Abstract: Provided herein is a tyrosine selection marker system, and uses thereof. In some embodiments, nucleic acid constructs, vectors, host cells and related compositions and methods for generating and selecting tyrosine prototroph cells are provided.

Abstract: The disclosure describes methods, compositions, and kits for high throughput DNA assembly reactions in vitro. The disclosure further describes modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa are also disclosed.

Abstract: The present disclosure provides methods, automated modules, and instruments for enrichment of live cells that have been edited by nucleic acid-guided nuclease genome editing. The disclosure provides improved methods and modules—including high throughput methods and modules—for enriching for cells that have been subjected to editing.

Abstract: The present disclosure is generally related to compositions and methods for obtaining Bacillus licheniformis cells/strains having increased protein production capabilities. Certain embodiments of the disclosure are related to genetically modified Bacillus licheniformis cells/strains derived from parental B. licheniformis cells/strains comprising a variant rghR2 gene.

Abstract: The present invention relates to materials and methods for the production of ethanol. More particularly, the present invention provides genetically modified strains of Saccharomyces cerevisiae exhibiting decreased level of BCY1 protein activity and capable of anaerobic fermentation of xylose into ethanol without the need for cell growth. Also provided are methods of using such genetically engineered yeast strains for improved anaerobic xylose fermentation in the yeast for industrial-scale production of various fuels, chemical feedstocks, and synthetic polymers.

Abstract: The invention provides DNA molecules and constructs, including their nucleotide sequences, useful for modulating gene expression in plants and plant cells. Transgenic plants, plant cells, plant parts, seeds, and commodity products comprising the DNA molecules operably linked to heterologous transcribable polynucleotides are also provided, 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 the recombinant DNA molecules operably linked to heterologous transcribable DNA molecules, as are methods of their use.

Abstract: The present invention relates to the field of agriculture. In particular, the invention provides a promoter, a recombinant gene, plants comprising the recombinant genes and a method to improve yield of a cotton plant under stress conditions.

Abstract: The present invention relates to diacylglycerol acyltransferase genes and proteins, and methods of their use. In particular, the invention describes genes encoding proteins having increased diacylglycerol acetyltransferase activity compared to prior art proteins, specifically for transferring an acetyl group to a diacylglycerol substrate to form acetyl-Triacylglycerols (acetyl-TAGS), for example, a 3-acetyl-1,2-diacyl-sn-glycerol. The present invention encompasses both native and recombinant wild-type forms of the transferase, as well as mutants and variant forms. The present invention also relates to methods of using the diacylglycerol acyltransferase genes and proteins, including their expression in transgenic organisms at commercially viable levels, for increasing production of 3-acetyl-1,2-diacyl-sn-glycerols in plant oils and altering the composition of oils produced by microorganisms, such as yeast, by increasing acetyl-TAG production.

Abstract: Methods and materials for modulating low-nitrogen tolerance levels in plants are disclosed. For example, nucleic acids encoding low nitrogen tolerance-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also disclosed are plants having increased low-nitrogen tolerance levels and plant products produced from plants having increased low-nitrogen tolerance levels.

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 a cucumber plant (Cucumis sativus L.) that is resistant to Pseudomonas syringae pv. lachrymans, a pathogen that causes angular leaf spot disease in cucumber. The invention further relates to markers linked to the resistance and the use of markers to identify resistant plants. The invention also relates to seed and progeny of such plants and to propagation material derived from such plants and for obtaining such plants. Furthermore, the invention relates to methods for producing, identifying and selecting Pseudomonas resistant cucumber plants, and for producing hybrid plant seed. The invention further relates to the use of a gene and/or QTLs and sequences thereof to identify/select Pseudomonas resistant cucumber plants.

Abstract: The present invention relates inter alia to a rodent or rodent cell having a genome comprising: i) one or more companion animal IGH V region genes, one or more companion animal D region genes and one or more companion animal J region genes; and (ii) optionally one or more companion animal IGL kappa V region genes and one or more companion animal IGL kappa J region genes; and/or one or more companion animal IGL lambda V region genes and one or more companion animal IGL lambda J region genes, wherein the rodent or rodent cell is capable of expressing the companion animal variable region gene(s) to form an antibody chain and wherein the companion animal species is not a rodent.

Abstract: The present invention provides systems and methods wherethrough a cancer cell's metabolic activities attract a vector to the cell to provide the cell with tools and instructions for self-destruction. A vector is engineered for attraction to and reaction with cells of higher temperature, a characteristic result of hypermetabolism inherent in the uncontrolled or extreme growth of cancerous and precancerous cells. A second engineered feature relates to the increased acidity resulting from a cancer cell's reduced reliance of mitochondrial ATP production. The engineered vector then stimulates the body's natural intracellular and extracellular innate immune responses to effect death and destruction of the targeted hypermetabolizing cells.

Abstract: Aspects of the disclosure relate to compositions and methods useful for treating ocular ciliopathies, for example Leber congenital amaurosis (LCA). In some embodiments, the disclosure provides isolated nucleic acids comprising a transgene encoding a CEP290 protein fragment, and methods of treating ocular ciliopathies using the same.

Abstract: A rAAV vector is described herein which has an AAVhu68 capsid and at least one expression cassette in the capsid. The at least one expression cassette comprises nucleic acid sequences encoding a functional SMN protein and expression control sequences that direct expression of the SMN sequences in a host cell. Also provided are compositions containing this rAAVhu68.SMN vector and methods of using same for spinal muscular atrophy in a patient.

Abstract: Methods of modifying a frataxin gene are disclosed, comprising removing some or all of endogenous GAA trinucleotide repeats within the frataxin gene, e.g., within an intron (e.g., intron 1) of the frataxin gene. The removal may be effected using a CRISPR/CAS nuclease system. Such modification may be used to increase frataxin expression in the cell, and also to treat a subject suffering from Friedreich ataxia. Reagents, kits and uses of the method are also disclosed, for example to modify a frataxin gene and to treat a subject suffering from Friedreich ataxia.

Abstract: The present invention relates in part to nucleic acids encoding proteins, therapeutics comprising nucleic acids encoding proteins, methods for inducing cells to express proteins using nucleic acids, methods, kits and devices for transfecting, gene editing, and reprogramming cells, and cells, organisms, and therapeutics produced using these methods, kits, and devices. Methods and products for altering the DNA sequence of a cell are described, as are methods and products for inducing cells to express proteins using synthetic RNA molecules. Therapeutics comprising nucleic acids encoding gene-editing proteins are also described.

Abstract: Engineered nucleic acids encoding genome editing system components are provided, as are engineered RNA-guided nucleases that include inserts encoded in part by cellular genomic or other sequences recognized by guide RNAs.

Abstract: The present disclosure provides DNA-guided CRISPR systems; polynucleotides comprising DNA, RNA and mixtures thereof for use with CRISPR systems; and methods of use involving such polynucleotides and DNA-guided CRISPR systems.

Abstract: Described herein is a method of producing drimenol and/or drimenol derivatives, the method including contacting at least one polypeptide with farnesyl diphosphate (FPP). The method may be performed in vitro or in vivo. Also described herein are amino acid sequences of polypeptides useful in the methods and nucleic acids encoding the polypeptides described. Also described herein are host cells or organisms genetically modified to express the polypeptides and useful to produce drimenol and/or derivatives of drimenol.

Abstract: The present disclosure provides compositions and methods for rapid production of chemicals in genetically engineered microorganisms in a large scale. Also provided herein is a high-throughput metabolic engineering platform enabling the rapid optimization of microbial production strains. The platform, which bridges a gap between current in vivo and in vitro bio-production approaches, relies on dynamic minimization of the active metabolic network.

Abstract: This invention relates to a fermentation process for producing D-lactic acid or its salts. The said process comprises the following steps: cultivating of Sporolactobacillus laevolacticus bacteria strain by fermentation with sugarcane juice in order to obtain the seed culture; fermenting of the obtained seed culture in sugarcane juice, wherein the cultivation step is operated for the time that the final concentration of Sporolactobacillus laevolacticus strain in the cultivation step is in a range of 400 to 1,600 mg of dry cell per liter. The said process according to the invention can provide high productivity and yield of the D-lactic acid with a high optical purity. Moreover, the said process can be easily done and reduces the complicate steps.

Abstract: A process for producing an organic aliphatic product (such as butanol) from lignocellulosic biomass is provided, comprising: (a) fractionating lignocellulosic biomass in the presence of a solvent for lignin, a hydrolysis catalyst, and water, to produce a liquor containing hemicellulose, cellulose-rich solids, and lignin; (b) washing the cellulose-rich solids and separating the cellulose-rich solids from the liquor; (c) enzymatically hydrolyzing the cellulose-rich solids to generate a hydrolysate comprising glucose; (d) detoxifying the hydrolysate by neutralizing the hydrolysate, removing insoluble solids, and removing or oxidizing residual hydrolysis catalyst, thereby generating a purified hydrolysate; (e) fermenting the purified hydrolysate using a suitable microorganism to produce a dilute organic aliphatic product, wherein the microorganism is recycled with a membrane; (f) extracting the dilute organic aliphatic product into a water-immiscible extractant, to generate an intermediate material; and (g) disti

Abstract: A PHA copolymer which is slowly crystallized is improved in crystallization speed to improve the melt workability of the PHA copolymer in working such as injection molding, film molding, blow molding, fiber spinning, extrusion foaming or bead foaming, thereby improving the resultant articles in productivity. A method for the improvement is a method for producing a PHA mixture, including the step of culturing a microorganism having both of a gene encoding a PHA synthase that synthesizes a copolymer PHA (A) and that is derived from the genus Aeromonas, and a gene encoding a PHA synthase that synthesizes a PHA (B) different in melting point from the copolymer PHA (A) by 10° C. or more to produce, in a cell of the microorganism, two or more PHAs different in melting point from one another by 10° C. or more simultaneously.

Abstract: The present invention relates to engineered carbohydrate-active enzyme constructs that are useful for glycan polymers synthesis. The construct comprises a CD domain from a GH, wherein the domain is conjugated to CBM3a via a peptidic linker. The invention also relates to a method of improving glycan polymer synthesis by using engineered carbohydrate active enzymes comprising a CD domain and CBM3a.

Abstract: The present compositions and methods relate to a beta-glucosidase from Glomerella graminicola, polynucleotides encoding the beta-glucosidase, and methods of making and/or use thereof. Formulations containing the beta-glucosidase may be suitable for use in hydrolyzing lignocellulosic biomass substrates.

Abstract: A technology regarding the production, formulation and use of conditioned media and the factors included therein is disclosed. The conditioned media may be inoculated with animal cells, plant cells and any combination thereof. The inoculations may occur simultaneous or at different times. Cells retrieved from different areas of the animal and/or the plant may also be cultured together to form conditioned media and associated growth factors.

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: Devices for microbial detection of microorganisms are provided including a body member including a substrate having a first major surface and a second major surface. The device further includes a substantially dry, first microbial growth nutrient composition disposed on a portion of the first major surface, a first adhesive composition adhered to the first microbial growth nutrient composition, and a cold-water-soluble first hydrogel-forming composition adhered to the first adhesive composition. The device also includes a cover sheet attached to the body member, where the cover sheet includes a first major surface facing the body member. Devices including a water-proof pouch are also provided. Methods for detecting and enumerating at least one microorganism in a sample are additionally provided, using the devices.

Abstract: A method of data collection includes culturing a sample that was generated from a raw sample. The raw sample was taken from a patient and the sample includes a pathogen when the raw sample included the pathogen. An assay sample is generated from a portion of the sample such that the assay sample includes the pathogen when the sample included the pathogen. The sample is cultured for a time period that less than hours and greater than or equal to 0.0 hours before the portion of the test sample was taken from the test sample. The assay sample is assayed so as to determine whether the pathogen is present in the assay sample.

Abstract: The present invention provides an in vitro method for concentrating infectious pathogens found in a biological sample obtained from an individual who is suspected of being infected with the pathogens. Provided herein is also an in vitro method for reducing or eliminating blood cells from a sample obtained from an individual suspected to being infected with an infectious pathogen. The present invention also provides a method for diagnosing malaria and a method for determining if an individual is infected with a pathogen. Provided herein is also a concentrator and a kit for use with the methods.

Abstract: Compounds having chemiluminescent flash and glow properties. Also disclosed are methods using the compounds to generate light, detect and/or quantify enzymes, antigens, and/or nucleic acids. Also disclosed are kits relating to these compounds.

Abstract: Provided herein are compositions and methods for cellular analysis. Nucleic acid from single cells may be processed in one or more partitions. A partition may comprise a cell bead and one or more enzymes for nucleic acid processing. A partition may comprise a functionalized polymer. In some cases, single cells may be subjected to epigenetic analysis, thereby generating an epigenetic profile for each cell from a plurality of cells.

Abstract: Transposase-based barcoding of DNA for improved efficiency, high-accuracy sequencing is described. Transposases including transposable barcodes can be used to fragment and barcode target DNA in a single step.

Abstract: The present invention relates to a method of diagnosing chronic obstructive airway disease such as asthma, COPD, and the like through bacterial metagenomic analysis, and more particularly, to a method of diagnosing chronic obstructive pulmonary disease and asthma by analyzing an increase or decrease in content of extracellular vesicles derived from specific bacteria through bacterial metagenomic analysis using a subject-derived sample. Extracellular vesicles secreted from bacteria present in the environment are absorbed into the human body, and thus may directly affect inflammatory responses, and it is difficult to diagnose chronic obstructive airway diseases such as asthma, COPD, and the like early before symptoms occur, and thus efficient treatment therefor is difficult.

Abstract: The present invention relates to a method of diagnosing Parkinson's disease through bacterial metagenomic analysis, and more particularly, to a method of diagnosing Parkinson's disease by analyzing an increase or decrease in content of extracellular vesicles derived from specific bacteria by bacterial metagenomic analysis using a subject-derived sample. Extracellular vesicles secreted from microorganisms such as bacteria, archaea, and the like present in the environment are absorbed into the human body and distributed in the brain, and thus may directly affect inflammatory responses and brain functions, and since it is difficult to implement early diagnosis for Parkinson's disease, which is characterized by inflammation, before symptoms appear, efficient treatment therefor is difficult.

Abstract: Described herein various PCR based assays that can detect H. penaei and/or V. parahaemolyticus that causes AHPND in a nucleic acid sample obtained from one or more shrimp. In some aspects, the PCR based assays can detect one or more of the following genes: the fIgE gene from H. penaei, the shrimp 18s rRNA gene, the shrimp beta actin gene from shrimp, a bacterial 16S rRNA gene from bacteria (any type of bacteria) the Vibrio pirA gene, and the Vibrio pirB gene. The assays described herein can be single assays or can be multiplexed such that more than one gene and/or more than one bacterial species can be detected in a single reaction. Other compositions, compounds, methods, features, and advantages of the present disclosure will be or become apparent to one having ordinary skill in the art upon examination of the following drawings, detailed description, and examples.

Abstract: The present invention addresses the issue of providing a target base sequence detection method, etc., whereby a determination can be readily made regarding whether or not a target base sequence is present in a nucleic acid sample. A fluorescent-labeled detection probe and a competitive probe are added to a nucleic acid sample and caused to hybridize with the nucleic acid in the sample, the fluorescence intensity is measured while changing the temperature of the reaction sample, and first order differentiation is performed on a temperature-fluorescence intensity curve.

Abstract: The invention is a method of sequencing polymers in which the sequence of one or more polymers is determined through an emergent property of the binding interactions of a repertoire of molecular probes to the polymer(s).

Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.

Abstract: Comparison of common sequencing reads from sequencing based on partition-based barcoding can be used to improve sequencing results. Increased loading of barcodes per partition can also improve sequencing results.

Abstract: This disclosure describes, in one aspect, methods for DNA sequencing and performing epigenomic analyses. Generally, the methods include immobilizing a plurality of copies of a DNA molecule on a surface, stretching at least a portion of the immobilized DNA molecules, and sequencing at least a portion of the immobilized, stretched DNA molecules.

Abstract: Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared from dsDNA alone.

Abstract: The present invention relates to a method for determining a survival probability of a subject comprising a) detecting the methylation status of at least two CpG sites selected from the list consisting of cg24704287, cg08362785, cg25983901, cg06126421, cg05575921, cg23665802, cg01612140, cg19572487, cg14975410, and cg10321156 in a sample of said subject and, b) based on the methylation status detected in step a), determining the survival probability of said subject. The present invention further relates to uses, data collections, kits, devices and methods related to the aforesaid method.

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: Provided are polynucleotides that find use, e.g., for detecting RNase activity. In certain embodiments, the polynucleotide comprises a tRNA operably linked to a pre-microRNA (pre-miRNA), and an aptamer that binds to a detectable label. According to some embodiments, the detectable label is a fluorescent dye, non-limiting examples of which include malachite green, tetramethylrosamine, sulforhodamine B, and a triphenylmethane dye. Also provided are compositions that include the polynucleotides of the present disclosure. Also provided are kits that include a polynucleotide of the present disclosure and a detectable label to which the aptamer of the polynucleotide binds.

Abstract: Disclosed are methods of isolating paired T cell receptor (TCR) alpha and beta chain sequences, or an antigen-binding portion thereof. Also disclosed are methods of automatically identifying the TCR alpha and beta chain V segment sequences and CDR3 sequences of a TCR having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation. Methods of preparing a population of cells that express paired TCR alpha and beta chain sequences, or an antigen-binding portion thereof, are also disclosed. Isolated pairs of TCR alpha and beta chain sequences and isolated populations of cells prepared by the methods are also disclosed.

Abstract: Compositions and methods for the diagnosis and treatment of lymphatic anomaly are disclosed.

Abstract: This document provides methods and materials for detecting genetic and/or epigenetic elements. For example, methods and materials for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, methods and materials for detecting the amount of target nucleic acid containing a genetic or epigenetic element within a sample, kits for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, kits for detecting the amount of target nucleic acid containing a genetic or epigenetic element present within a sample, and methods for making such kits are provided.