Patents Issued in December 28, 2017
  • Publication number: 20170369898
    Abstract: Methods and compositions are provided which allow for genetic modification of host cells including, plants and plant cells. The various methods and composition employ a recombinant DNA construct comprising SEQ ID NO: 1 and/or 2 or active variants and fragments thereof. Such polynucleotides find use in facilitating integration of polynucleotides of interest into the DNA of a host cell, including a plant or plant cell. Vectors, host cells, bacterium and plants comprising the recombinant DNA construct or fragments thereof are provided. Further provided are methods of introducing into a host cell or a plant cell a polynucleotide of interest. The method comprises contacting the host cell with a bacterium competent for the transformation of the host cell, wherein the bacterium comprises a transformation vector comprising a recombinant DNA construct.
    Type: Application
    Filed: December 18, 2015
    Publication date: December 28, 2017
    Inventors: Vadim Beilinson, James R. Henriksen
  • Publication number: 20170369899
    Abstract: Provided are mutated acetohydroxyacid synthase (AHAS) nucleic acids and the proteins encoded by the mutated nucleic acids. Also provided are cassava plants, cells, and seeds comprising the mutated genes.
    Type: Application
    Filed: January 8, 2016
    Publication date: December 28, 2017
    Applicants: CIBUS US LLC, CIBUS EUROPE B.V.
    Inventors: Tracey A. LINCOLN, Gregory F.W. GOCAL
  • Publication number: 20170369900
    Abstract: The invention relates to genes which may be utilized for resistance to soybean cyst nematode. More specifically the present disclosure relates to identification of gene(s) that can confer upon a soybean plant resistance to soybean cyst nematode (SCN) and methods to use these loci and genes to obtain soybean strains that are resistant to SCN.
    Type: Application
    Filed: December 30, 2015
    Publication date: December 28, 2017
    Inventors: Tarek Abdel HEWEZI, Aditi RAMBANI, C. Neal STEWART, JR., Mitra MAZAREI, Vincent PANTALONE
  • Publication number: 20170369901
    Abstract: Methods and compositions for enhancing the resistance of plants to plant pests are provided. Chimeric pesticidal polypeptides and nucleic acid molecules encoding the chimeric pesticidal polypeptides are provided. The chimeric pesticidal polypeptides comprising a solubility-enhancing polypeptide operably linked to a polypeptide comprising pesticidal activity. The nucleic acid molecules can be used in expression cassettes for making transformed plants with enhanced resistance to plant pests. Further provided are transformed plants, plant tissues, plant cells, other host cells, and seeds as well as pesticidal compositions.
    Type: Application
    Filed: September 1, 2017
    Publication date: December 28, 2017
    Applicant: PIONEER HI-BRED INTERNATIONAL, INC.
    Inventors: RUTH CONG, TAKASHI YAMAMOTO, YI ZHENG
  • Publication number: 20170369902
    Abstract: Manipulation of male fertility in a polyploid species requires attention to the interaction of male-fertility alleles of multiple genomes. In hexaploid wheat, single-genome heterozygotes for Ms26 provide differential levels of male fertility across genomes. Hexaploid wheat homozygous for mutations in the Ms26 gene on the A, B, and D genomes is male-sterile. Male fertility may be restored by sufficient levels of expression of Ms26 using native Ms26 or a transgene, which may be native to wheat or to another species, or a combination of native and transgenic alleles. CRISPR/Cas9 technology may be used to generate mutations in Ms26 in wheat or rice.
    Type: Application
    Filed: December 15, 2015
    Publication date: December 28, 2017
    Applicant: PIONEER HI-BRED INTERNATIONAL, INC.
    Inventors: ANDREW MARK CIGAN, MANJIT SINGH
  • Publication number: 20170369903
    Abstract: Simultaneous expression of a plurality of foreign genes by using a stealthy RNA gene expression system that is a complex that does not activate the innate immune mechanism and is formed from an RNA-dependent RNA polymerase, a single-strand RNA binding protein, and negative-sense single-strand RNAs including the following (1) to (8): (1) a target RNA sequence that codes for any protein or functional RNA; (2) an RNA sequence forming a noncoding region and derived from mRNA; (3) a transcription initiation signal sequence recognized by the RNA-dependent RNA polymerase; (4) a transcription termination signal sequence recognized by the polymerase; (5) an RNA sequence containing a replication origin recognized by the polymerase; (6) an RNA sequence that codes for the polymerase; (7) an RNA sequence that codes for a protein for regulating the activity of the polymerase; and (8) an RNA sequence that codes for the single-strand RNA binding protein.
    Type: Application
    Filed: January 18, 2016
    Publication date: December 28, 2017
    Applicants: NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY, TOKIWA-BIO INC.
    Inventors: Mahito Nakanishi, Minoru Iijima
  • Publication number: 20170369904
    Abstract: The present invention describes a method for increasing transfection efficiency of cells. The present invention further provides a method for increasing the efficiency of stem cell reprogramming.
    Type: Application
    Filed: June 21, 2017
    Publication date: December 28, 2017
    Inventors: James LIM, Luke CASSEREAU
  • Publication number: 20170369905
    Abstract: The present invention relates to a mammalian cell comprising a gene encoding a polypeptide of interest, wherein the polypeptide of interest is expressed comprising one or more posttranslational modification patterns. These modifications are useful for example in glycoprotein production where the antibodies with the modifications have an enhanced antibody-dependent cell-mediated cytotoxicity (ADCC). The present invention also relates to methods for producing the glycoproteins and compositions comprising the glycoproteins, and their uses.
    Type: Application
    Filed: December 11, 2015
    Publication date: December 28, 2017
    Inventors: Henrik Clausen, Zhang Yang, Adnan Fevzi Halim, Eric Bennett, Carsten Behrens, Malene Bech Vester-Christensen, Shamim Herbert Rahman
  • Publication number: 20170369906
    Abstract: A highly efficient ethanol-fermentative yeast having high efficiency in ethanol production is provided without introducing a foreign gene. The highly efficient ethanol-fermentative yeast features a fermentative yeast effectively producing ethanol from pentose and hexose and being deposited to NITE Patent Microorganisms Depositary under the accession number NITE BP-01963.
    Type: Application
    Filed: December 5, 2014
    Publication date: December 28, 2017
    Inventors: Yoshiki Tsuchida, Ikumi Kurihara, Tomohiro Imai, Iku Koike
  • Publication number: 20170369907
    Abstract: This document describes biochemical pathways for producing one or more of pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine and 1,7-heptanediol by forming one or two terminal functional groups, comprised of carboxyl, amine or hydroxyl groups, in a C7 aliphatic backbone substrate produced from succinate semialdehyde or pyruvate. These pathways, metabolic engineering and cultivation strategies described herein rely on the aldol condensation of succinate semialdehyde and pyruvate.
    Type: Application
    Filed: June 29, 2017
    Publication date: December 28, 2017
    Inventors: Alex Van Eck Conradie, Adriana Leonora Botes, Changlin Chen, Paul S. Pearlman
  • Publication number: 20170369908
    Abstract: Embodiments of the invention relate generally to methods to generate microorganisms and/or microorganism cultures that exhibit the ability to produce polyhydroxyalkanoates (PHA) from carbon sources at high efficiencies. In several embodiments, preferential expression of, or preferential growth of microorganisms utilizing certain metabolic pathways, enables the high efficiency PHA production from carbon-containing gases or materials. Several embodiments relate to the microorganism cultures, and/or microorganisms isolated therefrom.
    Type: Application
    Filed: July 7, 2017
    Publication date: December 28, 2017
    Inventor: Markus D. Herrema
  • Publication number: 20170369909
    Abstract: Provided is ?3 desaturase having high enzymatic activity even at normal temperature. A polypeptide which consists of an amino acid sequence having an identity of 80% or more with the amino acid sequence represented by SEQ ID NO: 2 and has ?3 desaturation activity on C20 fatty acid, and a gene thereof.
    Type: Application
    Filed: December 24, 2015
    Publication date: December 28, 2017
    Applicants: KYOTO UNIVERSITY, NISSHIN PHARMA INC.
    Inventors: Jun OGAWA, Akinori ANDO, Eiji SAKURADANI, Sakayu SHIMIZU, Shigeru HIRAMOTO, Masataka HARATA, Yuki TAKEMOTO
  • Publication number: 20170369910
    Abstract: Disclosed are transformed cells comprising one or more genetic modifications that affect the lipid content of the cell, e.g., by increasing the concentration of oleic acid in the cell relative to an unmodified cell of the same type. Also disclosed are methods for modifying the lipid content of a cell by increasing the activity of one or more proteins in the cell and/or by decreasing the activity of one or more proteins in the same cell.
    Type: Application
    Filed: December 9, 2015
    Publication date: December 28, 2017
    Inventors: Vasiliki TSAKRAKLIDES, Elena E. BREVNOVA, Jonathan FRIEDLANDER, Annapurna KAMINENI, Arthur J. SHAW, IV
  • Publication number: 20170369911
    Abstract: The present invention concerns an oleaginous yeast variant of the species Rhodosporidium azoricum characterized by higher biomass yields and intra- cellular lipid accumulation useful for the production of bio-fuels higher, in determined conditions, with respect to the wild type strain of the same species. Furthermore, the invention concerns a method through which said oleaginous yeast variant of the species Rhodosporidium azoricum was obtained. The invention further concerns the lipid production by means of said variant strain of oleaginous yeast of the species Rhodosporidium azoricum.
    Type: Application
    Filed: December 29, 2015
    Publication date: December 28, 2017
    Applicant: ENI S.p.A.
    Inventors: Giuliana FRANZOSI, Daniela CUCCHETTI, Daniele BIANCHI, Silvia GALAFASSI, Concetta COMPAGNO
  • Publication number: 20170369912
    Abstract: Disclosed are transformed cells comprising one or more genetic modifications that increase the lipid content of the cell, e.g., relative to an unmodified cell of the same type. Also disclosed are methods for increasing the lipid content of a cell by increasing the activity of one or more proteins in the cell and/or by decreasing the activity of one or more proteins in the cell.
    Type: Application
    Filed: December 29, 2015
    Publication date: December 28, 2017
    Inventors: Arthur J. SHAW, IV, Johannes Pieter VAN DIJKEN, Annapurna KAMINENI, Jonathan FRIEDLANDER, Vasiliki TSAKRAKLIDES, Maureen HAMILTON, Elena E. BREVNOVA
  • Publication number: 20170369913
    Abstract: Provided is a method of producing and isolating a diamine produced by microbial fermentation that minimizes undesirable salt formation to provide a lower cost process.
    Type: Application
    Filed: December 22, 2015
    Publication date: December 28, 2017
    Inventors: Lauri H. Suominen, Connor J. Galleher, Michael Japs, Mark J. Burk, Cara Tracewell
  • Publication number: 20170369914
    Abstract: This document describes biochemical pathways for producing 2-aminopimelate from 2,6-diaminopimelate, and methods for converting 2-aminopimelate to one or more of adipic acid, adipate semialdehyde, caprolactam, 6-aminohexanoic acid, 6-hexanoic acid, hexamethylenediamine, or 1,6-hexanediol by decarboxylating 2-aminopimelate into a six carbon chain aliphatic backbone and enzymatically forming one or two terminal functional groups, comprised of carboxyl, amine or hydroxyl group, in the backbone.
    Type: Application
    Filed: July 6, 2017
    Publication date: December 28, 2017
    Inventors: Alex Van Eck Conradie, Adriana Leonora Botes
  • Publication number: 20170369915
    Abstract: The present invention provides a method of producing lysergic acid and other ergot alkaloids by genetic modification of a fungus. A strain of fungus comprising Aspergillus fumigatus (A. fumigatus) or any fungus having a pathway similar to Aspergillus fumigatus and expressing one or more genes of the ergot alkaloid biosynthesis pathway from one or more fungus selected from the group consisting of Epichloë festucae var. lolii×Epichloë typhina isolate Lp1 (E. sp. Lp1); Claviceps species; Claviceps africana (C. africana); Claviceps gigantea (C. gigantea); Epichloë coenophiala and Periglandula species, wherein gene easA or gene easM is inactivated in said A. fumigatus or said fungus having a pathway similar to Aspergillus fumigatus, is provided.
    Type: Application
    Filed: September 11, 2017
    Publication date: December 28, 2017
    Inventors: Daniel G. Panaccione, Sarah L. Robinson
  • Publication number: 20170369916
    Abstract: A genetically modified microorganism of the genus Gluconacetobacter has decreased pyrroloquinoline-quinone (PQQ)-dependent glucose dehydrogenase (GDH) activity of and increased glucose permease activity. The microorganism has enhanced productivity cellulose and is useful for the manufacture of microbial cellulose.
    Type: Application
    Filed: April 5, 2017
    Publication date: December 28, 2017
    Inventors: Jieun Kim, Hongsoon Rhee, Jiae Yun, Jinkyu Kang, Jinhwan Park
  • Publication number: 20170369917
    Abstract: The invention relates to a process for the preparation of a sugar and/or fermentation product from lignocellulosic material.
    Type: Application
    Filed: December 16, 2015
    Publication date: December 28, 2017
    Inventor: Bertus NOORDAM
  • Publication number: 20170369918
    Abstract: The present invention provides for a method of fermenting or saccharifying a biomass comprising: (a) (i) contacting a biomass comprising a polysaccharide, and an ionic liquid (IL) to form a first solution, or (ii) providing the first solution comprising the biomass and the IL, (b) contacting the first solution and carbon dioxide such that the first solution results in a lower pH, (c) introducing (i) an enzyme capable of enzymatically to breakdown at least one bond in the polysaccharide or a breakdown product of the polysaccharide, and/or (ii) a microorganism that capable of producing the enzyme and/or fermenting the polysaccharide or a breakdown product of the polysaccharide, such that the polysaccharide is at least partially broken down and the first solution is transformed into a second solution.
    Type: Application
    Filed: December 23, 2015
    Publication date: December 28, 2017
    Inventors: Jian Sun, Jian Shi, Blake A. Simmons, Seema Singh
  • Publication number: 20170369919
    Abstract: The process for the hydrolysis of ligno-cellulosic biomass comprises the steps of A) Contacting a ligno-cellulosic feedstock, the feedstock comprised of biomass having a dry content and water with at least a portion of a solvent, the solvent comprised of water soluble hydrolyzed species; wherein at least some of the water soluble hydrolyzed species are the same as the water soluble hydrolyzed species obtainable from the hydrolysis of the biomass in the feedstock; B) maintaining the contact between the feedstock of the feedstock stream and the solvent at a temperature in the range of 20° C. to 200° C. for a time in the range of 5 minutes to 72 hours to create a hydrolyzed product from the biomass in the feedstock.
    Type: Application
    Filed: September 1, 2017
    Publication date: December 28, 2017
    Applicant: Beta Renewables S.p.A.
    Inventors: Marco COTTI COMETTINI, Paolo Torre, Francesco Cherchi, Alberto Riva, Simone Ferrero, Piero Ottonello, Mirko Garbero
  • Publication number: 20170369920
    Abstract: The invention relates to a method for selective crystallization of 2?-FL from an aqueous solution comprising 2?-FL and one or more other fucosylated carbohydrates by adding acetic acid to the solution.
    Type: Application
    Filed: December 16, 2015
    Publication date: December 28, 2017
    Inventors: Gyula DEKANY, Györgyi OSZTROVSZKY, Martin MATWIEJUK, Pierre CHASSAGNE, Markus HEDEROS
  • Publication number: 20170369921
    Abstract: Provided herein are methods and compositions for analyzing nucleic acids associated with single cells using nucleic acid barcodes. According to some embodiments, a method for producing one or more polynucleotides of interest comprises: obtaining a plurality of RNAs associated with one or more samples, wherein the samples are obtained from one or more subjects, each RNA is associated with a single sample, and the RNAs associated with each sample are present in a separate reaction volume; adding an adapter molecule to the RNAs associated with each sample, wherein the adapter molecule is generated using an enzymatic reaction and comprises a universal priming sequence, a barcode sequence, and a binding site; and incorporating the barcode sequence into one or more polynucleotides associated with each sample, thereby producing the one or more polynucleotides of interest.
    Type: Application
    Filed: February 8, 2017
    Publication date: December 28, 2017
    Inventors: Yann Chong Tan, Gary Withey
  • Publication number: 20170369922
    Abstract: The invention relates to recombinant microorganisms and methods for producing steviol glycosides, glycosylated ent-kaurenol, and glycosylated ent-kaurenoic acid.
    Type: Application
    Filed: January 29, 2016
    Publication date: December 28, 2017
    Inventors: Kim Olsson, Ernesto Simon, Michael Dalgaard Mikkelsen, Simon Carlsen, Veronique Douchin, Swee Chuang Lim, Louis During
  • Publication number: 20170369923
    Abstract: The invention provides means and methods for producing one or more Ig-like molecules in a single host cell. Novel CH3 mutations enabling the production of monospecific and/or bispecific Ig-like molecules of interest are also provided.
    Type: Application
    Filed: May 16, 2016
    Publication date: December 28, 2017
    Inventors: Cornelis Adriaan DE KRUIF, Linda Johanna Aleida HENDRIKS, Ton LOGTENBERG
  • Publication number: 20170369924
    Abstract: The present invention is directed to methods for the growth, enrichment and isolation of microbes within a sample for further use in presumptive identification of pathogenic bacteria that may therein be contained.
    Type: Application
    Filed: June 22, 2017
    Publication date: December 28, 2017
    Inventors: Linda Pilarski, Alexey Atrazhev, Jana Lauzon, Cammika Manage
  • Publication number: 20170369925
    Abstract: A rapid one-pass liquid filtration system efficiently concentrates biological particles that are suspended in liquid from a dilute feed suspension. A sample concentrate or retentate suspension is retained while eliminating the separated fluid in a separate flow stream. Suspended biological particles include such materials as proteins/toxins, viruses, DNA, and/or bacteria in the size range of approximately 0.001 micron to 20 microns diameter. Concentration of these particles is advantageous for detection of target particles in a dilute suspension, because concentrating them into a small volume makes them easier to detect. Additional concentration stages may be added in “cascade” fashion, in order to concentrate particles below the size cut of each preceding stage remaining in the separated fluid in a concentrated sample suspension. This process can also be used to create a “band-pass” concentration for concentration of a particular target size particle within a narrow range.
    Type: Application
    Filed: August 18, 2017
    Publication date: December 28, 2017
    Inventors: David S. Alburty, Andrew E. Page, Zachary A. Packingham, Daniel B. Marske
  • Publication number: 20170369926
    Abstract: The inventors have identified several proteases and a protease inhibitor that are overexpressed in ovarian cancer tumors. They have developed monoclonal antibodies against the proteins and shown that they can be detected in serum and the levels of the proteins in serum fluctuate during cancer treatment. They have shown that serum assays for the proteases and protease inhibitor can be used for early detection of ovarian cancer, and for monitoring cancer treatment.
    Type: Application
    Filed: August 30, 2017
    Publication date: December 28, 2017
    Inventors: Timothy J. O'Brien, John Beard, Wilbur C. Hitt, JR.
  • Publication number: 20170369927
    Abstract: A method for quantifying a plurality of target molecules in a sample may include releasing a target molecule from a non-covalent bond of a conjugate by using a fusion molecule. A kit may include a detection conjugate, a release reagent, nucleic acid amplification agents, and an amplification detection probe. A device may be designed to perform the methods.
    Type: Application
    Filed: June 27, 2017
    Publication date: December 28, 2017
    Inventors: Michael Adler, Hendrik Schroeder, Mark Spengler
  • Publication number: 20170369928
    Abstract: The present disclosure provides a method for evaluating DNA damage by an analyte and a method for screening a DNA damage inhibitor. According to the present invention, the present invention can quantitatively evaluate the extent of DNA damage by an analyte through visualization.
    Type: Application
    Filed: December 28, 2016
    Publication date: December 28, 2017
    Inventor: Kyu Bong JO
  • Publication number: 20170369929
    Abstract: A composition for reducing the inhibitory effects of contaminants on nucleic acid amplification is provided. The composition includes effective amounts of ferric iron, an organic iron-chelating reagent, and a non-ionic surfactant. Optionally, the composition includes polyvinylpyrrolidone. The composition has a pH of about 8.45 to 8.85. The organic iron-chelating reagent has a first affinity constant greater than or equal to 104.2 with respect to ferric iron and a second affinity constant less than 103.8 with respect to magnesium. The first affinity constant and the second affinity constant are determined in deionized water at pH 8.45 and 20° C. Methods of using the composition to prepare a sample for nucleic acid amplification are also provided.
    Type: Application
    Filed: December 21, 2015
    Publication date: December 28, 2017
    Applicant: 3M INNOVATIVE PROPERTIES COMPANY
    Inventors: GREGORY W. SITTON, NEIL PERCY
  • Publication number: 20170369930
    Abstract: The present invention relates to a method for predicting causative factors (bacteria) of serious bacterial infectious diseases in a clinical sample containing bacteria-derived nano-sized extracellular vesicles, that is, nanovesicles, through the analysis of the genes contained in the nanovesicles. According to the present invention, information on bacteria of serious bacterial infection can be provided, a causative factor of the bacterial infection can be predicted, and the resistance of the bacteria to antibiotics can be predicted.
    Type: Application
    Filed: December 10, 2015
    Publication date: December 28, 2017
    Applicant: MD HEALTHCARE INC.
    Inventors: Young Koo JEE, Yoon-Keun KIM, Young-Ju KIM, Hyeonil CHOI, Mina RHO, Sungmin KIEM
  • Publication number: 20170369931
    Abstract: The invention is directed to compositions, kits, and methods for amplifying and detecting a Zika virus nucleic acid sequence in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.
    Type: Application
    Filed: June 26, 2017
    Publication date: December 28, 2017
    Inventors: Matthew Frankel, George Schneider
  • Publication number: 20170369932
    Abstract: The present invention relates to a method for detecting a target nucleic acid derived from a pathogen in a subject. The method comprises (a) amplifying the nucleic acid sequence of the target nucleic acid, which is obtained from a cell-free fraction of a blood sample from the subject, to produce a double stranded DNA is produced, and (b) detecting the double stranded DNA. The presence of the double stranded DNA indicates the presence of the target nucleic acid in the subject. Also provided are kits for detecting a target nucleic acid derived from a pathogen in a subject.
    Type: Application
    Filed: July 31, 2017
    Publication date: December 28, 2017
    Applicant: Occam Biolabs, Inc.
    Inventor: Mingwei QIAN
  • Publication number: 20170369933
    Abstract: A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Application
    Filed: August 17, 2017
    Publication date: December 28, 2017
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman
  • Publication number: 20170369934
    Abstract: Disclosed is a method of designing a valid primer pair satisfying a specificity condition. The method includes searching for an identifier of a base sequence from a genetic information index based on a query language associated with a gene, searching for a candidate primer from a provided candidate primer set index to satisfy the specificity condition based on the identifier of the base sequence, filtering the candidate primer based on primer-related filtering conditions, and providing information about a primer pair satisfying the query language and the filtering conditions based on a result of the filtering.
    Type: Application
    Filed: April 26, 2017
    Publication date: December 28, 2017
    Applicant: Daegu Gyeongbuk Institute of Science and Technology
    Inventors: Min Soo Kim, HYERIN KIM, JAEHYUNG KOO, Na Na Kang, KyuHyeon An
  • Publication number: 20170369935
    Abstract: The invention provides compositions comprising nucleic acid complexes for use in monitoring binding interactions and in measuring association and/or dissociation kinetics, detecting analytes including low concentration analytes, and screening library members. In some instances, the nucleic acid complexes are double-stranded nicked nucleic acids comprising a scaffold nucleic acid hybridized to one or more oligonucleotides. In some instances, a first, a second, a third, and optionally a fourth oligonucleotide are linked to moieties that are known to interact with each other or which are suspected of interacting with each other or of interacting with a common moiety such as an analyte. Changes in topology of the complex are used to determine the binding interactions of the various binding partners.
    Type: Application
    Filed: November 16, 2015
    Publication date: December 28, 2017
    Applicants: Children's Medical Center Corporation, President and Fellows of Harvard College
    Inventors: Mounir Ahmad Koussa, Kenneth Anders Halvorsen, Andrew Ward, Wesley Philip Wong
  • Publication number: 20170369936
    Abstract: The invention provides a novel array method for nucleic acid sequence detection with improved specificity which allows for detection of genetic variation, from simple SNPs (where the variation occurs at a fixed position and is of limited allelic number) to more complex sequence variation patterns (such as with multigene families or multiple genetic strains of an organism where the sequence variation between the individual members is neither fixed nor consistent). The array is comprised of short, synthetic oligonucleotide probes attached to a solid surface which are hybridized to single-stranded targets. Single stranded targets can be produced using a method that employs primers modified on the 5? end to prohibit degradation by a 5?-exonuclease that is introduced to degrade the unprotected strand. The invention further provides for printing buffers/solutions for the immobilization of oligonucleotide probes to an array surface.
    Type: Application
    Filed: February 6, 2017
    Publication date: December 28, 2017
    Inventors: Kerry B. Gunning, Mark Aaron Behlke
  • Publication number: 20170369937
    Abstract: The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.
    Type: Application
    Filed: June 15, 2017
    Publication date: December 28, 2017
    Inventors: Job Dekker, Erez Lieberman Aiden, Nynke Van Berkum, Andreas Gnirke, Eric Lander, Chad Nusbaum, Louise Williams, Alexandre Melnikov, Georgia Giannoukos
  • Publication number: 20170369938
    Abstract: A method of producing a replicate or derivative of an array of molecules, the array having a spatial arrangement of separate samples of molecules, includes creating, for each sample, at least one spatially limited effective area which is separate from the effective areas of the other samples, a surface, provided with a binding adapter or binding properties, of a carrier bordering on the effective areas. The molecules are amplified by means of amplifying agents in the effective areas for creating replicates or derivatives of the samples. The replicates or derivatives of the samples are bound to the carrier by means of the binding adapter or the binding properties, so that a spatial arrangement of the replicates or derivatives of the samples on the carrier corresponds to the spatial arrangement of the samples in the array. The carrier having the copies of the samples is removed from the array.
    Type: Application
    Filed: July 4, 2017
    Publication date: December 28, 2017
    Inventors: Roland ZENGERLE, Felix von Stetten, Guenter Roth, Jochen Hoffmann
  • Publication number: 20170369939
    Abstract: Provided are systems, kits, and methods for the quantitative detection of single nucleotide polymorphisms or variants to identify malignant neoplasms. The methods include use of modified oligonucleotide blockers with peptide nucleic acid backbones that hybridize to and block logarithmic amplification of the wild-type alleles of a target, and incorporation of locked nucleic acids into probes that are complementary to a mutant allele of the target sequence to increase specificity. The methods include detection of variants in sequences with high GC content and/or low complexity, such as the TERT promoter, IDH1, BRAF, NRAS, GNAQ, GNA11 and H3F3 A gene variants. The methods include sensitive detection and staging of cancers with low cellularity, and can be used intraoperatively such as for glioma, or to detect cell-free circulating tumor DNA, such as for melanoma.
    Type: Application
    Filed: December 22, 2015
    Publication date: December 28, 2017
    Applicants: THE BROAD INSTITUTE, INC., DANA-FARBER CANCER INSTITUTE, INC., THE GENERAL HOSPITAL CORPORATION
    Inventors: MATTHEW MEYERSON, GANESH M. SHANKAR, JOSHUA M. FRANCIS, DANIEL P. CAHILL, MIKAEL L. RINNE
  • Publication number: 20170369940
    Abstract: According to one embodiment, there is provided a nucleic acid primer set that amplifies a ZEBOV gene. An F1 sequence includes at least 13 consecutive bases included in SEQ ID NO: 31 or 64. An F2 sequence includes at least 13 bases included in SEQ ID NO: 62 or 63. An F3 sequence includes at least 13 bases included in SEQ ID NO: 29, 36, 38, 55, 56, 57, 58, 59, 60, 61 or 61. A B1c sequence includes at least 13 bases included in SEQ ID NO: 68, 69, 70, 71, 72, 73, 74 or 75. A B2c sequence includes at least 13 bases included in SEQ ID NO: 65 or 66. A B3c sequence includes at least 13 bases included in SEQ ID NO: 34, 67, 82 or 83.
    Type: Application
    Filed: June 19, 2017
    Publication date: December 28, 2017
    Applicants: Nagasaki University, Toshiba Medical Systems Corporation
    Inventors: Jiro YASUDA, Yohei Kurosaki
  • Publication number: 20170369941
    Abstract: The present invention relates to a method which prevents undesirable binding of ddNTPs to double stranded polynucleotides when in the presence of a polymerase. Such methods may be used to prevent the appearance of false positives in methods employing ddNTPs, e.g. in sequence detection methods. The present invention also provides a method of avoiding a false Tm reading or false FRET effects (such as false positive quenching), for example in a melting curve analysis method. In particular a method is provided in which a target nucleotide sequence in a test polynucleotide is detected using a method in which a double stranded molecule is generated which may or may not comprise two labels depending on whether the target sequence is present in which the presence of the two labels is determined, preferably by performing a melting curve analysis.
    Type: Application
    Filed: February 1, 2016
    Publication date: December 28, 2017
    Applicants: NORWEGIAN UNIVERSITY OF LIFE SCIENCES, HEDMARK UNIVERSITY OF APPLIED SCIENCES
    Inventors: Knut RUDI, Robert C. WILSON
  • Publication number: 20170369942
    Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed therebetween. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide.
    Type: Application
    Filed: June 16, 2017
    Publication date: December 28, 2017
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
  • Publication number: 20170369943
    Abstract: A method for sequencing a nucleic acid strand, comprising the steps of: providing a solution containing truncated strands having lengths different from one another terminating with a respective dideoxynucleotide from among ddATP, ddTTP, ddGTP, and ddCTP; functionalizing first masses by a donor molecule and second masses by an acceptor molecule such as to generate a light emission when they come into mutual contact; coupling a first mass to a first end of each truncated strand; coupling the second masses to a respective terminal dideoxynucleotide of each strand; applying an AC electrical field having variable frequencies that are such as to generate, on each second mass, a net movement directed towards the first mass; acquiring a plurality of light radiations for each frequency value; and associating each light radiation acquired to a respective dideoxynucleotide and, thus, to a respective nucleotide base.
    Type: Application
    Filed: December 29, 2016
    Publication date: December 28, 2017
    Inventors: Alessandro Paolo Bramanti, Marco Angelo Bianchessi
  • Publication number: 20170369944
    Abstract: A method of analyzing a molecule is disclosed. A lipid bilayer is formed such that it divides a first reservoir characterized by a first reservoir osmolarity from a second reservoir characterized by a second reservoir osmolarity. An electrolyte solution is flowed to the first reservoir that tends to make a first change to a ratio of the first reservoir osmolarity to the second reservoir osmolarity. A voltage is applied across the lipid bilayer, wherein the lipid bilayer is inserted with a nanopore, and wherein a net transfer of ions between the first reservoir and the second reservoir tends to make a second change to the ratio of the first reservoir osmolarity to the second reservoir osmolarity, and wherein the first change to the ratio and the second change to the ratio tends to counter-balance each other.
    Type: Application
    Filed: June 22, 2017
    Publication date: December 28, 2017
    Inventors: Geoffrey BARRALL, Jason KOMADINA, Marcin ROJEK
  • Publication number: 20170369945
    Abstract: Methods of screening subjects for genetic markers associated with autism spectrum disorders are disclosed. In particular, the invention relates to methods of diagnosing autism spectrum disorders by detecting the presence of deleterious mutations or aberrant expression of genes associated with autism spectrum disorders. The present invention relates to genetic markers associated with ASD and methods of screening subjects for such genetic markers. In particular, the invention relates to methods of diagnosing ASD by detecting the presence of deleterious mutations or aberrant expression of genes associated with ASD.
    Type: Application
    Filed: December 28, 2015
    Publication date: December 28, 2017
    Inventors: Jingjing Li, Minyi Shi, Michael Snyder
  • Publication number: 20170369946
    Abstract: Methods and kits for diagnosing and/or treating a lower respiratory infection in a subject include obtaining a biological sample from the subject; detecting RNA expression levels of one or more biomarkers in the biological sample and comparing the expression levels of the one or more three biomarkers to at least one invariant control marker wherein an increase or decrease in the level of expression of the one or more biomarkers as compared to the at least one invariant control marker is indicative of a lower respiratory infection.
    Type: Application
    Filed: January 12, 2016
    Publication date: December 28, 2017
    Applicant: The George Washington University a Congressionally Chartered Not-for-Profit Corporation
    Inventors: Timothy A. Mccaffrey, Lakhmir S. Chawla
  • Publication number: 20170369947
    Abstract: Provided herein are a kit and method for detecting mutations in CTNNB1 and hTERT, and their use in detection and management of hepatocellular carcinoma (HCC). The kit comprises a first pair of primers, configured to specifically bind sequences flanking the genomic region for amplifying the genomic region in a first PCR reaction; and at least one clamp, each configured to bind to one first allele but not any second allele at an annealing temperature in the first PCR reaction to thereby selectively suppress amplification of the one first allele but still allow amplification of other second allele(s). Kits and methods for detecting mutations in CTNNB1 and hTERT are also provided. A method for detecting or monitoring recurrence of HCC is further disclosed, which comprises determining levels of five DNA markers, including CTNNB1 mutations, hTERT mutations, TP53 mutations, RASSF1A methylation, and GSTP1 methylation.
    Type: Application
    Filed: April 20, 2017
    Publication date: December 28, 2017
    Applicant: JBS Science Inc.
    Inventors: Wei Song, Surbhi Jain, Jamin Dean Steffen, Jeremy Wang