Abstract: Methods for the treatment of Angelman Syndrome autism spectrum disorders are provided. The methods comprise administrating to a subject an agent that increases the expression of, or increases activity of, ?-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) at neuronal synapses.

Abstract: The present invention is related to a nucleic acid capable of binding to hepcidin.

Abstract: This present invention provides methods for the detection of small molecules in samples comprising the steps a) coupling a nanoparticle (NP) or microparticle (MP) to an aptamer specific for the small molecule to be detected to form a NP-aptamer conjugate b) contacting the NP-aptamer conjugate with the sample; and c) detecting a change in the size, surface potential, or mobility of the NP-aptamer conjugate, wherein the change is indicative of the presence of the small molecule. The present invention also provides for and a biosensor comprising nanoparticles coupled to aptamers to provide nanoparticle aptamer-conjugates (NP-aptamer).

Abstract: Disclosed herein are methods of treating a patient at risk of developing an inflammatory joint disease. In exemplary embodiments, the method involves inhibiting MCPIP levels in a patient in need, wherein said patient in need is exhibiting pre-arthritic or pre-osteoporotic symptoms.

Abstract: The invention features polynucleotide constructs containing one or more components (i) containing a disulfide linkage, where each of the one or more components is attached to an internucleotide bridging group or a terminal group of the polynucleotide construct, and each of the one or more components (i) contains one or more bulky groups proximal to the disulfide group. The invention also features polynucleotide constructs containing one or more components (i) containing a disulfide linkage, where each of the one or more components (i) is attached to an internucleotide bridging group or a terminal group of the polynucleotide construct, and each of the one or more components (i) contains at least 4 atoms in a chain between the disulfide linkage and the phosphorus atom of the internucleotide bridging group or the terminal group; and where the chain does not contain a phosphate, an amide, an ester, or an alkenylene.

Abstract: The present invention relates to compounds, compositions, and methods for the study, diagnosis, and treatment of traits, diseases and conditions that respond to the modulation of IDH1 and mutant IDH1 gene expression and/or activity, and/or modulate an IDH1 or mutant IDH1 gene expression pathway. Specifically, the invention relates to double-stranded nucleic acid molecules, including small nucleic acid molecules such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules, that are capable of mediating or that mediate RNA interference (RNAi) against IDH1 or mutant IDH1 gene expression.

Abstract: RNA interference is provided for inhibition of spleen tyrosine kinase (Syk) mRNA expression, in particular, for treating patients having a Syk-related inflammatory condition or at risk of developing a Syk-related inflammatory condition such as allergic conjunctivitis, ocular inflammation, dermatitis, rhinitis, asthma, allergy, or mast-cell disease.

Abstract: This invention relates to the field of biotechnology or genetic engineering. Specifically, this invention relates to the field of gene expression. More specifically, this invention relates to novel substitution mutant receptors and their use in a Group H nuclear receptor-based inducible gene expression system and methods of modulating the expression of a gene in a host cell for applications such as gene therapy, large scale production of proteins and antibodies, cell-based high throughput screening assays, functional genomics and regulation of traits in transgenic organisms.

Abstract: The present disclosure generally relates to novel polynucleotide molecules for use in regulating gene expression in recombinant cells, such as labyrinthulomycetes cells. The disclosure further relates to nucleic acid constructs, such as vectors and expression cassettes, containing a regulatory element operably linked to a heterologous nucleotide sequence. The disclosure further relates to methods for stably transforming a host cell, such as a labyrinthulomycetes cell with transgenes. Stably transformed recombinant cells, progeny, biomaterials derived therefrom, and methods for preparing and using the same are also provided.

Abstract: Disclosed herein are a transformed Synechococcus elongatus strain having improved capability of producing acetone and a method for producing acetone and a method for removing carbon dioxide using the same. In an aspect, the transformed Synechococcus elongatus strain of the present disclosure can produce acetone with high selectivity using carbon dioxide as a carbon source. The present disclosure is economical because the Synechococcus elongatus strain can economically produce high value-added acetone using carbon dioxide existing in the atmosphere as a carbon source without requiring an additional catalytic reaction. Also, the present disclosure is environment-friendly because carbon dioxide in the atmosphere can be removed or reduced using the microorganism.

Abstract: A method for deleting a region of DNA in a plant. In some embodiments, the method comprises transforming a plant with a nucleic acid molecule, wherein the nucleic acid molecule encodes one or more zinc finger nuclease(s) (ZFNs) operably linked to one or more tissue-specific promoter(s), e.g., a pollen-specific promoter. Methods include excising native genes in a plant. Accordingly, in some embodiments, ZFNs are engineered that recognize sequences that flank native plant genes. In further embodiments, ZFNs are expressed under the control of developmental stage-specific promoters, such that, for example, nucleic acid sequences are specifically excised in plants during relatively late stages of development. Nucleic acid molecules useful for carrying out disclosed methods and plants produced by the methods are included.

Abstract: A recombinant DNA construct is disclosed. When the recombinant DNA construct is expressed in a plant or a plant cell, endogenous HD-Zip class II proteins become less able to repress DNA transcription of the genes they typically regulate. The recombinant DNA construct can be expressed in plant cells to produce plants with enhanced phenotypes. Methods of making transgenic plants comprising the recombinant DNA construct, and plants produced thereby are also disclosed.

Abstract: A method to generate siRNAs in vivo is described, as are constructs and compositions useful in the method. The method does not depend on the use of DNA or synthetic constructs that contain inverted duplications or dual promoters so as to form perfect or largely double-stranded RNA. Rather, the method depends on constructs that yield single-stranded RNA transcripts, and exploits endogenous or in vivo-produced miRNAs or siRNAs to initiate production of siRNAs. The miRNAs or siRNAs guide cleavage of the transcript and set the register for production of siRNAs (usually 21 nucleotides in length) encoded adjacent to the initiation cleavage site within the construct. The method results in specific formation of siRNAs of predictable size and register (phase) relative to the initiation cleavage site. The method can be used to produce specific siRNAs in vivo for inactivation or suppression of one or more target genes or other entities, such as pathogens.

Abstract: The present application discloses an isolated nucleic acid sequence comprising (a) at least about 500 consecutive nucleotides of SEQ ID NO: 1; (b) a nucleotide sequence with at least 95% sequence identity to the nucleotide sequence of (a); (c) a nucleotide sequence hybridizing under stringent conditions to the nucleotide sequence of (a) or (b); and (d) a nucleotide sequence complementary to the nucleotide sequence of any one of (a) to (c). Further disclosed herein is a chimeric gene comprising the isolated nucleic acid described herein operably linked to a nucleic acid coding for an expression product of interest, and a transcription termination and polyadenylation sequence. Also disclosed herein are a vector, a transgenic plant cell, a transgenic plant and a seed as characterized in the claims.

Abstract: Compositions and methods comprising polynucleotides and polypeptides having glyphosate-N-acetyltransferase (GLYAT) activity are provided. In specific embodiments, the sequence has an improved property, such as, but not limited to, an improved specificity for glyphosate when compared to an appropriate control resulting in decreased off target acetylation of, e.g. an amino acid such as aspartate. Further provided are nucleic acid constructs, plants, plant cells, explants, seeds and grain having the GLYAT sequences. Various methods of employing the GLYAT sequences are provided. Such methods include methods for producing a glyphosate tolerant plant, plant cell, explant or seed and methods of controlling weeds in a field containing a crop employing the plants and/or seeds disclosed herein.

Abstract: Disclosed are methods of preparing FV vector particles. In some aspects, the disclosed methods may include the steps of transfecting a population of eukaryotic cells by contacting said population of eukaryotic cells with one or more transfection reagents to form a transfection mixture, and incubating the transfection mixture to form a transfected cell population; harvesting the FV vector particles from said transfected cell population; purifying the FV vector particles; and concentrating the FV vector particles.

Abstract: Methods for use with Type II CRISPR-Cas9 systems for increasing Cas9-mediated genome engineering efficiency are disclosed. The methods can be used to decrease the number of off-target nucleic acid double-stranded breaks and/or to enhance homology-directed repair of a cleaved target nucleic acid.

Abstract: The invention relates to an approach for introducing one or more desired insertions and/or deletions of known sizes into one or more predefined locations in a nucleic acid (e.g., in a cell or organism genome). They developed techniques to do this either in a sequential fashion or by inserting a discrete DNA fragment of defined size into the genome precisely in a predefined location or carrying out a discrete deletion of a defined size at a precise location. The technique is based on the observation that DNA single-stranded breaks are preferentially repaired through the HDR pathway, and this reduces the chances of indels (e.g., produced by NHEJ) in the present invention and thus is more efficient than prior art techniques. The invention also provides sequential insertion and/or deletions using single- or double-stranded DNA cutting.

Abstract: This invention relates to metabolically engineered microorganism strains, such as bacterial strains, in which there is an increased utilization of malonyl-CoA for production of a fatty acid or fatty acid derived product, wherein the modified microorganism produces fatty acyl-CoA intermediates via a malonyl-CoA dependent but malonyl-ACP independent mechanism.

Abstract: The present invention relates to a method for preparing a recombinant microorganism simultaneously comprising genes encoding enzymes used in the biosynthesis pathway of 6-aminocaproic acid, which is a precursor of caprolactam, biosynthesizing 6-aminocaproic acid from the microorganism, and producing the same so as to synthesize caprolactam.

Abstract: The present invention relates to methods for improving fermentation processes, including increasing product yield, reduced viscosity, and/or reduced foaming.

Abstract: The present invention relates to the field of biotransformation of furanic compounds. More particular the present invention relates to novel genetically modified cells with improved characteristics for biocatalytic transformation of furanic compounds and a vector suitable for the genetic modification of a host cell. Further aspects of the invention are aimed at processes for biotransformation of 5-(hydroxymethyl)furan-2-carboxylic acid (HMF-acid) and its precursors with the use of the cell according to the invention.

Abstract: Some variations provide a method of enzymatically converting biomass-derived cellulose to glucose, comprising exposing the biomass-derived cellulose to (i) cellulase enzymes, to hydrolyze the cellulose to glucose; and (ii) an external sulfur-containing compound, to deter bacterial and/or yeast contamination during cellulose hydrolysis. In some embodiments, the sulfur-containing compound includes sulfur dioxide or lignosulfonates. When the sulfur-containing compound includes lignosulfonates, the lignosulfonates may also function as an enzyme surfactant to assist hydrolysis, in addition to deterring bacterial and/or yeast growth/contamination. This method may be applied to cellulose-rich solids obtained from the AVAP® fractionation process, the Green Power+® pretreatment process, or any other source of cellulose-rich solids.

Abstract: Disclosed herein are enzymes useful for the degradation of cellobiosan in materials such a pyrolysis oils. Methods of degrading cellobiosan using enzymes or organisms expressing the same are also disclosed.

Abstract: Provided are processes for treating crop kernels which comprising the steps of a) soaking kernels in water to produce soaked kernels; b) grinding the soaked kernels; c) treating the soaked kernels in the presence of a polypeptide having protease activity.

Abstract: The present disclosure relates to a process for extracting sugars from a pretreated lignocellulosic biomass. This process consists of contacting the pretreated lignocellulosic biomass with low charges of an aqueous peroxy acid (PA) solution to produce a liquid fraction (containing a small amount of lignin and hemicellulose degradation products) and a solid fraction containing cellulose, hemicellulose and lignin. The solid fraction can then be subjected to enzymatic hydrolysis with a variety of cell wall-degrading enzymes to produce a lignin-rich residue and a sugar solution that can be fermented to a variety of (bio)chem icals.

Abstract: A process for the production of a glycoconjugate by N-glycosylation of a protein or peptide comprising the sequence D/E-X—N—X—S/T, wherein each X is the same or different and is any natural amino acid other than proline, wherein the process comprises reacting the protein or peptide with a polyisoprenyl pyrophosphate of formula (I), or a salt thereof, in the presence of PglB: (I) to produce the glycoconjugate comprising the protein or peptide having a saccharide [SI] linked to the asparagine in the sequence D/E-X—N—X—S/T. Polyisoprenylpyrophosphates used as substrates in the biocatalytic process are also provided, as well as certain glycoconjugates.

Abstract: This disclosure provides methods for preparing a sequencing library including the steps of providing a template nucleic acid sequence, dNTPs, dUTP, a primer, a polymerase, a dUTP excising enzyme, and a plurality of beads including oligonucleotide adapter sequence segments; amplifying the template nucleic acid with the polymerase, dNTPs, dUTP and random hexamer to provide a complementary nucleic acid sequence including occasional dUTPs; and excising the incorporated dUTPs with the dUTP excising enzyme to provide nicks in the complementary nucleic acid sequence to provide a sequencing library.

Abstract: The present disclosure provides systems, processes, articles of manufacture, and compositions that relate to the use of degradable adaptors for background reduction in various nucleic acid manipulations. In particular, adaptors are provided that can be degraded to an extent that the degradation products are incapable or are substantially incapable from participating in subsequent reactions, such as ligation, primer extension, amplification, and sequencing reactions.

Abstract: Antibiotic susceptibility profile and the bacterial species identification are reported and determined in a single diagnostic test. The method simultaneously reports for a sample of bacteria the identities of the bacteria and their respective antibiotic susceptibilities, the method comprising step(s): contacting the bacteria with antibiotics, a phenotypic fluorescent sensor of antibiotic susceptibility and species- or strain-specific affinity probes, wherein the probes and sensor simultaneously report, respectively, the identities of the bacteria and their respective antibiotic susceptibilities.

Abstract: The present invention relates to a method for isolating and optionally detecting microorganisms from a sample comprising mammalian cells, comprising the use of a lysis buffer comprising Benzonase® Nuclease. The invention further relates to a lysis buffer comprising Benzonase® Nuclease and its use.

Abstract: The present invention relates to indicator molecules containing multiple cleavage sites for use in detecting enzyme cleavage activity. The invention also relates to various applications of these indicator molecules, for example in enzyme detection devices, particularly although not exclusively, devices for use in the detection of enzyme activity in a test sample. The invention also relates to using the indicator molecules in methods for detecting the presence of enzyme activity in a test sample.

Abstract: A device is disclosed for conducting a non-invasive analysis of a bodily fluid to determine the presence and level of a certain constituent carried by the bodily fluid. An indicator formulation of the device changes color in response to exposure to the constituent to provide a visible indication of the presence and level of the constituent carried by the bodily fluid. A carrier substrate of the device is constructed of a material having voids providing a high void volume within the substrate. The device is made by applying a chromagen to the carrier substrate to create a chromagen-ladencarrier member. Then, a selected reagent having a particular constituent-specific formulation is applied to the chromagen-laden member. The selected reagent then combines with the chromagen thereby establishing the indicator formulation within the carrier substrate in place for reception of a sample of the bodily fluid.

Abstract: A method of detecting a target and quantifying the concentration of the same within a sample includes generating a plurality of fractionated volumes, wherein at least some of the fractionated volumes contain the target bound to a first detector molecule connected to a first reaction component (R1) and a second detector molecule connected to a second reaction component (R2). The fractionated volumes that contain the target, first detector molecule, second detector molecule, and a probe or other reporter molecule emit light and are imaged. Fractionated volumes emitting radiation can be used to detect the presence of the target within the sample. The number of fractionated volumes emitting a positive emission signal can be counted from the image and the concentration (or range of calculations) of the target can be calculated based at least in part on the number of fractionated volumes emitting a positive emission signal from the image.

Abstract: A method for performing a rolling circle amplification (RCA) reaction includes at least two rounds of RCA. The method includes providing a concatemeric first RCA product having a multiplicity of monomer repeats, each repeat representing a complementary copy of a first RCA template, wherein the nucleic acid molecule to be detected and/or analyzed, or its compliment, is contained in the first RCA template. The first RCA product is cleaved into monomer units which are reduced in size compared to the monomer repeat of the first RCA template. Monomer units resulting from the cleavage are circularized to form second RCA templates, which are smaller than the first RCA template. A second RCA reaction is performed on the second RCA template and a primer for the second RCA to form a second RCA product. The second RCA product, or a monomer unit derived from it, is detected or analyzed.

Abstract: Disclosed is a DNA detection device that detects a target DNA by detecting fluorescence output from sample droplets flowing through a flow path in a surface of a sensor chip, and that includes a fluorescence detector that detects fluorescence output from sample droplets flowing through the flow path, and a DNA detector that determines a type of fluorescent probe solution contained in each of the sample droplets based on a duration of the detected fluorescence and determines whether or not the sample droplet contains the target DNA based on whether intensity of the fluorescence is higher or lower than a threshold value.

Abstract: Embodiments provided herein relate to methods and compositions for labeling a nucleic acid in a sample with a stochastic barcode. Some embodiments relate to methods and compositions for characterizing a sample by identifying the TCR alpha chain or beta chain of a T cell.

Abstract: The present invention relates to a scalable multiplex PCR method that can simultaneously amplify overlapping amplicons without the drawbacks of conventional multiplex PCR. The method selectively amplifying target nucleic acid fragments having an overlapping region. The method comprises the steps of: obtaining a first nucleic acid sequence comprising a first tag t2 and a first forward primer F1, obtaining a second nucleic acid sequence comprising a second tag t1 and a first reverse primer R1, obtaining a third nucleic acid sequence comprising the second tag t1 and a second forward primer F2, obtaining a fourth nucleic acid sequence comprising a third tag t3 and a second reverse primer R2, wherein each primer is a gene-specific primer; performing initial cycles of PCR; and then performing later cycles of PCR at higher annealing temperatures to obtain amplification products.

Abstract: A composition and method for preserving a urine sample and a preservative delivery vessel are disclosed wherein treatment of the urine sample aids in preserving circulating cell-free nucleic acids in urine over a wide range of dilution ratios within temperature fluctuations that can occur during urine sample handling, storage and transportation. The urine sample preservation composition and method and preservative delivery vessel provide a method for obtaining high quality stabilized urinary cell-free nucleic acids for clinical diagnostics development and application.

Abstract: Markers of caloric restriction (CR) can be identified in a selected tissue by exposing an animal to CR conditions and selecting one or more genes differentially expressed in response to CR conditions in multiple subject groups. A candidate compound can be screened for likely ability to mimic the effects of CR when administered to an animal by comparing the tissue levels of expression products of the genes in animals treated with the candidate compound to those of animals subjected to CR.

Abstract: This application pertains to methods for the whole-cell analysis of gram-positive bacteria. The methods are capable of making a determination of whether or not a sample (e.g., a clinical sample) comprises one or more select gram-positive bacteria as well as, for example, whether or not none, some or all of said select gram-positive bacteria in said sample, or possibly other bacteria in said sample, possess a select trait or traits of interest. In some embodiments, the methods can be used to determine methicillin-resistant (the select trait) staphylococcus aureus (the select gram-positive bacteria), coagulase-negative staphylococci (another select gram-positive bacteria) and/or methicillin-sensitive staphylococcus aureus (MSSA) in said sample. The whole-cell analysis can be performed, for example, by in-situ hybridization (ISH), fluorescence in-situ hybridization (FISH), immunocytochemistry (ICC), or any combination of two or more of the foregoing.

Abstract: Compositions and methods for detecting Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are provided. The present invention also provides methods and compositions for screening for infection/inflammation based on genomic copy number. Described herein is a method that entails assaying a sample obtained from the urogenital tract of the mammal for an indicator of genomic copy number, wherein a genomic copy number level that is higher than a control genomic copy number level is indicative of the presence of infection or inflammation of the urogenital tract.

Abstract: Disclosed is a thermostable DNA polymerase preparation which can illimitably reduce the risk of false positivity in the detection of a subject microorganism utilizing a gene amplification reaction and therefore enables the selective amplification of DNA for detecting the subject microorganism even when the amount of the subject microorganism is small and therefore the amount of DNA collected therefrom is extremely small, and can be produced at a reduced cost. Also disclosed is a method for quantifying or quantifying/identifying a subject organism to be detected rapidly, conveniently and with high sensitivity using the preparation of the present invention.

Abstract: The present invention relates to nucleic acids and methods for detecting pathogens and beneficial microorganisms.

Abstract: Provided herein are kits for performing for nucleic acid sequences.

Abstract: Provided herein is a method for making a pool of probes by primer extension. In certain embodiments, the method comprises hybridizing a first population of oligonucleotides comprising a top strand sequence having the following formula V1-B-3? with a second population of oligonucleotides comprising a bottom strand sequence having the following formula V2?-B?-3? to provide a population of duplexes. After hybridizing, the 3? ends of the oligonucleotides in the duplexes are extended to produce a population of double stranded products comprising a top strand sequence having the following formula V1-B-V2, where V2 is complementary to V2?.

Abstract: The present application relates to detection units and methods for detecting one or more target analytes in a sample using a complex formed by a target and first and second probes, wherein the complex comprises an elongated region, a particle that is coupled to the first probe, and a solid support that is coupled to the second probe. Specific binding of a target analyte can be distinguished from non-specific binding of the particle by measuring the displacement of the particle.

Abstract: According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I): In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

Abstract: The present invention provides a method for improved fluorescent in situ hybridization (FISH) methodology which allows for quantifiable signals to be obtained in a short period of time. In certain embodiments, the method provides for a shorter hybridization time, thereby allowing the present method to be used in screening and rapid diagnostic methods. The present invention also provides a device and reagents for use with the methods of the invention.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.