Abstract: The present invention relates to a new method for improving glyphosate resistance of a plant. The method encompasses providing one or more specific mutations in a specific nucleotide sequence in said plant. In comparison to a plant not manipulated according to the method, the plant obtained by the method displays (improved) glyphosate resistance. Also provided are a (transgenic) plant, including a seed thereof, and a plant product that can be obtained by the method according to the invention.

Abstract: The present invention relates to the field of spinach breeding, in particular to a new dominant resistance gene, designated RPF11, which confers resistance against races 7 to 14 of Peronospora farinosa and to spinach plants comprising said gene.

Abstract: The present invention discloses gene targets, constructs and methods for the genetic control of plant disease caused by nematodes of the genus Meloidogyne (root knot nematodes). The present invention relates to achieving a plant protective effect through the identification of target coding sequences and the use of recombinant DNA technologies for post-transcriptionally repressing or inhibiting expression of the target coding sequences in the cells of plant-parasitic nematodes. The disclosed gene targets show significant conservation at the nucleotide level between orthologs from different Meloidogyne species, facilitating genus-wide targeting by RNA interference.

Abstract: Methods and compositions for modifying stem cells using one or more ZFPs are disclosed. Such methods and compositions are useful for facilitating processes such as, for example, dedifferentiating cells, differentiating stem cells into the desired phenotype, propagating stem cells and/or facilitating cloning.

Abstract: This disclosure provides replication-incompetent adenoviral vectors useful in vaccine development and gene therapy. The disclosed vectors comprise a selective deletion of E3 and are particularly useful for preparation of vaccines development and for gene therapy using toxic transgene products that result in vector instability that occurs when the entire E3 domain is deleted.

Abstract: Described are single-stranded new sequences of TT viruses, rearranged TTV sequences and hybrid molecules of a specific TT virus sequence and host cell DNA that are capable of replicating autonomously for use in diagnosis, prevention and treatment of diseases like cancer and autoimmunity. In addition, it relates to the use of such molecules as gene vectors and artificial chromosomes.

Abstract: The invention relates to the production of products such as alcohols and acids by microbial fermentation, particularly microbial fermentation of substrates comprising CO. It more particularly relates to methods and systems for improving efficiency of products by microbial fermentation. In particular embodiments, the invention provides a method of optimizing production of desired products including the step of ascertaining the proportion of CO converted to CO2.

Abstract: The present invention relates to a process for producing a dicarboxylic acid comprising fermenting a fungal cell in a vessel comprising a suitable fermentation medium, comprising adding a gas flow which comprises 20 to 35 v/v % of oxygen and less than 0.1 v/v % of carbon dioxide to the fermentation medium, and maintaining an average partial carbon dioxide pressure of at least about 0.35 bar in the fermentation medium, and producing the dicarboxylic acid.

Abstract: An isolated fungus is described. The isolated fungus produces at least one compound selected from the group consisting of 1,8-cineole, 1-methyl-1, 4-cyclohexadiene, and (+)-?-methylene-?-fenchocamphorone. A method for producing at least one compound selected from the group consisting of 1,8-cineole, 1-methyl-1, 4-cyclohexadiene, and (+)-?-methylene-?-fenchocamphorone is also described. The method includes culturing a fungus on or within a culturing media in a container under conditions sufficient for producing the at least one compound.

Abstract: A method produces a sugar liquid by repeating a sugar liquid production process including (1) to (3): (1) adding a filamentous fungus-derived cellulase to cellulose to perform primary hydrolysis; (2) adding a fresh filamentous fungus-derived cellulase to the hydrolysate in Step (1) to perform secondary hydrolysis; and (3) subjecting the hydrolysate in Step (2) to solid-liquid separation to obtain a sugar liquid, from which a recovered enzyme is obtained; wherein the recovered enzyme obtained in Step (3) is used for Step (1) of the next and later sugar liquid production processes.

Abstract: Materials and methods are described to produce xylitol from a mixture of hemicellulosic sugars by several routes. Examples include either as a direct co-product of a biorefinery or ethanol facility, or as a stand-alone product produced from an agricultural or forestry biomass feedstock including using, e.g. ethanol waste streams.

Abstract: The present invention relates to methods for degrading or converting a cellulosic material and for producing substances from the cellulosic material under high temperature conditions.

Abstract: An embodiment of a method for generating a population of amplified concatamer products is described that comprises amplifying a template nucleic acid molecule using a first nucleic acid primer immobilized on a bead substrate and a second nucleic acid primer in solution to generate a population of substantially identical copies of the template nucleic acid molecule immobilized on the bead substrate; and amplifying the population of substantially identical copies of the template nucleic acid molecule using a concatamer primer that comprises a first region complementary to an end region of the population of substantially identical copies of the template nucleic acid molecule and a second region to generate a population of immobilized concatamer products of the substantially identical copies of the template nucleic acid molecule.

Abstract: Disclosed herein is pyrroline-carboxy-lysine (PCL), a pyrrolysine analog, which is a natural, biosynthetically generated amino acid, and methods for biosynthetically generating PCL. Also disclosed herein are proteins, polypeptides and peptides that have PCL incorporated therein and methods for incorporating PCL into such proteins, polypeptides and peptides. Also disclosed herein is the site-specific derivatization of proteins, polypeptides and peptides having PCL or pyrrolysine incorporated therein. Also disclosed herein is the crosslinking of proteins, polypeptides and peptides having PCL or pyrrolysine incorporated therein.

Abstract: This invention relates to the production of 7-dehydrocholesterol, 25-hydroxy-7-dehydrocholesterol, and 25-hydroxy ergosterol in yeast such as Saccharomyces cerevisiae. It also relates to various enzymes catalyzing the reduction of the double bond at position 24 of lanosterol, dimethyl zymosterol, methyl zymosterol, zymosterol, cholesta-7, 24-dienol, or cholesta-5,7,24-trienol; or the hydroxylation at position 25 of ergosterol, 7-dehydrocholesterol, cholesta-8-enol, and cholesta-7-enol. It also relates to various nucleic acids encoding cholesterol C25-hydroxylases and sterol ?24-reductases and their use to produce and hydroxylate 7-dehydrocholesterol or ergosterol. It also relates to the yeast strains so produced, and methods of making these sterols that include the steps of cultivaton a transformed yeast cell, and harvesting the resulting sterol(s).

Abstract: The disclosure also relates to novel compositions and methods for the single, direct detection of Hemoglobin A1c percentage in a sample, using conversion of functional groups attached to a transitional metal complex, resulting in quantifiable electrochemical signal at two unique potentials, Eo1 and Eo2.

Abstract: The present invention provides a simple culture device that is designed for manufacture and use in areas of limited resources. The device is useful for cell culture in such environments with limited resources because cells grow in paper just as they do in a culture dish. Also provided is a binding assay that employs an activatable dormant bacteriophage carrying a reporter gene to qualitatively or quantitatively detect the presence of a substance of interest in a sample.

Abstract: The application discloses methods, materials, and compositions for the labeling of molecules, for example, proteins, in living cells or in subcellular compartments of living cells. In particular, the application relates to proteomic analysis methods; materials and compositions and means based on direct tagging of unknown proteins with tagging enzymes (such as biotin ligase or a peroxidase) within the vicinity of a tagging substrate (such as a tyramide) within living cells, with optional targeting to specific subcellular locations by expression of genetic constructs.

Abstract: A method of utilizing the chymotrypsin level of an individual as a measure of the success of neuropeptides, and peptides or digestive enzyme administration to such individuals, and in particular, as a prognosticative of potential neuropeptides, peptides, and digestive enzyme administration for persons having ADD, ADHD, Autism and other PDD related disorders. A method for determining the efficacy of neuropeptides, peptides, or digestive enzymes for the treatment of an individual diagnosed with a pervasive developmental disorder (PDD) comprises obtaining a sample of feces from an individual, determining a quantitative level of chymotrypsin present in the sample, and correlating the quantitative level of chymotrypsin determined to be present in the sample with the PDD to determine the efficacy of treating the individual with neuropeptides, peptides, or digestive enzyme administration.

Abstract: A method of utilizing the chymotrypsin level of an individual as a measure of the success of neuropeptides, and peptides or digestive enzyme administration to such individuals, and in particular, as a prognosticative of potential neuropeptides, peptides, and digestive enzyme administration for persons having ADD, ADHD, Autism and other PDD related disorders. A method for determining the efficacy of neuropeptides, peptides, or digestive enzymes for the treatment of an individual diagnosed with a pervasive developmental disorder (PDD) comprises obtaining a sample of feces from an individual, determining a quantitative level of chymotrypsin present in the sample, and correlating the quantitative level of chymotrypsin determined to be present in the sample with the PDD to determine the efficacy of treating the individual with neuropeptides, peptides, or digestive enzyme administration.

Abstract: The invention provides methods and mass-labeled peptides for use in said methods for quantifying the presence of a one or more viral proteins in a sample of a preparation containing agents which bind to said viral protein, using mass-spectroscopic analyzes of the sample and standards containing known amounts of labeled and unlabeled signature peptides, in particular wherein said viral proteins are antigens in a vaccine for porcine circovirus.

Abstract: A method of determining the thrombogenicity of an implantable medical device is disclosed. The implanted device is exposed in vitro to platelet rich plasma, the activity of an indicator is assayed, and the thrombogenicity is determined.

Abstract: A cell based assay for detection for protease activity is disclosed. In the assay a cell is engineered to express a protease substrate with at least one label, preferably on its C-terminus. Cleavage of the substrate by the protease that recognizes it results in a C-terminal fragment and a N-terminal fragment, where the fragment having the label is subject to ubiquitin proteasome degradation. The assay measures the disappearance of the label due to degradation of the fragment to which it is attached. A cell free assay is also described for detection of protease activity. In the cell free assay, the protease substrate is expressed in a solution that includes the elements of the ubiquitin proteasome pathway for degradation of the fragment. The assay measures the disappearance of the label attached to the fragment that results from cleavage by the protease.

Abstract: The present invention relates to methods and kits for preserving genomic DNA sequence complexity within chemically and/or enzymatically converted DNA by an enzyme or series of enzymes that adds a methyl group to a cytosine outside of CpG dinucleotide sequences of genomic DNA. Further, the present invention relates to methylation analysis of the genomic DNA.

Abstract: Apparatuses for preparing a sample are disclosed herein. The apparatuses include a chamber, a first valve at least partially disposed in the first chamber, a second valve at least partially disposed in the first chamber, and a pump comprising an actuator and nozzle.

Abstract: This invention allows ultra-low levels of virtually any biological analyte to be detected and quantified rapidly, simply and inexpensively with an electrochemical biosensor using a novel electrochemical signal amplification technique. The invention amplifies detection signals from low level analytes using an innovative sandwich ELISA structure that replaces optical labels with a massive amount of electrochemically detectable guanine rich oligonucleotide tags. Selective binding is achieved with matched pairs of either commercial or custom analyte binding materials such as monoclonal antibodies or single strand DNA. The guanine tags are eluted from the sandwich structures and hybridize with complementary cytosine rich oligonucleotide recognition probes attached to the surface of a biosensor working electrode. An electrochemical technique generates a signal in proportion to the guanine level on the working electrode which is also proportional to the analyte level in the sample.

Abstract: Methods for multiplex ligation-dependent probe amplification include (a) providing a sample tissue to query different target nucleic acids, (b) providing different probe sets for each of the target nucleic acids, each probe set including a first locus specific probe having a first adapter sequence and a first target specific portion and a second locus specific probe having a second adapter sequence, and a second target specific portion adjacent to the first target specific portion, (c) hybridizing the probe sets to the target sequences to form hybridization complexes, (d) ligating the hybridization complexes to form ligated probes, (e) amplifying the ligated probes to form amplicons, the amplifying step being carried out with a first universal primer including a region complementary to the first adapter sequence and a second universal primer including a region complementary to the second adapter sequence, and (f) detecting the amplicons in a detection system by sequencing each of the amplicons.

Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.

Abstract: The invention provides a method for converting non-methylated cytosine in a single-stranded DNA into uracil by a bisulfite reaction with a high conversion efficiency from non-methylated cytosine into uracil. The invention also provides a method for amplifying the single-stranded DNA in which non-methylated cytosine has been converted into uracil, as well as a method for detecting methylated cytosine in the single-stranded DNA.

Abstract: A microfluidic chip for use in multiplexed analysis of samples is described. The microfluidic chip comprises a plurality of sensing chambers and further comprises at least a first fluid supply channel for providing a first fluid and a plurality of microfluidic channels. These are in fluid communication with at least one sensing chamber and with the first fluid supply channel for delivery of said first fluid to the at least one sensing chamber. The microfluidic channels are branching off from the supply channel in the neighborhood of the sensing chamber that can be provided with the first fluid through the microfluidic channel. The different channels thus form a tree-like delivery distribution system for supplying the first fluid to said plurality of sensing chambers.

Abstract: The invention is directed to methods and apparatus for detecting sequences of optical signals from parallel reactions on an array of nanostructures, such as nanopores, nanowells, or nanoparticles. In accordance with the invention, an array of nanostructures is provided, each nanostructure comprising a reaction site and each capable of confining a reaction that generates a sequence of optical signals, and the nanostructures of the array being arranged in clusters each comprising a number of nanostructures. Each different cluster is disposed within a different resolution limited area and the number of nanostructures in each cluster is either greater than one or a random variable with an average value greater than zero. Optical signals from reactions in the nanostructures are detected by an optical system operatively associated with the array.

Abstract: The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

Abstract: This invention provides nucleoside triphosphate analogs having the structure: wherein B is a base and is adenine, guanine, cytosine, uracil or thymine, wherein R? is an OH or an H, and wherein R? is azidomethyl, a hydrocarbyl, or a substituted hydrocarbyl, and which has a Raman spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1 or a Fourier transform-infrared spectroscopy spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1, and also to methods of DNA sequencing and SNP detection.

Abstract: Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include integrated illumination elements and optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

Abstract: The application concerns means for determining the stage of hepatic tissue damage, in particular the hepatic fibrosis score of subjects infected with one or more hepatitis viruses. In particular, the means of the invention involve measuring the levels of expression of selected genes, said selected genes being: SPP1, and at least one gene from among A2M and VIM, and at least one gene from among IL8, CXCL10 and ENG, and optionally, at least one gene from among the list of the following sixteen genes: IL6ST, p14ARF, MMP9, ANGPT2, CXCL11, MMP2, MMP7, S100A4, TIMP1, CHI3L1, COL1A1, CXCL1, CXCL6, IHH, IRF9 and MMP1.

Abstract: Methods of reliably quantifying telomere length in cells or tissues that have been formalin fixed and paraffin embedded (FFPE) samples by quantitative polymerase chain reaction protocol and kits for use with such various methods are provided. The methods of the present invention may be used to predetermine an individual's response to treatment with a telomerase inhibitor, a telomere damaging agent or a telomerase activator.

Abstract: The present invention is related to the novel discovery of a number of genes that were identified as systemic markers of pulmonary inflammation. This discovery allows for development of a novel tool for reliable, rapid and efficient assessment of therapeutic responses and enables design of novel therapies targeted against diseases associated with pulmonary inflammation. In one embodiment, the present invention allows quantification of therapeutic response in patients who have a disease associated with pulmonary inflammation. In preferred embodiments, the genes are CD64, ADAM9, CD36, IL32, HPSE, PLXND1, HCA112, CSPG2, TLR2, and CD163.

Abstract: The present invention provides methods, kits, and compositions for detecting mutations in transient receptor potential cation channel, subfamily V, member 4 (TRPV4). In particular, mutations are detected in TRPV4 to detect diseases such as scapuloperoneal spinal muscular atrophy (SPSMA) and hereditary motor and sensory neuropathy type IIC (HMSN IIC) or Charcot-Marie-Tooth disease type 2C (CMT2C).

Abstract: Methods and compositions disclosed herein generally relate to methods of treating eosinophilic esophagitis (EE) and eosinophilic disorders by providing or enhancing a diagnosis of EE and eosinophilic disorders. In particular, the invention relates to obtaining a sample from a patient, then quantifying from the sample an amount of one or more microRNAs (miRNAs) associated with EE, wherein an altered level of the miRNA correlates with a positive diagnosis of EE. An EE diagnosis can then be provided or enhanced, based upon the quantifying step, and an appropriate treatment can be administered to the patient. The invention further relates to diagnostic kits, tests, and/or arrays that can be used to quantify the one or more miRNAs associated with EE, as well as treatments developed to up-regulate or down-regulate one or more miRNAs and/or their downstream pathways relevant to EE or asthma. The invention further relates to the use of IGF1 and IGF1R inhibitors for the treatment of EE and eosinophilic disorders.

Abstract: Disclosed are screening methods and sequences related thereto. Disclosed are methods for detecting mutations in the MYH gene of an individual. Also disclosed are methods of genotyping and methods of predicting for an individual the likelihood of developing certain cancers, such as colorectal cancer.

Abstract: Presented herein are biomarkers related to breast cancer. The presently identified salivary biomarkers create the basis for a breast cancer detection bioassay with sensitivity and specificity. Means and methods for evaluating the data generated using multiple biomarkers in order to validate findings and further use of the multiplexed breast cancer assay in clinical, diagnostic and therapeutic uses is also included.

Abstract: Described are bladder cancer specific biomarkers and lung cancer specific biomarkers comprising the nucleic acid sequence of the Engrailed-2 (EN2) gene or the amino acid sequence of the encoded EN2 protein. Also described are uses of the biomarkers in the treatment, diagnosis, monitoring and imaging of bladder cancer and lung cancer.

Abstract: A method for determining genes in breast cancer that are stable in copy number, expression and sequence in tumors from nearly all patients. Certain stable genes are targets of standard chemotherapy. The effectiveness of therapies that act upon these targets depends on maintaining the stability and integrity of these genes in tumors. Mutations in these targets result in poor response to therapies that target these gene products. In the instant invention, ordinarily stable gene targets are characterized as either normal or mutant for the purpose of determining whether to include or exclude particular drugs as potential treatments.

Abstract: A method for preparing a criterion for identifying the habitat of insects of the same kind, comprising the steps of: (a) determining the nucleotide sequences of DNA of one or more insects from two or more habitats; (b) aligning the nucleotide sequences determined in said step (a); (c) eliminating sites consisting of one or more nucleotides conserved in all of the nucleotide sequences aligned in said step (b) from the nucleotide sequences; (d) defining all or a part of the sites remaining upon elimination in said step (c) as type-discriminating sites; (e) comparing nucleotides corresponding to each other in the type-discriminating sites obtained in said step (d) to classify completely identical type-discriminating sites as the same type and incompletely identical type-discriminating sites as one or more different types; and (f) determining the habitat of each type classified in said step (e) on the basis of the habitats of insects belonging to each type, thereby defining the type-discriminating site of each

Abstract: The disclosure relates to a method of generating catalytic nucleic acid probes useful for detecting microorganisms such as bacterial pathogens. In one embodiment, the catalytic nucleic acid probes are fluorogenic DNAzymes. The disclosure also relates to catalytic nucleic acid probes and methods of using the probes for detecting microorganisms.

Abstract: A method of diagnosing bacterial vaginosis in a woman, which involves determining an amount of each of more than one BV-associated bacterium in a vaginal sample obtained from the female and assessing a BV status of the female based on the amount of each of the more than one BV-associated bacterium in the sample.

Abstract: This disclosure relates to methods of identifying and/or selecting wheat plants or germplasm by detecting markers associated with flowering date, anther-extrusion, heading date and/or fusarium head blight resistance.

Abstract: We have created novel engineered genetic counter designs and methods of use thereof that utilize DNA recombinases to provide modular systems, termed single invertase memory modules (SIMMs), for encoding memory in cells and cellular systems. Our designs are easily extended to compute to high numbers, by utilizing the >100 known recombinases to create subsequent modules. Flexibility in our engineered genetic counter designs is provided by daisy-chaining individual modular components, i.e., SIMMs together. These modular components of the engineered genetic counters can be combined in other network topologies to create circuits that perform, amongst other things, logic and memory. Our novel engineered genetic counter designs allow for the maintenance of memory and provide the ability to count between discrete states by expressing the recombinases between their cognate recognition sites.

Abstract: Nucleic acid amplification primers and methods for specific detection of influenza A and influenza B nucleic acid targets are disclosed. The primer-target binding sequences are useful for detection of influenza A and influenza B targets in a variety of amplification and hybridization reactions. The oligonucleotide sequences are able to differentiate between influenza A and influenza B strains through specific hybridization to one or the other virus strain, enabling specific detection of the presence of influenza A and/or influenza B in a specimen.

Abstract: Described herein are novel polynucleotides associated with viral infections. The polynucleotides are miRNAs and miRNA precursors. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of viral infections.