Abstract: The present invention relates generally to methods for identifying cancer patients with a poor prognosis, and to therapeutic modalities for improving prognosis by combating metastasis and abrogating chemoresistance in cancer cells. Embodiments of the present invention provide an objective means of prognostication regarding the long-term outcome of an incident of cancer, breast cancer in particular. Therapeutic modalities include immunotherapy and anti-sense therapy. Prognosis is determined by measuring the number of copies of the metadherin gene in the patient's cells.

Abstract: The invention refers to an oligonucleotide consisting of 10 to 20 nucleotides of selected regions of the TGF-beta1, TGF-beta2 or TGF-beta3 nucleic acid sequence, which comprises modified nucleotides such as LNA, ENA, polyalkylene oxide-, 2?-fluoro, 2?-O-methoxy and/or 2?-O-methyl modified nucleotides. The selected regions are preferably the region of nucleic acid no. 1380 to 1510, no. 1660 to 1680, no. 2390 to 2410, or no. 2740 to 2810 of the TGF-beta2 nucleic acid sequence of SEQ ID NO. 1, specific regions of the TGF-beta1 nucleic acid sequence of SEQ ID NO. 149, or specific regions of the TGF-beta3 nucleic acid sequence of SEQ ID No. 267. The invention further relates to pharmaceutical compositions comprising such oligonucleotide, wherein the composition or the oligonucleotide is used in the prevention and/or treatment of a malignant and/or benign tumor, an immunologic disease, fibrosis, glaucoma, etc.

Abstract: Disclosed herein are chimeric polypeptides, including compositions thereof, expression vectors, and methods of use thereof, for the generation of transgenic cells, tissues, plants, and animals. The compositions, vectors, and methods of the present invention are also useful in gene therapy techniques.

Abstract: Provided herein are immunogenic compositions containing recombinant proteins capable of presenting all, or antigenic portions of, the Eimeria tenella Elongation Factor 1 alpha, or EF-1?, protein in the development of active immunity to, and control of, coccidiosis. Also provided are methodologies of using the immunogenic compositions for administration to poultry and other animals in the control of coccidiosis. In some instances, the EF-1? protein utilized in the immunogenic composition presented herein is molecularly manipulated or combined with adjuvants to increase effectiveness.

Abstract: Compositions and methods are provided for introducing transgenic target sites for Site Specific Integration (SSI) and/or polynucleotides of interest into at least one double-strand break target site of a double-strand-break inducing agent in a genomic window of a plant genome. Also provided are methods and compositions for producing a complex trait locus in a genomic window of a plant comprising at least one transgenic target site for site specific integration integrated in at least double-strand-break target site. The double-strand-break target site can be, but is not limited to, a target site for a zinc finger endonuclease, an engineered endonuclease, a meganuclease, a TALENs and/or a Cas endonuclease. The genomic window of said plant can comprise at least one genomic locus of interest such as a trait cassette, a transgene, a mutated gene, a native gene, an edited gene or a site-specific integration (SSI) target site.

Abstract: A method for inducing a structural change in a plant mitochondrial genome is provided. The invention relates to a method for inducing a structural change in a mitochondrial genome in a plant cell by introducing a double-strand break into a target sequence region on mitochondrial genomic DNA in a plant cell, which is present in individual molecule species of the mitochondrial genomic DNA. In addition, the present invention also relates to a method for deleting a gene that is present in mitochondrial genomic DNA in a plant cell by introducing a double-strand break into the gene or a region near the gene, which is present in individual molecule species of the mitochondrial genomic DNA. Moreover, the invention also relates to a plant cell having a mitochondrial genome, in which a structural change has been induced by the method, and a seed and a plant having the plant cell.

Abstract: The invention provides recombinant DNA molecules and constructs, as well as their nucleotide sequences, useful for modulating gene expression in plants. The invention also provides transgenic plants, plant cells, plant parts, and seeds comprising a recombinant DNA molecule comprising a DNA molecule operably linked to heterologous transcribable DNA molecule, as are methods of their use.

Abstract: The invention provides recombinant DNA molecules and constructs, as well as their nucleotide sequences, useful for modulating gene expression in plants. The invention also provides transgenic plants, plant cells, plant parts, and seeds comprising a recombinant DNA molecule comprising a DNA molecule operably linked to heterologous transcribable DNA molecule, as are methods of their use.

Abstract: The invention relates to the field of plant improvement, in particular of the improvement of yield for plants, by using a transgene containing an root-specific promoter driving expression of a MYB-related protein.

Abstract: Provided are methods of increasing nitrogen use efficiency, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality and/or abiotic stress tolerance of a plant by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO:1-467, 785-3047; or an exogenous polynucleotide encoding a polypeptide at least 80% identical to SEQ ID NO:468-784, 3048-4333, 4335-4682. Also provided isolated polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-467, 785-3047, which can be used to increase nitrogen use efficiency, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality and/or abiotic stress tolerance of a plant.

Abstract: This disclosure provides plants having enhanced traits such as increased yield, increased nitrogen use efficiency and increased water use efficiency: propagules, progeny and field crops of such plants; and methods of making and using such plants. This disclosure also provides methods of producing seed from such plants, growing such seed and selecting progeny plants with the composition, or with enhanced traits. Also disclosed are plants with altered phenotypes which are useful for screening and selecting events for the desired enhanced trait.

Abstract: Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NOs: 710-1153 and 9276-15726, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-709 and 1157-9275, 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: Soybean plant and seed comprising soybean transgenic event SHZD32-01 and DNA molecules unique to the event. Also provided are use of the plant parts, seeds; the soybean transgenic event SHZD32-01 comprises at least one of the nucleic acid molecules of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 9, and their complete complementary sequences. The method of use include the method for producing soybean with tolerance to herbicide glyphosate, producing a soybean-based commercial product, and controlling weeds in a field comprising soybean plants. Soybean strains comprising the soybean event SHZD32-01 exhibits strong tolerance to glyphosate and is helpful for weeds control. DNA detection of the soybean event SHZD32-01 is useful for identifying the soybean event SHZD32-01 in a sample and may be applied to methods for breeding soybean plants comprising the DNA.

Abstract: A newly identified protein that is encoded by a polynucleotide sequence associated with cytoplasmic male sterility restorer activity (Rf3) is described. The cytoplasmic male sterility restorer gene can be inserted through breeding introgression into plant genomes to restore cytoplasmic male sterility in plants. Further applications of the newly identified polynucleotide sequence associated with cytoplasmic male sterility restorer activity include a mutation (rf3) which results in cytoplasmic male sterility. The cytoplasmic male sterility restorer gene can be inserted through breeding introgression into plant genomes to result in cytoplasmic male sterility in plants. Methods for detecting the cytoplasmic male sterility restorer (Rf3) and the cytoplasmic male sterility (rf3) gene sequences are further described.

Abstract: The invention relates to dendritic cells, the NF?B signaling pathway of which has been manipulated by RNA transfection, to the manufacture thereof and to use thereof.

Abstract: The present disclosure relates to nucleic acid vaccine compositions and methods for preventing or treating pathological conditions, such as cancer or infectious disease. Further, the disclosure provides methods for more efficient production of antigens via mRNA containing one or more non-conventional start codons to promote multiplex initiation of translation in eukaryotic cells.

Abstract: Compositions and methods for treating type II diabetes in a subject. A viral vector is provided which includes a nucleic acid molecule comprising a sequence encoding a propeptide and the active portion of GLP-1, wherein, when expressed, the N-terminal amino acid of GLP-1 immediately follows the C-terminal amino acid of the propeptide. In desired embodiments, the subject is a cat or dog.

Abstract: The present invention relates to viral particles which exhibit self-regulatory or regulatable features.

Abstract: This disclosure provides methods and compositions for treating disorders or injuries that affect motor function and control in a subject. In one aspect, the invention a transgene product is delivered to a subject's spinal cord by administering a recombinant viral vector containing the transgene to the spinal cord. The viral vector delivers the transgene which expresses the encoded recombinant viral gene product. The viral gene product comprises HIF1-alpha. Also provided are compositions for delivery of a transgene product to a subject's spinal cord.

Abstract: The invention provides methods and compositions for the expression of small RNA molecules within a cell using a lentiviral vector. The methods can be used to express doubles stranded RNA complexes. Small interfering RNA (siRNA) can be expressed using the methods of the invention within a cell, which is capable of down regulating the expression of a target gene through RNA interference. A variety of cells can be treated according to the methods of the invention including embryos, embryogenic stem cells, allowing for the generation of transgenic animals or animals constituted partly by the transduced cells that have a specific gene or a group of genes down regulated.

Abstract: Described herein are methods and vectors for rational, multiplexed manipulation of chromosomes within open reading frames (e.g., in protein libraries) or any segment of a chromosome in a cell or population of cells, in which various CRISPR systems are used.

Abstract: Described herein are methods and vectors for rational, multiplexed manipulation of chromosomes within open reading frames (e.g., in protein libraries) or any segment of a chromosome in a cell or population of cells, in which various CRISPR systems are used.

Abstract: The present invention relates to methods to improve the absolute rate of homology-directed repair (HDR) and/or to improve the relative rate of HDR compared with non-homologous end joining (NHEJ).

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Abstract: In one aspect there is provided a method for producing ethanol and distiller's dried grains and solubles (DDGS). This method comprises the steps of: providing a plurality of feedstocks; milling said feedstocks; mixing the milled feedstocks into a feedstock blend; producing ethanol from the feedstock blend using a dry milling process; and collecting the DDGS by-product, after the ethanol is produced. In another aspect, the method further comprises providing barley as one of the feedstocks and peas as a second feedstock, wherein the barley feedstock and pea feedstock is mixed in a ratio of between 2:1 and 3.5:1 to make the feedstock blend. In yet another embodiment, antifoaming enzymes are added during the dry milling process to reduce foaming during the fermentation stage of the dry mill process.

Abstract: The present invention provides methods for producing cannabinoids and cannabinoid analogs as well as a system for producing these compounds. The inventive method is directed to contacting a compound according to Formula I or Formula II with a cannabinoid synthase. Also described is a system for producing cannabinoids and cannabinoid analogs by contacting a THCA synthase with a cannabinoid precursor and modifying at least one property of the reaction mixture to influence the quantity formed of a first cannabinoid relative to the quantity formed of a second cannabinoid.

Abstract: The present invention relates to a new process of vanillin production from a substrate by bioconversion and that allows a continuously producing and removing vanillin from the fermentation broth as it is formed. In particular, the invented process advantageously allows to reduce the residence time of vanillin in the fermenter and to maintain the vanillin concentration, in the fermentation broth, below its toxic level for the microorganism.

Abstract: A method comprising a series of selective extraction techniques for the parallel production of biodiesel and isolation of several valuable co-products including an alkenone hydrocarbon mixture of the kerosene/jet fuel range (primarily C10-, C12-, and C17-hydrocarbons) and fucoxanthin, a high-valued carotenoid, from the marine alkenone-producing microalgae Isochrysis.

Abstract: The present invention provides a method for producing N?-dodecanoyl-L-lysine using an enzyme having properties suitable for the industrial production of N?-dodecanoyl-L-lysine. More specifically, the present invention provides a method for producing N?-acyl-L-lysine including reacting a carboxylic acid or a salt thereof and L-lysine or a salt thereof in the presence of a protein having an amino acid sequence of SEQ ID NO: 1; a protein having an amino acid sequence in which one or several amino acid residues are inserted, added, deleted, or substituted in the amino acid sequence of SEQ ID NO: 1 and having N?-acyl-L-lysine-specific aminoacylase activity; and a protein which has 90% or higher homology with the amino acid sequence of SEQ ID NO: 1 and having N?-acyl-L-lysine-specific aminoacylase activity.

Abstract: A process for the production of carbohydrate cleavage products, characterized by a combination of the measures that a lignocellulosic material is treated with an aqueous solution containing an alcohol, in particular a C1-4-alcohol or a phenol, and having a pH-value of between 11.0 and 14.0 in order to cleave lignocellulose and separate cleavage products from the material, whereby a material enriched with cellulose and hemicellulose is obtained, and the obtained material enriched with cellulose and hemicellulose is treated with at least one carbohydrate-cleaving enzyme in order to obtain the carbohydrate cleavage products.

Abstract: Disclosed are methods for producing steviol glycosides, such as rebaudioside D and rebaudioside M, using engineered yeast. The methods include growing yeast on non-fermentative carbon sources. Other methods include growing yeast on one or more polysaccharides in which saccharification and fermentation of the polysaccharides occurs simultaneously.

Abstract: A recombinant host capable of producing a steviol glycoside which overexpresses a polypeptide which mediates steviol glycoside transport and which polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 35 or SEQ ID NO: 38 or an amino acid sequence having at least about 50% sequence identity to either thereto. A recombinant host capable of producing a steviol glycoside which has been modified, preferably in its genome, to result in a deficiency in the production of a polypeptide which mediates steviol glycoside transport and which polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 35 or SEQ ID NO: 38 or an amino acid sequence having at least about 50% sequence identity to either thereto.

Abstract: The present invention relates to methods and compositions for preventing incorporation of norleucine into proteins during recombinant protein production in bacteria. The present invention also provides microorganism host cells and nucleic acid molecules for use with the methods and compositions provided herein.

Abstract: Provided herein are methods for identifying and obtaining environmental isolates of microorganisms that maintain viability following seed treatment components or seed treatment processes and storage.

Abstract: The invention, in different embodiments, relates to a device for treating fluids, particularly body fluids, which comprises a receiving container for receiving the fluid from a body, a filter device which comprises a filter element for filtering out pathogenic particles from the fluid, and a cultivation device configured to incubate the filtered pathogenic particles on a nutrient medium, said filter device being coupled to the cultivation device such that the pathogenic particles can be transferred from the filter element into the cultivation device without contamination. A corresponding method is also provided.

Abstract: This disclosure describes techniques to improve the sequencing of polynucleotides by decreasing the likelihood of errors occurring during a sequencing calibration process. In implementations, regions of polynucleotides that are used for the calibration process can be modified to reduce a number of polynucleotides that have a same nucleotide at one or more positions of the calibration regions. In some cases, the calibration regions can be modified by adding a sequence to the polynucleotides that replaces the original calibration regions. Also, the calibration regions can be modified by rearranging the nucleotides at the different positions of the calibration regions. Additionally, the calibration regions can be modified by adding sequences of varying length to the polynucleotides being sequenced to produce polynucleotides having varying length with different calibration regions.

Abstract: A method for analyzing genomic DNA includes introducing a plurality of samples comprising human cells into individual vessels in each of a plurality of multi-vessel well plates. At least a subset of the human cells in the plurality of samples is lysed without the use of heat. DNA in the at least a subset of lysed human cells is isolated with the use of a plurality of paramagnetic beads. The isolated DNA is analyzed to identify one or more single nucleotide polymorphisms (SNPs), wherein the lysing, isolating, and analyzing steps are performed substantially in parallel for each of the plurality of samples.

Abstract: The present teachings relate to a method and system for normalizing spectra across multiple instruments. In an embodiment of the present invention, the method comprises at least one reference instrument and a test instrument. Each instrument comprises at least one excitation filter and at least one emission filter arranged in pairs. Each instrument further comprises a pure dye plate comprising a plurality of wells. Each well contains a plurality of dyes where each dye comprises a fluorescent component. Fluorescent spectra are obtained from each instrument for each dye across multiple filter combinations to contribute to a pure dye matrix Mref for the reference instrument and pure dye matrix M for the test instrument. The pure dye spectra can then be multiplied by correction factors for each filter pair to result in corrected pure dye spectra, then normalized and the multicomponenting data can be extracted.

Abstract: Microfluidic devices are provided for trapping, isolating, and processing single cells. The microfluidic devices include a cell capture chamber having a cell funnel positioned within the cell capture chamber to direct a cell passing through the cell capture chamber towards one or more a cell traps positioned downstream of the funnel to receive a cell flowing. The devices may further include auxiliary chambers integrated with the cell capture chamber for subsequent processing and assaying of the contents of a captured cell. Methods for cell capture and preparation are also provided that include flowing cells through a chamber, funneling the cells towards a cell trap, capturing a predefined number of the cells within the trap, interrupting the flow of cells, flowing a wash solution through the chamber to remove contaminants from the chamber, and sealing the predefined number of cells in the chamber.

Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.

Abstract: The present disclosure relates to improved methods for the isolation of genomic material and detection of disease related single nucleotide polymorphisms. In some aspects, these methods increase the total recovery of genomic DNA from buccal cell samples by improving cell lysis conditions. In other aspects, these methods allow for the reuse of patient buccal swab samples, reducing the likelihood of having to collect additional patient samples for re-testing. Finally, in some aspects, these methods increase the sensitivity of SNP detection using an improved real-time PCR assay protocol.

Abstract: The present disclosure relates to a method for reducing quantification errors caused by an optical artefact in digital polymerase chain reaction (dPCR) and to a method for determining the amount or concentration of a nucleic acid of interest in a sample with dPCR.

Abstract: Disclosed are compositions and methods for the preparation of RNA libraries for sequencing, gene expression profiling, microarray and other uses and for simplification of the library preparation process. The disclosure provides blocking oligonucleotides which bind to byproduct nucleic acid molecules formed during the ligation of adapters to nucleic acid segments prior to sequencing and inhibit or block amplification of the byproduct nucleic acid molecules in subsequent amplification reactions. Methods for library preparation using blocking oligonucleotides are also provided.

Abstract: First and second sets of receptacles containing reagents for first and second amplification reactions, respectively, are placed in first and second receptacle holders, each associated with a thermal element. The receptacles are subjected to different first and second incubation processes resulting in the first and second amplification reactions in each of the first and second sets of receptacles that contain a first or a second target nucleic acid, respectively. The presence or absence of the first or second target nucleic acid, if any, is determined for each receptacle of the first and second sets of receptacles.

Abstract: In one embodiment, a polymerase chain reaction (PCR) system includes a mixture chamber, a denature chamber, an annealing chamber, an extension chamber, and a product chamber, that are fluidically coupled to one another through a plurality of microfluidic channels. An inertial pump is associated with each microfluidic channel, and each inertial pump includes a fluid actuator integrated asymmetrically within its associated microfluidic channel. The fluid actuators are capable of selective activation to circulate fluid between the chambers in a controlled cycle.

Abstract: The present disclosure describes methods and kits for selecting treatments for, and treating, an oral infection in a patient. Oral samples are collected from multiple locations of the patient's oral cavity and include saliva, tongue biofilm, and interproximal biofilm. The samples are analyzed to determine a pathogen profile of the oral cavity, using nucleic-acid based analysis. Based on the pathogen profile, an antibiotic rinse is selected as the treatment of the oral infection.

Abstract: Some pairs of primers are provided, being used for detection of carbapenemase genes and carbapenemase-producing bacterial strains, and a diagnosis method using said set of primers. Furthermore, there is also disclosed, preferably, the use of probes within each amplification reaction, more preferably multiplex PCR, for selective identification and detection of carbapenemase genes from a biological sample. The primers object of this invention may be used for preparing a kit for carbapenemase genes identification and detection, preferably carbapenemases contained in bacterial strains producing said enzymes.

Abstract: The present invention compositions, methods and systems to identify, detect, and/or quantify bacterial DNA in the presence of contaminating non-bacterial DNA. In particular, the present invention provides oligonucleotides configured to detect a relatively small amount of bacterial DNA in the presence of an overwhelmingly large amount of contaminating human DNA.