Abstract: The present disclosure provides expression vectors containing a nucleic acid encoding an RNA polymerase III promoter, a ribozyme, a CRISPR-Cas9 single guide RNA, and an RNA polymerase III terminator, where the ribozyme is 5? to the CRISPR-Cas9 single guide RNA, as well as ribonucleic acids encoded thereby. Further provided are fungal cells containing an expression vector described herein, as well as methods of fungal genome engineering through use of an expression vector described herein.

Abstract: Technology to optimize plant architecture is critical for future efforts to increase planting density in a wide range of crops. Little is known regarding the molecular mechanisms governing this basic plant developmental feature, particularly in fruit trees. Recently, a pair of distantly related genes called LAZY1 and TILLER ANGLE CONTROL 1 (TAC1) was shown to have opposing effects on lateral branch angle in monocots and dicots. We have characterized the LAZY1 gene in both Arabidopsis and plum (Prunus domestica) and assessed its functional relationship with TAC1. Both lazy1 and tac1:lazy1 Arabidopsis plants showed a previously unreported weeping phenotype. Transgenic plum lines silenced for LAZY1 showed horizontal branch angles, sometimes marked by rootward lateral branch growth. Our results establish that manipulation of LAZY1 gene function results in changes in tree shape and can be used to engineer fruit or ornamental trees with desired branch angles.

Abstract: Two novel cDNAs for two different genes, HDT1 and HDT2, are isolated from red clover and sequenced. Both HDT1 and HDT2 encode hydroxycinnamoyl-CoA:L-DOPA/tyrosine hydroxycinnamoyl transferase (HDT) which enzymatically produces clovamide and/or related hydroxycinnamoyl amides. Clovamide and related hydroxycinnamoyl amides reduce post-harvest protein degradation. Genetically altered alfalfa plants containing an expression cassette containing a cDNA encoding HDT1 or HDT2 are generated. These genetically altered alfalfa plants produce hydroxycinnamoyl-CoA:L-DOPA/tyrosine hydroxycinnamoyl transferase, which in turn produces clovamide and/or related hydroxycinnamoyl amides.

Abstract: A method for synthesizing influenza virus-like particles (VLPs) within a plant or a portion of a plant is provided. The method involves expression of influenza HA in plants and the purification by size exclusion chromatography. The invention is also directed towards a VLP comprising influenza HA protein and plant lipids. The invention is also directed to a nucleic acid encoding influenza HA as well as vectors. The VLPs may be used to formulate influenza vaccines, or may be used to enrich existing vaccines.

Abstract: The TaNAC2 gene can promote uptake and utilization of nitrogen in a plant. A method for improving the uptake, transport and/or assimilation of nitrogen element in the plant includes: introducing a gene encoding a protein represented by SEQ ID NO:4 into a primary plant to obtain a transgenic plant. Compared to the primary plant, the uptake, transport and/or assimilation of the nitrogen element in the transgenic plant are improved. The method provides advantages in that: the TaNAC2 gene, as a nitrate nitrogen responsive regulatory factor, which can regulate the expression of a series of genes in nitrogen element uptake pathways of wheat, greatly promotes the study of the metabolism and utilization of the nitrogen element in a plant; and it is possible to improve the assimilation efficiency of nitrogen element by increasing the expression of TaNAC2, thereby reducing fertilizer application and increasing yield.

Abstract: Methods and compositions to introduce a synthetic pathway based on the 3-hydroxypropionate bicycle into an organism such as the model cyanobacterium, Synechococcus elongatus sp. PCC 7942. The heterologously expressed pathway acts as a photorespiratory bypass as well as an additional carbon fixation cycle orthogonal to the endogenous Calvin-Benson cycle. We demonstrate the function of all six introduced enzymes, which not only has implications on increasing net-photosynthetic productivity, but also key enzymes in the pathway are involved in high-value products that are of biotechnological interest, such as 3-hydroxypropionate.

Abstract: Provided are methods and compositions for improving the growth characteristics of plants.

Abstract: Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NOs: 552-897 and 6029-10629, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-551 and 898-6028, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

Abstract: Isolated polynucleotides and polypeptides, and recombinant DNA constructs are useful for conferring drought tolerance and/or improved nitrogen use efficiency. Compositions (such as plants or seeds) comprise these recombinant DNA constructs; and methods utilize these recombinant DNA constructs. The recombinant DNA constructs comprise a polynucleotide operably linked to a promoter that is functional in a plant, wherein said polynucleotides encode glutamate receptor polypeptides.

Abstract: A method of increasing tolerance of a plant to an abiotic stress or increasing biomass, vigor or yield of a plant is disclosed. The method comprising upregulating within the plant an exogenous polynucleotide of a microRNA or a precursor thereof, wherein the microRNA is selected from the group consisting of miR-156, miR-169, miR-164, miR-159, miR-167, miR-529, miR-168, ppt-miR395, sof-miR408a, ath-miR408, miR-1039, miR-1091, miR-1118, miR-1134 and miR-1129, thereby increasing the tolerance of the plant to the abiotic stress or increasing the biomass, vigor or yield of the plant.

Abstract: The present disclosure relates to the use of a grass-active herbicide postemergently applied to AAD1-transformed turfgrasses to selectively control grass weeds in a turf grass crop. Also described is the use of AAD1 as a selectable marker in the production of transgenic turfgrass.

Abstract: Methods and compositions are provided for editing the genome of a cell without the use of an exogenously supplied nuclease. Aspects of the methods include contacting a cell with a targeting vector comprising nucleic acid sequence to be integrated into the target locus, where the cell is not also contacted with a nuclease. In addition, reagents, devices and kits thereof that find use in practicing the subject methods are provided.

Abstract: This application discloses methods of treating, preventing, and diagnosing colorectal cancer and IBD in a subject comprising administering an effective dose of antisense miR-133? or AFTPH to the subject or detecting expression levels of miR-133? and AFTPH.

Abstract: Sequences of a serotype 8 adeno-associated virus and vectors and host cells containing these sequences are provided. Also described are methods of using such host cells and vectors in production of rAAV particles.

Abstract: The present invention provides new adenoassociated virus vectors and pharmaceutical compositions containing the same for the treatment of lysosomal storage disorders and specially, for the treatment of mucopolysaccharidoses Type IIIB.

Abstract: Bioconversion processes are disclosed in which biocatalysts including microorganisms or isolated enzymes that are substantially irreversibly retained in the interior of an open, porous, highly hydrophilic polymer are cycled between at least two different fluid media for the bioconversion of one or more substrates to one or more bioproducts. The processes are particularly attractive for using gas phase or using liquid feedstocks containing the substrate.

Abstract: A recombinant yeast cell, fermentation compositions, and methods of use thereof are provided. The recombinant yeast cell includes at least one heterologous nucleic acid encoding one or more polypeptide having phosphoketolase activity; phosphotransacetylase activity; and/or acetylating acetaldehyde dehydrogenase activity, wherein the cell does not include a heterologous modified xylose reductase gene, and wherein the cell is capable of increased biochemical end product production in a fermentation process when compared to a parent yeast cell.

Abstract: The invention relates to recombinant microorganisms that have been engineered to produce various chemicals using genes that have been repurposed to create a reverse beta oxidation pathway. Generally speaking, the beta oxidation cycle is expressed and driven in reverse by modifying various regulation points for as many cycles as needed, and then the CoA thioester intermediates are converted to useful products by the action of termination enzymes.

Abstract: The present invention is related to recombinant host cells comprising: (i) at least one deletion, mutation, and/or substitution in an endogenous gene encoding a polypeptide that converts pyruvate to acetaldehyde, acetyl-phosphate or acetyl-CoA; and (ii) a heterologous polynucleotide encoding a polypeptide having phosphoketolase activity. The present invention is also related to recombinant host cells further comprising (iii) a heterologous polynucleotide encoding a polypeptide having phosphotransacetylase activity.

Abstract: High conversion efficiency processes are disclosed for the anaerobic bioconversion of syngas to alcohol. The processes use bioreactors that have a non-uniform gas composition and a substantially uniform liquid composition such as deep tank bioreactors. By maintaining certain electron to carbon mole ratios in the syngas feed to the bioreactors and certain partial pressures of carbon dioxide in the off gas from the bioreactors, at least about 80 percent of the hydrogen and at least about 95 percent of the carbon monoxide in the feed can be consumed.

Abstract: The present invention provides methods for producing a product of one or more enzymatic pathways. The pathways used in the methods of the invention involve one or more conversion steps such as, for example, an enzymatic conversion of guluronic acid into D-glucarate (Step 7); an enzymatic conversion of 5-ketogluconate (5-KGA) into L-Iduronic acid (Step 15); an enzymatic conversion of L-Iduronic acid into Idaric acid Step 7b); and an enzymatic conversion of 5-ketocluconate into 4,6-dihydroxy 2,5-diketo hexanoate (2,5-DDH) (Step 16). In some embodiments the methods of the invention produce 2,5-furandicarboxylic acid (FDCA) as a product. The methods include both enzymatic and chemical conversions as steps. Various pathways are also provided for converting glucose into 5-dehdyro-4-deoxy-glucarate (DDG), and for converting glucose into 2,5-furandicarboxylic acid (FDCA).

Abstract: Presented herein are oleaginous strains of yeast such as Saccharomyces cerevisiae that have been modified to allow for xylose utilization. Such strains are also modified to allow for higher lipid accumulation utilizing a broad range of sugar monomers such as those released during pretreatment and enzymatic saccharification of lignocellulosic biomass. Methods of producing lipids and ethanol using these yeast strains are also disclosed.

Abstract: Process for the production of lipids from biomass including at least one polysaccharide comprising: —subjecting said biomass to hydrolysis to obtain a mixture comprising a first solid phase and a first aqueous phase; —preparing an inoculum comprising at least one oleaginous microorganism in a first fermentation device to obtain a first fermentation broth; —feeding said first aqueous phase and said first fermentation broth to a second fermentation device to obtain a second fermentation broth; —subjecting at least a portion of said second fermentation broth to microfiltration to obtain a first retentate and a first permeate; —feeding said first retentate to said second fermentation device; —subjecting said first permeate to a purification treatment to obtain a second permeate and a second retentate; —feeding said second retentate to said second fermentation device; —at the end of said fermentation, subjecting said second fermentation broth to separation to obtain an aqueous suspension of oleaginous cellular bio

Abstract: The present disclosure relates to polypeptides having transaminase activity, polynucleotides encoding the polypeptides, and methods of using the polypeptides.

Abstract: The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a liquor. The present invention also relates to methods of using the compositions.

Abstract: The present invention relates to a fractionated coupled apparatus for saccharifying biomass and a method for saccharifying biomass using the apparatus, and more particularly, to a fractionated coupled apparatus and method for saccharifying biomass, in which biomass mixed with enzyme is first saccharified in a single-tubular plug-flow reactor (PFR) unit, and then distributed into and saccharified in a second multi-tubular PFR unit comprising 2-100 PFRs, each having a diameter smaller than that of the single-tubular PFR unit. According to the present invention, biomass is first saccharified in a PFR having a relatively large diameter, and then distributed into and saccharified in PFRs having a relatively small diameter. Thus, a high concentration of a sugar compound can be obtained without having to use an additional mixer.

Abstract: This invention relates to the production of RNA by co-expressing a tRNA ligase and a chimeric RNA molecule comprising a target RNA and a plant viroid scaffold, such as Eggplant latent viroid, in a host cell. This co-expression causes the production of large amounts of the chimeric RNA molecule in the host cells and may be useful for example in the production of RNA aptamers and other RNA molecules.

Abstract: The present invention provides compositions and methods for biosynthetically producing podophyllotoxin intermediates and derivatives including enzymes and their equivalents involved in the biosynthetic production of podophyllotoxin intermediates and derivatives.

Abstract: This invention provides an improved process for manufacturing a Rabies monoclonal antibody (HuMab 17C7) that results in low osmolality, minimum secondary metabolites like ammonia and lactate, enhanced cell growth and productivity, minimum aggregation or degradation of monoclonal antibody during purification, thereby improving potency of monoclonal antibody (HuMab 17C7) as compared to human rabies immunoglobulin (hRIG).

Abstract: The present invention relates to methods of upregulating the high mannose glycoform content of a recombinant protein during a mammalian cell culture by manipulating the mannose to total hexose ratio in the cell culture media formulation.

Abstract: Certain embodiments are directed to sensors that enable the use of optimized biocompatible materials such as pre-anodized paper printed electrode transducer to detect binding of a target agent, wherein the surface is modified or functionalized through zero length cross-linker so that it interacts with or specifically binds a target such as sugars (glucose) or glycated proteins (HgbA1c).

Abstract: A novel class of hydroxylases is described having the amino acid sequence of SEQ ID NO: 2, 4, 6 and 8, and variants and fragments thereof having HIF hydroxylation activity. The polypeptides of the invention have in particular prolyl hydroxylase activity. An assay method monitors the interaction of the HIF hydroxylase with a substrate. Modulators of HIF hydroxylase are provided for use in the treatment of a condition associated with increased or decreased HIF levels or activity or for the treatment of a condition where it is desirable to modulate HIF levels or activity.

Abstract: A mutant hydrolase optionally fused to a protein of interest is provided. The mutant hydrolase is capable of forming a bond with a substrate for the corresponding nonmutant (wild-type) hydrolase which is more stable than the bond formed between the wild-type hydrolase and the substrate. Substrates for hydrolases comprising one or more functional groups are also provided, as well as methods of using the mutant hydrolase and the substrates of the invention. Also provided is a fusion protein capable of forming a stable bond with a substrate and cells which express the fusion protein.

Abstract: A method for the generation of oligomers or a mixture of oligomers to form a chemical library by amide-forming oligomerization comprises the steps of 1) reacting a mixture of at initiator (I) with monomer (M) to form a dimer of the initiator (I) and the monomer (M) or a pre-oligomer with an initiator (I) attached to a chain of more than one monomer (M) or a mixture thereof by amide-bond formation; 2) optionally adding at least one terminator (T) for the formation of a linear oligomer or a mixture of linear oligomers by amide-bond formation; or, for the formation of a cyclic oligomer or a mixture of cyclic oligomers by amide-bond formation, changing the reaction conditions relative to step 1) so as to form a linking covalent bond between the at least one initiator (I).

Abstract: Systems and methods are described for quantifying a target nucleic acid. A sample comprising a target nucleic acid is segregated into a first plurality of the reaction volumes containing at least one target nucleic acid molecule and a second plurality of the reaction volumes containing no target nucleic acid molecules. The reaction volumes are subjected to an amplification assay, wherein the amplification assay is configured to amplify the target nucleic acid. An indicator of amplification is detected or measured in at least some of the plurality of reaction volumes. The target nucleic acid is quantified based on the detection or measurement. After discontinuing the amplification assay, the plurality of reaction volumes may be heated and changes in the indicators of amplification of two or more of the at least some of the reaction volumes may be detected or measured.

Abstract: A device for processing a biological sample includes a first substrate having a first cavity, a second substrate having a second cavity, a filter element having a plurality of perforations, and an electrically conductive structure. The first cavity forms a first chamber segment of a chamber for accommodating the biological sample. The second cavity forms a second chamber segment of the chamber for accommodating the biological sample. The filter element is formed between the first cavity and the second cavity in order to hold back a plurality of organic cells of the biological sample on the plurality of perforations when the biological sample moves between the first cavity and the second cavity through the filter element. The electrically conductive structure is arranged on the filter element and is configured to cause lysis of the organic cells and/or to duplicate and/or detect defined segments of exposed DNA.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: A carrier for detecting food poisoning bacteria that is used to simultaneously detect Escherichia coli, Salmonella, Staphylococcus aureus, and Vibrio parahaemolyticus includes a plurality of probes comprising: a probe from a region of pyrH gene of Escherichia coli; a probe from a region of vtx1 gene of Escherichia coli; a probe from a region of vtx2 gene of Escherichia coli; a probe from a region of invA gene of Salmonella; a probe from a region of dnaJ gene of Staphylococcus aureus; a probe from a region of toxR gene of Vibrio parahaemolyticus; a probe from a region of tdh gene of Vibrio parahaemolyticus; a probe from a region of trh1 gene of Vibrio parahaemolyticus; and a probe from a region of trh2 gene of Vibrio parahaemolyticus, wherein the probes are immobilized on the carrier.

Abstract: A sensor comprising a semiconductor layer having a two dimensional electron gas (2DEG) and an oxide layer in electronic contact with the semiconductor layer is provided. A method of detecting an analyte molecule using such sensor is also provided.

Abstract: The present invention provides a method for detecting the presence or absence of a guanine-abasic site, the method being a process for detecting guanine opposite at least one abasic sites generated in a double-stranded DNA, comprising: (1) step 1 of site-selectively cleaving at least one abasic sites in a double-stranded DNA using an enzyme; (2) step 2 of modifying the amino group at position 2 of guanine opposite the abasic sites using a modifier; and (3) step 3 of performing polymerase chain reaction on the modified double-stranded DNA obtained by conducting step 1 and step 2, which serves as a template, to search for the presence or absence of an amplification product, the sequence of steps 1 and 2 being not limited to the order presented.

Abstract: Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including a method of preventing a significant reduction in duplexes detectable in a hybridization assay involving (i) selecting probe lengths for sets of oligonucleotide probes, wherein probes include different subsequences such that at least one subsequence is complementary to a subsequence in a cognate target; wherein probes for longer cognate targets are longer in length than probes for shorter cognate targets, (ii) selecting, for each set of probes, a density of oligonucleotides probes attached per unit area on a solid phase carrier which is below a limit at which the significant reduction in detectable duplexes is predicated to take place, (iii) producing the probes and affixing them to different solid phase carriers at the selected density, and (iv) annealing targets to the probes, wherein signal intensities of probes and targets of different lengths are about the same.

Abstract: Systems, methods and compositions of matter according to the present invention, can be used in capture/enrichment, gene expression profiling and targeted sequencing. Provided are systems, methods and compositions concerning the enhancement of nucleic acid hybridization specificity and controlling the shapes of melting curves revealed by nucleic acid hybrid pairs to optimize nucleic acid analysis. These systems, methods and compositions comprise producing a positively charged surface or surface coating, on the surface of microarray slides or other types of surfaces similarly purposed, which enhances melting curve analysis to the point of allowing detection or differentiation of small changes in sequences between nucleic acid binding partners. The accuracy or resolution of melting curve analysis was to be sufficient to distinguish between the melting of perfect matched dsDNA and dsDNA with the smallest possible change in sequence, a one base pair mismatch.

Abstract: The present disclosure describes a method of adapter ligation to the ends of fragmented double-stranded DNA molecules.

Abstract: A method of nucleic acid processing that comprises providing an adapted nucleic acid fragment having a triazole linkage therein, and transcribing the adapted nucleic acid fragment with reverse transcriptase. The invention further relates to kits and uses associated with the method.

Abstract: A method for characterizing at least a portion of the biodiversity of a sample. The method includes the steps of: (i) obtaining a sample having nucleic acid from a plurality of different organisms; (ii) extracting at least a portion of the nucleic acid from the sample; (iii) optionally performing a whole-genome amplification of the extracted nucleic acid; (iv) optionally performing a second, targeted amplification; (v) sequencing the amplified nucleic acid to obtain sequence data comprising a nucleic acid sequence for at least some of the plurality of different organisms; (vi) querying, using the obtained sequence data, a sequence database, where querying the sequence database identifies one or more of the plurality of different organisms; and (vii) determining, using the identified one or more of the plurality of different organisms, a characteristic of the sample.

Abstract: Described herein are engineered alpha-hemolysin subunits having mutated oligomerization domains for assembling into heptameric nanopores in lipid bilayers.

Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.

Abstract: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.

Abstract: Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.

Abstract: A method for assessing risk of losing a transplanted organ by a patient having an episode of acute rejection of the transplanted organ is described. The method includes obtaining from the patient a cell sample from the transplanted organ or peripheral blood, determining a level of FOXP3 in the cell sample, and correlating the level with the risk of loss of the transplanted organ, wherein, compared to a control level, a significantly greater level of FOXP3 in the cell sample from the transplanted organ or a significantly lower level of FOXP3 in the cell sample from the peripheral blood correlates with a decreased risk of loss of the transplanted organ.