Abstract: The invention provides compositions and methods for inhibiting the expression of the gene XAX1 in grass plants. Plants with inhibited expression of XAX1 have use, e.g., in biofuel production by increasing the amount of soluble sugar that can be extracted from the plant.

Abstract: Provided are methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

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

Abstract: The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of improved plant size, vegetative growth, growth rate, seedling vigor and/or biomass in plants challenged with saline conditions. The present invention further relates to the use of these nucleic acid molecules and polypeptides in making transgenic plants, plant cells, plant materials or seeds of a plant having plant size, vegetative growth, growth rate, seedling vigor and/or biomass that are improved in saline conditions with respect to wild-type plants grown under similar conditions.

Abstract: The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of improved plant size, vegetative growth, growth rate, seedling vigor and/or biomass in plants challenged with saline and/or oxidative stress conditions. The present invention further relates to the use of these nucleic acid molecules and polypeptides in making transgenic plants, plant cells, plant materials or seeds of a plant having plant size, vegetative growth, growth rate, seedling vigor and/or biomass that are improved in saline and/or oxidative stress conditions with respect to wild-type plants grown under similar conditions.

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: 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: The present invention relates generally to immunization and immunotherapy for the treatment or prevention of HIV. In particular, the methods include in vivo and/or ex vivo enrichment of HIV-specific CD4+ T cells.

Abstract: As disclosed herein, optimal native genomic loci have been identified in dicot plants, such as soybean plants, that represent best sites for targeted insertion of exogenous sequences.

Abstract: Methods and system for producing a slip stream of sugar, for example for use in the production of one or more chemicals, in ethanol fermentation facilities. In some embodiments, the methods and systems have little to no impact on the level of production of ethanol, despite also producing a slip stream of sugar. The methods and systems can be implemented in dry mill ethanol, wet mill ethanol, and lignocellulosic ethanol fermentation facilities and processes.

Abstract: Methods and systems for the production of alcohols are described. A two stage process is utilized, where fermentation in a first stage produces an intermediate product, such as an amino acid or organic acid, from a carbon containing feedstock. A second stage produces alcohol by fermentation of this intermediate product.

Abstract: An object of the present invention is to provide a microorganism strain that accumulates a high molecular weight PHA, and a PHA production method using the microorganism. The present invention provides a method for producing a PHA copolymer, which includes culturing a microorganism, wherein at least a portion of either of the following genes (a) and (b) of the microorganism has been altered by substitution, deletion, insertion, and/or addition to reduce or eliminate the activity of a PHA degrading enzyme encoded by the gene: (a) a PHA degrading enzyme gene encoding the amino acid sequence of SEQ ID NO:2 in the sequence listing; and (b) a gene encoding a polypeptide having at least 85% sequence identity to the amino acid sequence of SEQ ID NO:2 in the sequence listing and having PHA degrading enzyme activity.

Abstract: Process for extracting volatile fatty acids (VFA), organic molecules called precursors produced by microorganisms (M) in a fermentation reactor (2) by anaerobic fermentation (3) using fermentable biomass (1), said molecules being fermentative metabolites, comprising at least the following steps: a) selecting an extraction means (8) from extraction means that is, at least, insoluble in the fermentation medium and the processing conditions of which preserve the capacity of the microorganisms (M) present in the fermentation medium to produce the molecules, b) bringing the chosen extraction means (8) into contact (9) with the fermentation medium without interrupting the fermentation (3), c) recovering (12) the extracted molecules, at a pH lower than 4.5, by the extraction means (8) outside the fermentation reactor (2). The invention also relates to an installation for implementing the method.

Abstract: Recombinant photosynthetic microorganisms that convert inorganic carbon to secreted fatty acids are described. Methods to recover the secreted fatty acids from the culture medium without the need for cell harvesting are also described.

Abstract: The invention relates to methods of preconditioning pretreated cellulosic material in the presence of a combination of phenol oxidizing enzyme and glucoamylase. The invention also relates to processes of producing sugars and fermentation products including a preconditioning step. Finally the invention relates to a composition suitable for preconditioning.

Abstract: Disclosed is a method for preparing a mixture of malto-oligosaccharides. Generally, a dry-milled corn fraction, such as a corn flour from which germ and fiber have been removed, is subjected to hydrolysis, typically catalyzed with acid or an enzyme such as an ?-amylase enzyme, under conditions suitable to form a mixture of malto-oligosaccharides. A gluten fraction is removed and the enzyme is inactivated, such as with heat. The mixture of malto-oligosaccharides then may be recovered from remaining solids and purified.

Abstract: The present invention relates to recombinant filamentous fungal host cells producing cellulolytic enzyme compositions and methods of producing and using the compositions.

Abstract: This document describes materials and methods for, for example, producing 6-hydroxyhexanoic acid using a ?-ketothiolase or synthase and an alcohol O-acetyltransferase to form a 6-acetyloxy-3-oxohexanoyl-CoA intermediate. This document describes biochemical pathways for producing 6-hydroxyhexanoic acid using a ?-ketothiolase or synthase and an alcohol O-acetyltransferase to form a 6-acetyloxy-3-oxohexanoyl-CoA intermediate. 6-hydroxyhexanoic acid can be enzymatically converted to adipic acid, caprolactam, 6-aminohexanoic acid, hexamethylenediamine or 1,6-hexanediol. This document also describes recombinant hosts producing 6-hydroxyhexanoic acid as well as adipic acid, caprolactam, 6-aminohexanoic acid, hexamethylenediamine and 1,6-hexanediol.

Abstract: The present invention relates to a cell for the production of an antibody molecule such as an antibody useful for various diseases having high antibody-dependent cell-mediated cytotoxic activity, a fragment of the antibody and a fusion protein having the Fc region of the antibody or the like, a method for producing an antibody composition using the cell, the antibody composition and use thereof.

Abstract: An apparatus (1) for analyzing a contaminated surface has a transfer device (2) with a mount (3) and a porous disk-shaped medium (5) having a contact side (6) arrangeable on the contaminated surface. The mount (3) is bindable to the medium on its side (8) facing away from the contact side (6) via a first fixing edge (7a). An analytical device (11) is bindable to the medium (5) on its contact side (6) via a second fixing edge (7b) to remove the medium (5) from the mount (3). The first fixing edge (7a) is bindable to the medium (5) via a first adhesive bond and the second fixing edge (7b) is bindable to the medium (5) via a second adhesive bond. The first adhesive bond is breakable by a lower application of force than the second adhesive bond.

Abstract: The field of the invention is the analysis of target microorganisms in a complex sample. The present invention more particularly relates to a culture medium for the detection of at least one target microorganism including: at least one natural or synthetic fermentation or enzymatic activity substrate, and at least one selective agent, which inhibits non-target microorganisms, constituted by para-amino benzoic acid, one of its derivatives or one of their salts, at a concentration of between 0.05 and 1 g/L.

Abstract: A process is provided that is effective for reducing CO2 emissions, enhancing STY and/or increasing cell density. The process allows for utilization of syngas from different sources by controlling concentration levels of CO, CO2 and H2 in syngas provided to the fermentation and by controlling relative concentrations of CO, CO2 and H2 in the syngas provided to the fermentation. The process includes providing syngas to a first fermentation zone and fermenting the syngas. If the first fermentation zone off-gas includes about 4 mole % or more CO, then at least a portion of the first fermentor off-gas is provided to one or more subsequent fermentation zones.

Abstract: Devices, systems and methods including a sonicator for sample preparation are provided. A sonicator may be used to mix, resuspend, aerosolize, disperse, disintegrate, or de-gas a solution. A sonicator may be used to disrupt a cell, such as a pathogen cell in a sample. Sample preparation may include exposing pathogen-identifying material by sonication to detect, identify, or measure pathogens. A sonicator may transfer ultrasonic energy to the sample solution by contacting its tip to an exterior wall of a vessel containing the sample. Multipurpose devices including a sonicator also include further components for additional actions and assays. Devices, and systems comprising such devices, may communicate with a laboratory or other devices in a system for sample assay and analysis. Methods utilizing such devices and systems are provided. The improved sample preparation devices, systems and methods are useful for analyzing samples, e.g. for diagnosing patients suffering from infection by pathogens.

Abstract: Devices, systems and methods including a sonicator for sample preparation are provided. A sonicator may be used to mix, resuspend, aerosolize, disperse, disintegrate, or de-gas a solution. A sonicator may be used to disrupt a cell, such as a pathogen cell in a sample. Sample preparation may include exposing pathogen-identifying material by sonication to detect, identify, or measure pathogens. A sonicator may transfer ultrasonic energy to the sample solution by contacting its tip to an exterior wall of a vessel containing the sample. Multipurpose devices including a sonicator also include further components for additional actions and assays. Devices, and systems comprising such devices, may communicate with a laboratory or other devices in a system for sample assay and analysis. Methods utilizing such devices and systems are provided. The improved sample preparation devices, systems and methods are useful for analyzing samples, e.g. for diagnosing patients suffering from infection by pathogens.

Abstract: An optical measurement instrument is an integrated instrument that includes an optical cavity with a light source, a sample cuvette, and an optical sensor. The light source and sensor are on a bench that is on a translational or rotational mechanical platform such that optical beam can be moved to multiple sample containers. The instrument can be used for taking measurements of organism concentration in multiple samples as a production tool for microbiology. Preferably, the instrument holds multiple, individually-loaded, independent fluid samples and determines bacteria concentration via a forward-scattering signal. The instrument can incorporate onboard incubation to promote bacterial growth in the samples during the test. In another aspect, the instrument can be a part of a network for medical diagnostic testing data where data is stored in a manner that is inherently untainted by patient identifiable information.

Abstract: A sample of produce wash water containing an antimicrobial sanitizer fluid, and a reference pathogen fluid are both injected into a pathogen inactivation region of a micro-fluidic mixer. The produce wash water (i.e. sanitizer fluid/pathogen fluid mix) is directed through mixer elements in the pathogen inactivation region of the micro-fluidic mixer. In the sanitizer deactivation region, a sanitizer deactivation solution is added to the sanitizer fluid/pathogen fluid mix to produce a deactivated solution. The deactivated solution is evaluated for the presence of the pathogen and the characteristics of the sanitizer. In the preferred embodiment, the sanitizer comprises chlorine and the pathogen comprises E. coli bacteria.

Abstract: Methods are provided for performing antibiotic susceptibility testing based on the detection of RNA, such as tmRNA, from microbial cells after exposure to antibiotics. In some embodiments, aliquots are obtained from a sample, one of which contains a selected antibiotic. The aliquots, which include growth media, are incubated under conditions suitable for microbial growth, and the microbial cells in each aliquot are removed and lysed, and the lysate is subjected to reverse transcription and amplification in infer the effect of the selected antibiotic on the microbial cells. In one embodiment, a sample containing microbial cells is incubated in the presence of a selected antibiotic and a stimulus is provided to induce the production on m RNA within the microbial cells. The microbial cells are subsequently lysed without substantial degradation of the m RNA within the lysate, and the m RNA is detected to determine the effect of the antibiotic on the microbial cells.

Abstract: Disclosed herein are methods and systems for detection of a microorganism of interest using an amplification assay. The methods and systems utilize the specificity of binding agents, such as antibodies, to rapidly detect low levels of a specific microorganism present in a sample. In certain embodiments, antibodies are bound to a large number of the available binding sites on a microorganism.

Abstract: A polynucleotide encoding a modified luciferase polypeptide. The modified luciferase polypeptide has at least 60% amino acid sequence identity to a wild-type Oplophorus luciferase and includes at least one amino acid substitution at a position corresponding to an amino acid in a wild-type Oplophorus luciferase of SEQ ID NO:1. The modified luciferase polypeptide has at least one of enhanced luminescence, enhanced signal stability, and enhanced protein stability relative to the wild-type Oplophorus luciferase.

Abstract: A method of detecting a state of a lipid membrane in a cell of a nanopore based sequencing chip is disclosed. A lipid membrane is coupled with an integrating capacitor, wherein the lipid membrane is between a working electrode and a counter electrode. An alternating current (AC) voltage is applied to the counter electrode. A voltage across the integrating capacitor is periodically sampled by an analog-to-digital converter (ADC). A change in the sampled voltage across the integrating capacitor in response to an intermediate change in the AC voltage is determined. A state of the lipid membrane is determined based on the determined change in the sampled voltage across the integrating capacitor in response to the intermediate change in the AC voltage.

Abstract: A method of generating deformable gel beads that contain a single colloidal particle is described. Gel beads containing a particle are isolated from those that do not contain a particle, based on differences between the buoyant density of these gel bead populations. The gel beads containing a particle are subsequently co-encapsulated at a high efficiency into droplets that can comprise additional objects such as cells, other particles, or reagents. The gel coating on the rigid particle prevents clogging in narrow channels, such as those of a droplet generator.

Abstract: Novel methods of generating a localized population of immobilized clonal amplicons on a support are provided.

Abstract: Provided herein are products and processes for detecting the presence or absence of minor nucleic acid species in a sample containing a mixture of minor nucleic acid species and one or more major nucleic acid species, where the amount (frequency or copy number) of the minor nucleic acid species is less than that of the major nucleic acid species. Certain methods include amplifying the mixture and extending the resulting amplicons using chain terminating reagents and extension primers that specifically hybridize to the amplicons, where a chain terminating reagent specific for the major nucleic acid species has a concentration that is less than a chain terminating reagent that is specific for a minor nucleic acid species.

Abstract: The disclosure relates to methods for obtaining nucleic acid sequence information by constructing a nucleic acid library and reconstructing longer nucleic acid sequences by assembling a series of shorter nucleic acid sequences.

Abstract: This disclosure provides, among other things, a cartridge comprising: (a) a cartridge body comprising a malleable material and having, disposed on a surface of the body, at least one valve body comprising a valve inlet and a valve outlet, each fluidically connected to a fluidic channel; and (b) a layer comprising a deformable material bonded to a surface of the cartridge body and sealing the at least one valve body at points of attachment, thereby forming at least one valve; wherein the at least one valve body is depressed in the cartridge body relative to the points of attachment and wherein the deformable material covering the at least one valve body retains sufficient elasticity after deformation such that in a ground state the valve is open.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

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.

Abstract: This document provides methods and materials related to genetic variations of developmental disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Autism Spectrum Disorder.

Abstract: The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—, e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization.

Abstract: Methods for determining the presence or absence of expansion of CGG repeat sequence in the FMR1 gene presence or absence of expansion of CCG repeat sequence in the FMR2 gene are provided. The methods are useful in identifying an individual with normal/intermediate, versus premutation or full mutation allele of FMR1 gene and FMR2 gene due to the expansion of CGG repeats and CCG repeats in the 5?-untranslated region respectively. The methods are also useful for screening newborns for fragile X syndrome or for screening women to determine heterozygosity status with full premutation of the CCG repeat tract. The methods are also useful in estimating the premutation and full mutation carrier frequency and estimating the prevalence of FXTAS AND FXPOI in a population. The methods are simple, rapid and require small amount of sample.

Abstract: The invention described herein relates to methods of treating emphysema and COPD with a GHK tripeptide. The invention further relates to methods of determining the state of the lungs using biomarkers described herein.

Abstract: The present invention provides novel mutations identified in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that can be used for a more accurate diagnosis of cystic fibrosis (CF) and CF related disorders. Methods for testing a sample obtained from a subject to determine the presence of one or more mutations in the CFTR gene are provided wherein the presence of one or more mutations indicates that the subject has CF or a CF related disorder, or is a carrier of a CFTR mutation.

Abstract: The invention relates to the identification of mircoRNAs associated with rosacea and to the uses thereof. More specifically, the invention relates to a method of diagnosing rosacea in a subject, comprising the determination, in a sample from said subject, of the expression of at least the combination of the following seven microRNAs: hsa-miR-3201, hsa-miR-4423-3p, hsa-miR-3128, hsa-miR-3163, hsa-miR-606, hsa-miR-4776-5p and hsa-miR-635.

Abstract: The present invention relates generally to the identification of subjects with a predisposition to recurrent depression, predicting a subject's responsiveness to therapy, and determining whether a subject has remitted from depression following therapy. In particular, provided herein are biomarkers, methods, and kits for such uses.

Abstract: Biomarkers are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer. In addition, kits are provided for measuring expression levels or the presence of the biomarkers associated with thymic cancer for detecting, diagnosing and prognosing thymic cancer. Furthermore, methods are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer via the biomarkers.

Abstract: The invention relates to methods and reagents for the identification of the origin of a carcinoma of unknown primary origin (CUP) based on the determination of the methylation profile in the genome of the CUP. The invention relates as well to methods for selecting a suitable therapy for a patient suffering a CUP as well as to methods for personalized medicine of patient suffering a CUP based on the use of a treatment which is adequate for the primary tumor from which the CUP is derived. The invention also relates to kits comprising reagents adequate for performing the above methods as well as to computer systems and programs which can be used for implementing the methods of the invention.

Abstract: Disclosed herein are methods and compositions (e.g., oligonucleotide primers) for isothermal amplification and detection of M. pneumoniae nucleic acids in a sample. In some embodiments, the methods include contacting a sample with a set of LAMP primers specific for a M. pneumoniae CARDS toxin-encoding nucleic acid under conditions sufficient to produce an M. pneumoniae nucleic acid amplification product and detecting the resulting M. pneumoniae amplification product. Kits including sets of LAMP primers for detection of M. pneumoniae CARDS toxin nucleic acids are also provided herein.

Abstract: The present invention is concerned with PCR-based detection methods and kits for the identification, differentiation, and quantification of different bacterial strains (e.g., Gram-negative bacterial strains), and also association of two or more PCR-positive genes to a single genome. The methods generally comprise carrying out PCR reactions using at least a first PCR primer set and/or probe for at least one target nucleic acid; and a second PCR primer set and/or probe for at least a second target nucleic acid. Positive PCR reaction products are then detected to determine test samples containing positive PCR reaction products for both the first and second target nucleic acids. This information can be used to calculate the gene association rate to determine whether the sample contains, for example, Shiga toxin-producing E. coli of the O-type serogroup.

Abstract: Compositions and methods for detecting Trichomonas vaginalis are provided.

Abstract: The present disclosure provides a transgenic corn comprising event MON87403 that exhibits increased grain yield. The disclosure also provides cells, plant parts, seeds, plants, commodity products related to the event, and DNA molecules that are unique to the event and were created by the insertion of transgenic DNA into the genome of a corn plant. The disclosure further provides methods for detecting the presence of said corn event nucleotide sequences in a sample, probes and primers for use in detecting nucleotide sequences that are diagnostic for the presence of said corn event.