyes Miriam, Tisone Thomas C.
Принадлежит:

Methods for forming cell arrays of multiple cell samples arranged substantially in a monolayer on a single substrate particularly suited for diagnostic analysis are disclosed. The cell arrays are formed with a high-speed dispensing apparatus capable of dispensing small volumes in precise, complex patterns. Also disclosed are substrates upon which cell arrays may be formed, and methods for conducting diagnostic analyses on the formed cell arrays. 150-. (canceled)51. A method of forming a cell array comprising a plurality of discrete cell samples on a single substrate , comprising:aspirating a cell suspension from a source;providing relative motion between the cell suspension and the substrate;metering a predetermined amount of the cell suspension using a direct current fluid source;dispensing the metered amount of the cell suspension in the form of droplets onto the substrate so as to form a plurality of discrete cell samples, each discrete cell sample being arranged substantially in a monolayer on the substrate; anddispensing a predetermined amount of probe or stain to interact with at least one of the discrete cell samples.52. The method of claim 51 , wherein metering a predetermined amount of the cell suspension involves using a positive displacement pump.53. The method of claim 51 , wherein providing relative motion between the cell suspension and the substrate involves transporting the cell suspension relative to the substrate.54. The method of claim 51 , wherein the method further comprises dispensing a predetermined amount of a cover fluid sufficient to substantially cover the plurality of discrete cell samples arranged on the substrate claim 51 , and wherein the cover fluid is selected from the group consisting of inert liquids claim 51 , immiscible liquids claim 51 , and mineral oil.55. The method of claim 51 , wherein the cell array that is formed comprises at least one test sample and at least one control sample on the substrate.56. The method of claim 51 ...

Подробнее
Номер записи: 95
02-01-2014 дата публикации

Methods for Identifying and Isolating Cells Expressing a Polypeptide

Номер: US20140005076A1
Автор: Bond Christopher J., GURNEY AUSTIN L., Lazetic Alexandra L.L.
Принадлежит: OncoMed Pharmaceuticals, Inc.

The invention relates to novel polypeptides and cells comprising the polypeptides. The polypeptides and cells are used in methods to identify and/or isolate cells producing a protein with specific biological functions. In particular, the methods may be used for identifying, selecting, and isolating cells producing antigen-specific monoclonal antibodies. 1216-. (canceled)217. A cell library , each cell comprising: (i) an extracellular portion comprising an immunoglobulin heavy chain constant region comprising CH2 and CH3 domains; and', '(ii) a non-immunoglobulin transmembrane portion; and, '(a) a first polypeptide comprising(b) a second polypeptide comprising an immunoglobulin heavy chain constant region comprising CH2 and CH3 domains,wherein the first and second polypeptides form a heterodimeric molecule that is expressed on the surface of the cell.218. The cell library of claim 217 , wherein the extracellular portion of the first polypeptide comprises SEQ ID NO:2 claim 217 , SEQ ID NO:4 claim 217 , SEQ ID NO:6 claim 217 , or SEQ ID NO:8.219. The cell library of claim 217 , wherein the transmembrane portion of the first polypeptide comprises at least a portion of the transmembrane domain selected from the group consisting of CD4 claim 217 , CD8 claim 217 , Class I MHC claim 217 , Class II MHC claim 217 , CD19 claim 217 , T-cell receptor α and β chains claim 217 , CD3 claim 217 , zeta chain claim 217 , ICAM1 (CD54) claim 217 , ICAM2 claim 217 , ICAM3 claim 217 , ICAM4 claim 217 , ICAM5 claim 217 ,CD28, CD79a, CD79b, and CD2.220. The cell library of claim 217 , wherein the transmembrane portion of the first polypeptide comprises SEQ ID NO:13 or SEQ ID NO:16.221. The cell library of claim 217 , wherein the first polypeptide comprises a sequence at least 80% identical to SEQ ID NO:10 claim 217 , SEQ ID NO:12 claim 217 , SEQ ID NO:22 claim 217 , SEQ ID NO:23 claim 217 , SEQ ID NO:26 claim 217 , SEQ ID NO:28 claim 217 , SEQ ID NO:30 claim 217 , SEQ ID NO:31 claim 217 , or ...

Подробнее
Номер записи: 96
02-01-2014 дата публикации

Methods for Identifying and Isolating Cells Expressing a Polypeptide

Номер: US20140005077A1
Автор: Bond Christopher J., GURNEY AUSTIN L., Lazetic Alexandra L.L.
Принадлежит: OncoMed Pharmaceuticals, Inc.

The invention relates to novel polypeptides and cells comprising the polypeptides. The polypeptides and cells are used in methods to identify and/or isolate cells producing a protein with specific biological functions. In particular, the methods may be used for identifying, selecting, and isolating cells producing antigen-specific monoclonal antibodies. 1216-. (canceled)217. A method of identifying a cell that produces a heterodimeric molecule of interest comprising:(a) fusing a first cell with a second cell, wherein the first cell expresses a first polypeptide comprising (i) an extracellular portion comprising an immunoglobulin heavy chain constant region comprising CH2 and CH3 domains; and (ii) a non-immunoglobulin transmembrane portion, wherein the first polypeptide comprises a sequence at least 80% identical to SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, or SEQ ID NO:32; and the second cell expresses a second polypeptide comprising an immunoglobulin heavy chain constant region comprising CH2 and CH3 domains;(b) incubating the fused cell to allow expression of a heterodimeric molecule on the surface of the cell, wherein the heterodimeric molecule comprises the first polypeptide and the second polypeptide;(c) contacting the fused cell with a detection molecule, wherein the detection molecule binds the heterodimeric molecule; and(d) identifying the fused cell bound by the detection molecule.218. The method of claim 217 , comprising transfecting the first cell with a polynucleotide that encodes the first polypeptide.219. The method of claim 218 , wherein the polynucleotide encoding the first polypeptide is transiently transfected or stably transfected into the cell.220. The method of claim 217 , wherein the first cell is a fusion partner cell line.221. The method of claim 217 , wherein the second cell is an antibody-producing cell.222. The method of claim 221 , wherein the antibody-producing cell is ...

Подробнее
Номер записи: 97
02-01-2014 дата публикации

Optical system for chemical and/or biochemical reactions

Номер: US20140005078A1
Автор: Benjamin Masterman Webster, James Richard Howell, Mark Quentin Clark, Richard Alfred Howell
Принадлежит: IT IS International Ltd

An apparatus for detecting light emanating from chemical or biochemical reactions occurring in at least one reaction vessel of a plurality of reaction vessels is disclosed. Each reaction vessel has a receptacle portion having an emitting area from which light can emanate. A plurality of light waveguides are arranged to guide light from apertures in a masking element to a light dispersing device for dispersing the light from each waveguide into a dispersed spectrum. A light detecting device detects specific spectra in the dispersed spectra of light substantially simultaneously In one embodiment, the light waveguides have a diameter that tapers from a first end substantially similar in diameter to the area of the top of the reaction vessel to a second end that is substantially smaller in diameter.

Подробнее
Номер записи: 98
09-01-2014 дата публикации

Scalable Bio-Element Analysis

Номер: US20140011690A1
Автор: Baer Thomas M., Dimov Ivan K.
Принадлежит: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY

A method is provided for detecting one or more analytes in a sample. The method relies, in part, on the ability of functionalized particles added to the sample to partially or completely inhibit the transmission of electromagnetic radiation into and out of the sample through a detection surface in a reaction vessel containing the sample. In a microarray format, the invention can be used to screen millions, billions or more biological elements, such as an organism, cell, protein, nucleic acid, lipid, saccharide, metabolite, or small molecules. Methods, apparatuses and kits are described. 1. A method for detecting an analyte in a sample , comprising:adding to a reaction vessel comprising a sample solution, first particles and a first label that emits electromagnetic radiation, wherein the first label is bound to the first particles or the first label becomes bound to the first particles as a result of the presence or absence of the analyte in the sample,accumulating the first particles at a first detection surface to inhibit the transmission of electromagnetic radiation into and out of the sample through the surface, anddetecting the presence or amount of electromagnetic radiation emitted from the first detection surface.2. The method of claim 1 , wherein the vessel comprises a microcavity and the first surface comprises a first meniscus of the sample solution.3. The method of claim 1 , wherein the label is released from the particle as a result of the presence or absence of the analyte in the sample.4. The method of claim 1 , wherein the first particles accumulate at the detection surface as a result of a force applied to the sample claim 1 , wherein the force is selected from the group consisting of gravitational claim 1 , magnetic claim 1 , electrical claim 1 , centrifugal claim 1 , convective and acoustic.5. The method of claim 2 , further comprising mixing the sample by applying a magnetic field to move the first particles within the sample solution claim 2 , ...

Подробнее
Номер записи: 99
09-01-2014 дата публикации

Methods and Compositions for Tagging and Identifying Polynucleotides

Номер: US20140011708A1
Автор: Brenner Sydney
Принадлежит: POPULATION GENETICS TECHNOLOGIES LTD

The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by specific hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive specific hybridizations of labeled word complements, or the like. 121-. (canceled)22. A composition of nucleic acid molecules made by the following method:ligating a discriminatory oligonucleotide tag to fragmented genomic DNA so that substantially every target polynucleotide in said fragmented genomic DNA receives a tag that comprises a unique nucleotide sequence, to produce a tagged sample; andamplifying the target polynucleotides in said tagged sample by polymerase chain reaction to produce a plurality of amplicons that each comprise a unique tag.23. The method of claim 22 , wherein said fragmented genomic DNA is fragmented by digestion with a restriction enzyme.24. The method of claim 22 , wherein said fragmented genomic DNA is fragmented mammalian genomic DNA. This application is a continuation-in-part of U.S. patent application Ser. No. 11/055,187 filed 10 Feb. 2005, which is incorporated by reference in its entirety; this application also claim priority form U.S. provisional patent application Ser. No. 60/ ...

Подробнее
Номер записи: 100