Abstract: The present disclosure identifies new genes which have the potential to increase broad acre yield in crops. This disclosure is based upon our fundamental knowledge of light signal transduction and our understanding of the roles these genes play in regulating plant growth and development in response to light. Transgenic plants with gain- or loss-of-function of one of these genes, or in combination, are expected to show significant improvements in broad acre yield and stress tolerance.

Abstract: A method of controlling tolerance to drought stress in a plant includes regulating expression of a gene encoding Oryza sativa branched-chain amino acid aminotransferase 2 (OsBCAT2) protein derived from rice in a plant cell. A genome-edited rice plant having enhanced tolerance to drought stress is prepared by carrying out genome editing by introducing guide RNA specific to target nucleotide sequence in a gene encoding OsBCAT2 protein, and endonuclease protein to a rice plant cell, and regenerating a plant from the genome-edited rice plant cell.

Abstract: The present disclosure provides methods and compositions for increasing resistance of plants to a disease caused by infection with bacteria of a Liberibacter species.

Abstract: Pesticidal proteins exhibiting toxic activity against Lepidopteran pest species are disclosed, and include, but are not limited to, TIC6757, TIC6757PL, TIC7472, TIC7472PL, TIC7473, and TIC7473PL. DNA constructs are provided which contain a recombinant nucleic acid sequence encoding one or more of the disclosed pesticidal proteins. Transgenic plants, plant cells, seed, and plant parts resistant to Lepidopteran infestation are provided which contain recombinant nucleic acid sequences encoding the pesticidal proteins of the present invention. Methods for detecting the presence of the recombinant nucleic acid sequences or the proteins of the present invention in a biological sample, and methods of controlling Lepidopteran species pests using any of the TIC6757, TIC6757PL, TIC7472, TIC7472PL, TIC7473, and TIC7473PL pesticidal proteins are also provided.

Abstract: The disclosure provides compositions and methods for the Vectored Augmentation of the Destruction, Expression and/or Regulation of proteins, e.g., VA-DER systems and methods.

Abstract: Compositions and methods are described for the delivery of a fully human post-translationally modified therapeutic monoclonal antibody that binds to CGRP or CGRP receptor to a human subject for the treatment or prevention of migraines and cluster headaches. The antibodies may be delivered by gene therapy vectors, particularly rAAV vectors. Also provided are dual transgene constructs for the delivery of anti-CGRP and anti-CGRP receptor antibodies or antigen binding fragments thereof.

Abstract: The present invention relates to CRISPR-mediated means and methods, e.g., for adjustably induction of multiple gene expression and subsequent cell reprogramming. Particularly, the CRISPR-mediated means and methods of the present invention relate to conversion of endogenous glial cells into GABAergic neurons representing an effective method for cell reprogramming.

Abstract: This document provides AAVs and methods and materials for making and using AAVs. For example, AAVs containing a VP1 polypeptide, a VP2 polypeptide, and a VP3 polypeptide having a heterologous amino acid segment having the ability to bind to a binding partner are provided. This document also provides compositions containing an AAV described herein, a vector system encoding an AAV described herein, and methods for making a composition that includes two or more different AAVs covalently linked together.

Abstract: A method of treating X-linked juvenile retinoschisis (XLRS) in a human subject includes subretinally delivering to the human subject a therapeutically effective amount of an rAAV vector. The rAAV vector includes a nucleic acid sequence comprising coding sequence for human RS1 protein. The rAAV vector can further include a mutated AAV2 VP3 capsid protein having a phenylalanine (F) for tyrosine (Y) substitution at each of the positions corresponding to Y444, Y500 and Y730 in a wild type AAV2 VP3 capsid protein.

Abstract: Disclosed herein is a recombinant adeno-associated virus (AAV) vector comprising (a) a variant AAV2 capsid protein, wherein the variant AAV2 capsid protein comprises at least four amino acid substitutions with respect to a wild type AAV2 capsid protein; wherein the at least four amino acid substitutions are present at the following positions in an AAV2 capsid protein sequence: 457, 492, 499 and 533; and (b) a heterologous nucleic acid comprising a nucleotide sequence encoding a gene product.

Abstract: In certain aspects, the present invention provides methods for inducing a stable gene modification of a target nucleic acid via homologous recombination in a primary cell, such as a primary blood cell and/or a primary mesenchymal cell. In certain other aspects, the present invention provides methods for enriching a population of genetically modified primary cells having targeted integration at a target nucleic acid. The methods of the present invention rely on the introduction of a DNA nuclease such as a Cas polypeptide and a homologous donor adeno-associated viral (AAV) vector into the primary cell to mediate targeted integration of the target nucleic acid. Also provided herein are methods for preventing or treating a disease in a subject in need thereof by administering to the subject any of the genetically modified primary cells or pharmaceutical compositions described herein to prevent the disease or ameliorate one or more symptoms of the disease.

Abstract: The present disclosure provides improved compositions for the homology directed repair of the human globin locus for the prevention, treatment, or amelioration of at least one symptom of a hemoglobinopathy.

Abstract: Compositions and methods for editing, e.g., introducing double-stranded breaks, within the TTR gene are provided. Compositions and methods for treating subjects having amyloidosis associated with transthyretin (ATTR), are provided.

Abstract: A CRISPR-Cas3 system was successfully established in a eukaryotic cell.

Abstract: Enzymes and methods are described herein for manufacturing terpenes, including terpenes.

Abstract: Processes, systems, and methods for producing combustible gas from wet biomass are provided. In one aspect, for example, a process for generating a combustible gas from a wet biomass in a closed system is provided. Such a process may include growing a wet biomass in a growth chamber, moving at least a portion of the wet biomass to a reactor, heating the portion of the wet biomass under high pressure in the reactor to gasify the wet biomass into a total gas component, separating the gasified component into a liquid component, a non-combustible gas component, and a combustible gas component, and introducing the liquid component and non-combustible gas component containing carbon dioxide into the growth chamber to stimulate new wet biomass growth.

Abstract: A method of producing bioethanol in a bioethanol system and a control system for a bioethanol system is disclosed, the control system comprising a controller comprising one or more processors and an interface, wherein the one or more processors are configured to obtain a primary amino nitrogen (PAN) measurement; determine an input scheme based on the PAN measurement; and control one or more input devices of the bioethanol system according to the input scheme.

Abstract: Described herein are recombinant fermenting organisms having a heterologous polynucleotide encoding an alpha-amylase and/or a heterologous polynucleotide encoding a trehalase. Also described are processes for producing a fermentation product, such as ethanol, from starch or cellulosic-containing material with the recombinant fermenting organisms.

Abstract: The present disclosure provides methods for producing fuels, such as biofuels, and commodity chemicals. In some embodiments, the methods comprise pretreating cellulosic biomass with a sugar acid. In some embodiments, the methods further comprise recycling sugar acids that are produced during fermentation for use in the subsequent pretreatment of cellulosic biomass. In some embodiments, the methods further comprise utilizing one or more components produced during pretreatment for subsequent fermentation. Fuels and commodity chemicals produced according to the methods of the present invention are also provided herein.

Abstract: ?The invention is directed to a non-naturally occurring microbial organism comprising a first attenuation of a succinyl-CoA synthetase or transferase and at least a second attenuation of a succinyl-CoA converting enzyme or a gene encoding a succinate producing enzyme within a multi-step pathway having a net conversion of succinyl-CoA to succinate.

Abstract: Provided is a nucleic acid comprising a recombinant bacterial or archaeal geranyl pyrophosphate synthase (GPPS) gene, codon optimized for production in yeast. Also provided is a yeast cell comprising an expression cassette comprising the above nucleic acid. Additionally provided is a method of producing a terpene or cannabinoid in a yeast, the method comprising incubating the above yeast cell in a manner sufficient to produce the terpene or cannabinoid.

Abstract: The disclosure relates to the technical field of food and medical chemical production, and provides a method of preparing an extract of chayote. The method includes: step 1, adding water and a pretreatment agent of ethoxylated p-tert-octylphenol to a chayote powder to obtain a pretreatment mixture; step 2, adding a stabilizer and a cellulase to the pretreatment mixture to perform an enzymolysis treatment to obtain an enzymatic hydrolysate, and centrifuging the enzymatic hydrolysate to obtain a crude extraction liquid; step 3, concentrating the crude extraction liquid to obtain a concentrate, purifying and drying the concentrate to obtain the extract of chayote.

Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of histamine and provides novel engineered microbial cells and cultures, as well as related histamine production methods.

Abstract: A method for preparing (S)-nicotine by reduction includes conducting a reduction process on an alkene compound as shown in Formula I and/or an iminium cation compound as shown in Formula II, thereby producing (S)-nicotine. The method is simple, safe, reliable, and yields both high purity and high quantities of (S)-nicotine production.

Abstract: Provided is a composition and a fructose production method, wherein the composition contains: sucrose phosphorylase or a microorganism expressing same; or a culture or lysate of the microorganism whereby fructose can be produced at low cost with high yield.

Abstract: Disclosed are methods, systems, components, and compositions for synthesis of sequence defined polymers. The methods, systems, components, and compositions may be utilized for incorporating novel substrates that include non-standard amino acid monomers and non-amino acid monomers into sequence defined polymers. As disclosed herein, the novel substrates may be utilized for acylation of tRNA via flexizyme catalyzed reactions. The tRNAs thus acylated with the novel substrates may be utilized in synthesis platforms for incorporating the novel substrates into a sequence defined polymer.

Abstract: The present invention relates to an enzyme-catalyzed process for producing GDP-fucose from low-cost substrates guanosine and L-fucose or guanosine and D-Mannose in a single reaction mixture. Said process can be operated (semi)continuously or in batch mode. Further, said process can be adapted to produce fucosylated molecules and biomolecules including glycans, such as human milk oligosaccharides, proteins, peptides, glycoproteins or glycopeptides.

Abstract: This invention provides a novel protein deamidating enzyme.

Abstract: Disclosed herein include methods, compositions, and kits suitable for use in signal amplification. There are provided, in some embodiments, protease-based signal amplification modules. Disclosed herein include amplifier proteins comprising a first part of a first protease domain, a first dimerization domain, a first cut site a protease in a protease active state is capable of cutting, a second dimerization domain, a second cut site a protease in a protease active state is capable of cutting, and a first caging domain. Disclosed herein include companion amplifier proteins comprising a second part of a first protease domain, a third dimerization domain, a third cut site a protease in a protease active state is capable of cutting, a fourth dimerization domain, a fourth cut site a protease in a protease active state is capable of cutting, and a second caging domain.

Abstract: This disclosure relates to novel thermophilic amplification compositions and methods, in particular for use in nucleic acid amplification and sequencing.

Abstract: The invention relates to a new method of delivering an analyte to a transmembrane pore in a membrane. The method involves the use of microparticles.

Abstract: The present disclosure relates to a nanoparticle including a first layer including a first polymer and a first plurality of accessory oligonucleotides, a second layer including a second polymer and a single template site for bonding a template polynucleotide, and a third layer including a third polymer and a second plurality of accessory oligonucleotides. Also described herein is a method of making said nanoparticle, including “dip-coating,” e.g., successively dipping a surface with wettable nanodomains in different polymer solutions. Further described herein is a method of making the nanoparticles by forming them in nanowells and subsequently releasing them from the nanowells. Also described herein is a method of attaching the nanoparticle to a substrate and amplifying the template polynucleotide using a polymerase.

Abstract: Rapid, sensitive, and specific point-of-care testing for pathogens is crucial for disease control. Lateral flow assays (LFAs) have been employed for nucleic acid detection, but they have limited sensitivity and specificity. A fusion of catalytically inactive Cas9 endonuclease and a relaxase for example, VirD2 are used for sensitive, specific nucleic acid detection by LFA. VirD2-dCas9 specifically binds the target nucleic acid sequence via dCas9 and covalently binds to a FAM-tagged oligonucleotide via VirD2. The biotin label and FAM tag are detected using a LFA. This system, termed Vigilant (VirD2-dCas9 guided and LFA-coupled nucleic acid test) is coupled to reverse transcription-recombinase polymerase amplification to detect pathogenic nucleic acid of interest in a sample, it exhibits an impressive limit of detection and shows no cross-reactivity, thus reducing incidents of false positives. Vigilant offers an easy-to-use, rapid, cost-effective, and robust detection platform for SARS-CoV2.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more non-nucleic acid targets of interest in a sample. The compositions and methods provide signal boost upon detection of non-nucleic acid targets of interest in less than one minute and in some instances instantaneously at ambient temperatures down to 25° C. or less, allow for massive multiplexing, high accuracy, minimal non-specific signal generation, and are easily reprogrammable.

Abstract: A method of conducting an assay for a set of targets, the method comprising: providing a set of targets; subjecting each target of the set of targets to a recognition event, in which each target is uniquely recognized by and bound to a recognition element associated with a code from a set of codes, thereby yielding a set of coded targets comprising the target and the recognition element; subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element produces a modified recognition element, thereby yielding a set of modified recognition elements comprising the code; subjecting each code of the set of modified recognition elements to an amplifying event, in which each code is amplified, thereby yielding a set of amplified codes; subjecting each amplified code of the set of amplified codes to a detection event, thereby determining the nucleic acid sequence of the code.

Abstract: Detecting analytes using proximity-induced tagmentation, strand invasion, restriction, or ligation is provided herein. In some examples, detecting an analyte includes coupling a donor recognition probe to a first portion of the analyte. The donor recognition probe includes a first recognition element specific to the first portion of the analyte, a first oligonucleotide corresponding to the first portion, and a transposase coupled to the first recognition element and the first oligonucleotide. An acceptor recognition probe is coupled to a second portion of the analyte. The acceptor recognition probe includes a second recognition element specific to the second portion of the analyte and a second oligonucleotide coupled to the second recognition element and corresponding to the second portion. The transposase is used to generate a reporter polynucleotide including the first and second oligonucleotides. The analyte is detected based on the reporter including comprising the first and second oligonucleotides.

Abstract: The invention provides methods and compositions for hybridizing at least one molecule to a target. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in hybridization. Compositions for use in the invention include an aqueous composition comprising at least one nucleic acid sequence and at least one polar aprotic solvent in an Camount effective to denature double-stranded nucleotide sequences.

Abstract: A method of determining whether one or more forms of a nucleic acid analyte are present in a sample. The method includes dissolving an amplification reagent with a first solvent, where the amplification reagent contains oligonucleotides sufficient to amplify and detect a first region of a first form of the analyte, where the first solvent contains one or more oligonucleotides which, in combination with the oligonucleotides of the amplification reagent, are sufficient to amplify and detect a second region of a second form of the analyte, where the one or more oligonucleotides of the first solvent are insufficient to amplify and detect the first or second form of the analyte, and where the first and second regions each comprise a different nucleotide base sequence.

Abstract: The present disclosure relates to methods and compositions for enhanced assessment of exogenous polynucleotide and/or polypeptide-mediated transcriptional perturbations at high throughput and single cell/droplet levels of resolution. In embodiments, nucleic acid fusions of exogenous polynucleotide(s) and associated target transcript(s) are produced within individually sequestered or discretely identifiable cells/lysates and analyzed for exogenous polynucleotide mediated perturbations across a vast population of droplets/cells within individual reactions. Kits for performance of the methods are also provided.

Abstract: A method for assessing the status of degradation and/or integrity of one or more nucleic acids in a sample, which includes amplifying at least two overlapping regions within at least one locus and detecting the amount of the amplification products using at least two probes, where one probe binds to an overlapping region and the other probe binds to a non-overlapping region. Also, a method of designing primers and/or probes for amplifying at least two overlapping regions within at least one single copy locus or multicopy locus. Also a primer and a primer pair for amplifying at least two overlapping regions from one nucleic acid template which is a multicopy locus present in loci in the human genome. Also a kit including primers and/or probes for assessing the status of degradation and/or integrity of one or more nucleic acids in a sample.

Abstract: A method of characterizing a nucleic acid that includes steps of (a) contacting a primer-template nucleic acid hybrid with a polymerase and a mixture of nucleotides to produce an extended primer hybrid and to form a stabilized ternary complex including the extended primer hybrid, the polymerase and a nucleotide cognate of the next base in the template, wherein the mixture contains nucleotide cognates of four different base types, wherein the nucleotide cognate of the first base type has a reversible terminator, and wherein nucleotide cognates of the second, third and fourth base types are extendable; (b) detecting the stabilized ternary complex to distinguish the next base from other base types in the template; and (c) determining the presence of a base multiplet in the template nucleic acid, the base multiplet including the first base type followed by the next base.

Abstract: Methods and compositions are provided for improved nucleic acid amplification assays. In some embodiments, the nucleic acid amplification assay is a tagged amplicon primer extension (TAPE) nucleic acid amplification reaction.

Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.

Abstract: This disclosure relates to novel amplification compositions and methods, in particular for use in nucleic acid amplification and sequencing, preferably that do not involve reagents that are thermophilic.

Abstract: The present invention is related to a Template Switch Oligo construct and its use into a ligase free diagnostic and/or sequencing method and to the kit for performing the method of the invention.

Abstract: Materials and methods for the diagnosis of traumatic brain injury using miRNA biomarkers are disclosed. Amplification nucleotide chains amplify a detectable signal indicating the expression and/or upregulation of the biomarkers. Detection of the amplified signal is accomplished with capture nucleotide chains in a stem-loop conformation. The loop sequence of the capture nucleotide chains binds with the biomarkers and/or an indicator nucleotide chain released in the presence of one or more of the biomarkers. Binding is detected with indicators on one or more of indicator nucleotide chains released during amplification, the capture nucleotide chains, and signal nucleotide chains capable of complementary base-pair binding to the capture nucleotide chains. Incorporating the foregoing into a lateral flow assay permits point of care diagnosis.

Abstract: The disclosure provides a method for detecting a target analyte in a biological sample including contacting the sample with one or more probe sets each comprising a primary probe and a linker, contacting the sample with an initiator sequence, contacting the sample with a plurality of fluorescent DNA hairpins, wherein the probe binds the target molecule, the linker connects the probe to the initiator sequence, and wherein the initiator sequence nucleates with the cognate hairpin and triggers self-assembly of tethered fluorescent amplification polymers, and detecting the target molecule by measuring fluorescent signal of the sample.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: The invention provides DNA compositions that relate to transgenic insect resistant maize plants. Also provided are assays for detecting the presence of the maize DAS-59122-7 event based on the DNA sequence of the recombinant construct inserted into the maize genome and the DNA sequences flanking the insertion site. Kits and conditions useful in conducting the assays are provided.