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25-04-2013 дата публикации

METHODS OF USING CELLULASE FOR REDUCING THE VISCOSITY OF FEEDSTOCK

Номер: US20130098356A1

Автор: Geddes Claudia C., Ingram Lonnie O., Mullinnix Michael T., Peterson James J., Shanmugam Keelnatham

Принадлежит: UNIVERSITY OF FLORIDA RESEARCH FOUNDATION, INC.

The invention provides methods for treatment of feedstock to reduce the relative viscosity and promote release of fermentable sugars. 1. A method of decreasing the relative viscosity of feedstock comprising:incubating the feedstock with about 0.01 FPU to about 20 FPU cellulase/g dry weight of feedstock for about 10 minutes to about 10 hours at a pH of about 2 to about 6 at a temperature of about 40° C. to about 80° C.;thereby decreasing the relative viscosity of the feedstock.2. The method of claim 1 , wherein the feedstock is a bagasse claim 1 , corn fiber claim 1 , corn stover claim 1 , a plant waste material claim 1 , a processing or agricultural byproduct claim 1 , a sugar cane claim 1 , monoenergy cane claim 1 , sorghum sudan claim 1 , Miscanthus claim 1 , switchgrass claim 1 , wheat claim 1 , milo claim 1 , bulgher claim 1 , barley claim 1 , rice claim 1 , corn claim 1 , beet claim 1 , or tree.3. (canceled)4. The method of claim 1 , wherein the feedstock is incubated with; about 0.05 FPU to about 20 FPU cellulase/g dry weight of feedstock; about 0.50 FPU to about 5 FPU cellulase/g dry weight of feedstock; or about 5 FPU to about 10 FPU cellulase/g dry weight of feedstock; or more.5. (canceled)6. (canceled)7. The method of claim 1 , wherein the feedstock is incubated for; about 10 minutes to about 6 hours; or for about 15 minutes to about 2 hours.8. (canceled)9. The method of claim 1 , wherein the relative viscosity after treatment is: less than 8000 cP; less than 6000 cP; less than 3000 cP; or less than 1500 cP.1012-. (canceled)13. The method of claim 1 , wherein the pH is: about 2 to 6; about 2 to 5; about 2 to 4; about 2 to 3; or about 3 to 6.1417-. (canceled)18. The method of claim 13 , wherein the feedstock is incubated for about 10 minutes to about 6 hours or for about 15 minutes to about 2 hours.19. (canceled)20. The method of claim 13 , wherein the relative viscosity after treatment is: less than 8000 cP; less than 6000 cP; less than 3000 cP; or less ...

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Номер записи: 72

25-04-2013 дата публикации

VARIANTS OF GLUCOAMYLASE

Номер: US20130102035A1

Автор: Aehle Wolfgang, Bott Richard R., Degn Peter Edvard, Petersen Elin, Scheffers Martijn Silvan, Vroemen Casper Willem

Принадлежит: DUPONT NUTRITION BIOSCIENCES APS

The present invention relates to combinatorial variants of a parent glucoamylase that have altered properties for reducing the synthesis of condensation products during hydrolysis of starch. Accordingly the variants of a parent glucoamylase are suitable such as for use within brewing and glucose syrup production. Also disclosed are DNA constructs encoding the variants and methods of producing the glucoamylase variants in host cells. 34-. (canceled)5. The glucoamylase variant according to claim 1 , wherein the glucoamylase variant has at least 85% claim 1 , 90% claim 1 , 95% claim 1 , 98% claim 1 , or 99.5% sequence identity with SEQ ID NO: 1 or 2.67-. (canceled)8. The glucoamylase variant of claim 1 , comprising SEQ ID NO: 1098 or SEQ ID NO: 1099.9. (canceled)10. The glucoamylase variant according to claim 1 , wherein the glucoamylase variant has a starch binding domain that has at least 96% claim 1 , 97% claim 1 , 98% claim 1 , 99% claim 1 , or 99.5% sequence identity with the starch binding domain of SEQ ID NO: 1 claim 1 , 2 claim 1 , 11 claim 1 , 385 claim 1 , 386 claim 1 , 387 claim 1 , 388 claim 1 , 389 claim 1 , or 390.11. The glucoamylase variant according to claim 1 , wherein the glucoamylase variant has a catalytic domain that has at least 80% claim 1 , 85% claim 1 , 90% claim 1 , 95% claim 1 , or 99.5% sequence identity with the catalytic domain of SEQ ID NO: 1 claim 1 , 2 claim 1 , 3 claim 1 , 5 claim 1 , 6 claim 1 , 7 claim 1 , 8 claim 1 , or 9.1217-. (canceled)18. The glucoamylase variant according to claim 1 , which glucoamylase exhibit a reduced ratio between isomaltose synthesis and starch hydrolysis activity (IS/SH ratio) as compared to the parent glucoamylase.19. (canceled)20. The glucoamylase variant according to claim 1 , which glucoamylase exhibit an enhanced real degree of fermentation as compared to the parent glucoamylase.2125-. (canceled)26. A polynucleotide encoding a glucoamylase variant according to .27. A vector comprising the ...

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Номер записи: 73

02-05-2013 дата публикации

Nucleic Acid Amplification in the Presence of Modified Randomers

Номер: US20130109060A1

Автор: ANKENBAUER Waltraud, Heindl Dieter, Laue Frank

Принадлежит:

The present invention is directed to a composition comprising a DNA Polymerase which is preferably thermostable, Deoxynucleotides, at least one primer oligonucleotide or a pair of amplification primers, and randomized 5-8 mer oligonucleotide, characterized in that said oligonucleotide comprises a modification with an organic hydrophobic moiety Such a composition is specifically useful for performing hot start PCR. 17-. (canceled)8. A method for polymerase chain reaction (PCR) amplification of a specific target nucleic acid comprising the steps of providing a sample suspected of containing the target nucleic acid , adding a composition comprisinga DNA polymerase,deoxynucleotides,at least one primer oligonucleotide, anda randomized 5-8 mer oligonucleotide, wherein said oligonucleotide comprises a modification with an organic hydrophobic moiety, and performing at least a first primer extension reaction.91. The method for PCR amplification of a specific target nucleic acid according to claim wherein the DNA polymerase is thermostable and the composition further comprises a pair of amplification primers , andperforming a nucleic acid amplification reaction.10. The method according to claim 9 , wherein said nucleic acid amplification reaction is a polymerase chain reaction which is monitored in real time.11. The method according to wherein an amplification product generated by said amplification is subjected to a melting curve analysis.121. The method for PCR amplification according to claim wherein said modification is positioned at the 5′ end of said randomized oligonucleotide.131. The method for PCR amplification according to claim wherein said moiety is a pyrene or a stilbene.141. The method for PCR amplification according to claim wherein the composition further comprises a target nucleic acid sample.151. The method for PCR amplification according to claim claim 8 , wherein the randomized oligonucleotide are present in the composition in a concentration of between 10 ...

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Номер записи: 74

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 ...

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Номер записи: 75

09-05-2013 дата публикации

Low-viscosity reduced-sugar syrup, methods of making, and applications thereof

Номер: US20130112192A1

Автор: Guo-Hua Zheng, Lawrence E. Fosdick, Scott Helstad, Yauching W. Jasinski

Принадлежит: Cargill Inc

The invention provides a low-viscosity reduced-sugar syrup, methods of making such a low-viscosity reduced-sugar syrup, and uses of such syrup.

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Номер записи: 76

09-05-2013 дата публикации

Immunogenic Substances Comprising a Polyinosinic Acid - Polycytidilic Acid Based Adjuvant

Номер: US20130115244A1

Автор: Haixiang Lin, Lie Tao Victor Li

Принадлежит: Yisheng Biopharma Singapore Pte Ltd

The present invention provides a polynucleotide adjuvant (PICKCa) composition and methods of use in eliciting an immune response, in particular a mucosal immune response. The polynucleotide adjuvant comprises of a polyriboinosinic-polyribocytidylic acid (PIC), at least one antibiotic and at least one positive ion. The present invention also provides an immunogenic composition comprising the polynucleotide adjuvant composition together with other immunogenic compositions such as an antigen (e.g., as in a vaccine) selected from viral, bacterial, fungal, parasitic and/or cancer antigens. The present invention further contemplates methods of use of such adjuvant compositions, particularly in eliciting an immune response, in particular a mucosal immune response to an antigenic compound.

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Номер записи: 77

09-05-2013 дата публикации

METHOD FOR PREPARATIVE PRODUCTION OF LONG NUCLEIC ACIDS BY PCR

Номер: US20130115605A1

Автор: Erdmann Volker, Merk Helmut, Stiege Wolfgang

Принадлежит: RINA-NETZWERK RNA-TECHNOLGIEN GMBH

The invention relates to a method for preparative production of long nucleic acids by PCR. The method involves the following hybridization steps: a) a nucleic acid base sequence is hybridized on the 3′ and 5′ ends with an adapter primer; b) the product from step a) is hybridized on the 3′ and 5′ ends with an extension primer containing an extension sequence, wherein a nucleic acid with extension sequences amplified and enlarged in the 3′ and 5′ ends of the nucleic acid base sequence is then formed from the nucleic acid base sequence. The invention also relates to different applications of the inventive method. 1. A method for preparative production of long nucleic acids by means of PCR and involving the following hybridization steps:a) a nucleic acid base sequence is hybridized on the 3′ and 5′ ends with an adapter primer,b) the product from step a) is hybridized on the 3′ and 5′ ends with an extension primer containing an extension sequence,wherein a nucleic acid sequence enlarged by the extension sequences and amplified on the 3′ and 5′ ends of the nucleic acid base sequence is formed from the nucleic acid base sequence.2. A method according to claim 1 , wherein the product from step b) is hybridized in a step c) on the 3′ and 5′ ends with one amplification primer each claim 1 , an amplified nucleic acid end sequence being formed.3. A method according to claim 1 , wherein the adapter primers contains <70 nucleotides claim 1 , wherein the extension primers contain ≧70 nucleotides claim 1 , and/or wherein the amplification primers contain <70 nucleotides.4. A method according to claim 1 , wherein the steps a) claim 1 , b) and as an option the step c) are performed in a PCR solution containing the nucleic acid base sequence claim 1 , the adapter primers claim 1 , the extension primers and as an option the amplification primers.5. A method according to claim 1 , wherein the steps a) and b) in a method step A) are performed in a pre-PCR solution containing the nucleic ...

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Номер записи: 78

09-05-2013 дата публикации

Method of producing sugar

Номер: US20130115660A1

Автор: John Aikens, Robert J. Turner

Принадлежит: PROTERRO Inc

Provided herein is a transgenic bacteria engineered to accumulate carbohydrates, for example disaccharides. Also provided is a photobioreactor for cultivating photosynthetic microorganisms comprising a non-gelatinous, solid cultivation support suitable for providing nutrients and moisture to photosynthetic microorganisms and a physical barrier covering at least a portion of the surface of the cultivation support. Devices for the large scale and continuous cultivation of photosynthetic microorganisms incorporating photobioreactors and methods of use are disclosed. Also disclosed are methods of producing fermentable sugar from photosynthetic microorganisms using a photobioreactor of the invention.

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Номер записи: 79

16-05-2013 дата публикации

Solid lignocellulosic hydrolysate and methods to prepare a solid lignocellulosic hydrolysate

Номер: US20130118483A1

Автор: Benjamin Levie, Dwight Anderson, Johnway Gao

Принадлежит: Catchlight Energy LLC

The present disclosure provides a solid lignocellulosic hydrolysate and methods to prepare the solid lignocellulosic hydrolysate from a woody biomass or an herbaceous biomass. The solid lignocellulosic hydrolysate may be used in the production of biofuels, bioproducts, and food products. The solid lignocellulosic hydrolysate allows for ease of storage, ease of transportation and handling of the solid lignocellulosic hydrolysate, and ease of use in biological or fermentation processes or chemical processes for the production of biofuel, bioproducts, chemicals and food products due to the bulk handling characteristics (e.g., solubility and rate of dissolution) of the solid lignocellulosic hydrolysate.

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Номер записи: 80

16-05-2013 дата публикации

METHOD FOR PREPARING NOVEL PROCESSED GINSENG OR AN EXTRACT THEREOF, THE USUALLY MINUTE GINSENOSIDE CONTENT OF WHICH IS INCREASED

Номер: US20130122122A1

Автор: Bae Soo-Hyun, Choi Jung Hyo, Kim Jeom Yong, Kim Sun-Ok, Park Sun Kyu, Yoo Young-Hyo

Принадлежит: GREENCROSS HERB & PHARMACEUTICAL CO., LTD.

The present invention relates to a method for preparing a processed ginseng or processed ginseng extract. Specifically, the invention relates to a method for preparing a processed ginseng or processed ginseng extract having increased ginsenoside contents. More specifically, the invention relates to a method of preparing a novel processed ginseng or processed ginseng extract having increased ginsenoside contents by preparing saponinase, fermenting ginseng or red ginseng with the prepared saponinase and hydrolyzing the fermented ginseng or red ginseng with an organic acid and to an anticancer supplement composition or pharmaceutical composition comprising the processed ginseng or processed ginseng extract prepared thereby. 1. A method for preparing a processed ginseng or processed ginseng extract having increased contents of ginsenosides Rg3 and Rh2 , the method comprising the steps of:{'i': 'Aspergillus niger', '(a) inoculating an strain into a medium composed of ginseng and wheat bran;'}(b) culturing the strain of step (a);(c) purifying the cultured material of step (b) by ultrafiltration;(d) separating an enzyme from the purified material of step (c);(e) adding the enzyme of step (d) to ginseng, red ginseng or a ginseng or red ginseng extract to obtain a mixture;(f) fermenting the mixture of step (e);(g) separating the fermented material of step (f) to obtain a supernatant;(h) concentrating the supernatant of step (g);(i) reacting the concentrate of step (h) with at least one organic acid selected from the group consisting of acetic acid, lactic acid, citric acid, malic acid and tartaric acid; and(j) neutralizing, filtering, purifying, concentrating and drying the reaction product of step (i).2Aspergillus nigerAspergillus niger. The method of claim 1 , wherein inoculation of the medium with in step (a) is performed such that the number of spores in an spore suspension is 5×10spores per g of the medium and the initial water content of the medium is maintained at 50- ...

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Номер записи: 81

16-05-2013 дата публикации

Nucleic Acid Amplification Using A Reversibly Modified Oligonucleotide

Номер: US20130122507A1

Автор: Bi Wanli

Принадлежит:

The present invention provides a method for amplification of a target nucleic acid sequence or signal, wherein an amplification reaction mixture is used which contains at least one reversibly modified oligonucleotide having a non-hydroxyl group 3′ end which can be converted into a hydroxyl 3′ end upon exposure to a chemical and/or irradiation and/or a range of temperature. The present invention also provides a reversibly modified oligonucleotide as described above, and a nucleic acid amplification reaction mixture and kit comprising such an oligonucleotide. 143.-. (canceled)44. A method for regenerating a 3′ hydroxyl group , the method comprising:using a mixture comprising at least one reversibly modified oligonucleotide having a non-hydroxyl group 3′ end which can be converted into a 3′ hydroxyl group, wherein the oligonucleotide has a carboxylic acid ester group at its 3′ end;exposing the mixture to a first chemical and a first range of temperature, wherein the first chemical and the first range of temperatures regenerate the 3′ hydroxyl group, wherein the first chemical is an amine; andregenerating the 3′ hydroxyl group of the at least one reversibly modified oligonucleotide having a non-hydroxyl 3′ end.45. The method of claim 44 , wherein the amine is selected from the group consisting of methylamine claim 44 , ethylenediamine claim 44 , and triethylamine.46. The method of claim 45 , wherein the amine is methylamine.47. The method of claim 45 , wherein the amine is ethylenediamine.48. The method of claim 45 , wherein the amine is triethylamine.49. The method of claim 44 , wherein the carboxylic acid ester is maleic acid ester claim 44 , and the first chemical is methylamine.50. The method of claim 44 , wherein the carboxylic acid ester is maleic acid ester claim 44 , and the first chemical is ethylenediamine.51. The method of claim 44 , wherein the carboxylic acid ester is maleic acid ester claim 44 , and the first chemical is triethylamine.52. The method of ...

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Номер записи: 82

16-05-2013 дата публикации

RECOMBINANT PHAGE AND METHODS

Номер: US20130122549A1

Автор: Brownell Daniel Robert, Chevalier Brett Smith, Holder Jason Wyatt, Koeris Michael Sandor, Lu Timothy Kuan Ta, McKenzie Gregory John

Принадлежит: SAMPLE6 TECHNOLOGIES, INC.

This disclosure provided methods of cloning a phage genome. Also provided are methods of making a recombinant phage genome. In some embodiments the phage genome is engineered to comprise a heterologous nucleic acid sequence, for example a sequence comprising an open reading frame. In some embodiments the phage genome is cloned in a yeast artificial chromosome. Recombinant phage genomes and recombinant phage are also provided. In some embodiments the methods are high throughput methods such as methods of making a plurality of recombinant phage genomes or recombinant phage. Collections of recombinant phage genomes and recombinant phage are also provided. 1. A method of making a cloned phage genome , comprising:providing a vector;inserting a starting phage genome into the vector to provide a recombinant vector; andpropagating the recombinant vector in a vector host cell that is not a phage host cell to thereby provide the cloned phage genome.2. The method of claim 1 , wherein the recombinant vector comprising a starting phage genome is made by a method comprising:co-transforming the starting phage genome and the vector into a plurality of vector host cells, under conditions that allow insertion of the starting phage genome into the vector; andselecting a vector host cell comprising the recombinant vector as a result of insertion of the starting phage genome into the vector.3. The method of claim 1 , wherein the recombinant vector comprising a starting phage genome is made by a method comprising:transforming the starting phage genome into a plurality of vector host cells comprising the vector, under conditions that allow insertion of the starting phage genome into the vector; andselecting a vector host cell comprising the recombinant vector as a result of insertion of the starting phage genome into the vector.4. The method of claim 1 , further comprising isolating the recombinant vector.5. The method of claim 1 , further comprising removing the cloned phage genome from ...

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Номер записи: 83

16-05-2013 дата публикации

Reducing Template Independent Primer Extension and Threshold Time for Loop Mediated Isothermal Amplification

Номер: US20130122551A1

Автор: Evans, JR. Thomas C., Tanner Nathan

Принадлежит: NEW ENGLAND BIOLABS, INC.

Compositions and methods are provided for loop mediated isothermal amplification in which single stranded binding proteins are shown to protect primers from non-specific extension and to stimulate the rate of threshold amplification. 1. A preparation , comprising: a single stranded binding protein (SSB); a thermostable polymerase; at least four oligonucleotide primers , and a buffer.2. A preparation according to claim 1 , wherein the buffer has a pH in the range of pH6-pH9 claim 1 , and optionally a stabilization agent selected from the group consisting of BSA claim 1 , glycerol and detergent.3. A preparation according to wherein the buffer comprises a monovalent salt having a concentration in the range of 0-500 mM.4. A preparation according to wherein the buffer comprises a divalent metal cation having a concentration of 0.5 mM-10 mM.5. A preparation according to claim 1 , wherein the buffer has a pH in the range of pH6-pH9 claim 1 , a monovalent salt having a concentration in the range of 0-500 mM claim 1 , a divalent metal cation having a concentration of 0.5 mM-10 mM and optionally a stabilization agent selected from the group consisting of BSA claim 1 , glycerol and detergent.6. A preparation according to claim 1 , wherein the SSB is an extreme thermophile single strand binding protein (ET SSB).7. A preparation according to claim 1 , wherein the thermostable polymerase has strand displacement activity and is active at temperatures of greater than 50° C.8. A method of amplifying a nucleic acid claim 1 , comprising:{'claim-ref': {'@idref': 'CLM-00001', 'claim 1'}, 'adding to the preparation according to , dNTPs and template nucleic acid;'}performing loop mediated isothermal amplification (LAMP); andobtaining amplified template DNA.9. A method for inhibiting primer extension of a primer in an amplification reaction claim 1 , comprising:(a) combining a single stranded binding protein (SSB) with a thermostable polymerase, at least four primers and a template nucleic ...

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Номер записи: 84

16-05-2013 дата публикации

Tiacumicin Production

Номер: US20130123477A1

Автор: Chen Yuan-Ting, Chiou Ming-His, Du Chi-Jen Frank, Duffield Jonathan James, Okumu Franklin W., Shue Youe-Kong, Wu Mei-Chiao

Принадлежит: OPTIMER PHARMACEUTICALS, INC.

Methods, processes and materials for the production and recovery of Tiacumicins produced by culturing a microorganism belonging to the species subspecies having the ability to produce and accumulate one or more Tiacumicin in a nutrient medium comprising a carbon source, a nitrogen source, trace elements such as inorganic salts, and an adsorbent, wherein said nitrogen source comprises fish powder, and wherein said Tiacumicin is produced in a yield greater than about 50 mg/L broth. 1. A process for producing Tiacumicins that comprises culturing a microorganism having the ability to produce Tiacumicins in a nutrient medium and accumulating at least one Tiacumicin in the nutrient medium , wherein the yield of at least one Tiacumicin is greater than about 50 mg/L of whole fermentation broth.2. A process according to wherein said yield is greater than about 100 mg/L broth.3. A process according to wherein said yield is greater than about 200 mg/L broth.4. A process according to wherein said yield is from about 50 mg/L broth to about 500 mg/L broth.5. A process according to wherein said yield is from about 100 mg/L broth to about 500 mg/L broth.6Dactylosporangium aurantiacum. A process according to wherein said microorganism is NRRL 18085.7. A process according to wherein said Tiacumicin is Tiacumicin B.8. A process according to wherein said Tiacumicin is isolated from said nutrient medium using techniques selected from the group consisting of: sieving and removing undesired material by eluting with at least one solvent or a solvent mixture; extraction with at least one solvent or a solvent mixture; Crystallization; chromatographic separation; High-Performance Liquid Chromatography (HPLC); MPLC; trituration; and extraction with saturated brine with at least one solvent or a solvent mixture.9. A process according to wherein said microorganism is cultured at a temperature from about 25° to about 35° C. and at a pH from about 6.0 to about 8.0.10. A process according to ...

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Номер записи: 85

23-05-2013 дата публикации

Endoribonuclease compositions and methods of use thereof

Номер: US20130130248A1

Автор: Blake Wiedenheft, Jennifer A. DOUDNA, Martin Jinek, Rachel E. Haurwitz

Принадлежит: UNIVERSITY OF CALIFORNIA

The present disclosure provides variant Csy4 endoribonucleases, nucleic acids encoding the variant Csy4 endoribonucleases, and host cells genetically modified with the nucleic acids. The variant Csy4 endoribonucleases find use in a variety of applications, which are also provided. The present disclosure also provides methods of detecting a specific sequence in a target polyribonucleotide; and methods of regulating production of a target RNA in a eukaryotic cell.

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Номер записи: 86

23-05-2013 дата публикации

NUCLEIC ACID PRODUCTION AND SEQUENCE ANALYSIS

Номер: US20130130249A1

Автор: Klimasauskas Saulius, Stasevskij Zdislav

Принадлежит: Vilnius University

A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer, which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence, wherein the linking unit is attached to a target site in the template nucleic acid sequence with a covalent linkage. 1. A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer , which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence , wherein the linking unit is attached to a target site in the template nucleic acid sequence with a′ covalent linkage.2. A method according to comprising a step of forming the covalent linkage using a transferase enzyme.3. A method according to wherein the target site is within the template nucleic acid sequence and the linking unit is not attached with the covalent linkage to a terminal nucleotide of the template nucleic acid sequence.4. A method according to wherein the primer comprises four nucleotides or less which are complementary to the template nucleic acid at the start point of production of the nucleic acid molecule by the nucleic acid polymerase.5. A method according to wherein the primer is covalently linked to the linking unit claim 1 , or wherein the primer is non-covalently bound to the linking unit.6. A method according to wherein the linking unit comprises a nucleotide strand to which the primer is base paired.7. A method according to further comprising a step of forming the covalent linkage between the template nucleic acid sequence and the linking unit by ...

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Номер записи: 87

23-05-2013 дата публикации

Cells and methods for producing rhamnolipids

Номер: US20130130319A1

Автор: Anja Thiessenhusen, Mirja Wessel, Nadine Stein, Steffen Schaffer

Принадлежит: EVONIK GOLDSCHMIDT GMBH

The invention relates to cells and nucleic acids and also use thereof for producing rhamnolipids, and also methods for producing rhamnolipids.

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Номер записи: 88

23-05-2013 дата публикации

ENZYMES

Номер: US20130130320A1

Автор: Cozens Christopher, HOLLIGER PHILIPP, Pinheiro Vitor B.

Принадлежит:

The invention relates to a nucleic acid polymerase capable of producing a non-DNA nucleotide polymer from a DNA nucleotide polymer template, said polymerase comprising amino acid sequence having at least 36% identity to the amino acid sequence of SEQ ID NO:1, wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at one or more residues of the thumb region, said residues selected from: amino acids 651 to 679 (patch 10A); wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at residue E664. In one embodiment said polymerase comprises the mutations Y409G and E664K. In one embodiment said polymerase comprises amino acid sequence corresponding to SEQ ID NO:12. The invention also relates to A nucleic acid polymerase capable of reverse transcribing a HNA nucleotide polymer into a DNA nucleotide polymer, said polymerase comprising amino acid sequence having at least 36% identity to the amino acid sequence of SEQ ID NO:1, wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at residue I521. 1. A nucleic acid polymerase capable of producing a non-DNA nucleotide polymer from a DNA nucleotide polymer template ,said polymerase comprising amino acid sequence having at least 36% identity to the amino acid sequence of SEQ ID NO:1,wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at one or more residues of the thumb region, said residues selected from: amino acids 651 to 679 (patch 10A);wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at residue E664.2. A nucleic acid polymerase according to wherein said non-DNA nucleotide polymer is a RNA polymer; andwherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at residue Y409.3. A nucleic acid polymerase according to wherein said polymerase comprises the mutations Y409G and E664K.4. A ...

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Номер записи: 89

23-05-2013 дата публикации

Programmable Oligonucleotide Synthesis

Номер: US20130130321A1

Автор: Carapito Raphael, Staehler Peer

Принадлежит: Synthetic Genomics, Inc.

The invention relates to methods and devices for preparing synthetic nucleic acids. 2. The method as claimed in characterized in that a copy of the synthetic nucleic acids is provided by an RNA polymerase.3. The method as claimed in characterized in that the nucleic acid fragments produced are used for the modulation of gene expression by RNAi and/or antisense methods.4. The method as claimed in characterized in that the nucleic acid fragments produced are used for the production claim 2 , extraction claim 2 , purification claim 2 , isolation and/or preparation of analytes and/or samples (sample preparation).6. A method of production of a polypeptide claim 5 , comprising steps (a) claim 5 , (b) and (c) from . This application is a continuation application of U.S. application Ser. No. 13/441,186 filed Apr. 6, 2012, now pending; which is a divisional application of U.S. application Ser. No. 12/438,425 filed Feb. 23, 2009, now issued as U.S. Pat. No. 8,173,368; which is a 35 USC §371 National Stage application of International Application No. PCT/EP2007/007417 filed Aug. 23, 2007; which claims the benefit under 35 USC §119(a) to Germany Patent Application No. 10 2006 039 479.8 filed Aug. 23, 2006. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.1. Field of the InventionThe invention relates to methods and devices for preparing synthetic nucleic acids.2. Background InformationThere is a high demand for synthetic nucleic acids in molecular biology and biomedical research and development. Synthetic nucleic acids (DNA, RNA or their analogues) are mainly prepared using column-based synthesizers.Particularly important and widespread applications for synthetic nucleic acid polymers are primers for the polymerase chain reaction (PCR) (Critical Reviews in Biochemistry and Molecular Biology 26 (3/4), 301-334, 1991) and the sequencing method according to Sanger (Proc. Nat. Acad. Sci. 74, ...

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Номер записи: 90

23-05-2013 дата публикации

PREVENTION AND ALLEVIATION OF STERIC HINDRANCE DURING SINGLE MOLECULE SYNTHESIS

Номер: US20130130323A1

Автор: Ma Congcong, Wyatt Paul

Принадлежит: Pacific Biosciences of California, Inc.

The present invention provides compositions and methods for reducing steric hindrance in the product of nucleic acid polymerase reaction. Methods and compositions of the invention encompass application of exonucleases, endonucleases, and uracil-DNA glycosylases to a nucleic acid polymerase reaction such that newly formed nucleic acid strands are modified (e.g., cleaved) while the polymerase reaction continues to proceed. 1. A nucleic acid sequencing reaction mixture comprising:a. a nucleic acid polymerase, wherein said nucleic acid polymerase is immobilized on a substrate within a constricted volume reaction vessel;b. an enzyme selected from the group consisting of an endonuclease, an exonuclease, and a uracil-DNA glycosylase; andc. a template nucleic acid, wherein said enzyme is unable to modify said template nucleic acid.2. The composition of claim 1 , further comprising a set of differentially labeled nucleotides.3. The composition of claim 2 , wherein the differentially labeled nucleotides comprise a label attached at a phosphate group.4. The composition of claim 1 , wherein the constricted volume reaction vessel has a volume of less than one attoliter.5. The composition of claim 1 , wherein the constricted volume reaction vessel is a zero mode waveguide.6. The composition of claim 1 , further comprising uracil-containing nucleotides.7. The composition of claim 6 , further comprising thymine-containing nucleotides.8. The composition of claim 6 , further comprising at least one polyamine or AP endonuclease.9. The composition of claim 1 , wherein the template nucleic acid comprises a modification that prevents cleavage by the exonuclease or the endonuclease.10. The composition of claim 1 , wherein the template nucleic acid is a circular nucleic acid template.11. The composition of claim 1 , wherein the template nucleic acid is a single-stranded nucleic acid template.12. The composition of claim 1 , wherein the template nucleic acid is a double-stranded nucleic ...

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Номер записи: 91

23-05-2013 дата публикации

GENETICALLY ENGINEERED STRAIN WSJ-IA FOR PRODUCING ISOVALERYL SPIRAMYCIN I

Номер: US20130130324A1

Автор: Jiang Yang, WANG Yiguang, Yang Shengwu, ZHAO Xiaofeng

Принадлежит: SHEN YANG TONGLIAN GROUP CO., LTD.

A genetically engineered strain WSJ-IA for producing isovaleryl spiramycin I. Also provided is a method for preparing the strain, comprising the steps of: (a) constructing a recombinant plasmid comprising a double gene ist-acyB2; (b) transforming the plasmid into an isovaleryl spiramycin I—producing strain to obtain the strain WSJ-IA. The level of isovaleryl spiramycin I produced by fermentation of the strain WSJ-IA is increased 1.7 times and the fermentation potency thereof increased 4.14 times in comparison with the strain exclusively comprising a single gene ist. 1. A strain of genetically engineered bacterium producing high content of isovaleryl spiramycin I component with high productivity , wherein said genetically engineered bacterium is a clonal strain with isovaleryl transferase gene ist and the acyB2 regulatory gene linked with it co-expressed in isovaleryl spiramycin I producing bacterium WSJ-2.2. A method for constructing the strain of genetically engineered bacterium according to claim 1 , the method comprising:{'i': Streptomyces', 'Streptomyces thermotolarences, 'A) using total DNA of the heat-resistant (CGMCC4.1501) as a template, to design primers according to ist-acyB2 sequence announced by NCBI, carrying out PCR to obtain ist-acyB2 linked gene segment, inserting appropriate cleavage sites; or also, ligating ist and acyB2 gene fragments, respectively, with the integrative vector transferrable to the isovaleryl spiramycin I producing bacterium strain, to obtain recombinant plasmid containing ist-acyB2 gene; and'}B) transferring the recombinant plasmid containing ist-acyB2 into isovaleryl spiramycinl producing bacterium WSJ-2 by means of resistance screening to obtain transformant, after continuous passage under non-dosing conditions and testing with dosing to obtain stable expression of isovaleryl spiramycin I producing bacterium containing recombinant plasmid, and constructing a strain being named WSJ-IA, culture Collection No. CGMCC No.3942.32. The ...

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Номер записи: 92

23-05-2013 дата публикации

Polypeptides Having Beta-Glucosidase Activity, Beta-Xylosidase Activity, or Beta-Glucosidase and Beta-Xylosidase Activity and Polynucleotides Encoding Same

Номер: US20130130325A1

Автор: Morant Marc Dominique

Принадлежит:

The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides. 1. An isolated polypeptide having beta-glucosidase activity , beta-xylosidase activity , or beta-glucosidase and beta-xylosidase activity , selected from the group consisting of:(a) a polypeptide having at least 76% sequence identity to the mature polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, or SEQ ID NO: 12;(b) a polypeptide encoded by a polynucleotide that hybridizes under at least midium stringency conditions with (i) the mature polypeptide coding sequence of SEQ ID NO: 1 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 3 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 5 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 7 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 9 or the cDNA sequence thereof, or the mature polypeptide coding sequence of SEQ ID NO: 11 or the cDNA sequence thereof, or (ii) the full-length complement of (i);(c) a polypeptide encoded by a polynucleotide having at least 76% sequence identity to the mature polypeptide coding sequence of SEQ ID NO: 1 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 3 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 5 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 7 or the cDNA sequence thereof, the mature polypeptide coding sequence of SEQ ID NO: 9 or the cDNA sequence thereof, or the mature polypeptide coding sequence of SEQ ID NO: 11 or the cDNA ...

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Номер записи: 93

23-05-2013 дата публикации

Polypeptides Having Beta-Glucosidase Activity, Beta-Xylosidase Activity, or Beta-Glucosidase and Beta-Xylosidase Activity and Polynucleotides Encoding Same

Номер: US20130130326A1

Автор: Morant Marc Dominique

Принадлежит:

The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides. 1. An isolated polypeptide having beta-glucosidase activity , beta-xylosidase activity , or beta-glucosidase and beta-xylosidase activity , selected from the group consisting of:(a) a polypeptide having at least 80% sequence identity to the mature polypeptide of SEQ ID NO: 2, or the mature polypeptide of SEQ ID NO: 4;(b) a polypeptide encoded by a polynucleotide that hybridizes under at least high stringency conditions with (i) the mature polypeptide coding sequence of SEQ ID NO: 1 or the cDNA sequence thereof, or the mature polypeptide coding sequence of SEQ ID NO: 3 or the cDNA sequence thereof, or (ii) the full-length complement of (i);(c) a polypeptide encoded by a polynucleotide having at least 80% sequence identity to the mature polypeptide coding sequence of SEQ ID NO: 1 or the cDNA sequence thereof, or the mature polypeptide coding sequence of SEQ ID NO: 3 or the cDNA sequence thereof;(d) a variant of the mature polypeptide of SEQ ID NO: 2, SEQ ID NO: 4 comprising a substitution, deletion, and/or insertion at one or more (e.g., several) positions; and(e) a fragment of the polypeptide of (a), (b), (c), or (d) that has beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity.2. An isolated polynucleotide encoding the polypeptide of .3. A recombinant host cell comprising the polynucleotide of operably linked to one or more control sequences that direct the production of the polypeptide.4. A method of producing the polypeptide of claim 1 , comprising:(a) cultivating a cell, which in its wild-type form produces the polypeptide, under ...

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Номер записи: 94

23-05-2013 дата публикации

Method of treating plant biomass

Номер: US20130130328A1

Автор: Haruo Takahashi, Kazuhide Tabata, Nobuhiro Ishida, Risa Nakamura, Satoshi Katahira

Принадлежит: Toyota Motor Corp

Plant biomass is immersed in a solution that contains a polar solvent and an imidazolium salt that has a melting point of at least 100° C. As a result, the cellulose and hemicellulose present in the plant biomass are relaxed (decrystallized and depolymerized) and brought into an easy-to-degrade state. Reacting the immersed plant biomass with a cellulase produces saccharide at a high conversion efficiency.

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Номер записи: 95

23-05-2013 дата публикации

METHOD FOR EXTRACTING SUBSTANCES FROM SOAPBERRY FRUIT AND ITS SEEDS

Номер: US20130130329A1

Автор: Hsu Heng-Jui

Принадлежит:

An exclusive method for extracting active interface saponin and organic substances from soapberry; organic elements and oleic alcohol products from soapberry seeds through fermenting process, and end products made therefrom. By this method, every part of the soapberry is processed to become the raw material of varies of products and daily necessaries. Said method is toxin free and biologically safe, produce no solid and liquid wastage, zero carbon emissions, zero chemical pollution, low energy consumption and ecologically friendly. The end products produced by present invention are variables which can be applied in cosmetics, medicals, cleaning products, skin caring products and so on, thus, are with excellent economic value and industrial viability in mass production. 1. A method for extracting substances from soapberry fruit and its seeds , comprises following steps:{'b': 1', '1, 'Step : separate raw Soapberry fruits into pericarps and seeds, and store said pericarps under a constant temperature (T) for a predetermined time (S) to make them fermented naturally;'}{'b': 2', '1', '1', '1', '1, 'Step : put the fermented pericarps in step one inside a sealed tank, than fill in said sealed tank with liquid (W), then stand for 5-10 minutes, to make the foreign object attached on said pericarps being dissolved or moved by said liquid (W), supersonic vibrator or shifting the air pressure inside said sealed tank could be applied for speeding up the detachment of the foreign object on said pericarps, finally, take the pericarps out of the tank, and the liquid left in the tank becomes product which contains enzyme produced in step by fermenting;'}{'b': '3', 'Step : Put cleaned soapberry pericarps into a blender to grind them into the shattered mix of the pulp and fruit fiber;'}{'b': 4', '2', '2', '2, 'Step : Soak said shattered mix of the pulp and fruit fiber with liquid (W), then pouring them into an extractor; activate the extractor, and said pulp will be drained out of the ...

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Номер записи: 96

23-05-2013 дата публикации

Compositions Comprising High Molecular Weight Hyaluronic Acid and Methods For Producing Same

Номер: US20130131009A1

Автор: Andrei Seluanov, Christopher Hine, Vera Gorbunova

Принадлежит: UNIVERSITY OF ROCHESTER

This invention provides cell culture compositions which produce significant quantities of high molecular weight hyaluronic acid. The cell cultures are obtained from cells of mole rats, such as naked mole rats and blind mole rats. The high molecular weight hyaluronic acid can be collected in the conditioned media of these cell cultures. These cell cultures provide a convenient source of large quantities of high molecular weight hyaluronic acid.

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Номер записи: 97

30-05-2013 дата публикации

HIGH PURITY GENTIOOLIGOSACCHARIDES OBTAINED THEREFROM AND USES THEREOF

Номер: US20130136840A1

Автор: Ahn Sang Wook, Kim Kyeong Hee, LEE Jae Ho, Park Sang Jae

Принадлежит: CORN PRODUCTS DEVELOPMENT, INC.

The present invention relates to methods for preparing high purity gentiooligosaccharides, high purity gentiooligosaccharides obtained therefrom, and uses thereof. The methods of the present invention involve: adding a low purity gentiooligosaccharide to a liquid medium; subjecting the liquid medium to inoculation with a microorganism, followed by incubation and fermentation to consume glucose that is contained in the low purity gentiooligosaccharide; and subjecting the resulting fermentation broth to filtration and purification. According to the method of the present invention, high purity gentiooligosaccharides having a purity of at least 90% that can be used as alternatives to foods such as cocoa, chocolate, coffee, beer, tea, bread or confectionery product, and beverage or the main ingredients thereof. 1. A method for preparing a high purity gentiooligosaccharide comprising:adding a low purity gentiooligosaccharide to a liquid medium;subjecting the liquid medium to inoculation with a microorganism, followed by incubation and fermentation to consume glucose that is contained in the low purity gentiooligosaccharide;removing the microorganism from the obtained fermentation broth; andsubjecting the obtained broth to purification.2. The method of claim 1 , wherein the low purity gentiooligosaccharide contains 15 to 65% by weight of glucose and 35 to 85% by weight of gentiooligosaccharide.3. The method of claim 1 , wherein the low purity gentiooligosaccharide is added to the liquid medium at a concentration of 5 to 70% (w/v).4. The method of claim 1 , wherein the microorganism consumes glucose as a carbon source while not consuming gentiooligosaccharide.5. The method of claim 4 , wherein the microorganism is yeast claim 4 , bacteria or mold.6. A method for preparing a high purity gentiooligosaccharide comprising:adding a low purity gentiooligosaccharide to a liquid medium;subjecting the liquid medium to inoculation with a microorganism, followed by incubation and ...

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Номер записи: 98

30-05-2013 дата публикации

THERMAL CYCLING USING PHASE CHANGING FLUIDS

Номер: US20130137105A1

Автор: Zhang Rui

Принадлежит:

The invention provides systems, devices, and methods for heating and cooling chemical or biological samples, such as genetic materials during Polymerase Chain Reaction (“PCR”). The systems, devices, and methods comprise use of a fluid that performs repeated heating and cooling cycles, e.g., ‘thermal cycling’, on sample reactants with a phase changing fluid during evaporation and condensation. The systems, devices, and methods eliminate the need for a heating block as a means to obtain fast and uniform thermal cycling. The disclosure also describes the use of an optical system in conjunction with the thermodynamic cycler for real-time detection. Ultimately, uniformity and speed of the thermodynamic cycler provides for higher sensitivity and throughput of gene replication and detection. 1. A thermal cycling method for performing a polymerase chain reaction (PCR) comprising:i. providing a chamber adapted to fit a plurality of analyte samples;ii. providing a fluid inside said chamber; andiii. providing a component that regulates the thermodynamic phase of said fluid; andiv. changing the temperature of said samples during a phase change of said fluid in a manner predetermined by a PCR procedure.2. The method of wherein said samples comprise vessels containing temperature-sensitive substance.3. The method of wherein said samples are placed in direct contact with said fluid.4. The method of wherein said samples are partitioned from said fluid.5. The method of wherein said chamber comprises the component to provide heating inside thereof.6. The method of claim 1 , further comprising a component to provide fast and uniform transport of said fluid.7. The method of claim 1 , further comprising additional devices as a second component to regulate the said fluid phase.8. The method of claim 1 , further comprising a component that regulates the flow of said fluid in and out of said chamber.9. The method of claim 1 , further comprising a component that recirculates the flow of ...

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Номер записи: 99

30-05-2013 дата публикации

System and method including analytical units

Номер: US20130137110A1

Автор: Charles S. Kraihanzel

Принадлежит: Beckman Coulter Inc

Systems and methods for processing and analyzing samples are disclosed. The system may process samples, such as biological fluids, using assay cartridges which can be processed at different processing locations. In some cases, the system can be used for PCR processing. The different processing locations may include a preparation location where samples can be prepared and an analysis location where samples can be analyzed. To assist with the preparation of samples, the system may also include a number of processing stations which may include processing lanes. During the analysis of samples, in some cases, thermal cycler modules and an appropriate optical detection system can be used to detect the presence or absence of certain nucleic acid sequences in the samples. The system can be used to accurately and rapidly process samples.

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Номер записи: 100